Life Sciences Center

Sukurta: 09 April 2024

GMC 2 m Saulėtekio av. 7, LT-10257 Vilnius
Tel. +370 5 223 4419
E-mail:
Web: http://www.gmc.vu.lt
Director – Prof. Daumantas Matulis

STAFF
121 teachers (incl. 77 holding research degree), 262 research fellows (incl. 181 holding research degree).

DEPARTMENTS OF THE FACULTY
Institute of Biochemistry
Institute of Biosciences
Institute of Biotechnology
EMBL Partnership Institute
Doctoral School

RESEARCH AREAS
• Genomics, Biomolecules and Biotechnologies: Fundamental and Applied Research
• Ecosystems and Biodiversity, Preservation of Environment and Use of Natural Resources
• Investigation of Nervous System and Behaviour
• Structural biology and bioinformatics
• Signalling pathways and epigenetic regulation in tumour and stem cells
• Research and application of biocatalysts and self-organizing systems

DOCTORAL DISSERTATIONS MAINTAINED IN 2023
Leonavičienė Greta, Complex single-cell analysis using hydrogel microcapsules
Narmontė Milda, Method for high-resolution genome-wide analysis of 5-hydroxymethylcytosine and its application for epigenetic studies of human deseases
Paškevičius Šarūnas, Development and synthesis of plant-derived recombinant biopharmaceutical proteins active against gram-negative pathogenic bacteria
Ličytė Janina , Identification of oxidized 5-methylcytosine derivatives by novel technologies, their distribution and functions
Meškytė Erna Marija, Identification of the role of transcription factor ETV7 in breast cancer aggressiveness
Stulpinas Aurimas, Investigation of protein kinase MAPK and AKT crosstalk and dependencies on extracellular contacts in lung cancer-derived cell models
Ramonas Eimantas, Study of biocatalysts immobilized in three-dimensional structures
Kuliešiūtė Ugnė, Molecular mechanisms shaping neuronal networks during brain development and in neuropathology
Urbaitis Tomas, Identification and characterization of novel CRISPR-Cas nucleases
Survilienė Vaida, Social development and changes in steroid hormones during early ontogenesis of grey seals (Halichoerus grypus)
Rinkūnaitė Ieva, Study of molecular mechanisms of myocarditis and dilated cardiomyopathy
Sadzevičienė Ieva, Analysis of genetic and epigenetic biomarkers for breast cancer diagnosis and prognosis
Žilovič Diana, Genetical biomarkers of ovarian cancer
Matulevičius Augustinas, Innovative imaging technologies and genetic tests for the detection of clinically significant prostate cancer
Jarockytė Greta, Theranostic nanoparticles application for cancer diagnostica and treatment
Tarailis Povilas, Evalutation of electrical brain activity of the resting state: relation with subjective experience
Dankinas Denisas, Application of Artificial Intelligence for the Separation of Schizophrenic Patients from Healthy Subjects Using Response Preparation and Simulation Inhibition Estimates
Liang Wenming, The links of respiration with physical fitness, muscle tension, and executive functioning
Sakalauskas Andrius, Understanding inhibition of protein amyloid fibril formation
Sližienė Aistė, New monoclonal antibodies for fish allergen detection and testing

MAIN CONFERENCES ORGANIZED IN 2023
1. 2023-04-24/27 International scientific conference “The COINS”
2. 2023-05-24/25 international scientific conference “Frontiers in Molecular Life Sciences” in memory of Prof. Jędrzej Śniadecki in conjunction with the 13th International Conference on the History of Chemistry 2023
3. 2023-06-01/02 iNEXT-Discovery Regional Structural Biology Meeting
4. 2023-06-28/30 Lithuanian Biochemical Society conference “Medicinal Biochemistry”
5. 2023-09-20/21 International scientific conference Life Sciences Baltics (content committee)
6. 2023-10-11/13 5th Congress of Baltic microbiologists
7. 2023-11-24 15th International conference of the Lithuanian neuroscience association „Neurodiversity: from theory through artificial intelligence to clinical practice“

MAIN SCIENTIFIC ACHIEVEMENTS IN 2023
1. Article of Gintutas Tamulaitis research group "Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling " at the scientific journal "Science”.
2. Article of a team led by prof. Virginijus Šikšnys „TnpB Structure Reveals Minimal Functional Core of Cas12 Nuclease Family“ at the scientific journal “Nature”.
3. European Molecular Biology Organisation (EMBO) Installation Grants to Gytis Dudas and Patrick Pausch.
4. The European Research Council (ERC) Starting Grant and subsequently EMBO Installation Grant to Stephen Knox Jones Jr.

INSTITUTE OF BIOCHEMISTRY

7 Sauletekio av., LT-10257
Phone (+370 5) 223 4378
E-mail:
http://www.bchi.vu.lt

Director - Dr Kastis Krikštopaitis

STAFF
81 research fellows (61 holding research degree), 36 doctoral students.

DEPARTMENTS OF THE INSTITUTE
Department of Bioanalysis
Department of Bioelectrochemistry and Biospectroscopy
Department of Biological Models
Department of Molecular Cell Biology
Department of Molecular Microbiology and Biotechnology
Department of Xenobiotics Biochemistry
Laboratory of Bioorganic Compounds Chemistry
Proteomics Centre

RESEARCH AREAS
• Signalling pathways and epigenetic regulation in cancer and stem cells
• Investigation and application of biocatalysts and self-assembled structures

DOCTORAL DISSERTATIONS MAINTAINED IN 2023
E. Ramonas “Study of biocatalysts immobilized in three-dimensional structures”
A. Stulpinas “ Investigation of protein kinase MAPK and AKT crosstalk and dependencies on extracellular contacts in lung cancer-derived cell models”
E. Meškytė “ Identification of the role of transcription factor ETV7 in breast cancer aggressiveness ”
I. Rinkūnaitė “ Study of molecular mechanisms of myocarditis and dilated cardiomyopathy”

MAIN SCIENTIFIC ACHIEVEMENTS IN 2023
1. The funding of the project "Development of a bioelectrochemical L-amino-acid-urea analyser for the monitoring of intensive care patients” under the measure "Technological Development Programme" by the Lithuanian Research Council was granted to the research team of the Institute of Biochemistry (headed by Dr Dalius Ratautas) together with the company Bioanalizes sistemos. An enzymatic biosensor is being developed for the determination of total L-amino acids and blood urea levels, which should end up at the bedside of patients in intensive care units.
2. The research team from the Institute of Biochemistry Proteomic Center (headed by Dr Mindaugas Valius) awarded funding in the M-ERA.NET 3 network call, “Customised DNA-based nanocarriers to boost heart healing” (DNABEATS). The researchers will carry out studies on advanced DNA-based nanocarriers to unlock the potential of miR-based gene therapy which boost heart healing.

DEPARTMENT OF BIOANALYSIS

Sauletekio av. 7, LT-10257
Phone (+370 5) 223 4389
E-mail:
Head – Dr Marius Dagys

STAFF
Chief research associates: Dr J. Razumienė
Senior research associates: Dr M. Dagys, Dr G. Bagdžiūnas, Dr D. Ratautas, R. Žalneravičius
Research associates: Dr L. Tetianec, Dr I. Šakinytė, Dr A. Laurynėnas, Dr E. Ramonas
Junior research associates: I. Bratkovskaja, M. Butkevičius
Senior specialists: V. Gurevičienė.
Doctoral students: S. Serapinas, M. Katelynas, K. Ratkevičiūtė

RESEARCH INTERESTS
• Investigation of charge and energy transfer in biomolecules, bioreactor design
• Creation and investigation of biosensors and bioanalytical systems

RESEARCH PROJECTS CARRIED OUT IN 2023
Project Supported by the University Budget
Design and investigation of new systems for biocatalysis.
We specialise in application of the oxidoreductases for bioreactor applications and creation of mediatorless biofuel cells. The development of artificial nanocatalysts is a rapidly developing field in nanocatalysis and nanomaterials science. Our continuing research in this regard is the design of unique nanomaterials composed of several redox enzymes or nucleotides and nanoparticles. Properly wired biomolecules through the nanoparticle surface experience direct electrochemical “communication”, allowing electron transfer from one redox center to other.

National Research Projects
Research Council of Lithuania. Biosensor platform for fast, cheap and accurate quantification of amino acids in patients undergoing renal replacement therapy (DIALSENS) (No. 01.2.2-LMT-K-718-01-0019). Dr Dalius Ratautas. Partner – Vilnius University Hospital Santaros Klinikos. 2020 – 2023.

Research Council of Lithuania. Development of the electrochemical biosensor for the detection of single-nucleotide polymorphisms (FindSNPs) (No. S-MIP-23-127). Dr Dalius Ratautas. 2023 – 2025.

Research Council of Lithuania. Development of a bioelectrochemical L-amino acid-urea analyzer for monitoring of intensive care patients (AminoUreaSense) (No. S-TPP-23-3). Dr Dalius Ratautas. Partner – UAB “Bioanalizės sistemos”. 2023 – 2024.

Research Council of Lithuania. Ultrasensitive monitoring of medically relevant biomarkers on nanostructured surfaces (NanoBioSens) (No. P-PD-22-079). Dr Rokas Žalnėravičius. 2022 – 2024.

Central project management angency. Development of biosensor research and engineering competence and technology transfer centre (BIOSENSE) (No. 01.2.2-CPVA-K-703-03-0010). Dr Marius Dagys. 2020 – 2023.

Contractual Research
Contractual R&D works ordered by UAB Bioanalizės sistemos

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INOVATION) PARTNERS
Vilnius Gediminas Technical University (Lithuania)
Vilnius University Hospital Santaros Klinikos (Lithuania)
Malmo University (Sweeden)
Lund University (Sweden)
UAB Bioanalizės sistemos (Lithuania)
UAB Laboratorija 1 (Lithuania)

BEST REPORTS DELIVERED AT CONFERENCES ABROAD
1. J. Miškinis, E. Ramonas, V. Gurevičienė, J. Razumienė, M. Dagys, D. Ratautas. L-amino acid biosensors in clinical application: from concept to device. 33rd Anniversary World Congress on Biosensors, 2023 06 05 – 08, Busan, Pietų Korėja.
2. J. Razumienė. Application of amperometric biosensor for determination of glucose content in beverages. X International Scientific and Practical Conference ‘Modern Achievements of Pharmaceutical Technology’, dedicated to the 60th anniversary of Doctor of Pharmaceutical Sciences, Professor Yevgeny V. Gladukh, 2023 03 10.
3. J. Razumienė. Amperometric Biosensing of L-glutamate Using Reduced Graphene Oxide and Glutamate Oxidase. XXXV EUROSENSORS Conference, 2023-09-10 – 13, Lecce, Italija.

DEPARTMENT OF BIOELECTROCHEMISTRY AND BIOSPECTROSCOPY

Sauletekio av. 7, LT-10257 Vilnius
Phone (+370 5) 223 4394
E-mail:
Head – Dr Rima Budvytytė

STAFF
Chief research fellows: habil.Dr G. Niaura (part time).
Senior research fellow: DrR. Budvytytė, Dr G. Preta.
Research fellows: Dr M. Jankunec, Dr B. Pavliukevičienė, Dr T. Ragaliauskas, Dr T. Sabirovas, Dr M. Talaikis.
Young research fellows: F. Ambrulevičius, S. P. Arun.
Senior specialists: Dr A. Bulovas.
Doctoral students: S. Ganpule, E. Jankaitytė, R. Tamulytė, R. Bagdonaitė, A. Polita, A. Katkauskaitė.

RESEARCH INTERESTS
• Spectroelectrochemistry of proteins and biologically relevant redox species
• Self-organization in lipid systems
• Membranes/protein (peptide) interactions
• Measurement techniques and experimental data analysi
• Lipid-based nanoparticles for CRISPR/Cas9 delivery via membrane fusion
• Membrane lipid therapy

RESEARCH PROJECTS CARRIED OUT IN 2023
Project Supported by the University Budget
Spectroelectrochemical Studies of Biological Systems and their Models.
Properties and Function of self-assembled model systems. Properties and function of tethered bilayer membranes (tBLM), a biomimetic model of phospholipid membrane, depend on the structure of the self-assembled lipid-like monolayer that anchors tBLM to the surface. The tBLMs are also significantly influenced by environmental factors such as pH and the presence of various ions. Together these factors affect membrane’s functionality in applications ranging from biosensing to the study of membrane proteins.
Main publications:
1. Shivabalan, A.P.; Ambrulevicius, F.; Talaikis, M.; Pudzaitis, V.; Niaura, G.; Valincius, G. Effect of PH on Electrochemical Impedance Response of Tethered Bilayer Lipid Membranes: Implications for Quantitative Biosensing. Chemosensors 2023, 11, 1–19, doi:10.3390/chemosensors11080450.
2. Pudžaitis, V.; Talaikis, M.; Valincius, G.; Niaura, G. Formation of Tethered Bilayer Lipid Membranes on Gold Surface Probed by in Situ SEIRAS. Chemija 2023, 34, 1–7.
3. Polita, A.; Stancikaitė, M.; Žvirblis, R.; Maleckaitė, K.; Dodonova-Vaitkūnienė, J.; Tumkevičius, S.; Shivabalan A. P.; Valinčius, G. Designing a Green-Emitting Viscosity-Sensitive 4,4-Difluoro-4-Bora-3a,4a-Diaza- S -Indacene (BODIPY) Probe for Plasma Membrane Viscosity Imaging. RSC Advances 2023, 13 (28), 19257–19264. https://doi.org/10.1039/D3RA04126C.
4. Valiūnienė, A; Valinčius, G. Tethered bilayer membranes as impedimetric biosensors for detection of pore-forming biological agents. Current opinion in electrochemistry 2023,40: 2451-9111. DOI: 10.1016/j.coelec.2023.101344.
5. Valiūnienė, A.; Virbickas, P.; Gabriūnaitė, I.; Margarian, Ž.; Levinas, R.; Janarauskienė, D.; Valinčius, G. Titanium–platinum thin films as a tool for the electrooxidation of cyanide. Coatings: special issue: Fabrication of metallic micro-/nano-composite materials for environmental applications. Basel:MDPI 2023, 13 (11):1-18. DOI: 10.3390/coatings13111821.
Other publications:
1. Diliautas, R.; Karoblis, D.; Mazeika, K.; Baltrunas, D.; Niaura, G.; Talaikis, M.; Lukowiak, A.; Strek, W.; Zarkov, A.; Kareiva, A. Structural, Morphological and Magnetic Properties of Novel Sol-Gel Derived Bi1-XGdxFe0.85Mn0.15O3 Solid Solutions. Journal of Magnetism and Magnetic Materials 2023,570. https://doi.org/10.1016/j.jmmm.2023.170498.

Membrane/protein (peptide) interactions
Lipid-protein/protein interactions are essential in cell membrane organization and function. In collaboration with other research groups in the Life Sciences Center (Dr M. Zaremba, Dr V. Smirnovas, Dr M. Plečkaitytė), our group members continue to contribute to expand their knowledge about the lipid membrane/protein-related biological processes. Simultaneously, we adapt our technology as a diagnostic tool.
Main publication:
1. Tamulytė R.; Jankaitytė, E., Toleikis, Z.; Smirnovas, V.; Jankunec, M. Pro-inflammatory protein S100A9 alters membrane organization by dispersing ordered domains. Biochimica et Biophysica Acta-Biomembranes 2023,1865 (3): 184113.

Other topics. We also contributed through the collaborative initiatives to the research projects done at other departments of VU Life Sciences Center, VU Faculty of Chemistry and groups at the National Institute of Cancer, Center for Physical Science and Technology as well Lithuanian University of Health Sciences, Members of our group provide access to the unique scientific instruments and share their expertise in the areas of surface characterization (morphology and spectroscopy), material characterization (chromatography and spectroscopy) and data analysis.
Main publications:
1. Padrez Y., Golubewa L., Bahdanava A., Jankunec M.,. Matulaitienė I, Semenov D., Karpicz R., Kulahava T., Svirko Y., Kuzhir P. Nanodiamond surface as a photoluminescent pH sensor. Nanotechnology 2023, 34(19): 195702.
2. Stenqvist B., Ericson M., Gregoire S., Biatry B., Cassin G., Jankunec M., Engblom J., Sparr E. Membrane permeability based on mesh analysis. Journal of Colloid and Interface Science 2023, 633: 526-535.
3. Vaskevičius L., Malūnavičius V., Jankunec M.,. Lastauskienė E, Talaikis M., Mikoliunaitė L., Maneikis A., Gudiukaitė R. Insights in MICP dynamics in urease-positive Staphylococcus sp. H6 and Sporosarcina pasteurii bacterium. Environmental Research 2023, 234: 116588.

National Research Projects
Research Council of Lithuania. Improvement of scientific qualification through individual Horizon 2020 MTEP projects “Interactions of misfolded proteins and phospholipid membranes: possible key in neurodegeration (NeuroMisFolDe)”. No. 09.3.3-LMT-K-712-18-0003. Project leader: Dr Rima Budvytytė.
Main publication:
1. Budvytyte R., Valincius G. The interactions of amyloid β aggregates with phospholipid membranes and the implications for neurodegeneration. Biochemical Society Transactions. 2023,27;51(1):147-159. doi: 10.1042/BST20220434.

2022 – 2023 VU LSC-EMBL Partner Institute Associated Research Fellowship in EMBL Partnership Institute. This research was supported by the European Regional Development Fund under grant agreement No 01.2.2-CPVA-V-716-01-0001 with the Central Project Management Agency (CPVA), Lithuania. “Biomimetic lipid – based nanoparticles for CRISPR/Cas9 delivery via membrane fusion”. Project leader: Dr Rima Budvytyte.
Main publication:
1. Eimina Dirvelyte; Daina Bujanauskiene; Evelina Jankaityte; Neringa Daugelaviciene; Ugne Kisieliute; Igor Nagula; Rima Budvytyte; Urte Neniskyte. Genetically encoded phosphatidylserine biosensor for in vitro, ex vivo and in vivo labelling. Cellular & Molecular Biology Letters 2023, 28(1):59. DOI: 10.1186/s11658-023-00472-7. Impact factor: 8,712.
Patent application:
1. 2023 m, V83-131 PCT: Rima Budvytyte, Urte Neniškytė, Evelina Jankaitytė, Eimina Dirvelytė “Liposomal nanoparticles for CRISPR/Cas9 delivery”. Patent Application number: PCT/IB2023/063127.

2022-2024 P-PD-22-112. “Electroporation of tethered bilayer lipid membrane (EpoFoM)”. Project leader: Dr Rima Budvytyte. Project implementer: Dr Tomas Sabirovas

2022-2023 MSF-JM-2/2022. “Application of tethered bilayer lipid membranes for biofuel cells”. Project leader: Dr Tomas Sabirovas.

2023-2024 LMT Funding for student’s research projects during studies (studies scholarships). Project Nr: P-ST-23-385. "Investigation of the structural properties of tethered bilayer lipid membranes using viscosity-sensitive molecular markers." Project leader: Dr Tomas Sabirovas. Project implementer: master student Kajus Momgaudis.

2020-2023 01.2.2-LMT-K-718-03-0003. “Development of drug candidate compounds that inhibit BACE1 enzymatic activity and Aβ peptide aggregation for the treatment of Alzheimer's disease” Project leader: Dr Daumantas Matulis. Project implementer: Dr Rima Budvytyte and Evelina Jankaityte.

2020 -2023 01.2.2-CPVA-K-703 “Creation of a competence and technology transfer center for biosensor research and engineering” (BIOSENSE). Project leader: Dr Marius Dagys. Project implementer: Dr Rima Budvytyte, Dr Tadas Ragaliauskas, Dr Marija Jankunec, Dr Tomas Sabirovas.

2023-2024 LMT Funding for students research projects during studies (studies schollarships). Project Nr:P-ST-23-174. „Investigation of the mechanism of the interaction of the antimicrobial peptide colistin with the lipid membrane”. Project leader: Dr Rima Budvytyte. Project implementer: master student Modestas Mažerimas.

International Research Projects
2020-2023 COST Action CA18133 Action Title: “European Research Network on Signal Transduction – ERNEST” Management committe member – Rima Budvytyte.
2023-2027 COST action CA22153 Action title: “European Curvature and Biology Network (EuroCurvoBioNet)“. Grant holder institution – Paris lodron University of Salzburg, Austria. Management committe member – Dr Marija Jankunec

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INOVATION) PARTNERS
Faculty of Mathematics and Informatics, Vilnius University (Lithuania)
Institute of Neurosciences, Lithuanian University of Health Sciences (Lithuania)
Center for Physical Sciences and Technology (Lithuania)
Niels Bohr Insitute, University of Copenhagen (Denmark)
Institute for Biosciences and Biotechnology Research, University of Maryland, Rockville, MD (USA)
NIST Center for Neutron Research, Gaithersburg, MD (USA)
Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, Malmö (Sweden)
Department of Experimental Medicine, Sapienza University, Rome (Italy)

OTHER SCIENTIFIC ACTIVITIES
Dr G. Valinčius
• Member of the editorial Board of Scientific journal „Chemija “
• Member of the Lithuanina Biophysical society
• Member of the Lithuanian Biochemical Society
• Member of International Society of Electrochemistry
Habil.Dr G. Niaura
• Member of the Lithuanian Academy of Sciences
• Member of the editorial Board of the scientific journal „Chemija“
• Member of the editorial Board of the scientific journal “Materials”
• Member of the International Society of Electrochemistry
Dr R. Budvytytė
• VU MBA study committee member
• VU Intellectual property management and investment committee member
• Member of the American Biophysical Society
• Member of the Lithuanian Biophysical Society
Dr G. Preta
• Member of the editorial Board of the scientific journal ``Frontiers in Cell and Developmental Biology``

BEST REPORTS DELIVERED AT CONFERENCES ABROAD
1. 2023 April 09-14 EMBO Workshop “ImmunoBiophysics: From fundamental physics to understanding the immune response” Les Houches, France. Presenter: R. Budvytyte
2. 2023 July 31 – August 4, 14th EBSA congress, Stockholm, Sweden. Poster presentation: R. Tamulytė, E. Jankaitytė, D. Šulskis, M. Jankunec „The Effects of Calcium on Lipid-S100 Proteins Interactions“.
3. 2023 July 31 – August 4, 14th EBSA congress, Stockholm, Sweden. Poster presentation: R. Bagdonaitė, G. Valinčius „Lipid composition effects on membrane damage inflicted by alpha hemolysin from Staphylococcus Aureus“.
4. 2023 September 3-8, The 74th Annual Meeting of the International Society of Electrochemistry, Lyon, France. Oral presentation: T. Sabirovas, T. Raila, T. Meskauskas. G. Valincius “Local Electrochemical Impedance Spectroscopy for Pore Characterization in Tethered Bilayer Lipid Membranes”. Presenter: Dr Tomas Sabirovas.
5. 2023 September 3-8, The 74th Annual Meeting of the International Society of Electrochemistry, Lyon, France. Poster presentation: I Gabriunaite, T. Sabirovas, A. Valiuniene, G. Valincius “Comparison of Au and Thin Film Metal Oxides-based Biosensors for the Detection of Bacterial Toxins”.

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
G. Preta
• External reviewer for the 2023 Sapienza, University of Rome, Research Funding Call.
• Erasmus teaching mobility in Granada: 24/04/2023-28/04/2023

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. 2023 May 21 – 25, EMBO Workshop Cell polarity and membrane dynamics Sant Feliu de Guíxols, Spain. Poster presentation: Shivabalan A.P, Artūras Polita, Gintaras Valinčius
2. “Tethered Bilayer Lipid Membranes (tBLMs) from Lung Cancer Cells.”
3. 2023 August 21 – September 1, PhD Summer School Micro and Nano Sensors, Copenhagen, Denmark. Poster presentation: A. Katkauskaite, T. Ragaliauskas “Applications of biomimetic lipid membranes“.

DEPARTMENT OF BIOLOGICAL MODELS

Sauletekio av. 7, LT-10257 Vilnius
Phone (+370 5) 223 4408
E-mail:
Head – Dr Virginija Bukelskiene

STAFF
Chief researcher: Dr A. Burokas
Senior research fellows: Dr V. Bukelskienė, Dr D. Baltriukienė, Dr E. B.-M. Daliri
Research fellows: Dr M. Alksnė, Dr E. Šimoliūnas, Dr I. Rinkūnaitė
Postdoctoral researchers: Dr A. Atzeni, Dr B. Ravoitytė
Doctoral students: E. Baltrukonytė, V. Baranauskas, P. Barasa, M. Iešmantaitė, M. Grubliauskaitė, A. Kunevičius, V. O. Kyei-Baffour, A. Megur, J. Mingaila, M. Liudvinaitis, S. Samulėnaitė, A. K. Vijaya
Veterinary doctor: A. Ščerbavičienė
Assistants: J. Kernagytė, R. Balsienė, S. Razmus

RESEARCH INTERESTS
• Laboratory animals
• Cell culture
• Stem cells
• Tissues engineering
• Microbiota-gut-brain axis

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
Research Council of Lithuania. A complex-strategy for treating crtical size bone defects - an interdisciplinary approach to bone regeneration (No. P-MIP-23-149). Dr E. Šimoliūnas. 2023-2026
The most relevant problems in dentistry and maxillofacial surgery are the atrophy of alveolar bone and the formation of bone defects related to dental diseases, oncological surgeries, or trauma. Bone defects aggravate dental implant placement and impair the chewing, speech, and facial aesthetic appearance of the patient. Strategies for promoting bone regeneration include guided tissue regeneration, autogenous and allograft bone transplantation, also tissue engineering. However, all these techniques still have limitations. Autografts suffer from limited resources and donor-site morbidity due to potential infection and haematoma, also their harvesting requires an additional surgical procedure. Allografts can transfer pathogens to the patient and cause immunological rejection by the recipient's body. In comparison, tissue engineering combines bone graft materials with biological mediators to achieve predictable tissue regeneration. However, many scientists concentrate only on the development of an osteo-conductive and -inductive scaffold, while ignoring other possible ways of enhancing bone repair. Thus, we strive to develop not only novel materials/scaffolds for bone regeneration but more importantly to create a bone defect treatment strategy comprising post and pre-surgery procedures. During this project, a novel free-packed system will be created, in which the size and shape of the particles will be controlled to enhance osteogenesis. Additionally, the system will be enriched by low-intensity ultrasound stimulated (LIPUS) extracellular matrix (ECM) and extracellular vesicles (EV) extracted from mesenchymal stem cells (MSC), which should improve the regenerative properties of our created system. Finally, it will be verified whether the described freepacked system together with additional LIPUS treatment in vivo improves bone tissue regeneration.

Research Council of Lithuania. Artificial urethra for the treatment of hypospadias and urethral strictures. (No. 01.2.2-LMT-K-718-01-0087). Dr Virginija Bukelskienė. Partner – Vilnius University Hospital Santaros Klinikos. 2020 – 2023.
One of the most significant challenges of reconstructive surgery is the restoration of damaged tissues. This problem is also relevant in the treatment of urethral strictures and hypospadias, especially in cases of complex or recurrent damage. Current treatment practice involves skin or buccal grafts, but in both cases, the supply of tissue is limited, and the procedure can be problematic. The project developed artificial urethral tissue consisting of hydrogel, differentiated autologous stem cells and polymer-supported drugs and demonstrated its ability to restore function to the damaged urethra in the rabbit model organism. These results are promising for use in the treatment of urethral strictures and hypospadias in humans.
Main publication:
1. R. Žilinskaitė Tamašauskė, V. Kazlauskas, P. Barasa, N. Krestnikova, D. Dasevičius, V. Bilius, G. Verkauskas. (2023). Pilot Study on the Molecular Pathogenesis of Pyeloureteral Junction Obstruction: Underdevelopment or Fibrosis? Medicina, 59(10):1729. doi: 10.3390/medicina59101729.
Patent application:
1. P. Barasa et al. Polycaprolactone-polylactic acid electrospunmesh for drug delivery. Patent application No.: EP23211624.4

Research Council of Lithuania. Targeting the microbiota-gut-brain axis in Alzheimer’s disease: the role of the endocannabinoid system (No. 01.2.2-LMT-K-718-02-0014). Dr A. Burokas. 2019-2023.
Recently, the growing number of facts about the role of the gut microbiota in neurodegenerative disorders led us to focus on exploration of the microbiota and the mechanism of progression of Alzheimer’s disease. The gut microbiota can trigger the immune cells residing in the brain and can activate the immune response leading to neuroinflammation. The project has identified possible biomarkers of the gut microbiota that are under the validation process.
Main publication:
1. Mingaila J., A. Atzeni, A. Burokas. (2023). A comparison of methods of gut microbiota transplantation for preclinical studies. International Journal of Molecular Sciences 24 12005.
Patent application:
1. Burokas, A. Atzeni, E. N-M. Daliri, D. Baltriukienė, J. Mingaila. A. Vijaya. Gut microbiota olsenella Umbonata as biomarker for early detection of Alzheimer’s disease Patent application No.: EP23199177.9

Research Council of Lithuania. Biomarkers of the gut microbiota in autistic spectrum disorders (No. 01.2.2-LMT-K-718-01-0099). Dr A. Burokas. Partner – Center for physical sciences and technology, 2020-2023.
The project aimed to investigate faecal microbiota transfer therapy in children with autism spectrum disorder and to identify potential biomarker targets of the gut microbiota in this pathology in order to create a system that allows these biomarker targets to be regulated.
Patent application:
1. Burokas, V. Bukauskas, A. Kunevičius, V. Urbonas, T. Daugalas, V. Strazdienė. Method for detection of most important time points for the changes in the microbiota after various interventions. Patent application No.: EP23220189.7

Research Council of Lithuania. Black soldier fly larvae as the next generation nutritional supplement: microbiological implications and the impact on the gut microbiota in aging. (No. S-PD-22-93). Dr D. Baltriukienė, postdoctoral researcher Dr B. Ravoitytė. 2022-2024.
The goal of the project is to improve the qualification of scientific fellow by carrying out high-level research dealing with the composition of the microbiota of industrially reared black soldier fly larvae, antimicrobial potential of larvae-derived compounds, and the impact of black soldier fly meal on the health in aging mouse model. Metagenomic analysis of insect larvae-associated microorganism communities and employment of microbiological and molecular methods to identify cultivable microorganisms are planned. The efficiency of compounds extracted from Hermetiaillucens larvae for suppression of the growth of model Gram-positive and Gram-negative bacteria and yeasts will be analyzed. Tests of cognitive and physiological functions, metagenomic, and metabolomic analyses in aging mouse model fed with black soldier fly meal will be conducted. Expected results will aid to design more effective strategies for the introduction of biological origin materials or live microorganisms to expand the application of the black soldier fly.

Research Council of Lithuania. Development of anti-diabetic functional product that modulates the gut microbiota. (No. 09.3-LMT-K-712-23-0117). Dr A. Burokas, postdoctoral researcher Dr E. B.-M. Daliri. 2021-2023.
The study aimed to develop an antidiabetic product from beetroot that could modulate the gut microbiota. For this purpose, lactic acid bacteria isolated from traditionally fermented Lithuanian foods were analysed for their ability to improve the antidiabetic potential of beetroot in vitro. The antidiabetic and gut modulatory capabilities of the fermented product was ascertained using streptozotocin induced and diet-induced diabetic C57BL/6J mice models. Feeding the fermented product to both models significantly reduced blood glucose levels and increased the levels of beneficial microbes as well as short chain fatty acids in their gut. Also in an in vitro model of the distal colon, the product reduced the levels of pathobionts in prediabetic human stool samples and increased the levels of short chain fatty acid as observed in the mice. These results indicate that the fermented product could serve as a potent antidiabetic functional food for humans.
Main publications:
1. Daliri, E. B. M., D. Baltriukienė, A. Burokas. (2023). Beetroot for managing diabetes and its associated gut dysbiosis: Current findings and challenges. Trends in Food Science & Technology 142: 104216.
2. Daliri E. B.-M., T. Balnionytė, J. Stankevičiūtė, E. Lastauskienė, R. Meškys, A. Burokas. (2023). High temperature lacto-fermentation improves antioxidant and antidiabetic potentials of Lithuanian red beetroot. LWT – Food Science and Technology 185: 115122.
3. Megur A., E.B.-M. Daliri, T. Balnionytė, J. Stankevičiūtė, E. Lastauskienė, A. Burokas. (2023). In vitro screening and characterization of lactic acid bacteria from Lithuanian fermented food with potential probiotic properties. Frontiers in Microbiology 14:1213370.

Central project management angency. Center for Genetic Modeling of Animals (No. 01.2.2-CPVA-K-703-03-0032). Dr Daiva Baltriukienė. 2020 – 2023
Since small rodents used in biomedical studies do not fully mimic various human pathologies, the focus is given to genetically modified animal models that can provide insights into the mechanisms of origin of many diseases and the development of new innovative treatment strategies. Therefore, the project aimed to develop molecular tools to generate genetically modified rodent models to study the mechanisms of cardiomyopathy, neuroinflammation, and oncogenesis.
Patent applications:
1. D. Baltriukienė, I. Iešmantaitė, E. Baltrukonytė, V. Bukelskienė. Method for generation of endocannabinoid receptor gene knockout microglia cells. Patent application No.: EP23207226.4.
2. D. Baltriukienė, E. Baltrukonytė, I. Iešmantaitė, V. Bukelskienė. Cardiac fibroblast cell line containing knockout of the fhl1 gene. Patent application No.: EP23207224.9.
3. N. Krestnikova, D. Baltriukienė, V. Bukelskienė, E. Baltrukonytė, M. Iešmantaitė. The method for the generation of immortalized intestinal epithelial cells. Patent application No.: EP23207196.9.

Other topics
Resistance to the chemotherapeutic agents in the clinical management of cancer remains a significant challenge, and the mechanical environment of cancer cells is one of the major determinants of this. Stiffening of the environment is usually associated with increased chemoresistance of cancer cells, although this process depends on the type of cancer. Breast cancer is the most frequently diagnosed cancer, and more than half a million people die from it each year worldwide. In this study, we used the most frequent (70% of diagnosed cases) breast cancer phenotype, representing the MCF-7 cell line, to investigate the influence of surface stiffness on its sensitivity to one of the most commonly used anticancer drugs—doxorubicin. We showed that the mechanical environment affected MCF-7 proliferation, adhesion, and the expression and activation of mitogen-activated protein kinases (MAPKs). Furthermore, the role of MAPKs in response to doxorubicin was dependent on surface stiffness; nevertheless, surface stiffness did not affect MCF-7 resistance to doxorubicin.
Main publication:
1. Šimoliūnas, E., Jasmontaitė, D., Skinderskis, A., Rinkūnaitė, I., Alksnė, M., Liudvinaitis, M., & Baltriukienė, D. (2023). Surface Stiffness Has No Impact on MCF-7 Sensitivity to Doxorubicin. International Journal of Molecular Sciences, 24(12), 10192.

Providing a 3D environment that mimics the native extracellular matrix is becoming increasingly important for various applications such as cell function studies, regenerative medicine and drug discovery. Among the most critical parameters to consider are the intricate microscale geometry and material properties of the scaffold. Therefore, stereolithography based on photopolymerization is an emerging technique as it is able to selectively form volumetric structures from liquid resin through localized polymerization reactions. However, one of the most important parameters of the scaffold is biocompatibility, which depends not only on the material but also on the exposure conditions and post-processing, which is currently underestimated. In collaboration with Faculty of Physics and Center for Physical Science and Technology, a systematic investigation of the biocompatibility of optically 3D-printed microporous scaffolds, their improvement by post-processing and analysis with Raman microspectroscopy were performed.
Main publication:
1. Jersovaitė J., U. Šarachovaitė, I. Matulaitienė, G. Niaura, D. Baltriukienė, M. Malinauskas. (2023). Biocompatibility enhancement via post-processing of microporous scaffolds made by optical 3D printer. Frontiers in Bioengineering and Biotechnology 11: 1167753.

International Research Projects
Platform “European Innovative Research & Technological Development Projects in Nanomedicine (EuroNanoMed3). A liquid corneal glue-filler as an alternative to transplantation in high-risk patients. (No. S-Euronanomed-19-1). The Coordinator - Université de Montréal, Centre de recherche Maisonneuve Rosemont (Canada), May Griffith; Partner 1 - Estonian University of Life Sciences (Estonia), Illimar Altosaar; Partner 2 - OZ Biosciences SAS (France), Olivier Zelphati; Partner 3 - Vilnius University, Life Sciences center, Institute of Biochemistry (funded by Research Council of Lithuania), Virginija Bukelskiene. 2019-2022.
The aim of this project was to confirm feasibility of the concept of patching corneal defects to avoid the need for transplantation. In this project, we used the high-risk pathology, Herpes Simplex Keratitis, caused by Herpes simplex virus serotype I (HSV-1) infection12. The efficacy of 3 composites consisting of (1) CLP-PEG-fibrin (liquid filler, which is hereinafter referred to as LiQD Cornea), (2) LiQD Cornea enriched with silicon nanoparticles coated with antiviral peptide GF19 (hereinafter referred to as SiNP-GF19) and (3) LiQD Cornea + SiNP-GF19 plus SiNPs with GF19 in an ointment to treat HSV-1 infection with inflammation has been conducted.
Main publication:
1. Malhotra, K., Buznyk, O., Islam, M. M., Edin, E., Basu, S., Groleau, M., ... & Šimoliūnas E., Liszka A., Patra H.K., Griffith, M. (2023). Phosphorylcholine and KR12-Containing Corneal Implants in HSV-1-Infected Rabbit Corneas. Pharmaceutics, 15(6), 1658.

The EU Joint Programme – Neurodegenerative Disease Research (JPND). Multicellular organoids: modelling, mechanisms and therapy development for C9ORF72-associatedd neurodegeneration. The coordinator – the University of Sheffield; Partner - Vilnius University, Life Sciences center, Institute of Biochemistry; Dr D. Baltriukienė. 2020-2023.
The goal of the JPND project is to create a 3D-bioprintable, neural cell-laden microfluidic system for studying neurodegenerative disorders, such as Alzheimer's and frontotemporal dementia.
COST action CA21139 3Rs concepts to improve the quality of biomedical science (IMPROVE). Dr D. Baltriukienė. 2022-2026.
The project aims to establish a network that will work on the refinement, harmonisation and promotion of 3R concepts, data and documents to improve the quality of biomedical science.

Contractual Research
Study of the regenerative properties of allogeneic bioactive substances using a critical size skin defect model in vivo. Customer: J. Stučinskaitė-Maračinskienė. Executor: Dr Egidijus Šimoliūnas

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INOVATION) PARTNERS
Maj Institute of Pharmacology, Polish Academy of Sciences, Poland
Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundacio de Recerca Clinic Barcelona-Institut d'Investigacions Biomediques August Pi i Sunyer, Spain
The Dairy Research Institute of Asturias (IPLA-CSIC), Asturias, Spain
University Pompeu Fabra, Barcelona, Spain
Universite de Montreal, Canada
Universidade do Porto, Portugal
Uppsala University, Sweden
Center for physical sciences and technology (FTMC), Vilnius, Lithuania
Vilnius University, Faculty of Physics, Laser Research Centre
Vilnius University, Faculty of Medicine
Vilnius University, Faculty of Physics
Vilnius University Hospital Santaros Klinikos,
Vilnius University Children‘s Hospital
UAB „Prodentum“
UAB „Experimentica“

OTHER SCIENTIFIC ACTIVITIES
Dr M. Alksnė
• Member of Baltic Laboratory Animal Sciensce Association (Balt-LASA)
• Member of the Lithuanian Biochemical Society
Dr D. Baltriukienė
• President of Baltic Laboratory Animal Science Association (Balt-LASA)
• Board member of the FELASA (Federation of European Laboratory Animal Science Associations)
• Member of the Lithuanian stem cell researchers association
• Member of the Lithuanian Biochemical Society
• Scientific supervisor of the section of Bioshemistry and Biology at the National Academy of Schoolchildren, https://nmakademija.lt/mokomieji-dalykai/
Dr V. Bukelskienė
• Member of Baltic Laboratory Animal Sciensce Association (Balt-LASA)
• Board member of FELASA (Federation of European Laboratory Animal Science Associations)
Dr A. Burokas
• Board member of Baltic Laboratory Animal Science Association (Balt-LASA)
• Member of the Lithuanian Microbiology Society (LMD)
• Member of the Lithuanian Neuroscience Association (LNA)
Dr I. Rinkūnaitė
• Board member of Baltic Laboratory Animal Sciensce Association (Balt-LASA)
• Member of the Lithuanian Biochemical Society
Dr E. Šimoliūnas
• Member of Baltic Laboratory Animal Sciensce Association (Balt-LASA)
• Member of the Lithuanian Biochemical Society

BEST REPORTS DELIVERED AT CONFERENCES ABROAD
1. D. Baltriukienė. Diet and Aging Induce Neuroinflammation and its Modulation by Prebiotics. ARC2023 (Aging and Rejuvenation Conference). July 17-18, 2023. Frankfurt, Germany.
2. E. B-M. Daliri. High temperature lacto-fermentation improves the antidiabetic activities of red beetroot. 16th International Scientific Conference on Probiotics, Prebiotics, Gut Microbiota and Health. June 20-22, 2023. Bratislava, Slovakia.
3. A. Megur. In vitro screening and characterization of Lactic acid bacteria from Lithuanian fermented foods with potential probiotic properties. IPC 2023 – International Scientific Conference on Probiotics, Prebiotics, Gut microbiota and Health. June 20-22, 2023. Bratislava, Slovakia.
4. E. Šimoliūnas. Bone tissue engineering: secretomes, ECM as a boosting tools. CED/NOF-IADR Oral Health Research Congress. September 21-23, 2023. Rhodes, Greece

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
Dr V. Bukelskienė
• Member at the Committee on genetically modified organisms, Ministry of Environmentof the Republic of Lithuania
• Member of the Lithuanian Ethics Commission for the Use of Experimental Animals at the State Food and Veterinary Service

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. D. Baltriukienė. How artificial tissues and organs are created? https://www.lrt.lt/mediateka/irasas/2000298941/mokslas-be-pamokslu-kaip-kuriami-dirbtiniai-audiniai-ir-organai (in Lithuanian)
2. Burokas. Psychobiotics - the future of humanity? A scientist explains why they are worth using for being both healthy and sick. At LRT.lt https://www.lrt.lt/naujienos/sveikata/682/1983139/psichobiotikai-zmonijos-ateitis-mokslininkas-paaiskino-kodel-juos-verta-naudoti-ir-sveikiems-ir-ligotiems (in Lithuanian)

DEPARTMENT OF MOLECULAR CELL BIOLOGY

Sauletekio av. 7, LT-10257 Vilnius
Phone (+370 5) 223 4409
E-mail:
Head – Prof. Rūta Navakauskienė

STAFF
Chief research associate: prof. Dr R. Navakauskienė
Senior research fellow: Dr V. V. Borutinskaitė, Dr A. Kalvelytė
Research fellows: Dr A. Zentelytė, Dr N. Krestnikova, Dr G. Valiulienė, Dr A. Imbrasaitė
Junior research fellows: A. Stulpinas, E. Valatkaitė
Doctoral students: R. Baušytė, G. Skliutė, A. Stulpinas, B. Vaigauskaitė, D. Žukauskaitė
Assistants: D. Andriūnienė, V. Novikienė

RESEARCH AREAS
• Evaluation of proliferation, differentiation and apoptosis signaling in human cancer and stem cells ex vivo, in vitro and in vivo
• Determination of epigenetic regulation in stem cells during self-renewing and differentiation
• Manipulation of signaling molecules in chemotherapeutic drugs-induced pathway for establishment of new strategies for targeted anti-cancer treatment of many tumors

RESEARCH PROJECTS CARRIED OUT IN 2023
Projects Supported by the University Budget

“Evaluation of the applicability of extracellular vesicles from mesenchymal stem cells for medication-resistant depression disorder treatment”, project No. MSF-LMT-3/2020, 2020-2024. Project leader Dr Giedrė Valiulienė.
In this study, our objective is to explore the neurogenic potential of human amniotic fluid stem cells (hAFSCs) and assess the applicability of extracellular vesicles derived from hAFSCs for the cell-free treatment of medication-resistant depression (TRD). Additionally, we will evaluate the effects of combining hAFSCs extracellular vesicle therapy with conventional TRD treatment, incorporating neural stimulation techniques.
Main publications:
1. Valiuliene, G., Valiulis, V., Zentelyte, A., Dapsys, K., Germanavicius, A., & Navakauskiene, R. (2023). Anti-neuroinflammatory microRNA-146a-5p as a potential biomarker for neuronavigation-guided rTMS therapy success in medication resistant depression disorder. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie, 166, 115313. https://doi.org/10.1016/j.biopha.2023.115313
2. Valiulienė, G., Zentelytė, A., Beržanskytė, E., & Navakauskienė, R. (2023). Effect of 3D Spheroid Culturing on NF-κB Signaling Pathway and Neurogenic Potential in Human Amniotic Fluid Stem Cells. International journal of molecular sciences, 24(4), 3584. https://doi.org/10.3390/ijms24043584

„Search for markers of implantation potential in culture medium of human blastocysts“, project No. MSFJM-10/2022, 2022-2023. Principal investigator: Dr Aistė Zentelytė.
The aim of assisted reproductive technology procedures is a successful implantation of a well-developed embryo into the uterine lining. However, the only method of embryo quality evaluation relies only on microscopic evaluation performed by an embryologist and such evaluation can be subjective and depend on the experience of the specialist. To improve rates of embryo implantation, additional biomarkers that reflect embryo quality and implantation potential are required. Thus, we performed mass spectrometry analysis of secreted proteins in culture media, and the analysis revealed significantly elevated levels of proteins related to cell-cell adhesion, such as Junction plakoglobin (JUP) and desmoglein-1 (DSG1), in implanted embryo group when compared to non-implanted embryos. The identified proteins could potentially be used as biomarkers to predict embryo quality and implantation potential, although further studies are required to validate these proteins as biomarkers.

“The Effect of Probiotic Bacteria on Decidualization of Human Reproductive System Stromal Cells”, project No. MSF-JM-19/2023, 2023-2024. Principal investigator: Elvina Valatkaitė.
This project will investigate possible causes of infertility of unknown origin, because despite recent technological advancements infertility has still remained a growing problem globally. The results obtained during this project will help to determine the differences in the microbiota composition between pregnant and non-pregnant patients in the endometrial tissues and in endometriosis tissues. This study will expand the knowledge about the profile of the microbiota of the human reproductive system, because currently the most knowledge is accumulated about the bacterial ecosystem that prevails in the intestinal system. Also, the conducted research would be used for further research related to the treatment of infertility and explaining the possible causes of infertility of unknown origin.
The main goal of this project is to investigate the microbial profile of endometrial and endometriosis tissue and evaluate the effects of stromal cells derived from prenatal derivatives and reproduction system on endometrial functionality.

National Research Projects

Research Council of Lithuania. „Targeted Research in Smart Specialization Areas. Project Designing of the patient-specific, heterogeneous lung cell ex vivo model system for drug efficiency prediction in personalized oncotherapy“ (No. 01.2.2-LMT-K-718-01-0072). Dr A. Kalvelytė. 2018-2023.
Modeling different cellular states by using human lung tumor-derived cell models it was shown dependence of cell fate-determining signaling molecules on the contact with other cells or substrate as well as on the relative strength of the inducer. The 3D method for evaluating the dependence of the therapeutic sensitivity of cells on intercellular contacts called SFEROMET was developed and tested. Scientific research and methodology, which incorporates cell phenotypic heterogeneity and is designed for in vitro screening of anticancer drugs, was conducted and submitted for patenting.
Main publication:
1. Stulpinas A, Sereika M, Vitkeviciene A, Imbrasaite A, Krestnikova N and Kalvelyte AV. Crosstalk between protein kinases AKT and ERK1/2 in human lung tumor-derived cell models. Frontiers in. Oncology. 2023, 12:1045521.

VU LSC-EMBL Partnership Institute - Associated Research Fellowship “Epigenomic analysis of genome engineered therapeutic cells – CAR-NK” 2022-2023, Dr V.Borutinskaitė, D.Žukauskaitė (funded by project „EMBL partnership Institute“ (Nr. 01.2.2-CPVA-V-716-01-0001)): the goal of the project was to study through epigenetic analyses how CAR-NK cells can be better engineered to integrate the activating pathways of a CAR into the effector properties of the vehicle cell – Natural Killer, as well as to resist inhibitory signals or utilize positive signals from epigenetic feedback loops. We will pursued this goal through two approaches: First, comparing the epigenetic marks of activated CAR-NK and inactive CAR-NK through histone-modifications immunoprecipitation and sequencing, as well as DNA methylation analysis. Second, through genetically engineering the vehicle cell to better account for the resulting epigenetic modifications, and their consequential stimulatory & inhibitory feedback loops.

Research project funded by Private Investment Fund “Ateities biomedicinos fondas”: “CAR-NK cell molecular research in in vitro and in vivo”, 2023-2025, Dr V.Borutinskaitė: during this project we will analyze the molecular profiles of engineered CAR cells, which have not been studied in detail so far. Also, this work will aim for the first time to modulate CAR cells according to established molecular mechanisms and different factors that change during CAR-engeneered cells activation. This would allow the development of more efficient CAR cell model lines. Cytotoxicity of the new CAR cell lines will be evaluated in vitro and in vivo model systems.

Project „Effect of stem cell therapy on in vivo recovery of ovarian reserve depletion after chemotherapy“, Programme "Development of Scientific Competence of Researchers, Other Researchers, Students through Practical Research Activities", supported by the Research Council of Lithuania, S-SV-23-44, Dr Borutinskaitė, I.Krastinaitė (2023 summer): during this study, the effects of MSC cells isolated from placenta, menstrual blood, endometrial tissue and follicular fluid on the POI model of mice was investigated. The aim of the study was to determine changes in the expression of proteins related to the folliculogenesis process in vivo after stem cell transplantation. This study is important for elucidating the mechanisms of MKL in PKN and would contribute to the development of further treatment strategies for PKN.
Results presented during a talk at The 66th International Scientific Conference for Students of Physics and Natural Sciences „OpenReadings“ (2023 m. April 18–21 d.), „Folicullogenesis-Related Gene Expression In Chemotherapy-Induced Premature Ovarian Failure Model“.

Project „Therapeutic potential of immune cells for the treatment of premature ovarian failure“, Programme "Development of Scientific Competence of Researchers, Other Researchers, Students through Practical Research Activities", supported by the Research Council of Lithuania, P-ST-23-76, Dr Borutinskaitė, I.Krastinaitė (2023-2024): this project aims to evaluate the therapeutic potential of human immune T cells for ovarian function in an animal model of premature ovarian failure. During the study, a mouse model of premature ovarian failure created by chemotherapy drugs will be used to transplant T cells into the ovaries of mice, evaluate the ability to restore fertility in the mouse model, and also determine changes in the expression of genes and proteins related to the folliculogenesis process in vivo. This study could contribute to the further development of treatment strategies for premature ovarian failure and infertility.

International Research Projects
EUREKA Network Application E!13638 Innova-Fertility project "Advanced technologies for innovative infertility treatment" No. 01.2.2-MITA-K-702-12-0004. Prof. Rūta Navakauskienė. 2021-2023.
Project is aimed to stimulate international collaborative research between academic institution (Vilnius University, Life Sciences Center, Institute of Biochemistry, Dept. of Molecular Cell Biology) and two SMEs - an international partner LLC “Institute of Cell Therapy" in Ukraine and Nanodiagnostika, Ltd., in Lithuania that will be directed to the development of an innovative technology for infertility treatment.

European Cooperation in Science and Technology, COST Action CA17116 International Network for Translating Research on Perinatal Derivatives into into Therapeutic Approaches (SPRINT). Prof. R. Navakauskienė & Dr Veronika Borutinskaitė. 2018-2023.

European Cooperation in Science and Technology, COST Action CA20113 - A sound proteome for a sound body: targeting proteolysis for proteome remodelling. Dr Veronika Borutinskaitė. 2021-2025

European Cooperation in Science and Technology, COST Action CA21113 - Genome Editing to Treat Humans Diseases (GenE-Humdi). Dr Veronika Borutinskaitė. 2022-2026
Main publications:
1. Navakauskienė, Rūta; Žukauskaitė, Deimantė; Borutinskaitė, Veronika Viktorija; Bukreieva, Tetiana; Skliutė, Giedrė; Valatkaitė, Elvina; Zentelytė, Aistė; Piešinienė, Lina; Shablii, Volodymyr. Effects of human placenta cryopreservation on molecular characteristics of placental mesenchymal stromal cells // Frontiers in bioengineering and biotechnology. Lausanne : Frontiers Media S.A. ISSN 2296-4185. 2023, vol. 11, art. no. 1140781, p. [1-16]. DOI: 10.3389/fbioe.2023.1140781. [Science Citation Index Expanded (Web of Science); Scopus] [IF: 5,700; AIF: 7,200; IF/AIF: 0,791; Q1 (2022, InCites JCR SCIE)] [CiteScore: 6,70; SNIP: 1,212; SJR: 0,930; Q1 (2022, Scopus Sources)] [S.fld.: N 004] [Contribution: 0,112] Grants: No. 13.1.1-LMT-K-702-12-0001]
2. Vaigauskaitė-Mažeikienė, Brigita; Baušytė, Raminta; Valatkaitė, Elvina; Maželytė, Rūta; Kazėnaitė, Edita; Ramašauskaitė, Diana; Navakauskienė, Rūta. Assisted reproductive technology outcomes and gene expression in unexplained infertility patients // Frontiers in cell and developmental biology. Lausanne : Frontiers Media SA. eISSN 2296-634X. 2023, vol. 11, art. no. 1217808, p. [1-10]. DOI: 10.3389/fcell.2023.1217808. [Science Citation Index Expanded (Web of Science); Scopus] [IF: 5,500; AIF: 6,200; IF/AIF: 0,887; Q1 (2022, InCites JCR SCIE)] [CiteScore: 6,30; SNIP: 0,995; SJR: 1,418; Q2 (2022, Scopus Sources)] [S.fld.: N 004, M 001] [Contribution: 0,142]
3. Baušytė, Raminta; Vaigauskaitė-Mažeikienė, Brigita; Borutinskaitė, Veronika Viktorija; Valatkaitė, Elvina; Besusparis, Justinas; Valkiūnienė, Rūta Barbora; Kazėnaitė, Edita; Ramašauskaitė, Diana; Navakauskienė, Rūta. Human endometrium-derived mesenchymal stem/stromal cells application in endometrial-factor induced infertility // Frontiers in cell and developmental biology. Lausanne : Frontiers Media SA. eISSN 2296-634X. 2023, vol. 11, art. no. 1227487, p. [1-17]. DOI: 10.3389/fcell.2023.1227487.s001. [Science Citation Index Expanded (Web of Science); Scopus] [IF: 5,500; AIF: 6,200; IF/AIF: 0,887; Q1 (2022, InCites JCR SCIE)] [CiteScore: 6,30; SNIP: 0,995; SJR: 1,418; Q2 (2022, Scopus Sources)] [S.fld.: N 004] [Contribution: 0,111]

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Linköping University (Sweden)
Malta University (Malta)
Murcia University (Spain)
Northwestern University (USA)

OTHER RESEARCH ACTIVITIES
Prof. Rūta Navakauskienė
• Member of American Society for Cell Biology
• Member of Lithuanian Stem Cell Researchers Association
• Member of Federation of European Biochemical Society
• Member of International Perinatal Stem Cell Society
Dr Veronika Borutinskaitė
• Member of Lithuanian Stem Cell Researchers Association
• Member of Federation of European Biochemical Society
• Member of expert group, Research Council of Lithuania/ Agency for science, innovation and technology/ Expert at the Research Executive Agency (REA)/European Commission
• Guest Editor at special issue “Genetic Basis of Leukemia”, Genes (ISSN 2073-4425).
Dr Audronė Valerija Kalvelytė
• Member of Lithuanian Stem Cell Researchers Association
• Member of Federation of European Biochemical Society

DEPARTMENT OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Sauletekio av. 7, LT-10257 Vilnius
Phone (+370 5) 223 4386
E-mail:
Head – Dr Rolandas Meškys

STAFF
Chief research fellow: Dr R. Meškys.
Senior research fellows: Dr V. Časaitė, Dr L. Kalinienė, Dr L. Truncaitė, Dr J. Stankevičiūtė
Research fellows: Dr A. Aučynaitė, Dr R. Gasparavičiūtė, Dr V. Petkevičius, Dr S. Povilonienė, Dr R. Rutkienė, Dr M. Sadauskas, Dr R. Stanislauskienė, Dr E. Šimoliūnas, Dr N. Urbelienė, Dr A. Zajančkauskaitė.,
Junior research fellows: J. Vaitekūnas, A. Noreika, M. Šimoliūnienė
Doctoral students: V. Preitakaitė, R. Jamontas, A. Krupeckaitė, E. Žukauskienė, M. Koplūnaitė, G. Plakys, R. Statkevičiūtė.

RESEARCH INTERESTS
• Molecular biology and genetics of bacteria and bacteriophages
• Genetic and biochemical diversity of microorganisms, enzyme biotechnology

DEPARTMENT OF XENOBIOTICS BIOCHEMISTRY

Sauletekio av. 7, LT-10257 Vilnius
Phone (+370 5) 223 4392
E-mail:
Head – Habil. Dr Narimantas Čėnas

STAFF
Chief research fellow: habil. Dr N. Čėnas.
Senior research fellows: Dr Ž. Anusevičius, Dr K. Krikštopaitis, Dr J. Šarlauskas.
Research fellows: Dr M. Lesanavičius, Dr L. Misevičienė, Dr B. Valiauga.
Senior specialists: Dr A. Marozienė, Dr L. Kosychova.

RESEARCH INTERESTS
• Investigations of the molecular mechanisms of the antitumour activity and cytotoxicity of quinones, in particular the impact of their redox activity on their cytotoxic action.
• Investigations of the molecular mechanisms of cytotoxicity of novel nitroaromatic compounds, aromatic N-oxides and related compounds, in particular the impact of their redox properties and ability to inactivate antioxidant flavoenzymes.
• The studies of the catalytic mechanism of mamalian, parasite and bacterial quinone- and nitroreductases.
• The studies of redox reactions of flavo-heme, flavo-sulfo, and flavo-sulfo-selenium enzymes possibly participating in the bioreductive activation of quinones and aromatic nitrocompounds and N-oxides.

RESEARCH PROJECTS CARRIED OUT IN 2023
Project Supported by the University Budget
Molecular Mechanisms of Enzymatic Activation, Detoxification, Biodegradation, and Cytotoxicity of Redox Active Xenobiotics. Habil. Dr N. Čėnas. 2017–2025.
Our main results this year were following: i) we aimed to distinguish the roles of enzymatic redox cycling and the inhibition of thioredoxin reductase (TrxR) by nitroaromatic (ArNO2) anticancer agents Stattic, Tri-1, and NSC697923. It was found that the above compounds possess at least 10-fold greater cytotoxicity than can be expected from their redox cycling activity. This may be related to irreversible TrxR inhibition, however, a contribution of a parallel inhibition of glutathione reductase (GR) s also possible; ii) the studies of tirapazamine (TPZ)-resistant MH22a cells (resistance index, 5.64) revealed the increased expression of the antioxidant enzymes GR, aldehyde- and alcohol dehydrogenases, carbonyl reductases, catalase, and of xenobiotics conjugating glutathione-S-transferases. The expression of NADPH:cytochrome P450 reductase, which is mainly responsible for the single-electron reduction of TPZ, was decreased by 2.1 times. These data support the fact that the main mechanism of TPZ aerobic cytotoxicity is oxidative stress, which is mainly non-site-specific; iii) We proposed a modified quantum mechanical method of estimation of single-electron reduction potential (E17) of ArNO2 in aqueous medium, based on the use of the dielectric continuum model together with a certain number of H2O molecules at the vicinity of nitro group. It enabled us to calculate the E17 values for 19 ArNO2 (n = 19) with the insignificant deviation from the experimentally determined ones. Apart from nitrobenzene derivatives, this approach is suitable for the representatives of nitropyridines, nitrofurans, nitrothiophenes, and nitrothiazoles, and iv) the investigation of a series of polynitroaromatic secondary nitramines was performed to reveal the impact of incremental methylene groups on the oxygen balance, stability, mechanical sensitivity and energetic properties.
Main publications:

1. Nemeikaitė-Čėnienė, A., Misevičienė, L., Marozienė, A., Jonušienė, V., Čėnas, N. Enzymatic redox properties and cytotoxicity of irreversible nitroaromatic thioredoxin reductase inhibitors in mammalian cells. International Journal of Molecular Sciences, 2023. 24:12460.
2. Nemeikaitė-Čėnienė, A., Haberkant, P., Kučiauskas, D., Stein, F., Čėnas, N. Redox proteomic profile of tirapazamine-resistant murine hepatoma cells. International Journal of Molecular Sciences, 2023. 24:6863.
3. Tamulienė, J., Valiauga, B., Čėnas, N. Modified quantum mechanical approach fr the estimation of single-electron reduction potenttial of nitroaromatic compounds in aqueous medium. Free Radical Research, 2023. 57:153-160.
4. Tamulienė, J., Šarlauskas, J. Impact of incremental methylene groups on the energetic properties of aromatic nitramines. Energies, 2023. 16:3117.

Bilateral Research Projects
Research Council of Lithuania: NADH:ubiquinone reductase-II of Plasmodium falciparum as a target of redox active antiplasmodial agents (Bilateral Lithuanian-French project ‚Gilibert‘, No. S-LZ-23-2). Habil. Dr N. Čėnas. 2023-2024.
The aim of this project is to characterize the catalysis scheme and oxidant substrate specificity of NADH:ubiquinone reductase-II of malaria parasite P. falciparum (PfNdh2). It was found that this enzyme performs two-electron reduction of quinones and ArNO2, and follows a ‘ping-pong’ mechanism. There exists a scattered parabolic dependence of reactivity of these groups of oxidants on their E17. The derivatives of ubiquinone and potential antiplasmodial agents, derivatives of plasmodione, possess enhanced reactivity evidently due to their high lipophilicity.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INOVATION) PARTNERS
CNRS, Gif-sur-Yvette (France)
Kanazawa University, Kanazawa (Japan)
Universita degli Studi di Milano (Italy)
Universite de Strasbourg (France)
Victoria University of Wellington (New Zealand)

OTHER SCIENTIFIC ACTIVITIES
Habil.Dr N. Čėnas
• Member of Editorial Board of International Journal of Molecular Sciences (section Biochemistry);
• Member of the Management committee of COST action CA21111 ‘OneHealth drugs against parasitic vector borne diseases in Europe and beyond’, 2022-2026.
Dr J. Šarlauskas
• Nominated foreign member of Sweden Detonation Society.

LABORATORY OF BIOORGANIC COMPOUNDS CHEMISTRY

Mokslininku str. 12A, LT-08412 Vilnius
Phone (+370 5) 2729058
E-mail:
Head – Dr Mantas Jonušis

STAFF
Research fellows: Dr M. Jonušis
Senior researcher biochemist: Dr Algirdas Klimavičius
Researcher biochemists: Dr Regina Jančienė, Dr Zita Staniulytė, Jonas Meškauskas, Ričardas Rozenbergas
Junior research fellows: Simona Jonušienė
Junior administrator: Stanislava Palaikienė
Specialists: Kazimieras Vitkauskas
Laboratory technicians: Ilona Levutienė, Ala Peteraitienė, Olga Sivova, Juozas Puzas
Synthesis of heterocyclic, carbocyclic, amino acid and polyether derivatives, design and development of chemical process technology, total synthesis, scaleup of chemical processes, custom synthesis, green chemistry.

RESEARCH PROJECTS CARRIED OUT IN 2023
Project Supported by the University Budget
Investigation of the synthesis and structure of modulators and catalysts of biological processes (Dr M. Jonušis)
Synthesis and investigation of substituted 1,5-benzodiazepine derivatives.
Investigation and optimization of synthesis methods of polyethylene glycol modified indole derivatives.
Studies of C6 sugars conversion by establishing various catalytic processes.
1,5-Benzodiazepines are class of heterocyclic compounds that have received considerable attention due to their broad spectrum of biological activity. In order to better understand activity of 1,5-benzodiazepines, series of linker (ethanol amine, amino acid esters, propargylamine, etc.) modified (2nd position of benzodiazepine ring) derivatives were synthesized and studied on animal models. It was considered that compounds modified with ethanolamine were the most toxic due to the demise of mice at 24 h after single subcutaneous injection. One-time administration of other tested substances did not evoke any visible signs of toxicity, or statistically significant changes in counts of blood cells.
Indole compounds play an important role in pharmaceutical, dye and electronic industries. However, poor solubility of indole derivatives in water media is often encountered problem. We have investigated and optimized synthesis methods for polyethylene glycol modified indoles which are water soluble. Different length (n=3-9) of polyethylene glycol modified indoles were studied.
Increasing popularity of green chemistry and renewable resources made searching for a
new environmentally friendly plastics and monomers an important task for scientific community. Our goal was to study selective catalytic cleavage reactions of C6-Sugars. Cation exchangers (H form) were employed as catalysts in amounts ranging from 2.5% - 10%. The addition of NaCl resulted in a decrease in the pH of both water and organic solvent-based reaction media, leading to improved H+ exchange on cation exchangers.
Main publications:
1. Thuy Vu, Thi Tuyet; Liu, Shentan; Jonušis, Mantas; Jonušienė, Simona; Choi, Jinsik; Kawano, Riko; Rehnberg, Nicola; Hatti-Kaul, Rajni; Pyo, Sang-Hyun. Sustainable one-pot synthesis of 5(Hydroxymethyl)furfural from C6-sugars by enhanced H+ exchange heterogeneous catalysis // ACS sustainable chemistry & engineering. Washington : American Chemical Society (ACS). eISSN 2168-0485. 2023, 11, 48, 17130–17141.
2. Jonušis, Mantas; Vektarienė, Aušra; Mikulskienė, Gema; Jonušienė, Simona; Vektarytė, Dalia; Jančienė, Regina. Unexpected transformation of 1,5-benzodiazepine derivatives under imidazo-annulation reaction conditions // Chemistry of heterocyclic compounds. New York : Springer. ISSN 0009-3122. eISSN 1573-8353. 2023, vol. 59, no. (4/5), p. 283-288.
3. Vektarienė, Aušra; Jančienė, Regina; Jonušis, Mantas; Vektarytė, Dalia; Jonušienė, Simona. Ambidentinių anijonų aktyvumo tyrimas kvantinės chemijos metodais 1,4- ir 1,5- benzodiazepinonuose // 45-oji Lietuvos nacionalinė fizikos konferencija, 2023 m. spalio 25-27 d., Vilnius : programa ir pranešimų tezės. Vilnius : Vilniaus universiteto leidykla, 2023, abstract no.S1 - P61. eISBN 9786090709818. p. 142. (Vilnius University Proceedings, eISSN 2669-0233 ; vol. 38).

Contractual Research
The search for new enzymes for the decontamination of not self-decomposing in nature industrial waste. Contract with UAB Ekorama. Dr M. Jonušis

Investigation of the functionalization of cyano groups of 2-(p-cyanphenyl)-6-cyanindole by optimizing the DAPI synthesis scheme and the synthesis of experimantal samples of DAPI dihydrochloride. Contract with UAB Elymus. Dr R. Jančienė.

Investigation of used solvent regeneration processes and delivery of experimental examples". Contract with UAB Vilniaus Ventos puslaidininkiai. Dr M. Jonušis.

Optimization of synthesis technology of 3,6 -dichlorotetrazine. Contract with UAB Sanobiotech Novus. Dr R. Jančienė.

Synthesis of pantetine-4‘,4‘‘-diphosphate. Contract with UAB „Thermo Fisher Scientific Baltics“. Dr M.Jonušis.

Oxidation of condensed non-aromatic systems with air oxygen in the presence of different catalysts. Contract with UAB Sanobiotech Novus. Dr M Jonušis.

Development of a pathway for the organic synthesis of nicotinamide mononucleotide. Contract with UAB CMB Medicina. Dr M Jonušis.

Development, scaling up and optimization of technologies for the synthesis of isoxazole derivatives. Contract with MB Molecule projects. Dr M Jonušis.

Development of viable methods for the synthesis of various organic compounds and preparation of their experimental batches. Contract with Synthon Chemicals GmbH (Germany). Dr M. Jonušis.
Research in scaling up of a continous new method for making 5-hydroxymethylfurfural. Contract with Ramidus AB (Sweden). Dr M. Jonušis.

Synthesis of 2-Trimethyl-1,3-dithiane. Contract with TCI Europe N. V. (Belgija). Dr R. Jančienė.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INOVATION) PARTNERS
Center of Physical Sciences and Technology (Lithuania)
UAB „Thermo Fisher Scientific Baltics “(Lithuania)
Polypure AS (Norway)
Ramidus AB (Sweden)
Synthon Chemicals GmbH & Co.KG (Germany)
UAB Sanobiotech Novus (Lithuania)
UAB Elymus (Lithuania)
UAB Vilniaus Ventos puslaidininkiai (Lietuva)
UAB Ekorama (Lietuva)
UAB CMB medicina
TCI EUROPE N.V.
MB Molecule projects

PROTEOMICS CENTRE

Sauletekio av. 7, LT-10257, Vilnius
Phone (+370-5) 223 4410
E-mail:
Head – Dr Mindaugas Valius

STAFF
Chief research associate: Dr M. Valius
Research fellows: Dr A. Kaupinis, Dr M. Ger, Dr N. Dreižė, S. Urnikytė,
Doctoral students: J. Černuševič

RESEARCH INTERESTS
• Eukaryotic cell regulation mechanisms (signalomics)
• Mechanisms of anticancer drug resistance
• Drug repurposing to treat cancer
• Nanomaterials for therapy
• Cell senescence
• Proteomics, kinomics, phosphoproteomics

RESEARCH PROJECTS CARRIED OUT IN 2023
Projects Supported by the University Budget
Proteomic analysis of genome engineered therapeutic cells – CAR-NK, Associated Research Fellowship with VU LSC-EMBL Partnership Institute. 2022–2023.
CAR-T, which corresponds to T lymphocytes containing a synthetic therapeutic gene of the structure of Chimeric Antigen Receptors (CAR), is the leading example in the cell-based cancer therapeutics. In this study we aim to analuse through various proteomics technologies how CAR-NK cells can be better engineered to integrate the activating pathways of a CAR into the effector properties of the vehicle cell – Natural Killer.

National Research Projects
Research Council of Lithuania “Elucidation of cancer drug resistance molecular mechanisms to improve tumor therapy outcome” (CaDRez). Project leader Dr M. Valius, 2023–2026
Anticancer therapies frequently result in the rise of drug-resistant cells. Here we will develop global protein kinase network assessment approach to discover new drug resistance mechanisms and tackle them with PK inhibitors. The project will allow to develop proof-of-concept cancer treatment model based on primary drug and additional therapeutic that suppresses development of drug resistance in cancer cells.

Future Biomedicine Fund. “Innovative approach to identify pancreatic cancer signaling pathways for individual therapy selection using targeted therapy with repurposed drugs” (KDA-omika); Project leader Dr M. Valius, 2023–2025
Drug repurposing for cancer treatment is a fast and efficient strategy for the discovery of novel cancer and patient-specific drugs. Here we aim to develop an innovative method enabling the identification of cancer-related signaling pathways based on the detection of protein kinase activity changes in pancreatic cancer patient material and use it for the prediction of individual targets for the therapy with repurposed drugs.

International Research Projects

Research Council of Lithuania M-ERA.NET Call 2022. “Customised DNA-based nanocarriers to boost heart healing” (DNABEATS); work package of VU-LSC led by Dr M. Valius, 2023–2026.
The goal of the project is the development of advanced nanocarriers to unlock the potential of miR-based gene therapy and thus lead the fight against heart failure. We will develop customised DNA-based nanocarriers (DNCs) for a selective and efficient delivery of cardio-regenerative miR molecules to the heart, analyse the biological interaction of these DNCs with cardiac cells and their biodistribution and biocompatibility in terms of biodegradation, toxicity, immune and inflammatory response.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INOVATION) PARTNERS
University of Saragossa (Spain)
Aragon Health Research Institute (Spain)
Vilnius Unioversity Hospital Santaros Klinikos
National Cancer Institute (Lithuania)
University of North Carolina at Chapel Hill (USA)

OTHER SCIENTIFIC ACTIVITIES
Dr Mindaugas Valius, journal “Cells“ (MDPI), special issue editor.

INSTITUTE OF BIOSCIENCES

7 Saulėtekio ave, LT-10257 Vilnius
Tel. 239 8210, fax 239 8204
E-mail:
https://www.gmc.vu.lt/bmi
Dean – Prof. Dr Eglė Lastauskienė

DEPARTMENTS OF THE INSTITUTE
Department of Biochemistry and Molecular Biology
Department of Botany and Genetics
Department of Microbiology and Biotechnology
Department of Neurobiology and Biophysics
Department of Zoology
Centre for Ecology and Environmental Research

DEPARTMENT OF BIOCHEMISTRY AND MOLECULAR BIOLOGY

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 239 8225
E-mail:
Head – Dr Aušra Sasnauskienė

STAFF
Professors: Dr S. Serva, Dr V. Starkuvienė (part-time), Dr K. Sužiedėlis (part-time).
Associate professors: Dr J. Armalytė, Dr V. Jonušienė, Dr D. Labeikytė, Dr A. Markuckas, Dr A. Sasnauskienė, Dr A. Zimkus.
Assistant professors: Dr L. Aitmanaitė, Dr A. Konovalovas, Dr A. Mikalkėnas, Dr E. Žalytė.
Teaching assistant: V. Žitkutė.
Lecturer: Z. Žitkus.
Senior researchers: Dr J. Armalytė, Dr A. Sasnauskienė. Dr J. Skerniškytė.
Researchers: Dr V. Jonušienė, Dr A. Konovalovas, Dr D. Labeikytė, Dr A. Zimkus, Dr E. Žalytė.
Research assistants: Dr L. Aitmanaitė. V. Žitkutė.
Doctoral students: E. Celitan, A. Jasinevičius, L. Klimkaitė, T. Liveikis, G. Skinderytė.

RESEARCH INTERESTS
• Molecular virology: mechanisms and applications
• Bacterial pathogenesis, bacterial interaction with immune cells, antibiotic resistance, opportunistic pathogens
• Molecular mechanisms of resistance to anti-cancer treatment
• Molecular mechanisms of intracellular trafficking

RESEARCH PROJECTS CARRIED OUT IN 2023
Projects Supported by the University Budget:
Investigation of Mechanisms of Cellular Homeostasis and Their Clinical and Biotechnological Application. Groups of Dr J. Armalytė, Dr A. Sasnauskienė, Prof. Dr S. Serva, Prof. Starkuviene-Erfle.
Molecular analysis of viruses, bacterial and eukaryotic cells: 1) research on molecular biology of yeast dsRNA viruses and application of biologic nano-scaffolds for facilitated delivery of bioactive compounds; 2) microbial pathogenesis of gram-negative bacterial pathogens with the emphasis on opportunistic pathogens, molecular mechanisms of antibiotic resistance and its spread and evolution; 3) cellular and molecular mechanisms of cancer cell`s resistance to anti-cancer treatment; 4) molecular mechanisms of membrane trafficking.

Science Promotion fund of Vilnius University:
Project “Prevalence of genetic determinants of antibiotic resistance in the opportunistic pathogens Acinetobacter baumannii and Stenotrophomonas maltophilia” (MSF-JM-12/2023). Project leader – L. Klimkaitė, project participant – T. Liveikis, 2023-2024.
170 Acinetobacter baumannii and 69 Stenotrophomonas maltophilia isolates were collected from patients of Vilnius university hospital Santaros klinikos. Genetic similarity of isolates was determined using Pulsefield gel electrophoresis or BOX-PCR. Mobile genetic determinants (plasmids and integrons) were analysed.

Project “DNA engineering tools for pathogen identification in bioarchaeological samples” funded by Vilnius University Science promotion program (MSF-JM-14/2022); Project leader - A. Konovalovas, 2022-2023.
The project goal is to create a tool for identifying pathogenic microorganisms in bioarchaeological material and performing their genome sequencing.

Project “Development of model system of endometrial cancer” (MSF-JM-17/2022). Project leader – E. Žalytė, 2022–2023.
The aim of the project is to derive primary cell lines from the postoperative tissue of Lithuanian endometrial cancer patients. Established lines are characterized by assessing their doubling time, expression of cancer and stem cell markers, colony-forming efficiency, karyotype, mutations in cancer-related genes and sensitivity to anticancer drugs.
The permission from the Bioethics Committee (No. 2022/11-1464-938) for generation of endometrial cancer model using postoperative cancer tissue has been received (Head Dr V. Jonušienė).

VU LSC-EMBL Partner Institute Associated Research Fellowships:
Project “CRIPSR-based enrichment strategy for targeted long read sequencing“; 2022-2023, Project leader – A. Konovalovas.
The project objective is to develop simple and universal CRIPSR-based enrichment method for targeted long read sequencing and show that it can be used for the analysis of samples of different origins.

Project „Investigation of endocytosis-mediated off-targets effects of gene silencing“, 2022-2023. Project leader – V. Starkuviene-Erfle, participants, S. Liechocki, V. Žitkutė, E. Juciūtė.
The objective was to investigate the efficiency and dynamics of gene editing after delivering sgRNAs in cells stably expressing Cas9 and delivering sgRNA-Cas9 as RNP complexes. The appearance of on-target and off-target phenotypes in time were quantitatively assessed.

Research Council of Lithuania, Research Group Projects:
Project “Facilitated delivery of bioactive compounds: versatile toolkit for biomedical applications (DECORATION)”, Research Council of Lithuania, No. S-MIP-23-28 (2023-2026). Project leader – S. Serva.
Development of universal and multipurpose cargo delivery system is proposed by employing intrinsic yeast viruses. The special value of such system is in addressing diverse needs from fundamental research to biotechnology and medical engineering. Once developed, it presumes a great potential for outreach into healthcare by expanding into preparation of nanomaterials with unique properties and applications.

Project “Investigation of capsular polysaccharides and outer membrane vesicles as virulence factors in pathogenesis of opportunistic bacteria (CapOmBact)”, No. S-MIP-23-109 (2023-2026). Project leader – J. Skerniškytė.
The main virulence properties that allow bacteria to establish themselves in hospitals are: 1) ability to form biofilms on medical devices during the pre-infection phase and 2) resistance to the host's immune response during infection. The lack of knowledge about the specific virulence factors of opportunistic bacteria hinders the development of new antibacterial drugs. In this project, we propose a new approach to the study of the pathogenesis of opportunistic bacteria. We hypothesize that bacterial capsular polysaccharides (CPS) and outer membrane vesicles (OMVs) may be the key virulence factors during HAIs.

Project “Application of an integrated approach for the investigation of genetic causes of rare inherited disorders (ATGC)”, No. S-MIP-21-15 (2021-2023). Participant – A. Sasnauskienė.

Research Council of Lithuania. Target scientific research in smart specialization field (SMART):
Project Individualised nasal microbiome test – novel tool for diagnostics and health care (YourAirwayMicrobiome) (01.2.2-LMT-K-718-03-0079) (2021-2023). Project partner for research performed at Vilnius University Julija Armalytė.
The project was completed during the year 2023. At the end of the project, a thorough analysis of more than a 100 human respiratory tract microbiomes was performed, including the evaluation of lower respiratory tract microbiome composition of bronchiectasis patients, as well as comparison of upper respiratory tract microbiomes in healthy volunteers and people suffering from chronic respiratory tract conditions.

Future Biomedicine Fund:
Project “Modeling Endometrial Cancer for Personalized Therapy” (No. (1.78) SU-442). Project leader – Dr E. Žalytė. 2023-2026.
The aim of the project is to develop 2D and 3D in vitro systems of endometrial cancer and apply them for individualized treatment research.

Research Council of Lithuania, Projects for Development of Scientific Competences of Scientists, other Researchers and Students through Practical Research Activities:
Project “Biocontrol of wild berry microbiota composition by yeast counterpart (CONFIDENT)” (P-PD-22-058) (2022-2024). Project leader – S. Serva.
For the first time, comprehensive profiling of wild berry microbiomes will be performed and the relationship between the composition and functioning of microbial taxa addressed. The composition of eukaryotic counterpart will be further investigated to decipher the role of fungi in biocontrol of food safety.

Project “Linkage of biocidal phenomenon of natural yeast and native antiviral systems”, Research Council of Lithuania, No. S-ST-23-92 (2023-2024). Project leader – S. Serva.
The topic of the scientific research is the study of the dependence of the phenotypic expression of the yeast biocidal phenomenon, determined by two virus systems, on genomic antiviral systems. These systems have a clear evolutionary link with the corresponding prokaryotic systems and are extremely attractive targets for fundamental and applied studies. The project is dedicated to the identification of these systems in natural yeast isolates and further bioinformatic and biochemical study of these systems.

Project “Analysis of virulence factors of natural isolates of the opportunistic pathogen Stenotrophomonas maltophilia” (P -SV -23 -156) (2023). Project leader – J. Skerniškytė.
There is almost no information about the determinants of resistance and virulence, phenotypes and the ability to cause infections common to isolates of natural origin common in the world and in Lithuania. The aim of this project is to evaluate the antibiotic resistance phenotype of natural isolates of S. maltophilia isolated from different areas of Lithuania, by studying their sensitivity to antimicrobial substances, the prevalence of antibiotic resistance genes and genes encoding virulence factors.

Project “Characterization of proteases secreted by the opportunistic pathogen Stenotrophomonas maltophilia” (P -ST -23 -136) (2023-2024). Project leader – J. Skerniškytė.
Although bacterial proteases involved in tissue invasion and damage are thought to play an important role in the pathogenesis of opportunistic bacteria, the extracellular proteases synthesized by S. maltophilia are still poorly understood. The aim of this project is to describe the secreted proteases common in clinical isolates of S. maltophilia and to evaluate their role in the pathogenesis of the bacterium.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Lithuanian University of Health Sciences (Lithuania)
Nature Research Centre (Lithuania)
Centre for Innovative Medicine (Lithuania)
National Cancer Institute (Lithuania)
University of Ostrava (Czech Republic)
Masaryk University (Czech Republic)
Heidelberg University (Germany)
Universite Libre de Brussels (Belgium)
Université Paris-Saclay (France)
Université de Strasbourg (France)

OTHER RESEARCH ACTIVITIES
Prof. S. Serva
• CEO of Association Futura Scientia;
• Chairman of Lithuanian Biochemical Society; Head of organizing committee of XVI International LBS Conference “Biochemistry Targeting Diseases” (Taujėnai, Lithuania).

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
Prof. S. Serva
• Chairman of GMO Expert Commitee at Ministry of Environment of Lithuania;
• Member of Expert Board for Biomedical and Agrosciences at Agency for Science, Innovation and Technology of Lithuania.

BEST REPORTS DELIVERED AT CONFERENCES ABROAD
Oral presentations:
1. J. Armalytė. 5th Congress of Baltic Microbiologists (CBM2023) (Vilnius, Lithuania). Oral presentation “Insights into the microbial composition of the respiratory tract of bronchiectasis patients”;
2. Konovalovas. The Silent Architects of Yeast Genome. EMBO Workshop: The mobile genome: genetic and physiological impacts of transposable elements. 2023 November 8-11. Heidelberg, Germany;
3. S. Serva. COST Action CA17103 (DARTER) Congress in Bilbao, Spain;
4. S. Serva. Invited lecture at NanoTech Poland 2023 conference (Poznan, Poland);
5. S. Serva. Opening, session moderation and organization of the 2023 FEBS Education Ambassadors Meeting in Vilnius;
6. S. Serva. Moderation of session and closing discussion at the Jędrzej Sniadecki Memorial Conference “Frontiers in Molecular Life Sciences” (JSMC-2023) in Vilnius.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. Sasnauskienė:
https://www.15min.lt/gyvenimas/naujiena/sveikata/dr-a-sasnauskiene-kas-ivyksta-musu-lastelese-sergant-veziu-arba-retomis-genetinemis-ligomis-1028-2148706
2. J. Skerniškytė:
https://naujienos.vu.lt/spectrum-oportunistines-infekcijos-kam-pavojingos-ir-kaip-nuo-ju-apsisaugoti/

DEPARTMENT OF BOTANY AND GENETICS
Saulėtekio al. 7, LT-10257 Vilnius
Tel. 239 8257
E-mail:
Head – Prof. Dr Habil. Juozas Lazutka

STAFF
Professors: Dr S. Jarmalaitė, Dr E. Kutorga, Dr Habil. I. Pašakinskienė (part-time), Dr D. Žvingila.
Associate professors: Dr T. Čėsnienė, , Dr R. Šiukšta (part-time), Dr K. Daniūnaitė (part-time), Dr V. Dedonytė (part-time), Dr K. Noreikienė (part time), Dr R. Sabaliauskaitė (part time), Dr J. Butkuvienė (part time), Dr J. Patamsytė (part time), Dr R. Rimgailė-Voicik (part-time)
Lecturers: S. Juzėnas, A. Meldžiukienė, P. Venckus, A. Stapulionytė
Assistants: Dr I. Prigodina Lukošienė (part-time), Dr K. Šnipaitienė, Dr R. Kubiliūtė (part-time)
Junior Assistants (part time): B. Buragaitė Staponkienė, V. Mensonas, M. Babonaitė, V. Pukenytė, A.E. Clarke, R. Maleckaitė
Senior Researchers: Dr K. Noreikienė (part time), Dr K. Daniūnaitė (part time), Dr J. Patamsytė (part time), Dr R. Šiukšta (part-time)
Researchers: Dr V. Dedonytė (part-time), Dr J. Mierauskienė, Dr R. Rimgailė-Voicik, Dr K. Šnipaitienė. Dr R. Kubiliūtė (part-time), Dr D. Dabkevičienė (part time), Dr M. Rasimavičius
Senior biologists: Dr J. Rukšėnienė, Dr V. Kleizaitė, Dr V. Vaitkūnienė
Doctoral students: L. Šiaulienė, I. Vincerževskienė, M. Babonaitė, J. Gaiževska, R. Maleckaitė, A. Šeštokaitė, B. Buragaitė-Staponkienė, K. Žukauskaitė, I. Vaicekauskaitė, E. Vabuolė, V. Pukenytė, V. Mensonas, A.E. Clarke.

RESEARCH INTERESTS
• Search and application of the most effective biomarkers for genetic monitoring of human, animal and plant populations
• Investigation of mutagenic and antimutagenic effects of chemical compounds in human cells in vitro and experimental model systems in vivo
• Epigenomic and genomic profile of human diseases
• Studies of DNA polymorphism in plant populations
• Plant developmental, population genetics and phylogenetics
• Plant, algae and fungal species diversity, systematics, sociology, biology, ecology and distribution
• Research and monitoring of rare, protected and alien plant and fungal species
• Research in algal biotechnology
• Composition, structure and dynamics of lichen and plant populations
• Studies of fungal, algae, lichen and plant collections, maintained in the Herbarium of Vilnius University; study of the history of botany in Lithuania
• Mechanisms of animal adaptation to challenging environments
• Genetic diversity and distribution of complex life cycle parasites

RESEARCH PROJECTS CARRIED OUT IN 2023
Projects Supported by the University Budget
Function, Variability and Genome Structure in Higher Eukaryotes. Prof. J. R. Lazutka, Prof. S. Jarmalaitė.
Recent genome-scale analyses have provided novel insights into the genomic and epigenomic landscape of various diseases, including mutational profiles, DNA methylation, protein-coding and microRNA (miRNA) expression patterns. Despite the validation of previously known alterations, various newly discovered genetic and epigenetic features have been proposed as measures of cancer aggressiveness as well as tools for diagnosis. Using a variety of genome-wide and target-oriented methodologies, we aim at the development of (epi)genetic biomarkers of various human tumours (prostate, ovarian, etc.) and other chronic diseases, like periodontitis. These biomarker panels are used for liquid biopsy-based diagnostic and prognostic tests development. Genome alterations in other diseases sush as diabetes were investigated as well.
Main publications:
1. Žilovič D, Vaicekauskaitė I, Čiurlienė R, Sabaliauskaitė R, Jarmalaitė S. Uterine Cavity Lavage Mutation Analysis in Lithuanian Ovarian Cancer Patients. Cancers (Basel). 2023; 15(3), 868: 7-30. DOI: 10.3390/cancers15030868
2. Buragaite-Staponkiene B, Rovas A, Puriene A, Snipaitiene K, Punceviciene E, Rimkevicius A, Butrimiene I, Jarmalaite S. Gingival Tissue MiRNA Expression Profiling and an Analysis of Periodontitis-Specific Circulating MiRNAs. Int. J. Mol. Sci. 2023, 24(15), 11983: 1-18; DOI: 10.3390/ijms241511983 https://pubmed.ncbi.nlm.nih.gov/37569358/ 5.6 Q1
3. Šiaulienė L, Kazlauskaitė J, Jurkėnaitė D, Visockienė Ž, Lazutka JR. Influence of Body Mass Index and Duration of Disease on Chromosome Damage in Lymphocytes of Patients with Diabetes. Life. 2023; 13(9):1926. https://doi.org/10.3390/life13091926

Plant Polymorphism, Genome Stability and its Changing Factors. Prof. D. Žvingila.
Genetic polymorphism as a fundamental component of biodiversity is critical in the situation of the global climate change and is exploited in plant species conservation and breeding. We studied the natural and induced plant genome variability using genetic, biochemical, statistical and bioinformatical methods. Common reed is often used as a model plant to study anthropogenic impacts on ecosystems at local and global scales. As a community-forming species, it is directly exposed to the impacts of human activities on the ecosystem. The aim of our study was to evaluate the patterns of genetic diversity in common reed stands located in habitats differently affected by anthropogenic factors. We studied whether riverbed modifications, land cover in the neighborhood of the stand, and the chemical and physical parameters of the river water affect the genetic diversity of P. australis at the studied sites. Our study revealed a negative relationship between the concentration of nitrogen compounds and genotypic richness of P. australis populations, which means that increased nutrient availability may have promoted clonal growth and reduced seed recruitments at the studied sites.
Main publication:
1. Patamsytė, J., Lambertini, C., Butkuvienė, J., Naugžemys, D., Žvingila, D. Assessment of anthropogenic impacts on the genetic diversity of Phragmites australis in small-river habitats. Diversity. 2023, 15, 1116. https://doi.org/10.3390/d15111116

The Structure, Functioning in Ecosystems and Conservation of Vegetation, Algobiota and Mycobiota. Prof. E. Kutorga.
The Botany, Algology and Mycology Research Group focuses on the diversity, biology, distribution and ecology of plants, algae, fungi and lichens (https://www.gmc.vu.lt/en/ibs/departments/department-of-botany-and-genetics#botany-algology-and-mycology). Applying 'Survival analysis' statistical methods, we analyzed interval-censored data related to seedling emergence in 17 perennial indigenous plant species from Lithuanian meadows. Notably, Anthyllis vulneraria seedlings demonstrated a substantial 4.5-fold increase in emergence under NTP after 28 days, suggesting its potential as an additional approach to improve seedling emergence in specific species. However, the impact of NTP varied among species and, in some instances, resulted in significantly reduced seedling emergence. The characteristics of Equisetum variegatum populations occurring in natural and anthropogenic habitats were studied in four administrative districts of Lithuania. The ramet density, shoot height, total number of shoots and the number of fertile and sterile shoots and buds in a ramet were assessed. The density of E. variegatum ramets was significantly higher in natural habitats than in anthropogenic habitats. Silver nanoparticles are widely known for their antimicrobial activity in various systems from microorganisms to cell cultures. However, the data on their effects on microalgae are very limited. We used green microalga Haematococcus pluvialis as a model organism to test the influence of AgNPs on stress induction in unicellular algae, with visible phenotypic effects, such as astaxanthin synthesis and cell morphology. We observed decreased cell growth and division rate as well as a strong negative influence on cell morphology. Silver-induced stress did not increase accumulation of astaxanthin in H. pluvialis cells.

Main publications:
1. Gudynienė V., Juzėnas S., Stukonis V., Mildažienė V., Ivankov A., Norkevičienė E., 2023. Comparing Non-Thermal Plasma and Cold Stratification: Which Pre-Sowing Treatment Benefits Wild Plant Emergence? – Plants, 12 (18), art. no. 3220: 1-18. DOI: 10.3390/plants12183220
2. Rasimavičius M.; Naujalis J. R., Gudžinskas Z., 2023. Structure of Equisetum variegatum (Equisetaceae) populations in natural and anthropogenic habitats. – Botanica, 29 (2): 96-109. https://doi.org/10.35513/Botlit.2023.2.7
3. Venckus P., Endriukaitytė I., Čekuolytė K., Gudiukaitė R., Pakalniškis A., Lastauskienė E., 2023. Effect of biosynthesized silver nanoparticles on the growth of the green microalga Haematococcus pluvialis and astaxanthin synthesis. – Nanomaterials, 23 (10), art. no. 1618: 1-14. DOI: 10.3390/nano13101618

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Nature Research Centre (Lithuania)
Vytautas Magnus University (Lithuania)
National Cancer Institute (Lithuania)
Vilnius University Hospital Santaros Klinikos (Lithuania)
Institute for Ecosystem Studies, Florence (Italy)
Tampere University (Finland)
Portuguese Oncology Institute of Porto (Portugal)
Medical University of Gratz (Austria)
University of Milan (Italy)
Lithuanian Research Centre for Agriculture and Forestry (Lithuania)
University of Greifswald (Germany)
University of Tartu (Estonia)
Estonian University of Life Sciences (Estonia)
Swedish University of Agricultural Sciences (Sweden)

OTHER RESEARCH ACTIVITIES
Prof. J. R. Lazutka
• editor of the journal Open Life Sciences;
• editorial board member of the journal Current Issues in Molecular Biology.
• editorial board member of the journal Biologija
Prof. D. Žvingila
• member of GMO Expert Commitee at the Ministry of Environment of the Republic of Lithuania;
• member of the Standing Commission on National Plant Genetic Resources.
Prof. S. Jarmalaitė
• Council member of Life Sciences Centre, Vilnius University
• Research council member of National Cancer Institute, Lithuania
• A member of management committee of Lithuanian Society of Oncologists
• Acting editor of the Oncologija Journal
• Member of editorial group Acta Medica Lituanica Journal
• Full member of the Lithuanian Academy of Sciences
Prof. E. Kutorga
• editorial board member of multivolume edition Lietuvos grybai (Mycota Lithuaniae);
• chairman of the Council of Lithuanian Mycological Society;
Dr I. Prigodina Lukošienė
• member of the Scientific Council of Life Sciences Center;
• member of of Lithuanian Mycological Society;
• member of Nordic Lichen Society.
Dr M. Rasimavičius
• member of the International Equisetological Association (IEA).
Dr R. Rimgailė-Voicik
• member of American Fern Society.
Dr J. Rukšėnienė
• member of Lithuanian Mycological Society.
Dr J. Butkuvienė
• member of the International Union for Conservation of Nature (Fresh water plant specialists group).
Dr R. Sabaliauskaitė
• A member of Lithuanian Society of Oncologists
• A jury member of the National Biology Olympiad organizing group, jury member of the Lithuanian team in International Biology Olympiad (IBO)
Dr K.Noreikienė
• member of International Fish Biology and Fisheries Society
Dr K. Daniūnaitė
• member of Lithuanian Biochemical Society.
R. Maleckaitė
• member of Lithuanian Biochemical Society.

MOST IMPORTANT NATIONAL AND INTERNATIONAL AWARDS RECEIVED FOR R&D ACTIVITIES
1. S. Jarmalaitė St. Kristoforas award from Vilnius municipality for the contribution to the Oncology field
2. Ieva Vaicekauskaitė awarded for the 3rd place best presentation diploma (Title: “Studies of potential genetic markers for the diagnosis and prediction of ovarian cancer”) in the national conference “Bioateitis: gamtos ir gyvybės mokslų perspektyvos”. November 23, 2023, Vilnius, Lithuania

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS AND ORGANISATIONS, AND BUSINESS ENTITIES
1. Prof. S. Jarmalaitė - European Commission, Health and Food Safety EC Subgroup of Cancer, Expert; a member of Assembly BBMRI-ERIC; Committee member of National Health Council of the Seimas; Member of the National Cancer Prevention and Control Committee; a member of the Policy on Rare Diseases group under Health Ministry; a Member of Lithuanian Science Award Committee; Committee member of the Personalized Medicine Fund; a member of expert group under Smart Specialization priority „Health technologies and biotechnologies“ at the Innovation Agency of Lithuania
2. Prof. E. Kutorga - member of the Invasive Species Control Council of the Ministry of Environment of the Republic of Lithuania; member of the Lithuanian Red Data Book Commission of the Ministry of Environment of the Republic of Lithuania; member of the Sub-commission on Terminology of The State Commission of the Lithuanian Language (as expert in Mycology).
3. Prof. J. Lazutka – Chairman of of the Commission of Higher Education Institutions‘ Review (at the Centre for Quality Assessment in Higher Education)
4. Dr I.Prigodina Lukošienė - member of the Scientific Council of the Nature Research Center.
5. Dr M. Rasimavičius - member of the sub-commission on Terminology of The State Commission of the Lithuanian Language (as expert in Botany).
6. Dr R. Šiukšta – member of the Standing Commission on National Plant Genetic Resources.

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES
1. J. Butkuvienė. Consultations were provided for natural persons in the assessment of vegetation cover of water bodies and wetlands in cooperation with MB Ecojuris. Assessment reports and letters have been submitted to the State Service of Protected Areas under the Ministry of the Environment.
2. S. Jarmalaitė an expert of the National Governmental Strategic Analysis Center (STRATA) for the Personalized Medicine feasibility study

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. Butkuvienė J. Lecture to primary school students at Vyturys primary school "Plant hybrids in our rivers. Do monsters only exist in computer games? 2023-10-05.
2. S. Jarmalaitė: Lecture for senior citizens of Palangos on cancer and cancer vaccines organized by educational support service of Palanga; 15 min: Mokslas apie vėžį: kada sulauksime vakcinos ir kurias vėžio formas išgydyti sunkiausia?; L.rytas: Kova su vėžį sukeliančiu virusu: mergaitėms ir berniukams nuo šiol kompensuojama devyniavalentė vakcina
3. J. Lazutka. Participation in the science promotion TV broadcasting „Will we restore extinct dinosaurs“ (https://youtu.be/0n0d_PQloKc)
4. Kutorga E.: 10 articles (https://www.vle.lt/straipsnis/aksombaravykis/ , https://www.vle.lt/straipsnis/kartekle/, https://www.vle.lt/straipsnis/kugiabude/, https://www.vle.lt/straipsnis/skujagalve/, https://www.vle.lt/straipsnis/kiskiabude/, https://www.vle.lt/straipsnis/salmabude/, https://www.vle.lt/straipsnis/tauriabude/, https://www.vle.lt/straipsnis/auksliavarpis/, https://www.vle.lt/straipsnis/baltekle/, https://www.vle.lt/straipsnis/skyletbude/).
5. Rasimavičius M.: 3 exibitions (M. K. Čiurlionis National Museum of Art, Exhibition "Green", 2023 06 22 – 2024 01 21, https://ciurlionis.lt/activity/branches/paroda-zalia-en/; The Lithuanian National Museum of Art, Vilnius picture gallery, Exhibition Florentem, 2023 05 16 – 2024 01 28, https://www.lndm.lt/florentem-kunstkamera/?lang=en; Vilnius museum, rooms_of_vilnius_v.1.1, 21 07 2023–31 12 2023, https://vilniausmuziejus.lt/two-rooms/?lang=en).
6. Šiukšta R. Lecture for the students of National Student Academy on the topic “Ką slepia didžiausių genomų – augalų – savininkai?“ (“What are the owners of the largest known genomes – plants – hiding? ”). 2023-01-05, Vilnius University Life Sciences Centre, Vilnius.

DEPARTMENT OF MICROBIOLOGY AND BIOTECHNOLOGY

7 Saulėtekio ave, LT-10257 Vilnius
Tel. 8 5 2398213
E-mail:
Head: Prof. Dr Nomeda Kuisienė

STAFF
Professors: Dr N. Kuisienė, Dr E. Lastauskienė.
Associate professors: Dr A. Gegeckas, Dr R.Gudiukaitė, Dr V.Kašėta (part-time).
Associate professors-researchers: Dr A. Gricajeva.
Assistant professors: Dr R. Baranauskienė.
Assistant professors-researchers: Dr R. Kananavičiūtė, Dr T. Kirtiklienė.
Researchers: Dr A. Kaunietis.
Lecturers: J. Versockienė.
Postdoctoral researchers: Dr G. Gyraitė.
PhD students: R. Bikmurzin, K. Čekuolytė, G. Jansonaitė, L. Gegeckienė, J. Kavoliūnas, I. Lenkaitė, V. Malūnavičius, R. Mažylytė, V. Mažrimaitė, A. Slavinska.
Specialists: V. Dzekevičienė, J. Lekavičiūtė.

RESEARCH INTERESTS
• Genomics, Metagenomics, and Biotechnologies: Fundamental and Applied Microbial Research
• Research of Microorganisms for Innovative Biotechnologies
• Biocatalysts Selection for Biomass Conversion
• Prokaryotes for Biotechnology, Biopharmacy Efficiency, and Safety Food Production Development
• Strategies in Antimicrobial Therapy
• Protein Engineering

MAIN RESEARCH AREAS
• Antimicrobial peptides
• Bioactive compounds of microorganisms
• Bioremediation, biodegradation, waste treatment
• Electroporation and magnetoporation methods for the biocontrol of the skin colonizing microorganisms
• Microbial biotechnologies
• Microbial culture collections
• Microbial enzymes
• Molecular taxonomy of prokaryotes
• Photoinactivation of microbial biofilms, microfungi spores
• Yeast prions

RESEARCH PROJECTS CARRIED OUT IN 2023
Projects Supported by the University Budget
Selection and Research of Microorganisms for Innovative Biotechnology Creation. Prof. Dr L. Kalėdienė / Dr A. Gricajeva. 2023.
Our group work is dedicated to research in various domains of microbiology and biotechnology. Now our research mostly revolves around the following key areas: developing safe methods for bacterial biofilm control using antimicrobial photoinactivation (API) in combination with antimicrobial peptides (AP) and other compounds. The group is constantly participating in the research regarding safe bacterial biofilm and other resistant microbe forms (e.g., spores) control method development for European Space Agency (ESA). In collaboration with the Institute of Photonics and Nanotechnology (IPN), Faculty of Physics (Vilnius University), a novel API technology that is safe for the use in the confined systems such as spacecraft and food settings is being developed. The group is also adapting the API technology to create a prototype that could be used for the destruction of phytopathogenic microfungi infecting strawberries and other plant phytopathogens. Identification and characterization of novel quorum-sensing (QS) signal peptides and AI-2 produced in thermophilic and other gram-positive bacteria and search for quorum-quenching molecules (enzymes and other) to disrupt bacterial biofilms more efficiently is one of the newest research topics adapted by the research group in 2023.
Furthermore, although the potential for microbial degradation is ubiquitous, many organic contaminants, such as some pesticides, are not or often only poorly transformed in natural environmental conditions, thus, organic and other waste treatment and recycling (bioremediation of polluted environments) is also an important ongoing topic of the research group. Through exploitation of advances of conventional and molecular biology techniques, search, identification, and characterization of microbial enzymes (lipases and carboxylesterases) active towards fatty acid esters, pyrethroids and other compounds are done. Another emerging topic nowadays is alternative antibacterial compounds such as bacterial ribosomally synthesized peptides with antibacterial activity (bacteriocins). These natural compounds have considerable diversity with respect to their size, structure, mechanism of action, inhibitory spectrum, immunity mechanisms and targeted receptors and are also being studied in the laboratory. Eukaryotic microorganisms’ β-glucans, a diverse group of polysaccharides, exhibiting immunostimulating activity, are among the research group’s topics as well. Enzymes, antimicrobial and other biologically active compounds studied by our team are important to both, biotechnological applications and fundamental research. We actively contribute to scientific projects, collaborating with IPN (VU), and securing co-financing from sources like EU, ESA and the Research Council of Lithuania. Also, we actively include students in our research.
Main publications:
1. Gricajeva, A., Kalėdienė. Investigation of amino acids related to Staphylococcus saprophyticus AG1 EstAG1 carboxylesterase catalytic function revealed a new family of bacterial lipolytic enzymes. International Journal of Biological Macromolecules. 2023; 235:123791. doi: 10.1016/j.ijbiomac.2023.123791
2. Koniuchovaitė, A., Petkevičiūtė, A., Bernotaitė, E., Gricajeva, A., Gegeckas, A., Kalėdienė, L., Kaunietis, A. Novel leaderless bacteriocin geobacillin 6 from thermophilic bacterium Parageobacillus thermoglucosidasius. Frontiers in Microbiology. 2023; 14:1207367. doi: 10.3389/fmicb.2023.1207367
3. Bikmurzin, R., Maršalka, A., Kalėdienė, L. Solid-state 13C nuclear magnetic resonance study of soluble and insoluble β-glucans extracted from Candida lusitaniae. Molecules. 2023; 28: 8066. doi: 10.3390/molecules28248066

Molecular Microbiology of Prokaryotes for Modern Biotechnology and Biopharmacy. Prof. Dr N. Kuisienė. 2023.
In 2023, the main focus of our research was on the epidemiology of Neisseria meningitidis, Escherichia coli, Acinetobacter sp., Listeria monocytogenes, and Haemophilus influenzae. Using molecular genotyping methods as well as genome analysis, the dynamics, pathways and factors promoting the spread of different strains of these bacteria in society and healthcare institutions were studied. In order to contribute to the monitoring of antimicrobial resistance of clinically and epidemiologically important microorganisms, the genomic characteristics of invasive strains and the molecular factors determining drug resistance as well as virulence were evaluated.
Research of biotechnologically important proteins was another direction of our research in 2023. The main focus of our research was on those proteins that are related to human health. The primary emphasis in this investigation path was on the search and characterization of enzymes that synthesize bioactive substances (polyketide synthases and non-ribosomal peptide synthetases), enzymes that break down polysaccharides (mainly xylan and pectin) and collagen-like proteins encoded by bacteria. Investigation of psychrophilic polymer-degrading enzymes has also been started by our scientific group in 2023. Genome analysis and molecular methods were used for the research, allowing to identify unique unknown proteins in prokaryotic genomes, to determine their characteristics and to evaluate the potential of practical application.
Main publication:
1. Bagdonas, M., Čerepenkaitė, K., Mickevičiūtė, A., Kananavičiūtė, R., Grybaitė, B., Anusevičius, K., ... & Matulienė, J. Screening, synthesis and biochemical characterization of SARS-CoV-2 protease inhibitors. International journal of molecular sciences, 2023, 24(17): 13491. doi: 10.3390/ijms241713491

Strategies in Antimicrobial Therapy and Protein Engineering. Prof. Dr E. Lastauskienė. 2022.
The aim is a screening of the compounds exhibiting antibacterial and antifungal activity; determination of the mechanisms of the action of the new antimicrobial compounds and analysis of the cell death type; and construction of novel proteins with the potential application in biotechnology and biopharmacy.
New microbial producents synthesizing active compounds against pathogenic Candida yeasts and Fusarium spp. were discovered as well as active compounds against pathogenic Pseudomonas, Staphylococcus, and Streptococcus strains.
Lipolytic enzymes are extensively used in chemistry, food, pharmaceutical, detergent, cosmetics industries, and biodiesel production. Our research team applies different protein engineering methods (random and site-specific mutagenesis, DNA shuffling, epPCR, the designing of new fused biocatalysts) to investigate structure-function relationships of microbial lipolytic (lipases, carboxylesterases) and lipolytic-like (cutinases, PETases) enzymes to design more attractive polyesterases for industrial applications.
Metagenome research of the microbial population from various environments is carried out by our group. Two main strategies are held in this part of the research: determination of environmental pollution-related microbial communities and discovery of the micro-plastic degrading microorganisms and determination of the microbial populations in medical samples to understand the contribution of the microbiota to the progression of diseases: f.e. development of carcinoadenomas, colorectal cancer, diabetic foot and etc.
Main publications:
1. Malunavicius, V., Padaiga, A., Stankeviciute, J. Pakalniskis, A., Gudiukaite, R. Engineered Geobacillus lipolytic enzymes – attractive polyesterases that degrade polycaprolactones and simultaneously produce esters. Int J Biol Macromol. 2023. https://doi.org/10.1016/j.ijbiomac.2023.127656
2. Vaskevicius, L., Malunavicius, V., Jankunec, M., Lastauskiene, E., Talaikis, M., Mikoliunaite, L., Maneikis, A., Gudiukaite, R., Insights in MICP dynamics in urease-positive
3. Staphylococcus sp. H6 and Sporosarcina pasteurii bacterium, Environmental Research (2023), 234, 116588. https://doi.org/10.1016/j.envres.2023.116588.
4. K. Cekuolyte, R. Gudiukaite, V. Klimkevicius, V. Mazrimaite, A. Maneikis, E. Lastauskiene. Biosynthesis of Silver Nanoparticles Produced Using Geobacillus spp. Bacteria. Nanomaterials 2023, 13(4), 702; https://doi.org/10.3390/nano13040702
5. P. Venckus; I. Endriukaitytė; K. Čekuolytė; R. Gudiukaitė; A. Pakalniškis; E. Lastauskienė. Effect of biosynthesized silver nanoparticles on the growth of the green microalga haematococcus pluvialis and astaxanthin synthesis // Nanomaterials. Basel : MDPI. eISSN 2079-4991. 2023, vol. 23, no. 10, art. no. 1618, p. [1-14]. DOI: 10.3390/nano13101618.

National Research Projects
Agency for Science, Innovation and Technology 01.2.2-MITA-K-702 "Promotion of commercialization and internationalization of R&D results" (EUREKA) project Nanosilver and graphene oxide inks (No. 01.2.2-MITA-K-702-12-0002), Head of the project – Dr Eglė Lastauskienė. 2021-2022
The new antibacterial and antifungal inks for coating the different surfaces will be created in this project. The nanosilver particles are added to the graphene oxide inks and the antimicrobial properties are evaluated. The project is carried out together with Nature Research Center, JSC “Pro for Nano”, JSC „Graphene Composites“.

Research Council of Lithuania. PostDoc project Vibrio in Baltic Sea Coastal and transitional waters: virulence, antimicrobial resistance and prevalence in the microbial population. Supervisor prof. Eglė Lastauskienė 2022-2024, researcher – Dr Greta Gyraitė. Vibrio – microbes that are part of the natural bacterioplankton in temperate marine waters – stimulated by elevated surface water temperatures have in recent years flourished in the Baltic Sea. It is hence of great concern that Vibrio-related wound infections and fatalities have increased dramatically along the Baltic Sea coasts. Future climate change is predicted to accelerate this problem even more, posing a significant threat to bather’s health. Although Vibrio spp. are susceptible to most antibiotics of veterinary and human significance, many studies reported that multi-antibiotic resistance has emerged and evolved in many bacterial genera, including Vibrio, due to misuse of antibiotics in healthcare, agriculture, and aquaculture production.

Research Council of Lithuania. PhD project Analysis of the Geobacillus sp. Synthetized Silver Nanoparticles Mechanisms of Action on the Biocontrol of Pathogenic Skin Microbiota (No. KD-19142). Head of the project – prof. Eglė Lastauskienė. 2019–2023.
We evaluated the effect of pH in the inactivation protocol of Geobacillus sp. synthetized AgNPs and electroporation on Staphylococcus aureus and Streptococcus pyogenes bacteria. The results show that with some electroporation and pH values, lower concentrations of AgNDs are more effective against these bacteria than higher ones. By applying our improved methodology, we achieved effective inactivation rates of Pseudomonas aeruginosa biofilms. The evaluation of the AgNDs ability to supress the growth of Candida over time was tested as well. MICs have been shown to be ineffective in growing yeast culture in combination with AgNDs in the medium. Concentrations several times higher than the MIC were used to assess the time lapse effects of AgNDs.

"Development of scientific competence of scientists, other researchers, students through practical scientific activities", Funding for student’s research projects. Project “Development and analysis of cysteine as catalytic amino acid containing lipolytic enzymes from Geobacillus bacteria", No. P-ST-23-21; 2023 10 01 – 2024 03 31, leader – Dr R. Gudiukaitė, participant – Molecular biotechnology MSc student Laurynas Vaškevičius.
This project is focused on design of catalytic serine to cysteine mutants of two lipolytic enzymes, GD-95RM lipase and GDEst-95 esterase, and further directed evolution of these mutants to obtain new catalytic active variants.

"Development of scientific competence of scientists, other researchers, students through practical scientific activities", Funding for student’s research projects. Project “The effect of microgravity and telomere length on yeast cell viability and resistance to reactive oxygen species”, No. P-ST-23-58; 2023 10 01 – 2024 04 30, leader – Dr Eglė Lastauskienė, participant – Microbiology MSc student Irmantas Arūnas Čiužas.
The goal was to determine how microgravity conditions affect the resistance to reactive oxygen species and the type of cell death (apoptosis/necrosis) in yeasts with different telomere lengths.

"Development of scientific competence of scientists, other researchers, students through practical scientific activities", Funding for student’s research projects. Project „Optimisation of the synthesis of proteins with keratinolytic activity encoded by Streptomyces sp. SK-91 and purification of target proteins”, No. P-ST-23-339, 2023 10 01 – 2024 04 30, leader – Dr Audrius Gegeckas, participant – Microbiology MSc student Skaistė Jančauskytė.
Due to the increasing demand for keratinases in the industry, most research focuses on improving enzyme production. Heterologous expression of keratinases is a promising tool to achieve this goal. This approach allows genetic manipulation, protein engineering and the synthesis of large quantities of the target protein. Optimal tuning of the process conditions is essential for successful heterologous expression. The selection of the right expression organism, temperature and inducer concentration is important for the synthesis of the target protein. One of the main objectives of this project is to optimise a heterologous biosynthetic system for enzymes with keratinolytic activity and to perform the primary purification of target proteins.

Project funded by the science promotion fund of Vilnius University, MSF-JM-07/2023: “Development of a strategy to destroy biofilms formed by thermophilic bacteria using blue light and quorum-sensing disrupting substances“ (2023 05 01 – 2024 12 31), head of the project – Dr Alisa Gricajeva.
Thermophilic, biofilm-forming bacteria form a group of bacteria that are difficult to destroy and often cause food spoilage. The control of these bacterial biofilms in the food industry has so far received insufficient attention. Therefore, the aim of this project is to develop a safe method that will not induce emergence of resistance in bacteria for biofilm destruction of thermophilic bacteria using blue light and quorum-sensing disrupting agents.

Project of development of competences of scientists, other researchers and students through practical research financed by Lithuanian Research Council (LRC). Grant No. P-SV-23-186, Project “Search of bacteriocins active against phytopathogens” (2023 10 01 – 2024 04 30), head of the project – Dr A. Gricajeva.
Phytopathogenic bacteria pose a great threat to agricultural crops. Bacteriocins produced by bacteria have great potential in this area. The latter are antibacterial peptides and small proteins characterized by great stability, diversity and different mechanism of action. Bacteriocins are proposed for use in medicine, food industry and veterinary medicine as natural antimicrobial compounds that can replace traditional antibiotics, meanwhile, their use in agriculture to control phytopathogenic bacteria is studied insufficiently, so their potential in this field is not properly and fully evaluated. In this project, new biocontrol measures for horticulture would be developed, and new bacteriocins acting against phytopathogens would be sought. The identification of such antimicrobial peptides and the description of their properties would allow us to reveal their diversity and to better evaluate their properties and potential for use in agronomy.

Project of development of competences of scientists, other researchers and students through practical research financed by Lithuanian Research Council. Grant No. P-ST-22-233, Project „Antimicrobial photoinactivation of mold spores using natural photosensitizers“ (2022 09 15 – 2023 03 31), head of the project – prof. L. Kalėdienė.
Project’s aim is to determine the efficiency of the antimicrobial technology based on natural photosensitizers used in combination with blue light against phytopathgenic mold spores that are harmful to strawberries and other plants that are used as food.

Project funded by European Structural and Investment Funds via Central Project Management Agency of Lithuania (01.2.2-CPVA-K-703-03-0023) “New generation industrial enzyme engineering center (TVIRTAS)”, (2020-2023), project implementor – Dr A. Kaunietis.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Institute of Photonics and Nanotechnology, Faculty of Physics, Vilnius University (Lithuania)
Vilnius TECH (Lithuania)
Nature Research Centre (Lithuania)
State Research Institute Centre for Innovative Medicine (Lithuania)
Center for Physical Sciences and Technology (Lithuania)
National Public Health Surveillance Laboratory (Lithuania)
Vilnius University Hospital Santaros klinikos (Lithuania)
Republican Vilnius university hospital (Lithuania)
University of Greifswald (Germany)
University of Latvia (Latvia)
University of Ljubljana (Slovenia)
University of Milan (Italy)
National Institute of Chemical Physics and Biophysics (Estonia)
Jaypee University of Information Technology, Department of Biotechnology and Bioinformatics (India)
Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen (The Netherlands)
Norwegian University of Science and Technology, NTNU (Norway)
German Aerospace Center (DLR) (Germany)
Synthetic Biology Research Centre, The University of Nottingham, Biodiscovery Institute, Nottingham (United Kingdom).
JSC Avodės (Lithuania)
JSC Graphene Composites (UK)
JSC MKDS (Lithuania)
JSC Oda (Lithuania)
JSC Pro for Nano (Lithuania)
Company Audriaus Juškos ūkis (Lithuania)

OTHER RESEARCH ACTIVITIES
Prof. Dr N. Kuisienė
• member of the board of Lithuanian Microbiological Society, member of Lithuanian Biochemical Society.
Prof. Dr E. Lastauskienė
• member of the board of Lithuanian Microbiological Society, Head of FEMS Education group of Lithuanian Microbiological Society, member of Lithuanian Biochemical Society.
Assoc. Prof. Dr A. Gegeckas
• member of the board of Lithuanian Microbiological Society, FEMS delegate of Lithuanian Microbiological Society, member of Lithuanian Biochemical Society.
Assoc. Prof. Dr A. Gricajeva
• member of the board of Lithuanian Microbiological Society, Member of the scientific and organizing committees of the 5th International Congress of Baltic Microbiologists, 2023 (CBM2023).
Assoc. Prof. Dr R. Gudiukaitė
• member of the board of Lithuanian Microbiological Society, The secretary of Microbiologists Society of Lithuania; member of Lithuanian Biochemical Society
• Membership in Organizing committee of CBM2023 – 5th Congress of Baltic Microbiologists (https://cbm2023.com/committees)
Assist. Prof. Dr Rūta Kananavičiūtė
• member of Lithuanian Microbiological Society, Member of the organizing committees of the 5th International Congress of Baltic Microbiologists, 2023 (CBM2023).

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. Eglė Lastauskienė – "Mind experiments". The world of invisible microorganisms: the Eglė Lastauskienė – interviews and discussions: Scientist - about new threats: microplastics are even in the blood and why the Baltic Sea can become dangerous, 2023; Limaday Day | Lietuva 2023 Discussion: What can man and business learn from mutations in nature? VU researcher explained why there is no need to fear genetically modified products, but warned that not all mutations are beneficial, 2023. Overloading civilization. We gave up single-use plastic tools, but the packaging remained, 2023. Science without sermons. Microplastic damage: how to protect yourself from it? 2023 There is no place on earth where microplastics have not been found - even Mount Everest and our blood are contaminated, 2023. Microbiologist: Although bacteria are increasingly resistant to antibiotics, we would find other ways to fight them, 2023. Infections that are no longer affected by drugs, too sterile an environment and "good" bacteria. 2023. Scientist - about new threats: microplastics are even in the blood and why the Baltic Sea can become dangerous. 2023.
2. Alisa Gricajeva – practical activities and lectures for gymnasium pupils in the Center for non-formal education of Lithuanian pupils; member of the scientific project evaluation committee of the international students' VILIPO 2023 Olympiad in the category of Environmental Sciences.
3. Renata Gudiukaitė – contributed to the international conference The COINS 2023: Workshop for high school students. Workshop for school pupils as a part of the International Day of Microorganisms program.
4. Kotryna Čekuolytė – Excursions in the Department of Microbiology and Biotechnology for school pupils; making the Digital Bioguides for improving the competences of school teachers, showing various laboratory works. Educational lesson "Microorganisms around us" for school pupils as a part of the International Day of Microorganisms program.
5. Vilius Malūnavičius – Interview about the “5 second rule” for the young audience show “Čia dabar”. Contributed to the international conference The COINS 2023. Lectures for high school students “Microorganisms and the enzymes they produce”. Workshop, part of the international conference The COINS 2023. “How to prepare the best scientific poster”. Lecturer for the theoretic part of the workshop.
6. Justina Versockienė – Educational lesson "Microorganisms around us" for school pupils as a part of the International Day of Microorganisms program.

DEPARTMENT OF NEUROBIOLOGY AND BIOPHYSICS

7 Saulėtekio ave, LT-10257 Vilnius
Tel. 239 8222
E-mail:
Head - Prof. Dr Osvaldas Rukšėnas

STAFF
Professors: Dr A. Alaburda, Dr O. Rukšėnas, Dr V. Vengelienė, Dr I. Griškova-Bulanova.
Associate professors: Dr R. Buišas, Dr R. Grikšienė, Dr R. Guzulaitis, Dr V. Kisnierienė, Dr M. Mitkus, Dr K. Dapšys (Part-time), Dr G. Svirskis (part-time), Dr M. Korostenskaja (part-time), Dr U. Neniškytė, Dr A. Šoliūnas
Lecturers: Dr L. Bojarskaitė, Dr I. Lapeikaitė, Dr E. Pipinis, V. Gėgžna, V. Survilienė, V. Pupkis, D. Šimkutė, Dr A.Voicikas, R. Gaižauskaitė, I. Zelionkaitė.
Junior research fellows: V. Survilienė
Doctoral students: D. Dankin, V. Survilienė, A. Grabauskaitė, J. Kišonas, G. Jarockytė, D. Šimkutė, P. Tarailis, L. Saveikytė, V. Pupkis, D. Gabrielaitis, R. Gaižauskaitė, W. Liang, M. Plečkaitis, E. Voronovič, I. Zelionkaitė, D. Pamedytytė, U. Kuliešiūtė, G. Urbonaitė, K. Mickevičius, A. Shelest, R. Bagdonaitė, I. Brimienė, E. Jankaitytė, M. Ghodousi, V. Mažeika, E, Ilkevič, U. Jašinskytė, A. Polita, A. Mockevičius, I. Pocevičiūtė, I. Nagula, A. Dambrauskaitė, M. Potapovas, E. Dirvelytė.

RESEARCH INTERESTS
• Functional organization and realization of information coding/processing and decision making in human and animal nervous system and plant model, animal models for psychiatric disorders, electrical signalling in plant and animal cells
• Effect of sex and sex steroids on cognitive functions and socioemotional behaviour.
• Behavioural pharmacology, animal models of psychiatric disorders.
• Electrophysiological biomarkers and neurotechnological applications
• Targeted CRISPR-Cas delivery into mammalian nervous system

RESEARCH PROJECTS CARRIED OUT IN 2023
Projects Supported by the University Budget
Science Promotion Fund of Vilnius University. Glycocalyx profile and its changes on the neurons of human epileptic brain networks. 2022-2023, leader U. Kuliesiute

National Research Projects
Project: "Importance of microbiota-intestinal-brain connection in the development of Alzheimer's disease: influence of endocannabinoid system", Nr. 01.2.2-LMT-K-718-02-0014, 2019-2023, project leader Dr Aurelijus Burokas (VU BchI). (EU Funds Investment Action Program 2014-2020, Brain Attraction and Reintegration (SMART) Program). Participates from the department Dr Rokas Buišas, Gintarė Urbonaitė

“Screening for treatment of neurodegenerative disorders” (No. 01.2.2-LMT-K-718-03-0021). Funding: Research Council of Lithuania. Duration: 2020-2023. Head of project: Dr Evaldas Čiplys (GMC, BTI). Participants Dr R. Buišas, Dr V. Vengelienė, I. Pocevičiūtė, L. Saveikytė, D. Gabrielaitis

“Biomarkers of the gut microbiota in autistic spectrum disorders” (No. 01.2.2-LMT-K-718- -03-0099). Funding: Research Council of Lithuania. Duration: 2020-2023. Head of project: Dr Aurelijus Burokas (GMC, BChI). Participant Dr Rokas Buišas

„Yeast metabolic engineering for the biocatalytic synthesis of active substances or organic compounds, EU Funds, UAB "Sanobiotec". 2020-2023, Nr. 01.2.1-LVPA-K-856-01-0222. Head of project: Prof. O. Rukšėnas
A single injection of THCV had a statistically significant effect on distance traveled in males and females. The time spent in the center was not statistically significantly different between treatment groups in the males and females.
THCV reduced locomotor activity in male rats at doses as low as 1 mg/kg.
The new object recognition test showed that the used materials did not cause significant short-term memory changes.
None of the substances used altered the pain threshold of healthy rats as measured by the hot plate test.

„Application of genome editing tools for monogenic lysosomal storage diseases“. Lithuanian Research Council, 2023-2027, No. P-PAD-23-172. Head of the project: Dr Urtė Neniškytė

„Perception of stable and moving image: quantization mechanisms”, 2021-2024, No. S-MIP-21-56. Funding: Research Council of Lithuania. Head of project: Dr Rytis Stanikūnas (VU Psychology inst.). Participants: Dr A. Šoliūnas
Two psychophysical experiments were performed when the flickering light was presented during the saccade and the subjects reported the position and quantitative properties of perceived phantom area. The length of phantom area and the number of light dashes in the phantom area were distorted during saccade. The sequence of several dashes of the same color was perceptually aggregated into one dash percept. One publication has been submitted to the PierJ journal and is under review

„Men's mental well-being: A psychophysiological study of interactions between empathy, stress, and sex hormones“, The Research Council of Lithuania, 2023 10 – 2024 05 , Agreement No. P-ST-23-309, 4800 Eur. Project leader R. Grikšienė. Student D. Kontrimaite

International Research Projects
„ElectroMechanoActive Polymer-based Scaffolds for Heart-on-Chip (EMAPS-Cardio)“, international research project funded under the EU’s Horizon 2020 framework programme, contract 953138. International coordinator Dr Christian Bergaud (Centre National de la Recherche Scientifique (CNRS) Paris, France) coordinator in Lithuania Dr Eiva Bernotienė (Centre for Innovative Medicine), Vilnius. Participant from VU Dr Aidas Alaburda. 2021 – 2025.

„EMBL partnership institute“ (01.2.2-CPVA-V-716-01-0001), 2021-2023. Participant: U. Neniškytė (assigned funds €1 000 000)
The project aims to establish the partnership between Vilnius University Life Sciences Center and European Molecular Biology Laboratory for fundamental and applied research in the field of genome engineering and the development of CRISPR-Cas technologies. The group of U. Neniškytė is developing the methods for targeted CRISPR-Cas system delivery to mammalian nervous system.

„Rhythms in human body: the search for relationships between brain oscillations and fluctuations of sex hormones“, 2023.06–11, The Baltic-German University Liaison Office is supported by the German Academic Exchange Service (DAAD) with funds from the Foreign Office of the Federal Republic Germany. 5000 EUR. Project leader R. Grikšienė, participants PhD students: R. Gaižauskaite, I. Zelionkaitė.

„Interdisciplinary cooperation project to develop an EEG method to measure the function of the auditory cortex of patients with AD(H)D“, The Baltic-German University Liaison Office is supported by the German Academic Exchange Service (DAAD) with funds from the Foreign Office of the Federal Republic Germany. Project partner I. Griškova-Bulanova, participant PhD student M. Ghodousi.

Contractual Research
Determination of auto-antibodies against central nervous system by direct immunofluorescence of rat brain sections, Lithuanian Association of Neurologists (U. Neniškytė).

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Republican Vilnius Psychiatric Hospital (Lithuania)
University of Copenhagen (Denmark)
Florida Children Hospital (USA)
University of Lausanne (Switzerland)
Translational Research Center of University Hospital of Psychiatry Bern (Switzerland)
University of Poznan (Poland)
Kiev National Taras Shevchenko University (Ukraine)
Jagiellonian University (Poland)
Auckland University of Technology (New Zealand)
University of Southern Queensland (Australia)
Valparaiso University (Chile)
National Institute of Mental Health (Czech Republic)
Durham University (UK)
Manchester University (UK)
University of Saltzburg (Austria)
Tubingen University (Germany)
School of Physiology, University of Wollongong (Australia)
Department of Biophysics, Institute of Biology and Biochemistry, Maria Curie-Skłodowska University (Poland)
Lund University (Sweden)
Center for Information and Neural Networks (Japan)
Beijing Sports University (China)
The Florey Institute of Neuroscience and Mental Health (Australia)
Belgrade University (Serbia)
University of Freiburg (Germany)
European Molecular Biology Laboratory (Italy)
National Sun Yat-sen University (Taiwan)
Jāzeps Vītols Latvian Academy of Music (Latvia)
University of Azores (Portugal)
University of Tartu (Estonia)
University of Colorado School of Medicine (USA)
University of Freiburg (Germany)
Centre for Innovative Medicine (Lithuania)
University of Azores (Portugal)
Centre d'Ecologie Fonctionnelle et Evolutive, CEFE, University of Montpellier, CNRS (France)
Department of Physical Chemistry and Physicochemistry of Polymers, Nicolaus Copernicus University (Poland)
Institut Montpellier Management (France)
Tbilisi Medical Academy (Georgia)

OTHER RESEARCH ACTIVITIES
Prof. V. Vengelienė
• Associate Editor in the section Translational Pharmacology, within the journal of Frontiers in Pharmacology, https://loop.frontiersin.org/people/29567/overview
• Associate Editor in the section Addictive Behaviors, within the journal of Frontiers in Psychology, https://loop.frontiersin.org/people/29567/overview
• Editorial Board Member for Journal of Personalized Medicine, https://www.mdpi.com/journal/jpm/editors?search=vengeliene
Dr I. Griškova-Bulanova
• Editorial Board Member for Brian Sciences

BEST REPORTS DELIVERED AT CONFERENCES ABROAD
1. Dr Urtė Neniškytė, "Neuronal phosholipid scramblase Xkr8 guides neuron-microglia interaction in developing brain", XVIth European Meeting on Glial Cells in Health and Disease, Berlin, Germany
2. Dr I. Griškova-Bulanova „Psilocybin-mediated changes of gamma-range auditory steady-state responses", 16th International Congress of the Polish Neuroscience Society, Torun, Poland

MOST IMPORTANT NATIONAL AND INTERNATIONAL AWARDS RECEIVED FOR R&D ACTIVITIES
1. Urtė Neniškytė was selected as a member of FENS-Kavli Network of Excellence (FKNE).

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
Dr U. Neniškytė
• Board member of the Research Council of Lithuania
• Member of the Council for Science, Technology and Innovation
• Member of the State Progress Council. Member of the group for strengthening STEAM education (Ministry of Education, Science and Sport)

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES
Dr Urtė Neniškytė
• Consultant for Lithuanian National Commission for UNESCO on the ethics of neurotechnologies.
• Member of Horizon Europe Expert Advisory Group for MSCA at the Research Council of Lithuania.
• Member of Horizon Europe Expert Advisory Group for cluster Health at the Research Council of Lithuania.
Prof. V. Vengelienė
• Consultant for PAASP GmbH (Partnership for Assessment and Accreditation of Scientific Practice), Heidelberg, Germany

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. Igno Kėjaus straipsnis lrt.lt naujienų portalui “Vaistus nuo priklausomybės alkoholiui bandanti išrasti mokslininkė: aplinkos turėtume bijoti labiau nei genetikos”. https://www.lrt.lt/naujienos/mokslas-ir-it/11/2161927/vaistus-nuo-priklausomybes-alkoholiui-bandanti-israsti-mokslininke-aplinkos-turetume-bijoti-labiau-nei-genetikos
2. Igno Kėjaus laida LRT radijui „Minties eksperimentai“. https://www.lrt.lt/mediateka/irasas/2000311750/minties-eksperimentai-du-desimtmecius-vaistus-alkoholio-priklausomybei-bandanti-atrasti-mokslininke-jau-isbandeme-daugiau-nei-50-variantu
3. Žiedūnės Kiznytės straipsnis “Kada išgydysime priklausomybę nuo alkoholio?” VU mokslo naujienos. https://naujienos.vu.lt/kada-isgydysime-priklausomybe-nuo-alkoholio/
4. Dr U. Neniškytė:
TV programme LRT TV “Svarbi valanda” on the application of brain implants. https://www.lrt.lt/. 2023/05/26
Article on the membership at FENS-Kavli Network of Excellence and investigation of molecular mechanisms of glioblastoma https://www.lrytas.lt/it/laboratorija/2023/09/29/news/garsi-mokslininke-neuromoksliniai-tyrimai-lietuvoje-yra-sekmingai-vystomi-28550198 2023/09/29
Radio show on brain-computer interfaces. https://www.lrt.lt/mediateka/irasas/2000311075/sviesi-ateitis-smegenu-implantai-nuo-proverziu-medicinoje-iki-futuristiniu-scenariju. 2023/12/20
5. Dr I. Griškova-Bulanova:
Interview to Holistic portal https://holistic.news/en/the-online-brain-opportunity-or-trap/

DEPARTMENT OF ZOOLOGY

7 Saulėtekio ave, LT-10257 Vilnius
Tel. + 370 5 223 4430
E-mail: .
Head – Prof. Dr Virginija Podėnienė
STAFF
Professors: Dr V. Podėnienė, Dr S. Podėnas (part-time).
Associate professors: Dr J. Turčinavičienė, , Dr V. Sruoga (part-time), Dr A. Petrašiūnas, Dr A. Kaupinis (part-time).Dr A. Pašukonis (part-time)
Assistants: Dr G. Skujienė, Dr R. Aukštikalnienė.
Junior assistants: A. Lekoveckaite
Lecturers: Dr M. Biteniekytė, S. Skuja, I. Gorban (part-time)
Senior researchers: Dr J. Havelka, Dr V. Sruoga (part-time). Dr M. F. Torres Jimenez, Dr A. Pašukonis, Dr J. Sakalauskaitė
Junior researchers: A. Lekoveckaite,
Doctoral students: L. Stasiukynas. G. Mockevičienė, B. Masoit, M. Riepšaitė, B. Jukonis, D. Gul

RESEARCH INTERESTS
• Ecosystems and global change
• Mapping and catalogization of fauna
• Rare and endangered species both in terrestrial and aquatic systems
• Invasive species
• Species of medical and veterinary importance
• Biodiversity in tropics
• Biodiversity in dead wood
• Biosystematics studies in insects (Coleoptera, Hemiptera, Sternorrhycha: Aphididae, Diptera, Lepidoptera, Hymenoptera).
• Biomineralization in mollusc shells
• Biomolecular archaeology
• Morphological differentiation and population proteomics in coregonid fish
• Diversity and behavior of tropical frogs

RESEARCH PROJECTS CARRIED OUT IN 2023
Projects Supported by the University Budget
Animal Biodiversity, Ecology and Population Structure. Prof. Dr V. Podėnienė
A new genus Tauroconopa and two species new to science are described after taxonomic studies of the East Asian Limoniidae crane fl ies (Diptera: Tipuloidea). A review of the immature stages of the eastern Palaearctic crane flies Hexatoma (Diptera: Limoniidae) using morphological and molecular methods revealed the importance of an integrative approach to the phylogeny of this group. The diversity of saproxylic insect (Coleoptera) species and their dependence on dead wood in Lithuanian unmanaged forests was revealed. Taxonomic studies of Elastichidae and Gracillaridae (Lepidoptera) from the tropical region were carried out, and thirteen species new to science from sub-Saharan Africa and Bolivia were discovered and described. Parental roles in shaping sex differences in poisonous frogs of Neotropics were revealed. Key to the aquatic Tipuloidea of the Mediterranean Basin was compiled. Taxonomic revision of genus Eloeophila is performed.
Main publications:
1. Sruoga, V.; Prins, J. New species, new country distribution records, and a new generic combination of Afrotropical Acrocercopinae (Lepidoptera: Gracillariidae). Zootaxa. 2023, 5285(1): 75–115.
2. Sruoga, V.; Havelka, J. Review of the neotropical species of the Elachista praelineata species group (Lepidoptera, Elachistidae, Elachistinae) with identifi cation keys and description of a new species from Bolivia. Insects. 2023, 14(1): 62.
3. Lekoveckaitė, A.; Jimenez, M. F. T.; Trakimas, G.; Ferenca, R.; Podėnienė, V. Tree species affect beetle diversity on the common deciduous dead wood in Lithuanian unmanaged forests. Forests. 2023, 14: 1836.
4. Podenas, S.; Gelhaus, J.; Podeniene, V.; Devyatkov, V.; Yadamsuren, O.; Torres Jimenez, M. F. A new genus and two new species of short-palped crane fl ies (Diptera: Limoniidae) from Central Asia. Diversity. 2023, 15(9): 1–26.
5. Podeniene, V.; Podenas, S.; Park, S-J.; Bae, C-H.; Baek, M-J.; Havelka, J. Immature stages of genus Hexatoma (Diptera, Limoniidae) in the Korean Peninsula. Diversity. 2023, 15(6): 770.
6. Podeniene, V. Superfamily Tipuloidea. In: Maasri, A.; Thorp, J. H. (eds). Identifi cation and ecology of freshwater arthropods in the Mediterranean Basin. Elsevier, Amsterdam. 2023, 536–552.
7. Emelianova K, Riaño‐Pachón DM, Torres Jimenez MF. Making sense of complexity: Advances in bioinformatics for plant biology. Appl Plant Sci. 2023 Aug 9;11(4):e11538. doi: 10.1002/aps3.11538.
8. Hill, A., Jiménez, M. F. T., Chazot, N., Cássia-Silva, C., Faurby, S., Herrera-Alsina, L., & Bacon, C. D. (2023). Apparent effect of range size and fruit colour on palm diversification may be spurious. Journal of Biogeography, 50, 1724–1736. https://doi.org/10.1111/jbi.14683
9. Torres Jiménez, M. F., Chazot, N., Emilio, T., Uddling, J., Antonelli, A., Faurby, S., & Bacon, C. D. (2023). Functional and historical drivers of leaf shape evolution in palms (Arecaceae). Global Ecology and Biogeography, 32, 1495–1507. https://doi.org/10.1111/geb.13708
10. Podenas, S. 2023. Eloeophila of the World (Diptera, Limoniidae). National Institute of Biological Resources, Incheon: 1-245.

National Research Projects
Development of an Action Plan for the Regulation of the Population Abundance of the Invasive Species (Arion lusitanicus) (2022 03 24 No. A56(1)-389). Dr G. Skujienė, M. Adomaitis, S. Juzėnas, student A. Jucevičiūtė. 2022.
The invasive species Arion vulgaris in twelve years spread into the whole territory of Lithuania. Control strategies for this invasive species in settlements with high density of slugs prepared based on our results and data from other scientists.
Main publication:
1. Adomaitis M., Skujienė G., Račinskas P. Reducing the Application Rate of Molluscicide Pellets for the Invasive Spanish Slug, Arion vulgaris. Insects 2022, 13, 301. https://doi.org/10.3390/insects13030301

Research project “Shell Archaeochrome”, EMBO (No. ALTF 314-2022). Dr Jorūnė Sakalauskaitė, Prof. Virginijus Šikšnys
The aim of Shell Archaeochrome project is to study and characterise mollusc shell biochromes using an integrated molecular approach. Mollusc shells present an incredible diversity of colours and patterns and shell biochromes encode important biological information. They may play a role in immunity, shell strengthening, protection from thermal stress and UV radiation. Yet, despite the great diversity and complexity of shell colours, their durability in biomineral structures (e.g., they can persist in the fossil record), there is no complete molecular understanding of shell pigmentation in any mollusc system.
Shell archaeochrome project will carry out an in-depth study of mollusc shell biochromes. Focusing on Littorina sp. shells which display colour polymorphism, we will use cutting-edge ‘ShellOmic’ techniques - transcriptomics and proteomics, including for ancient samples (palaeoproteomics) coupled with the first application of CRISPR-Cas9 gene editing tools to elucidate the chemical nature of shell biochromes and associated proteins, and investigate which genes are involved in shell coloration and biomineralisation. Palaeoproteomics of archaeochromes (ancient chromoproteins) will shed light into biochrome stability over archaeological timescales. The project will be carried out in collaboration with the Biotechnology institute of Vilnius University and several international institutions: Department of Geobiology, Georg-August University of Göttingen (Germany), Tjärnö Marine Laboratory, University of Gothenburg (Sweden), CIBIO-InBIO, University of Porto (Portugal).
Main publication:
1. Alarashi H, Benz M, Gresky J, Burkhardt A, Fischer A, Gourichon L, Gerlitzki M, Manfred M, Sakalauskaite J, Demarchi B, Mackie M, Collins M, Odriozola CP, Garrido Cordero JÁ, Avilés MÁ, Vigorelli L, Re A, Gebel HGK. 2023. Threads of memory: Reviving the ornament of a dead child at the Neolithic village of Ba`ja (Jordan). PLoS One. 18(8):e0288075. doi: 10.1371/journal.pone.

International Research Projects
National Institute of Biological Resources (South Korea). Korean Fauna (No NIBR2022021111). Prof. S. Podėnas, Prof. V. Podėnienė.
The aim of the Korean Fauna project is to investigate fauna and flora of the Korean Peninsula (North and South Korea) and to complete National List of Species of Korea. Every year researchers from South Korea directed by scientists from NIBR collect and register different organisms and search for the specimens that are stored in scientific collections worldwide. Special attention is paid to endemic species. National Species List and List of Endemic species are updated and published constantly every five years. For the groups of organisms, that are less familiar for Korean researchers, foreign investigators are invited. We are working together with Korean colleagues on crane flies and related families of true flies (Diptera, Tipulomorpha) since 2012. Every year we add 15-20 new species for the Peninsula, some of them are new for science. We collect adult and preimaginal stages, teach Korean students and Master/PhD program students. Our goal is taxonomy, ecology and development of selected groups of organisms and evaluation of influence of climate change, agriculture, deforestation and fragmentation of habitats on distribution and abundance of separate species.

Main publications:
1. Podenas, S.; Park, S.-J.; Byun, H.-W.; Podeniene, V. 2022. Hexatoma crane flies (Diptera, Limoniidae) of Korea. ZooKeys 1105: 165-208. doi: 10.3897/zookeys.1105.82495
2. Podenas, S.; Park, S.J.; Byun, H.-W. 2022b. New record of Pilaria crane flies (Diptera: Limoniidae) new to Korea. Journal of Species Research 11: 38-46. DOI:10.12651/JSR.2022.11.1.038
3. Podenas, S.; Park, S.J.; Byun, H.-W. 2022c. Phylidorea crane flies (Diptera: Limoniidae) of Korea. Journal of Species Research 11: 47-60. DOI:10.12651/JSR.2022.11.1.047
4. Podenas, S.; Park, S.J.; Byun, H.-W. 2022d. Limnophila crane flies (Diptera: Limoniidae) of Korea. Journal of Species Research 11: 117-127. DOI:10.12651/JSR.2022.11.2.117
5. Podenas, S.; Park, S.J.; Byun, H.-W.; Aukstikalniene, R. 2022a. Prionolabis crane flies (Diptera: Limoniidae) new to Korea. Journal of Species Research 11: 29-37. DOI:10.12651/JSR.2022.11.1.029

BASF SE (Germany). Biodiversity Project on the Farm for Birds, Insects (Wild Bees and Other Aculeata and Beetles) and Spiders. R&D-SERVICE AGREEMENT No. (1.57)15600-INS-43. Assist. Dr G. Skujienė (project manager), S. Skuja, Dr M. Biteniekytė, V. Kuznecova, students J. J. Valiulis, T. Laurinaitis, J.A. Skuja, 2021–2025.
The aim of BASF SE (Germany) project is to investigate biodiversity in farmlands with the aim of documenting possible changes in birds, wild bees (pollinator) and other Aculeata, ground beetles and spider populations, as well as beneficial and pest populations over the years. Every year we add 2-4 new species for the Lithuania. The following questions are pursued: Which possible factors influence the bird, insects and spiders’ population in the study area (humans, pets, wild animals, hunters, diseases) outside of agriculture? Can the bird population be increased through the usual bird protection measures (nesting aids / perches) and other enhancement measures (flower strips, planting trees, hedges) in the respective study area? Our goal is taxonomy, ecology and development of selected groups of organisms and evaluation of influence of climate change, agriculture, deforestation and fragmentation of habitats on distribution and abundance of separate species.
Main publication:
1. Lazauskaitė M., Budrienė A., Budrys E., Skujienė G. Records of two southern bee species, Anthidium oblongatum (Illiger, 1806) and Xylocopa valga (Gerstaecker, 1872) (Hymenoptera: Megachilidae, Apidae) in Lithuania. Bulletin of the Lithuanian Entomological Society 2022, 6(34): 106-110. https://www.entomologai.lt/leidiniai/category/58-volume-6-34-2022

ERASMUS+ Project on Platform for innovation in Natural science online education (LINNEO). Partnership agreement No. 2022-1-IT02-KA220-SCH-000088667 between COSTA EDUTAINMENT S.P.A. (Coordinator, Italy), Be2Bit Ltd (Malta) and 6 others. VU represents Museum of Zoology staff: Dr G.Skujienė (VU project manager), V. Kuznecova, J.A. Skuja; I. Kančys; VU Botanical Garden staff: R. Ryliškienė. 2022/10/01-2024/09/30.
The LINNEO project aims to strengthen the capability of Primary School Teachers and Schools to provide innovative, effective and motivating digital education in NS, actually integrated in formal curricula and able to tackle the main obstacles raised by societal emergencies or other problems that prevent full access to learning opportunities for some groups of students. To achieve this, aim the LINNEO project will develop a web-based platform nurtured with high quality and engaging digital resources for primary education. To support teachers in the integration of the digital resources in their teaching practice LINNEO will develop Didactic Units and a set of reusable activities, that will result from the collaboration of the teachers of the schools’ partners in the project, experts in educational technologies and Natural Sciences Edutainment Institutions (NSEIs), using Natural Sciences resources from Museum of Zoology (LT), Botanical Garden (LT) and Marine aquarium (IT).

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS

Institute of Ecology, Nature Research Centre (Lithuania)
Kaunas Tadas Ivanauskas Museum of Zoology (Lithuania)
Silesian University, Katowice (Poland)
Zoological Institute of Russian Academy of Sciences, Saint Petersburg (Russia)
Drexel University (USA)
National Institute of Biological Resources (South Korea)
Korean Polar Research Institute, Seoul (South Korea)
University of Porto, Interdisciplinary Centre of Marine and Environmental Research (Portugal)
Kazimierz Wielki University, Bygdošč (Poland).
Senckenberg Museum of Natural History, Department of Görlitz and Deprtment of Dresden, (Germany)
Center for Adaptive Behavior and Cognition, Max Planck Institute for Human Development (Germany)
Institute of Systematic Biology, Daugavpils University (Latvia)
Trinity College of Dublin (Ireland)
The State Service for Protected Areas (Lithuania)
Baltic Environmental Forum (Lithuania)
Faculty of Medicine of Vilnius University, Department of Anatomy, Histology and Anthropology (Lithuania)
Finnish Museum of Natural History, University of Helsinki (Finland)
Vytautas Magnus University (Lithuania)
ArchaeoBiomics lab, Department of Life Sciences and Systems Biology, University of Turin (Italy)
Section for Geobiology, The GLOBE Institute, University of Copenhagen (Denmark)
Department of Geobiology, Georg-August University of Göttingen (Germany)
UMR CNRS/UBFC/EPHE 6282 Biogéosciences, University of Burgundy-Franche-Comté (France)
Bioarchaeology research centre, Vilnius University (Lithuania)
Tjärnö Marine Laboratory, University of Gothenburg (Sweden)
CIBIO-InBIO, University of Porto (Portugal)

BEST REPORTS DELIVERED AT CONFERENCES ABROAD
1. Virginija Podėniene. How a deep look into the morphology of crane fly larvae helps to solve taxonomic problems. 10th international Congresses of Dipterology, the ICDX, Reno, Nevada, USA, 16-21 July 2023.
2. Sigitas Podėnas. Diversity of Eloeophila crane flies (Diptera: Limoniidae. 10th international Congresses of Dipterology, the ICDX, Reno, Nevada, USA, 16-21 July 2023.

OTHER RESEARCH ACTIVITIES
Prof. V. Podėnienė
• assoc. researcher of the Academy of Natural Sciences of Drexel University, Philadelphia, PA (USA);
• expert of the Lithuanian Innovation Agency.
Prof. S. Podėnas
• true member of Lithuanian Academy of Sciences
• assoc. researcher of the Academy of Natural Sciences of Drexel University, Philadelphia, PA (USA);
• expert of the National Centre for Quality Assessment in Higher Education (Lithuania);
• director of Nature Research Centre (Lithuania).
Assoc. Prof. V. Sruoga
• member of the European Society of lepidopterology (Societas Europaea Lepidopterologica);
• member of the Lithuanian Entomological Society.
Assoc. Prof. J. Turčinavičienė
• expert of the Supervision Committee of Genetically Modified Organisms,
• editorial board member of the journal Bulletin of the Lithuanian Entomological Society;
• member of the Lithuanian Entomological Society.
Lect. Dr R. Aukštikalnienė
• member of the Lithuanian Morphological Society.
Assist. Dr G. Skujienė
• curator of the Museum of Zoology of Vilnius University;
• member of the Lithuanian Entomological Society;
• external expert of Molluscs of the State Commission of the Lithuanian Language;
• member of the Council of the Invasive Species of Lithuania;
• member of the Working Group on Wildlife Welfare;
• member of Bioethics Society;
• member of Lithuanian Rural Development Program 2021–2030 Program Monitoring Committee, delegated by the association Environmental Coalition.
Assoc. Prof. A. Petrašiūnas
• member of the Commission of the Lithuanian Red Data Book of the Ministry of Environment of the Republic of Lithuania;
• president of the Lithuanian Entomological Society;
• managing editor of the journal Bulletin of the Lithuanian Entomological Society;
• member of EAFE, European Association for Forensic Entomology.
• Head of the National Biology Olympiad organizing group, team leader of the Lithuanian team in International Biology Olympiad (IBO)
Lect. Dr M. Biteniekytė
• member of the Lithuanian Entomological Society.
Lect. S. Skuja
• member of the Lithuanian Ornithological Society;
• member of the Lithuanian Entomological Society.
Dr J. Sakalauskaitė
• Affiliated scientists at the ArchaeoBiomics lab, University of Turin;
• member of the Malacological Society of London;
• member of the International Society for Biomolecular Archaeology.
Dr Maria Fernanda Torres Jimenez
• Affiliated scientist at the Gothenburg Global Biodiversity Centre
• Invited editor for the Applications in Plants Sciences Journal
• Member of the Botanical Society of the Americas
• Marius Jakulis Jason Foundation Scholar

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
1. Prof. V. Podėnienė – member of the national committe of the UNESCO program „Man and the Biosphere“.
2. Assoc. Prof. A. Petrašiūnas - member of the Commission of the Lithuanian Red Data Book of the Ministry of Environment of the Republic of Lithuania;
3. Dr A. Pašukonis and L. Stasiukynas – members of the Zoo Inspection Commission.

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES
1. All staff – consultations by the scientists of Botany and mycology group and Zoology Department on the identification and use of animals, protists, plants, fungi and lichens, as well as nature protection.
2. Dr G. Skujienė – expertise and lectures of molluscs Vertigo geyeri monitoring – for specialists of protected areas. In-service training and abilities to perform assigned functions (state environmental monitoring) training Project of the Environmental Project Management Agency of the Ministry of Environment of the Republic of Lithuania No. LIFE16 IPE / LT / 016 “Optimization of NATURA 2000 network management in Lithuania” throw The Lithuanian Fund for Nature.
3. Dr G. Skujiene – moderator of practical events for teachers (biology) Public Institution “EduEducational Forum”, project “Development and testing of general education content and organization models in general education”, project No. 09.2.1-ESFA-V-726-04-0001
4. Dr G. Skujiene - Integrated science education in Lithuania: achievements and future perspectives. Project No. S-REP-21-3. Lithuanian Science Council. 2021-2022.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. Dr G. Skujienė - 2022 March 25/ YouTube with G.Skujiene ,, Biodiversity observations in farmers' fields - how and why is it done? Part 1, https://www.youtube.com/watch?v=nbGdDXSdHUI
2. Dr G. Skujienė - 2022-05-12 Verslas - 15: About research during the VU-BASF project "Modern farming and biodiversity can be combined" G. Skujienė
3. Dr G. Skujienė - Delfi: https://www.delfi.lt/uzsakomasis-turinys/agro/siuolaikini-ukininkavima-ir-bioivairove-galima-suderinti.d?id=90199613
4. Dr G. Skujienė - 2022-07-28 Valstietis.lt (interview with G. Skujiene): https://www.valstietis.lt/gamta/savivaldybes-raginamos-imtis-iniciatyvos-naikinti-invazinius-sliuzus/125247
5. Dr G. Skujienė - 2022-07-19 Jurbarkas district newspaper "Šviesa", J. Stanaitienė (interview with G. Skujiene). "Slugs climb through the windows, but the fight against them is left to the residents themselves": https://www.delfi.lt/agro/sodinu-auginu/sliuzai-lipa-pro-langus-taciau-kova-su-jais-palikta-patiems-gyventojams.d?id=90753959
6. Dr G. Skujienė - 2022-07-09 Rural Affairs Committee, press release, Chairman of the Seimas Rural Affairs Committee prof. Viktoras Pranckietis: ,,Progressive farming is ahead of time" (About research during the VU-BASF project) https://www.lrs.lt/sip/portal.show?p_r=38445&p_k=1&p_t=277452
7. Dr G. Skujienė - 2022 August 13 LRT RADIO journalist Agnė Skamarakaitė's show, "10-12" - G. Skujienė: Luzitaninis arionas, https://www.lrt.lt/mediateka/irasas/2000228751/jei-isiveise-invaziniai-sliuzai-naikinti-privvalu-kai- chemistry-doesn't-help-can-you-getanciu?fbclid=IwAR37QjFnu958LqhZtYFs3SvcLxEUjJtvCn7ughbTo9YtpRx_1u9A2ySwe-o
8. Dr G. Skujienė - 2022 August 3 LRT LT. Grita Skujienė
9. Dr G. Skujienė - 2022-09-11 Delfi TV show "Delfi theme" (interview with G. Skujiene): "Sad news for farmers - a new, insolent pest is invading their fields" https://www.delfi.lt/agro/sodinu-auginu/liudnos-zinios-ukininkams-i-ju-laukus-braunasi-naujas-izulus-kenkejas.d?id=88120453
10. Dr Maria Fernanda Torres Jimenez - 2022 March. Lecturer at the one-week workshop titled "Target capture for Illumina sequencing" at Tjärnö (Sweden). Organised by ForBio.
11. Dr Maria Fernanda Torres Jimenez - 2022 April. Online seminar titled "Mutualismos entre plantas y hormigas - evolución entre montañas" (Spanish) hosted by the Universidad del Rosario, Colombia. https://www.youtube.com/watch?v=rHmXTnBXThw
12. Dr Maria Fernanda Torres Jimenez - 2022 August. Scientific seminar titled "Of plants, fungi, and sequencing" at Royal Botanic Garden Kew, UK
13. Dr Maria Fernanda Torres Jimenez - 2022 October. "Zafire" Online documentary screening and discussion, hosted by the Paris-based L’Académie du Climat (The Climate Academy). During the event, we discussed the role of women in science, and the urge to protect the Amazonian forests
14. Dr Maria Fernanda Torres Jimenez - 2022 November. One-hour seminar "Lessons from Neotropical ant-plant interactions: associations, diversification, and a few fieldwork tales" for The City College of the City University of New York (US). Followed by one-hour interview with students from the M.Sc. program, one hour interview with Ana Carnaval's lab. https://www.ccny.cuny.edu/biology/department-biology-colloquium
15. Jun.asisst. I. Gorban - ARQUS Climate Workshop in Seggau/Graz (Austria) 26-29 April 2022 "Dead wood and Saproxylic flies (Nematocera, Diptera) ",

CENTRE FOR ECOLOGY AND ENVIRONMENTAL RESEARCH

7 Saulėtekio ave, LT-10257 Vilnius
Phone: 239 8299
E-mail:
Head – Assoc. Prof. Dr Alius Ulevičius

STAFF
Associate professors: Dr A. Ulevičius, Dr G. Ignatavičius, Dr V. Valskys, Dr G. Trakimas (part-time)
Assistant professors: Dr V. Kalcienė, Dr I. Nedveckytė, Dr A. Samas.
Senior researcher: Dr A. Judžentienė (part-time), DrG.Trakimas
Doctoral students: M. H. Ünsal, H. R. Hassan, L. Galinskaitė, A. Kovrigina, D. Šalkauskienė, D. Stancelytė.

RESEARCH INTERESTS
• Pollution of natural ecosystem components and anthropogenical environmental impact assessment
• Toxic impacts of environmental pollutants to ecosystems using tests of luminescent microorganisms and biomarkers
• Infochemical interactions and behaviour of organisms

RESEARCH PROJECTS CARRIED OUT IN 2023
Projects Supported by the University Budget

Pollution of natural ecosystem components and anthropogenic environmental impact assessment (Planned research topic of the Centre financed by University Budget). Participants – G. Ignatavičius, A. Ulevičius, V. Valskys, V. Kalcienė, A. Samas, M. H. Ünsal, H. R. Hassan, L. Galinskaitė, A. Kovrigina.
We assessed the composition of potentially toxic elements and their ecotoxicological effects as well as health risk in various environments using X-ray fluorescence spectrometry, geochemical analysis, GIS analysis, bacterial luminescence test, camera traps, ultrasonic detection and field survey techniques. Potentially toxic elements, heavy metals, organic and mineral sediments in various environments, indoor dust, test organisms, structure of habitats, vertebrates and mammals among study subjects. Our last findings demonstrate high geoaccumulation and pollution indices of indoor dust in schools of Vilnius. Composition and combination of potentially toxic elements in surface peat can be used as a tracer for the identification of past fire events that occurred in peatlands. Heavy metals in sapropel of lakes may reflect anthropogenic influence.
Main publications:
1. Valskys, Vaidotas; Kibirkštis, Gintautas; Taminskas, Julius; Ulevičius, Alius; Ignatavičius, Gytautas. Fires in raised bog: their influence and changes to geochemical elements in peat layers // Land. Basel: MDPI. 2023, vol. 12, iss. 10, art. no. 1948, p. [1-11].
2. Valskys, Vaidotas; Ignatavičius, Gytautas; Wolkowicz, Stanislaw; Satkūnas, Jonas; Rahidul Hassan, Howlader. Contamination and health risk assessment of potentially toxic elements in soils of different kinds of land use in Lithuania // Geological quarterly. Warsaw: Polish Geological Institute. ISSN 1641-7291. eISSN 2082-5099. 2023, vol. 67, art. no. 29, p. [1-13].
3. Unsal, Murat Hüseyin; Ignatavičius, Gytautas; Valskienė, Roberta; Valskys, Vaidotas. Long-term heavy metal accumulation in sediment dust of schools in Vilnius: a case study // 12th International conference "Environmental Engineering", 27-28 April 2023, Vilnius Gediminas Technical University, Lithuania. Vilnius: Vilnius Gediminas Technical University, 2023, art. no. enviro.2023.901.

Toxic impacts of environmental pollutants to ecosystems using tests of luminescent microorganisms and biomarkers (Planned research topic of the Centre financed by University Budget). Participants – V. Kalcienė
The set of different biochemical markers including acetylcholine esterase activity, levels of metabolites of polycyclic aromatic hydrocarbons, antioxidant power was employed to assess the impact of human activities on aquatic ecosystems.Toxic effects of emerging environmental pollutants – neonicotinoid pesticides, their commercial formations and their UV photolysis transformation products were analyzed using bacteria Aliivibrio fischeri luminescence inhibition test.

Infochemical interactions and behaviour of organisms (Planned research topic of the Centre financed by University Budget). Participants – I. Nedveckytė, A. Judžentienė, G. Trakimas, D. Stancelytė.
We are focused on search for bioactive compounds and antioxidant properties in diferent plant species extracts. Also we are evaluating allelopathic activity of various extracts and essential oils of native and alien/invasive plant species.
Allelopathy of various extracts and essential oils (EOs) of S. canadensis on seed germination and growth of lettuce (Lactuca sativa L.) and garden pepper cress (Lepidium sativum L.) was evaluated and compared with other Solidago species (S. virgaurea, S. × niederederi) collected from the same growing locality in Lithuania. Aqueous flower extracts of all studied Solidago species showed the highest inhibitory effect on model plants. Canadian goldenrod leaf water/diethyl ether extract showed highest inhibitory effect in all relative concentrations (1.0; 0.1; 0.01) suppressing growth of L. sativa (from 0 to 2.3 mm compared with 22.7 mm for control samples) and L. sativum (from 0.5 to 16.8 mm compared with 35.3 mm in control). It was noticed that garden pepper cress was more susceptible to Solidago spp. inhibitory effects than lettuce. S. canadensis root EOs comprised mainly of limonene (35.0%) and β-pinene (26.2%) and inflorescence oils containing α-pinene (21.6%), germacrene D (15.1%), limonene (10.2%) and lupenyl acetate (9.8%) exhibited the highest inhibitory effect on lettuce and garden pepper cress growth. Relative germination and vigor index of model plants was conducted. Chemical composition of extracts and EOs was determined by HPLC/DAD/TOF and GC/MS techniques.
Humans often provide food to wintering birds, thus, improving their winter survival. However, our study shows that excess underskin fat reserves of Great Tits wintering near permanent feeders can make them slow at take-off, which increases their exposure to predators. We suggest that caution should be taken when choosing a proper place to position bird feeders to prevent making birds at feeders easy prey for predators.
Main publications:
1. Judžentienė, A., Būdienė, J., Labanauskas, L., Stancelytė, D., & Nedveckytė, I. 2023. Allelopathic activity of Canadian goldenrod (Solidago canadensis L.) extracts on seed germination and growth of lettuce (Lactuca sativa L.) and garden pepper cress (Lepidium sativum L.). Plants, 12(7), 421.
2. Krama, T., Krams, R., Popovs, S., Trakimas, G., Rantala, M. J., Freeberg, T. M., & Krams, I. A. (2023). Permanent Ad-lib Feeders Decrease the Survival of Wintering Great Tits (Parus major). Birds, 4(2), 225-235.
3. Krama, T., Munkevics, M., Krams, R., Grigorjeva, T., Trakimas, G., Jõers, P., ... & Krams, I. A. (2023). Development under predation risk increases serotonin-signaling, variability of turning behavior and survival in adult fruit flies Drosophila melanogaster. Frontiers in Behavioral Neuroscience, 17, 1189301.

Projects of the Science Promotion Fund of Vilnius University

The effect of phthalates entering Lithuanian waters with sewage on the development of mammals. MSF-JM-18/2022. 07/01/2022 - 12/31/2023. Project leader - V. Valskys.
This project and the research carried out in it differ from other projects already implemented by other researchers in other countries in that long-term (multiple generations) complex studies of the effects of phthalates found in Lithuania on the development of a model organism - rats are planned, including not only histochemical and morphological-morphometric analysis, but also genotoxicity indicators. It is hoped that this will help to better understand the real situation faced by Lithuanian residents. These results may influence recommendations to allow or prohibit the use of some household products, products containing plastic, the components of which may be biologically active and dangerous.

The identification of aquatic vegetation genera in lakes using remote sensing data. MSF-JM-06/2023. 2023-06-01 – 2024-09-30. Researcher – V. Valskys, junior researcher – L. Galinskaitė.
Long-term monitoring will let us collect high quality information of plant genera during fieldwork and use it for validation of medium and high-resolution satellite data. At first, we will test satellite data in lakes of different ecological status and then will select 3-4 lakes for deeper spatial and temporal analysis. We will use Google Earth Engine to obtain medium resolution (10 m in visible bands) multispectral Sentinel-2, and Education and Research program of Planet to obtain high-resolution (3.7 m) PlanetScope satellite data. The data will be carefully processed before carrying out analysis. The area of lakes with aquatic vegetation will be segmented into areas with dominant vegetation types/genera. The spectral signatures of these areas will be determined. Data preparation and analysis will be carried out using the R programming language.

NATIONAL RESEARCH PROJECTS
Effect of polystyrene diet on survival, genotoxicity and microbiome of Tenebrio molitor (L.) larvae. Student research during the semester to implement the project, Research Council of Lithuania, S-ST-23-98 (2023-2024). Project leader – I. Nedveckytė.
Tenebrio molitor is one of four insect species allowed to be grown for human consumption in the European Union. This insect is an alternative to conventional animal protein and can also be used to break down plastic waste. It is still not clear whether the insects only break down the plastic or are able to digest it. There is a lack of scientific publications and studies on this topic, it is not known how much polystyrene insects are able to assimilate and what effect such a diet has on T. molitor larvae at different developmental stages. It is also not known what genotoxic and cytotoxic effects a plastic-supplemented diet causes and how such a diet changes the gut micro biome of the insect. The goal of this project is to evaluate the effect of different (experimental) diets on the viability of Tenebrio molitor larvae of different age groups. The results will add to the knowledge about the effects of the polystyrene diet on the test organisms.

INTERNATIONAL RESEARCH PROJECTS
Nordplus Higher education 2023 programme. BalticSeaBioMed, NPHE-2023/10225 (2023-2024). Dr Irena Nedveckytė - Co-Applicant.
BalticSeaBioMed forms today the collaborative network in the field of Biomedicine between Universities of Eastern Finland (UEF), Southern Denmark (SDU), Turku (UTU), Vilnius (UV), Åbo Akademi (ÅAU) and Karolinska Institutet (KI). Project goal is to train the students in the skills and competences required to solve complex problems of global health by using the challenges closer to us -the populations and well-being around the Baltic Sea- as an example.

EU Life programme. Algae – Economy Based Ecological Service of Aquatic Ecosystem (life17 env/lt/000407). 2018–2023. Dr Vaidotas Valskys - research group member.
The project AlgaeService for LIFE seeks to promote best practices in ecological service and the circular economics approach by implementing innovative complex system which has both demonstration and innovation character.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Nature Research Centre (Lithuania)
Vilnius Gediminas Technical University (Lithuania)
University of Latvia (Latvia)
Lithuanian Geological Survey (Lithuania)
Boston University (USA)
National Institute of Chemical Physics and Biophysics (NICPB) (Estonia)
Natural Resources Institute (Finland)
Swedish University of Agricultural Sciences (SLU) (Sweden)
Polish Geological Institute – National Research Institute (Poland)

OTHER RESEARCH ACTIVITIES
1. Fedukovičiūtė A., Nedveckytė I. The effect of polystyrene diet on the fitness of tenebrio molitor and zophobas morio larvae. International Conference of Life Sciences The Coins 2023, Vilnius 2023, 24th-27th of April, 2023, p: 87.
https://www.thecoins.eu/static/resources/booksofabstracts/COINS2023.pdf
2. Staknys N., Kalcienė V. Impact of UV light on toxicity and degradation of active substance thiametoxam in neonicotinoid pesticide Actara. International Conference of Life Sciences The Coins 2023, Vilnius 2023, 24th-27th of April, 2023, p:85
https://www.thecoins.eu/static/resources/booksofabstracts/COINS2023.pdf
3. Trakimas G., Krama T., Munkevics M., Krams R., Grigorjeva T., Joers P., Popovs S., Zants K., Sledevskis E., de Bivort B.L., Krams I. Effects of predator presence and 5-HT signaling on behavioural lateralization and survival in Drosophila melanogaster // 65th International scientific conference of Daugavpils University, Daugavpils, 20–21 April, 2023 : [book of abstracts]. Daugavpils : Saule. 2023, p. [13-14]. Prieiga per internetą: https://dukonference.lv/files/Tezes_65.konf_publicesanai.pdf
4. Unsal, Murat Hüseyin; Ignatavičius, Gytautas; Valskienė, Roberta; Valskys, Vaidotas. Long-term heavy metal accumulation in sediment dust of schools in Vilnius: a case study // 12th International conference "Environmental Engineering", 27-28 April 2023, Vilnius Gediminas Technical University, Lithuania. Vilnius : Vilnius Gediminas Technical University, 2023, art. no. enviro.2023.901.

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
1. Dr A. Ulevičius – member of expert group of wolf population management in Lithuania by the Ministry of Environment; member of expert group of Game and Trophies by the Lithuanian Council of Hunters and Fishermen.
2. Dr A. Ulevičius – member of Steering Committee by the Ministry of environment on the National Study preparation on Ecosystem Services.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. Dr A. Ulevičius – Invited lector at workshop of the VU interdisciplinary research excellence centre “Post-authoritarian landscapes”, Palanga, 03-05.12.2023.
2. Dr A. Ulevičius – Invited interview by the LRT organized podcast “Science without Sermons”, 12-2023.
3. Dr Doc. G. Ignatavicius. LRT Panorama 2023-05-23 Environmental damage of illegal landfills.
4. Dr Doc. G. Ignatavicius. LRT Klasika 2023-06-12 Impact of noise from concerts on the environment.
5. Dr Doc. G. Ignatavicius. Valstietis.lt (Valstiečių laikraštis) 2023-09-18 On the recurring accidents with hazardous and less hazardous waste
6. The excursion at laboratory of Ecotoxicology for Students of Life Sciences Center (2023-12-05)
7. The excursion at laboratory of Ecotoxicology for Researches and PhD Students of Life Sciences Center (2023-12-05)
8. Kalcienė V. – multiple meetings and educational excursions for secondary school students at the laboratory of Ecotoxicology;
9. Kalcienė V. – excursion at laboratory of Ecotoxicology for students of biochemical school;
10. Kalcienė V. – invited judge of poster presentation in an international conference of Life Sciences The Coins 2023 (2023-04-24 – 2023-04-27)
11. Kalcienė V. – invited judge in an international competition for students aged 14-19 „VILIPO OLIMPIAD 2023“ in the category of “Environment” (2023-05-01 – 2023-05-15);
12. Kalcienė V. – Submision of advisory opinion to attorney from Professional Law Partnership ‘Meidus ir Juzukonis’ regarding data requirements for ecotoxicological assessment of wastes according regulations of EU (2023-02-17 registration No. (1.4 E) 600000-S-9)
13. Nedveckytė I. – 2023 multiple meetings and educational excursions with secondary school students at Chemical ecology laboratory;
14. Nedveckyte I. – invited judge of poster presentation in an international conference of Life Sciences „The Coins“ 2023 (2023-04-24 – 2023-04-27)
15. Nedveckytė I. – invited judge in an international competition for students aged 14-19 „VILIPO OLIMPIAD 2023“ in the category of “Environment” (2023-05-01 – 2023-05-15);
16. Kalcienė V., member of the committee of the international student conference "OpenReadings 2023" in the fields of biology/genetics/biomedical sciences
17. Samas A., 2023 April 24 – 26, assessor of the posters in the international student conference „The COINS 2023“ in the field of ecology/biology.
18. Samas A., 2023 November 2023, Invited lector in lecture cycle of Lithuanian Association of Natural Sciences Olympiads.
19. Trakimas G. made a presentation: “Relationships between life history and personality in insects” at LSC Retreat Conference, Dubingiai, April 2-3, 2023.

INSTITUTE OF BIOTECHNOLOGY

Saulėtekio al. 7, LT-10257 Vilnius
Tel. +370 5 223 4365
E-mail:
https://www.gmc.vu.lt/bti

Director – Dr Vytautas Smirnovas

STAFF
19 chief research fellows, 34 senior research fellows, 36 research fellows, 44 junior research fellows, 37 other researchers and technical staff, 45 doctoral students.

DEPARTMENTS OF THE INSTITUTE
Department of Protein - DNA Interactions
Department of Bioinformatics
Department of Biothermodynamics and Drug Design
Department of Biological DNA Modification
Department of Eukaryote Gene Engineering
Department of Immunology
Department of Single Cell Analytics
Sector of Applied Biocatalysis
Chronoepigenetics Laboratory
Sector of Crystalography and Chemical Informatics
Sector of Amyloid Research

DOCTORAL DISSERTATIONS DEFENDED IN 2023
Greta Leonavičienė „Complex single-cell analysis using hydrogel microcapsules"
Milda Narmontė „Method for high-resolution genome-wide analysis of 5-hydroxymethylcytosine and its application for epigenetic studies of human diseases"
Šarūnas Paškevičius „Development and synthesis of plant-derived recombinant biopharmaceutical proteins active against gram-negative pathogenic bacteria"
Janina Ličytė „Identification of oxidized 5-methylcytosine derivatives by novel technologies, their distribution and functions"
Andrius Sakalauskas “Understanding inhibition of protein amyloid fibril formation”
Tomas Urbaitis "Identification and characterisation of novel CRISPR-Cas nucleases"
Aistė Sližienė "New monoclonal antibodies for fish allergen detection and testing"

DEPARTMENT OF PROTEIN - DNA INTERACTIONS
Saulėtekio al. 7, LT-10257 Vilnius
Tel. +370 5 223 4354
E-mail:

Head - Prof. Dr Virginijus Šikšnys

STAFF
Research professors: Prof. Dr V. Šikšnys, Dr Dr G. Sasnauskas, Dr M. Zaremba, Dr G. Tamulaitis
Senior researchers: Dr G. Tamulaitienė, Dr E. Manakova, Dr G. Gasiūnas, Dr A. Šilanskas, Dr T. Šinkūnas, Dr T. Karvelis, Dr M. Tutkus.
Researchers: Dr P. Toliušis, Dr E. Zagorskaitė, Dr M. Skapas, Dr I. Songailienė, Dr G. Bigelytė.
Junior researchers: E. Golovinas, I. Mogila, D. Smalakytė, J. Juozapaitis, M. Baltramonaitis,
G. Druteika.
Other researchers and technical staff: A. Tunevič, D. Klimavičius, J. Matulevič Ilinykh, D. Bakonytė.
Doctoral students: D. Smalakytė, D. Dakinevičienė, J. Juozapaitis, M. Štitilytė, G. Druteika, A. Kopūstas, M. Baltramonaitis, E. Jurgelaitis, R. Ivanickaitė, D. Sabonis, U. Gaižauskaitė, D. Klimavičius.

RESEARCH INTERESTS
• Structural and molecular mechanisms of restriction enzymes
• Bacterial antivirus defense systems Bacterial antivirus defense systems
• Structural and molecular mechanisms of CRISPR-Cas machinery
• CRISPR_Cas systems provide acquired immunity against viruses and plasmids. CRISPR represents a family of DNA repeats present in most bacterial and archaeal genomes. CRISPR loci usually consist of short and highly conserved DNA repeats, typically 21 to 48 bp, repeated from 2 to up to 250 times. The repeated sequences, typically specific to a given CRISPR locus, are interspaced by variable sequences of constant and similar length, called spacers, usually 20 to 58 bp. CRISPR repeat-spacer arrays are typically located in the direct vicinity of cas (CRISPR associated) genes. Cas genes constitute a large and heterogeneous gene family which encodes proteins that often carry functional nucleic-acid related domains such as nuclease, helicase, polymerase and nucleotide binding. The CRISPR/Cas system provides acquired resistance of the host cells against bacteriophages. In response to phage infection, some bacteria integrate new spacers that are derived from phage genomic sequences, which results in CRISPR-mediated phage resistance. Many mechanistic steps involved in invasive element recognition, novel repeat manufacturing, and spacer selection and integration into the CRISPR locus remain uncharacterized.

SELECTED PUBLICATIONS 2023
1. Mogila, I. et al. Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling. Science 382, 1036–1041 (2023).
2. Sasnauskas, G. et al. TnpB structure reveals minimal functional core of Cas12 nuclease family. Nature 616, 384–389 (2023).
3. Kauert, D. J. et al. The energy landscape for R-loop formation by the CRISPR–Cas Cascade complex. Nat Struct Mol Biol 30, 1040–1047 (2023).
4. Hino, T. et al. An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis. Cell (2023).
5. Aldag, P. et al. Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system. Nat Commun 14, 3654 (2023).

PATENTS 2023
Granted:
1. Siksnys, V. et al. RNA-directed DNA cleavage by the Cas9-crRNA complex. US11555187B2 (2023).
Applications:
1. Siksnys, V., Gasiunas, G. & Karvelis, T. RNA-directed DNA cleavage by the Cas9-crRNA complex. US20230123754A1 (2023).
2. Siksnys, V. et al. RNA-directed DNA cleavage by the Cas9-crRNA complex. US20230272394A1 (2023).

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
Characterization of Novel Cas12 Effectors for Targeted Genome Modification. (Project No. S-MIP-21-8). Research Council of Lithuania. Project leader Dr T. Karvelis 2021–2023.
Cas9 and Cas12a nucleases from CRISPR-Cas systems have revolutionized the genome editing field by enabling genome engineering in different model organisms at unprecedented simplicity, speed, and efficiency. Cas9-based genome editing technology is now rapidly progressing into the clinic for ex vivo treatment of inherited blood diseases. The large size of the Cas9 and Cas12a nucleases, however, becomes a bottleneck for direct in vivo applications because of the low DNA cargo packing capacity of adeno-associated viruses (AAVs), which are preferred delivery vehicles in human therapeutic applications. Therefore, smaller CRISPR-Cas nucleases are highly desirable to enable in vivo treatment of inherited genetic disorders using AAV delivery vectors. The extremely diverse Cas12 protein family contain Cas nucleases of different size including still uncharacterized Cas12 variants. It has been already established that while large (850-1300 amino acids (aa)) Cas12 proteins (maxi-Cas12) function both in in vitro and in human cells, the smallest Cas12 variants (400-500 aa) (mini-Cas12) are only active in vitro. The DNA cleavage efficiency and genome editing potential of the “medium-sized” (~600 aa) Cas12 nucleases (midi-Cas12), which still are compatible with AAV packaging remain to be established. In this project, we aim to biochemically characterize novel midi-Cas12 nucleases and evaluate their genome editing efficiency in the eukaryotic cells. Successful implementation of this project could provide novel genome editing tools compatible with AAV delivery and active in human cells thereby promoting clinical applications of genome editing technologies for in vivo treatment of inherited genetic diseases and contribute to our understanding of the fundamental mechanisms and evolution of CRISPR-Cas systems.

Structural and Functional Studies of Thoeris Bacterial Antiphage Defence Systems (Project No. S-MIP-21-6). Research Council of Lithuania. Project leader Dr G. Tamulaitienė, 2021–2024.
Bacteria, a major group of living organisms on earth, are outnumbered by a factor of 1 to 10 by bacteriophages that infect them. Due to the rapid evolution of phages, bacteria have evolved various mechanisms to defeat phage infection, as well as phages developed tools to escape bacterial defence systems, leading to an evolutionary arms-race. The mechanisms employed by bacteria include Restriction-Modification (RM), CRISPR-Cas, BREX, prokaryotic Argonautes, DISARM and other systems. Studies of such systems may result in creation of new molecular tools, like studies of RM and CRISPR-Cas systems, which caused revolutions in genetic engineering and genome editing, respectively. Thoeris is a recently (2018) discovered bacterial antiphage defence system, composed only of two genes, thsA and thsB. ThsA contains putative NAD+ binding domain (SIR2 or Macro domain), ThsB contains Toll/interleukin-1 receptor (TIR) domain, also found in eukaryotic receptors. thsB genes often are present in multiple, diverse copies around the single thsA gene. It was shown that SIR2 domain containing ThsA protein can cleave NAD+, while the function of the ThsB protein and the mechanism by which this system protects bacteria against phages remains to be elucidated. We will employ structural and biochemical methods to determine the defence mechanism of the Thoeris system.

Functional and structural studies of proteins involved in CRISPR-Cas signaling pathway (Project No. S-MIP-22-9). Research Council of Lithuania. Project leader Dr G. Tamulaitis, 2022–2025.
Cyclic mono- and di-ribonucleotides (cNT) are widely employed for controlling various biological processes by eukaryotes and especially prokaryotes. Prokaryotes employ c-mono-NT (cAMP, cGMP) and c-di-NT (c-di-AMP, c-di-GMP and 3’3’-cGAMP) as key secondary messengers for biofilm formation, quorum sensing, virulence and regulation of bacterial cell cycle. The c-mono- and c-di-NT-based signaling pathways are well understood. However, recent discoveries reveal an additional role of cNT signaling in prokaryotic antiviral defense systems as a new emerging paradigm. In 2017 we showed that in response to phage infection the type III CRISPR-Cas interference complex synthesizes cyclic oligoadenylates (cOAs) of various ring size. The cA4 or cA6 acts as a signaling molecule that binds to the CARF (CRISPR-Cas associated Rossmann Fold) domain of the CRISPR-Cas associated Csm6 or Csx1proteins and allosterically turns on the non-specific RNase activity of their HEPN domain. Further our comparative genome bioinformatic analysis revealed that proteins possessing CARF domain are widespread in prokaryotes. Therefore, the newly discovered cOAs might be universal signaling molecules and cOA binding CARF domain is a common sensor used to control the activity of different effectors and processes in the cell. The CARF and its divergent variant SAVED domains are found fused with different enzymatic or non-enzymatic domains and are often associated to type III CRISPR-Cas systems. The aim of this project is to determine novel activities by which type III CRISPR-Cas associated proteins provide additional immunity related to CRISPR-Cas signaling pathway. We plan to perform functional and structural analysis of selected uncharacterized type III CRISPR-Cas auxiliary protein candidates. The expected results will expand the knowledge of prokaryotic immunity modes, their regulation and interplay with other cellular functions.

Functional and structural studies of novel HEPN-domain-containing bacterial antiphage defence systems (Project No. S-MIP-22-13). Research Council of Lithuania. Project leader Dr G. Sasnauskas, 2022-2025.
Bacteria and archaea are frequently attacked by viruses (phages), and therefore must rely on dedicated antiphage defence systems to survive. The best-known examples of such systems are restriction-modification (RM) enzymes and CRISPR-Cas, fundamental studies of which led to development of new molecular tools that have revolutionized gene and genome engineering, respectively. Recently performed studies, including systematic analysis of conserved gene clusters in the so called "defence islands" in bacterial/archaeal genomes, resulted in the discovery of multiple (over 30) entirely new antiphage systems, the mechanism (and the potential for novel applications) for most of which remains unknown. In this project we plan to perform functional and structural studies of two novel bacterial antiphage systems called HEPN-MNT and ApeA. Both systems share the HEPN (higher eukaryotes and prokaryotes nucleotide-binding) RNase domain, which is widespread in both eukaryotes and prokaryotes, and is often associated with antiviral defence. Current knowledge on the mechanisms of HEPN-MNT and ApeA systems is either fragmented (HEPN-MNT) or absent (ApeA). Thus, understanding their mechanisms would add new chapters to the biology of bacterial antiviral defence. During implementation of this project, we will employ various in vitro and in vivo experimental techniques, including X-ray crystallography and cryogenic electron microscopy (cryo-EM).

The interplay of prokaryotic Argonautes with other antiphage defence systems. (Project No. S-MIP-23-131). Research Council of Lithuania. Project leader Dr M. Zaremba, 2023-2026.
Prokaryotic (bacterial and archaeal) cells, being the most abundant cellular life forms, are outnumbered 10 to 1 by viruses (phages) that infect them. To survive, prokaryotes rely on dedicated antiphage defence systems. The best known are restriction-modification (RM) and CRISPR-Cas (clustered regularly interspaced short palindromic repeats) systems, the fundamental studies of which led to the development of molecular tools that have revolutionized gene and genome engineering, respectively. Most studies on prokaryotic defence systems (currently there are known ~80 different such systems) have been carried out on individual systems in isolation, without any focus on their possible interplay when they coexist in the same cell. Indeed, today there are only few studies showing that different defence systems act together to enhance antiphage protection. Our objects of research are short prokaryotic Argonautes (pAgos) that in their operons are associated with two other proteins: an upstream encoded small protein showing distant similarities to N domains of long pAgos and a downstream encoded unknown function protein possessing a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) RNase domain. All these pAgo-HEPN systems are inserted between genes of the TypeI or TypeI-like RM systems. The aim of this project is to determine the defence mechanisms of the novel split pAgos-HEPN systems and their interplay with the associated TypeI-(like) RM systems. Therefore, such strict association of the split pAgo-HEPN systems with the TypeI-(like) RM systems indicates their possible functional relationship, and that the TypeI-(like) RM systems are obligatory for the function of the split pAgo-HEPN systems. This project will undoubtedly contribute to the understanding of the interactions of various prokaryotic defence systems, ensuring effective host protection against mobile genetic elements.

International Research Projects
Genetic therapy for EYS- and USH2A-associated retinal disease. (Project No. GET-READY EJPRD20-231). European Joint Program “Rare diseases”. One of the partners Dr V. Šikšnys, 2021-2024.
The retina is a tissue that lines the back of the eye, and is responsible for receiving, modulating and transmitting the incoming light signal to the brain for image interpretation. A disruption in any of these steps can result in visual impairment. An important cause of vision loss is mutations in one of many genes important for retinal structure and function. Such mutations cause the retina to degenerate over time and give rise to a group of rare diseases collectively named inherited retinal diseases (IRDs). Although there is no definitive cure, there has been much progress made over the last ten years in terms of genetic therapies. In particular, gene augmentation therapy, which consists of introducing a healthy copy of the mutated gene into the patient’s retina, has proven the most promising and has even been approved for the treatment of IRD due to mutations in one gene. This approach however is not applicable to genes exceeding the size of the currently used gene vehicles, including two of the most frequently mutated genes, EYS and USH2A. The aim of our proposal is to address these current limitations. We will develop alternative therapeutic approaches, and in parallel optimise novel larger vehicles that can ensure a proper delivery of EYS and USH2A coding sequences to the retina. If successful, our project will result in the treatment of a non-negligible patient population, and consequently improve the life-quality of these patients as well as reduce the socio-economic burden due to progressive vision loss.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Thermo Fisher Scientific Baltics (Lithuania)
Bristol University (UK)
Leipzig University (Germany)
Massachusetts Institute of Technology (USA)
Dana-Farber Cancer Institute (USA)
University of Copenhagen (Denmark)
DANISCO (France)
DuPont (USA)

OTHER RESEARCH ACTIVITIES
Prof. Dr V. Šikšnys
• member of the Lithuanian Academy of Sciences, https://www.lma.lt/asmsv/intranetas/index.php?m=profile&user=1454
• member of EMBO, https://people.embo.org/profile/virginijus-iknys
• member of EMBL council, https://www.embl.org/about/info/embl-council/embl-council-and-finance-committee-members/
• member of EMBC council, https://embc.embo.org/members-and-partners/embc-member-states/

MOST IMPORTANT NATIONAL AND INTERNATIONAL AWARDS RECEIVED FOR R&D ACTIVITIES
1. Dr Tautvydas Karvelis received Vilnius University Rector‘s Science Award for exceptional annual scientific achievements, contribution to the development of science at university and in Lithuania and raising the prestige of university's science globally in 2023.
2. Dr Inga Songailienė received Vilnius University Rector‘s Science Award for Junior Scientist for scientific acheivements.
3. Jonas Juozapaitis received Prof. V. Šikšnys fellowship for for internationally recognized outstanding results of their scientific activities.

DEPARTMENT OF BIOINFORMATICS

Saulėtekio 7, LT-10257 Vilnius
Tel. +370 5 223 4368
E-mail:
Website: https://bioinformatics.lt

Head - Dr Česlovas Venclovas

STAFF
Research professors: Dr Č. Venclovas.
Senior researchers: Dr V. Kairys, Dr M. Margelevičius, Dr J. Dapkūnas, Dr D. Kazlauskas, Dr K. Olechnovič
Researchers: Dr A. Timinskas
Junior researchers: S. Ašmontas
Other researchers: K. Timinskas, L. Valančauskas, R. Banciul
System administrator: R. Dičiūnas
Doctoral students: L. Valančauskas, S. Ašmontas, R. Banciul, J. Pachauri.

RESEARCH INTERESTS
• Development of computational methods for prediction and analysis of 3D structures for protein protein and protein-nucleic acid complexes
• Analysis of 3D structure of proteins and nucleic acids
• Analysis of genomes and proteomes
• Evolution of protein families, distant homology detection
• Protein-protein and protein-nucleic acids interactions
• Molecular mechanisms of DNA replication, recombination and repair in the context of 3D structures
• Structure, evolution and function of CRISPR-Cas systems

SELECTED PUBLICATIONS 2023
1. Mogila, I. et al. Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling. Science 382, 1036–1041 (2023).
2. Sasnauskas, G. et al. TnpB structure reveals minimal functional core of Cas12 nuclease family. Nature 616, 384–389 (2023).
3. Olechnovič, K. & Venclovas, Č. VoroIF-GNN: Voronoi tessellation-derived protein–protein interface assessment using a graph neural network. Proteins: Structure, Function, and Bioinformatics 91, 1879–1888 (2023).
4. Olechnovič, K., Valančauskas, L., Dapkūnas, J. & Venclovas, Č. Prediction of protein assemblies by structure sampling followed by interface-focused scoring. Proteins: Structure, Function, and Bioinformatics 91, 1724–1733 (2023).
5. Dapkūnas, J. & Margelevičius, M. The COMER web server for protein analysis by homology. Bioinformatics 39, btac807 (2023).

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
Expanding the CRISPR Toolbox for Rapid Detection and Genomic Surveillance of SARS-CoV-2 Variants of Concern (Project No 13.1.1-LMT-K-718-05-0021). Research Council of Lithuania. Project leader Dr D. Kazlauskas, 2021–2023.
SARS-CoV-2 variants of concern (VOCs) are dangerous because they can have lower efficacy for current vaccines. Early detection of VOCs allows for rapid intervention and minimizes the risk of spreading the disease. Currently, the most often used VOC detection methods are genome sequencing and RT-qPCR. These methods are expensive, slow and require highly trained personnel and costly equipment. To conquer shortcomings of genome sequencing, methods for detection of specific virus sequences based on CRISPR-Cas class 2 effector proteins (C2EP), namely Cas9, Cas12 and Cas13, are being developed. They offer significantly cheaper, faster and more accessible ways of SARS-CoV-2 diagnostics. However, to achieve that CRISPR nucleases should meet certain criteria, namely the mutation should be in a sequence called PAM (protospacer adjacent motif). Therefore, the major obstacle for widespread adoption of C2EP proteins for detection and genetic surveillance of VOCs is the limited mutation space which could be targeted. Currently known Cas9 and Cas12 proteins are restricted by their inability to recognize diverse PAMs. Our project aimed at expansion of the CRISPR toolbox for use in rapid detection and genomic surveillance of SARS-CoV-2 VOCs. We used state-of-the-art sequence search methods to collect C2EPs and machine learning to select the best candidates for experimental validation by our partner CasZyme. A comprehensive analysis of the diversity of C2EPs led to the identification of 481349 homologues. C2EP diversity analysis was presented at the 21st European Conference on Computational Biology. Machine learning method was developed to predict the thermostability of C2EP proteins from their sequences (https://github.com/ievapudz/TemStaPro). Thermostability of C2EP proteins was investigated using this method. C2EP representatives capable of operating at high temperatures (>55°C) were used for a test prototype that allows to distinguish SARS-CoV-2 variants.

Computational analysis and prediction of three-dimensional structures of protein complexes. (Project No. S-MIP-21-35). Research Council of Lithuania. Project leader Dr Č. Venclovas, 2021-2024.
Most proteins function not as isolated entities but as components of either stable or transient protein complexes. At present, advances in high-throughput experimental techniques result in rapid growth of protein-protein interaction (PPI) data. However, for comprehensive understanding of molecular mechanisms, the knowledge of three-dimensional (3D) structures of protein complexes is essential. The goal of this project is to consolidate available structural data on protein complexes and to provide new cutting-edge computational methods for both analysis and prediction of PPI structural properties. More specifically, the project entails the development of a non-redundant structural database of protein complexes, a computational pipeline for construction and analysis of template-based structural models of protein-protein and protein-nucleic acid complexes and a new method to predict protein-binding sites for individual protein structures. The results of the project are expected to make a major impact in the field of protein structural bioinformatics.

Lightning-fast protein structure alignment in the new era of structural biology. (Project No. S-MIP-23-104). Research Council of Lithuania. Project leader Dr M. Margelevičius, 2023-2026.
Knowledge of protein structure and function is crucial for understanding organisms and diseases. Protein structures, solved or predicted with high accuracy, have recently been made available for almost every known protein. Yet, mining large protein structure databases is long-lasting and becomes a bottleneck to exploiting these resources. To address this problem, this project aims to develop a novel, exceptionally fast method and software for protein structure search and alignment. The new software is expected to deliver up to four orders of magnitude speedup compared to the current state of the art. The solution is based on targeting performance from the perspective of structure comparison algorithms and leveraging the architecture of modern manycore processors, including the graphics processing unit (GPU). A specially developed prototype shows promising properties for large-scale single-chain structure alignments and superposition of protein complexes. The new method and software are thus expected to complement existing approaches and provide fast protein structure search and accurate alignment, demanded today.

International Research Projects
Comparative host and species-specific immune responses of macrophages infected with zoonotic Leptospira interrogans (LEPTIMMUNHOST). ERA-NET ICRAD project. Coordinator: Dr Catherine WERTS (Institut Pasteur, France), Lithuanian partner: Dr Česlovas Venclovas (Vilnius University), 2023-2026
The “One Health” concept recognizes that human, animal, and environment health are closely interrelated. Leptospira interrogans are the causative bacterial agent of leptospirosis, an emerging zoonotic disease affecting humans and animals, worldwide. The disease may appear as an acute, even fatal infection in accidental hosts, such as humans or livestock, or progress into a chronic, mainly asymptomatic infection in its natural hosts, such as mice and rats. In cattle, leptospirosis is responsible for high economic losses due to reduction in both, dairy and beef industry, and to high abortion rates. To improve on this, it is imperative to understand the innate immune responses elicited in different hosts. Many immunological experiments conducted in mice have allowed the understanding of some aspects of the immune responses during leptospirosis. However, recent studies have shown clear differences in the response seen in other mammalian hosts such as human and cattle. This proposal aims to apply a comparative analysis of the innate immune responses elicited by macrophages from divergent hosts such as bovines, pigs, mice, hamsters, and humans upon infection with various zoonotic Leptospira strains that are responsible for distinct outcomes of disease. The goal of this project is to understand differential and specific immunological processes and pathways. More specifically, the aim is to compare some Toll-like receptors recognition of membrane components of leptospires, using structural, biochemical, genomic, immunological, high content screening confocal microscopy and computational modeling approaches. This project should facilitate the understanding of the innate immune mechanisms driving host specificities of leptospirosis, and accordingly tailor host-directed intervention strategies.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Inria Grenoble – Rhone-Alpes Research Center (France)
VIB-VUB Center for Structural Biology (Belgium)
Institute of Molecular and Cell Biology, University of Tartu (Estonia)
National Center for Biotechnology Information (USA)
Institut Pasteur (France)
University of Cape Town (South Africa)

OTHER SCIENTIFIC ACTIVITIES
Dr Č. Venclovas
• editorial board member of Scientific Reports (Nature Publishing Group), https://www.nature.com/srep/about/editors;
• member of the Lithuanian Academy of Sciences, https://www.lma.lt/asmsv/intranetas/index.php?m=profile&user=2653

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
1. Dr K. Olechnovič was a member of the expert group organized by Research Council of Lithuania for “The current direction of competitive financing program for information technologies, including quantum technologies and provisions for implementation of the program”;
2. Dr K. Olechnovič was a member of the "Bioinformatics" bachelor study program committee at Vilnius University Faculty of Mathematics and Informatics.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

1. Article on the Vilnius University news website (Interview about bioinformatics, research carried out at the Department of Bioinformatics and the latest achievements of the team in CASP and CAPRI competititions – Dr Č. Venclovas https://naujienos.vu.lt/prof-c-venclovas-ateities-gyvybes-mokslu-srities-tyrimai-bus-neatsiejami-nuo-bioinformatikos/)

DEPARTMENT OF BIOTHERMODYNAMICS AND DRUG DESIGN
Saulėtekio al. 7, LT-10257 Vilnius
Tel. +370 5 223 4364
E-mail:

Head - Dr Asta Zubrienė

STAFF
Research professors: Dr D. Matulis.
Senior researchers: Dr A Zubrienė, Dr V. Petrikaitė, Dr V. Petrauskas, Dr J. Matulienė, Dr V. Dudutienė, Dr L. Baranauskienė, Dr E. Čapkauskaitė, Dr Š. Grincevičienė.
Researchers: Dr E. Kazlauskas, Dr V. Juozapaitienė, Dr A. Smirnov, Dr J. Kazokaitė, Dr J. Smirnovienė, Dr A. Toleikis.
Research assistants: A. Zakšauskas.
Other researchers and technical staff: J. Jachno, A. Mickevičiūtė, D. Lingė, L. Davidian.
Doctoral students: A. Petrošiūtė, V. Paketurytė, M. Gedgaudas, G. Žvinys, A. Vaškevičius, I. Paterylo, L. Stančaitis, G. Dabkevičiūtė, V. Siaurusevičiūtė, E. Urniežius.

RESEARCH INTERESTS
• We study the thermodynamics and kinetics of protein – small ligand binding and are interested in the fundamental understanding of the protein – ligand molecular recognition process. A system of 12 human carbonic anhydrases and over 900 synthetic sulfonamide-bearing ligands is being studied both energetically and structurally. Nearly 100 protein-ligand crystal structures were solved and deposited to the PDB. Over 5000 reactions were measured yielding the Gibbs energy, enthalpy, entropy, and volume correlations with the chemical and crystallographical structural features of the ligand and protein. Most promising compounds that bound CA IX, an anticancer target, with subnanomolar affinity and significant selectivity over other human isoforms, are being tested in cancer cell lines, and in animals for biological development as anticancer drugs.

SELECTED PUBLICATIONS 2023
1. Petrauskas, V. et al. Thermal shift assay for protein–ligand dissociation constant determination. TrAC Trends in Analytical Chemistry 170, 117417 (2024).
2. Bagdonas, M. et al. Screening, Synthesis and Biochemical Characterization of SARS-CoV-2 Protease Inhibitors. IJMS 24, 13491 (2023).
3. Hadi Ali Janvand, S. et al. Inhibitory effects of fluorinated benzenesulfonamides on insulin fibrillation. International Journal of Biological Macromolecules 227, 590–600 (2023).
4. Lingė, D. et al. PLBD: protein–ligand binding database of thermodynamic and kinetic intrinsic parameters. Database 2023, baad040 (2023).
5. Preikša, J., Petrikaitė, V., Petrauskas, V. & Matulis, D. Intrinsic Solubility of Ionizable Compounds from pKa Shift. ACS Omega (2023).

PATENTS 2023
Applications:
1. Matulis, D. et al. Carbonic anhydrase inhibitors synthesized on interconnecting linker chains. EP4255886A1 (2023).

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
Design of compounds inhibiting BACE1 enzymatic activity and Aβ peptide aggregation for the treatment of Alzheimer's disease. (No. 01.2.2-LMT-K-718-03). Research Council of Lithuania. Project leader Dr D. Matulis, 2020-2023.
The project goal is to design and patent pharmaceutical candidate substances that could be used in the development of anti-Alzheimer’s drugs. Europe faces the challenges of aging societies but there are no clinically validated anti-Alzheimer’s drugs in the market. The World Health Organization announced the decade of 2020-2030 to be the decade of Healthy Ageing – a goal that is hardly achievable without efficient anti-Alzheimer’s drugs. We will screen a library of proprietary compounds to determine if they possess both anti-aggregation and also inhibitory properties of enzymes performing a role in Alzheimer’s disease. The most promising compounds will be patented and promoted for drug development by pharmaceutical companies. The project will encompass production of recombinant proteins and peptides, their chromatographic purification and characterization by biophysical and biochemical methods, ligand binding studies and organic synthesis of lead compounds.

Design of pharmaceutical compounds for the treatment of cancer and neurodegenerative diseases (Project No. 01.2.2-CPVA-K-703-03-0006). Central Project Management Agency. Project leader Dr D. Matulis, 2020-2023.
The project intent is to create new chemical compounds, the leading drug candidates for cancer and neurodegenerative diseases. The current library of sulphonamide compounds will be screened to detect their ability to bind anti-cancer targets and to inhibit formation of amyloid fibrils. Based on the obtained data, new compounds will be synthesized, patented, and developed as drug candidates.

Design of Technological Prototype to Determine Compound Efficiency as Inhibitors of SARS CoV-2 Recombinant Viral Enzymes. (Project No. 01.2.2-LMT-K-718-05-0001). Research Council of Lithuania. Project leader Dr J. Matulienė, 2021 – 2023.
The goal of this project is to contribute to the worldwide effort in search of anti SARS-CoV-2 virus drug. This virus contains several enzymes such as proteases, RNA polymerase and methyltransferase that could be inhibited by screen-discovered or rationally designed chemical compounds. Potent inhibitors of such enzymes may stop viral enzyme functions and could be developed as antiviral drugs. In this project we will recombinantly prepare several of these viral enzymes and apply and develop the ThermoFluor methodology for screening compound libraries to determine chemical moieties that increase compound affinities for the enzymes. We have a library of 1200 unique chemical compounds that will be screened against the recombinantly prepared viral enzymes, and the resultant hits will be ranked according to their affinities and inhibitory potential. In addition, we plan to screen a set of pharmaceutical drugs against viral enzymes with the goal of testing the possibility to repurpose a drug as an antiviral.

Discovery and Design of Covalent Inhibitors as Anticancer Drugs. (Project No. S-MIP-22-35). Research Council of Lithuania. Project leader Dr D. Matulis, 2022-2025.
Conventional drug design strategies attempt to design inhibitors that would reversibly bind disease target proteins with high affinity and high selectivity. However, such inhibitors often lack both sufficient affinity and sufficient selectivity to be promoted as an actual drug. Here, in this project we would like to add on our preliminary results and design inhibitors that would have significantly greater affinity by forming an irreversible covalent bond with the target protein. Such inhibitors are in popularity in recent years. Their main advantages are improved affinity, prolonged duration of action, and exquisite selectivity when non-conserved nucleophilic amino acid residues are targeted. The functional groups that participate in the covalent reaction possess low chemical activity and thus covalent modification occurs only for the desired protein isoform after the compound high-affinity interaction with the protein. Here we have preliminary results that the covalently-binding compounds possess high affinity for the desired protein isoform. We plan to design highly selective covalently-binding compounds for two anticancer target proteins, carbonic anhydrase IX and histone deacetylase 8. We hypothesize that mild electrophiles might overcome the selectivity challenge among zinc-dependent carbonic anhydrase and histone deacetylase isoforms. We expect that such inhibitors could have high potential for further development and be used in anticancer therapy.

Mechanisms of DNA motors involved in different bacterial antiviral defense systems studied at a single-molecule resolution (Project No. S-MIP-23-83). Research Council of Lithuania. Project leader Dr A. Toleikis, 2023 – 2025.
DNA motors are proteins that use energy from ATP hydrolysis to produce mechanical work required in cells. They are found in all domains of life. Helicases, for instance, move along single-stranded DNA and translocases move along double-stranded DNA. They are involved in numerous DNA maintenance activities - DNA replication, DNA repair, chromatin remodeling etc. They are also crucial for bacterial antiviral defense systems: Restriction-Modification (RM) and CRISPR/Cas. The ultimate goal of the defense processes is to destroy the invading viral DNA, yet the indispensable role of DNA motors is not fully understood. The mechanical properties of DNA motors - especially force generation - are arguably the least understood aspect of the mechanism, even though producing force is required for mechanical work. In order to discern the physiological function of DNA motors, the mechanical properties must be better understood. Direct investigation of motor mechanics has been possible with the advent of single-molecule techniques, like magnetic tweezers (MTw). Here we aim to understand the activity of DNA motors by using a combination of techniques: magnetic tweezers, biochemistry and structural biology. We will be comparing different representatives of DNA motors from antiviral defense systems: Cas3, CasDinG (both from CRISPR) and H.CglI/H.NgoAVII (from RM). We will address the questions of force generation, activity coordination within the protein and with its functional partners, as well as translocation. This knowledge will help us to shed light on the mechanisms of DNA motors participating in defense systems. This, in turn, will facilitate the development of DNA motors as genome engineering tools.

International Research Projects
Project leader Dr A. Toleikis – EMBO Installation Grant. 2021-2024
A research grant to set-up an independent laboratory focusing on single-molecule studies of DNA motors.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Institute of Medical Technology, University of Tampere (Finland)
University of Kaiserslautern (Germany)
Lead Generation Biology at Johnson & Johnson Pharmaceutical Research and Development (USA)
Latvian Institute of Organic Synthesis (Latvia)
Umea University (Sweden)
Aarhus University (Denmark)
Hochschule Darmstadt (Germany)
University of Ljubljana (Slovenia)

OTHER RESEARCH ACTIVITIES
Dr D. Matulis
• editorial board member of the European Biophysics Journal with Biophysics Letters;
• BPS Publications committee member;
Dr V. Dudutienė
• Chair of Medicinal Chemistry thematic group within Lithuanian Chemical Society
Dr A. Toleikis
• Member of EMBO Young Investigator Network

BEST REPORTS DELIVERED AT CONFERENCES ABROAD
1. Oral presentation at 26th Congress and General Assembly of the International Union of Crystallography (IUCr 2023) in 2023/08/22-29, Melbourne, Australia. Title of presentation: “Protein-Ligand Binding Database (PLBD) of Crystal Structures and Intrinsic Thermodynamic Parameters“. Presenter: Dr D. Matulis.
2. Oral presentation at EMBO Sectorial meeting on AI, Bioinformatics, Computation, and Data (ABCD), 2023-11-20/24, Malta. Title: „Data challenges in single-molecule force measurements of molecular motors“. Presenter: Dr A. Toleikis.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. A publication in a science promotion journal "Spectrum": Sukurti naują vaistą trunka trečdalį mokslininko karjeros laiko” Dr J. Smirnovienė. https://naujienos.vu.lt/spectrum-sukurti-nauja-vaista-trunka-trecdali-mokslininko-karjeros-laiko/.
2. An interview in news portal "Delfi": Mokslininkė apie šiuolaikinį ugdymą: mokydamiesi iš praktikos vaikai supranta daug daugiau. Dr J. Smirnovienė. https://www.delfi.lt/uzsakomasis-turinys/premium/mokslininke-apie-siuolaikini-ugdyma-mokydamiesi-is-praktikos-vaikai-supranta-daug-daugiau-92416089.
3. Video interview to LRT about molecular motors. Dr A. Toleikis. 2023. https://www.lrt.lt/mediateka/irasas/2000304878/laba-diena-lietuva (from 26:10 to 33:20).
4. Interview to lrytas.lt about molecular motors. Dr A. Toleikis.
https://www.lrytas.lt/it/laboratorija/2023/10/31/news/lietuvis-mokslininkas-apie-tai-kas-yra-molekuliniai-motorai-kam-jie-mums-reikalingi-ir-ka-jie-turi-bendro-su-m-jacksonu-28946102
5. Interview to delfi.lt about molecular motors. Dr A. Toleikis.
https://www.delfi.lt/login/progresas/mokslas/kiekvienoje-musu-lasteleje-tukstanciai-molekuliniu-motoru-vu-biofizikas-paaiskino-kas-tai-ir-ka-jie-daro-94972531

DEPARTMENT OF BIOLOGICAL DNA MODIFICATION

Saulėtekio al. 7, LT-10257 Vilnius
Tel. +370 5 223 4350
E-mail:
Head - Prof. Habil. Dr Saulius Klimašauskas

STAFF
Research professors: Habil. Dr S. Klimašauskas, Dr G. Vilkaitis, Dr E. Kriukienė
Senior researchers: Dr M. Tomkuvienė, Dr V. Stankevičius
Researchers: Dr A. Osipenko, Dr R. Rakauskaitė, Dr L. Gasiulė, Dr R. Krasauskas, Dr M. Mickutė, Dr M. Narmontė, Dr J. Ličytė, Dr E. Jakubauskienė, Dr I. Pečiulienė.
Junior researchers: G. Urbanavičiūtė, Z. Staševskij, K. Kvederavičiūtė.
Other researchers and technical staff: D. Gedgaudienė, A. Rukšėnaitė, R. Bendorys, M. Rutkauskaitė, G. Jankauskaitė, A. Čečkauskas, J. Balčiūnas, K. Račaitė, T. Bareikis, K. Tučinskytė, K. Vaišvidaitė.
Doctoral students: B. Masiulionytė, K. Skardžiūtė.

RESEARCH INTERESTS
• Nucleic acids modification enzymes
• Epigenome profiling
• Enzyme engineering
• RNA capping

SELECTED PUBLICATIONS 2023
1. Vilkaitis, G., Masevičius, V., Kriukienė, E. & Klimašauskas, S. Chemical Expansion of the Methyltransferase Reaction: Tools for DNA Labeling and Epigenome Analysis. Accounts of Chemical Research, 56, 3188-3197 (2023).
2. Skardžiūtė, K. et al. One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci. Cell Chemical Biology, in press (2023).
3. Malikėnas, M., Masevičius, V. & Klimašauskas, S. Synthesis of S-Adenosyl-L-Methionine Analogs with Extended Transferable Groups for Methyltransferase-Directed Labeling of DNA and RNA. Current Protocols 3, e799 (2023).
4. Mickutė, M. et al. Interplay between bacterial 5′-NAD-RNA decapping hydrolase NudC and DEAD-box RNA helicase CsdA in stress responses. mSystems 8, e00718-23 (2023).

PATENTS 2023
Applications:
1. Kriukiene, E., Gordevicius, J., Narmonte, M. & Gibas, P. Methods and compositions for noninvasive prenatal diagnosis through targeted covalent labeling of genomic sites. EP4127223A1 (2023).
2. Kriukiene, E., GORDEVICIUS, J., NARMONTE, M. & GIBAS, P. Methods and compositions for noninvasive prenatal diagnosis through targeted covalent labeling of genomic sites. US20230151409A1 (2023).
3. Klimašauskas, S., Vilkaitis, G., Masiulionytė, B., Masevičius, V. Method for synthesizing S-adenosyl-L-methionine analogues. LT2023539

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
DNA Modification and Chromatin Dynamics during Growth and Differentiation of Healthy and Malignant Cells. (Project No. S-MIP-S-21-1). Research Council of Lithuania. Project leader Dr E. Kriukienė, 2021–2024.
Epigenomic analysis of various cells and tissues has revealed complex interactions between different epigenomic factors, such as DNA methylation and chromatin accessibility. To reveal their temporal relationships, innovative methods that are able to relate DNA modification and chromatin dynamics are needed. In this project, we will develop a novel and cost-efficient method for simultaneous profiling of DNA methylation and hydroxymethylation within open chromatin loci. The method makes use covalent labelling of genomic targets in nuclei and their genome-wide analysis by our recently elaborated economical approach for targeted sequencing, TOP-seq. The technology will be used to explore dynamical changes of epigenomic landscape during differentiation of embryonic cells and neuroblastoma cell lines. Neuroblastoma is a malignancy of the developing nervous system that is characterized by extreme clinical heterogeneity. Recent studies suggested that a few types of phenotypically divergent cells are dominant in neuroblastoma tumours which differ in differentiation stage and malignant potential. We will exploit unique properties of our method to study chemically-induced differentiation or treatment of neuroblastoma cells in order to comprehensively characterize their aberrant transformation states and to find potential targets for treatment monitoring in clinics. Our approach would make a universal tool for analysis of global epigenomic landscape in the context of various diseases.

Global analysis of post-transcriptional regulators of RNA-centered stress response networks in probiotics lactic acid bacteria. (Project No. S-MIP-22-11). Research Council of Lithuania. Project leader Dr G. Vilkaitis, 2022-2025.
Lactic acid bacteria (LAB) Lactobacillus casei and Lactococcus lactis are widely applied both in industry as starter cultures and medicine as natural probiotics. To exert their beneficial properties, these bacteria must survive the hostile environment of the human host as well as various stressors encountered during the manufacturing process. Small regulatory RNAs, sRNAs, have been shown to play a major role in the regulation of stress response pathways of model microorganisms. However, the function of these molecules in LAB remains largely unknown. In the current project we will attempt to perform a comprehensive characterization of sRNA-mediated posttranscriptional regulatory circuitry in selected LAB strains and delineate the relationship between sRNAs, their epitranscriptomic 5’-NAD modifications, and environmental stimuli. The precise functional characterization of sRNAs in L. lactis and L. casei will be performed by identifying their direct RNA targets and interacting proteins. RNA chaperones Hfq, ProQ, CsrA are the most widely spread sRNA specific RNA binding proteins (RBPs) that are critical for sRNAs function but with no orthologs determined in such an important group of bacteria as LAB. The experimental characterization of these RBPs will provide a valuable insight into the mechanistic control of sRNAs not only in LAB, but also in other strains of Gram-positive microorganisms. Finally, the knowledge gained will be adapted for the targeted construction of stress resistant LAB strains through the regulated overexpression of selected sRNAs and their interacting proteins, thus increasing bacterial stability in ever changing environments. When applied, the data obtained in the proposed study has the potential for the development of LAB plasmid systems encoding endogenous, highly strain-specific sRNAs conferring antimicrobial resistance and leading to a vast improvement in more efficient and safer application of LAB in food, medicine and other industries.

DNMT1-selective DNA methylation mapping in tumor cells using preclinical cancer models. (Project No. S-MIP-23-108). Research Council of Lithuania. Project leader Dr V. Stankevičius, 2023-2026.
5-methylcytosine is a critical epigenetic mark in mammalian DNA that regulates mammalian development and disease, including cancer. DNMT1, an AdoMet-dependent DNA methyltransferase, is required in mammalian cells to maintain established DNA methylation patterns throughout cellular proliferation. Through promoter hypermethylation of tumor suppressor genes, DNMT1 plays oncogenic roles in cancer cell proliferation and invasion, as well as the promotion of cancer stem cell self-renewal. However, the comprehensive relevance of DNMT1 activities in tumorigenesis remains unknown. In this effort, we will seek to explore the genome-wide DNMT1-selective enzymatic activity in cancer cells and identify key genome regions selectively regulated by DNMT1 in tumor-constituting cells. To circumvent current technical constraints, we will use a newly designed experimental platform (Dnmt-TOP-Seq) that allows for high-resolution selective monitoring of direct DNMT1 catalysis in live mammalian cells. To identify unique DNMT1 genome targets, we will establish mouse lung cancer and fibroblast cell lines containing engineered DNMT1 and covalently mark the genome in live cells with the synthetic cofactor Ado-6-azide by cellular electroporation. Following chemical genome tagging in cells utilized in a range of 3D cell culture models, a subsequent genome-wide characterization of DNMT1 enzymatic activity will provide valuable insights into epigenetic control events specifically driven by DNMT1 in a tumor microenvironment dependent manner. Finally, applying our selective genome tagging in tumor tissues will allow us to discover a collection of genomic elements solely controlled in vivo by DNMT1. The complete identification of distinct DNMT1 activities in tumor cells will allow us to establish an exclusive basis for preclinical research into comprehensive DNMT1-mediated cancer resistance, the development of new epidrugs, and may aid in diagnosis and boost targeted therapy in clinical applications.

International Research Projects
Epitrack - Single-Cell Temporal Tracking of Epigenetic DNA Marks (Project No. ERC-2016-ADG/742654). ERC Advanced Grant. Project leader Prof. S. Klimašauskas, 2017-2023.
DNA methylation is a prevalent epigenetic modification in mammals, which is brought about by enzymatic transfer of methyl groups from the S-adenosylmethionine (SAM) cofactor by three known DNA methyltransferases (DNMTs). The most dramatic epigenomic reprogramming in mammalian development occurs after fertilization, whereby a global loss of DNA methylation is followed by massive reinstatement of new methylation patterns, different for each cell type. Although DNA methylation has been extensively investigated, key mechanistic aspects of these fascinating events remain obscure. The goal of this proposal is to bridge the gap in our understanding of how the genomic methylation patterns are established and how they govern cell plasticity and variability during differentiation and development. These questions could only be answered by precise determination of where and when methylation marks are deposited by the individual DNMTs, and how these methylation marks affect gene expression. To achieve this ambitious goal, we will metabolically engineer mouse cells to permit SAM analog-based chemical pulse-tagging of their methylation sites in vivo. We will then advance profiling of DNA modifications to the single cell level via innovative integration of microdroplet-based barcoding, precise genomic mapping and super-resolution imaging. Using this unique experimental system we will determine, with unprecedented detail and throughput, the dynamics and variability of DNA methylation and gene expression patterns during differentiation of mouse embryonic cells to neural and other lineages.

Discovery of novel regulatory proteins via selective covalent tagging of CpG islands in mammalian cells. (Project No. S-LJB-23-2). Lithuania-Japan research and dissemination program. Project leader Dr S. Klimašauskas, 2023-2025.
Epigenetic mechanisms regulating gene activity in a mammalian cell underlie its identity, function, and thereby play key roles in mammalian development and disease. The majority of mammalian gene promoters are associated with CpG islands (CGIs) – genomic regions with high abundance of CpG dinucleotides. CGI promoters of developmental genes are regulated by large multi-subunit complexes (Polycomb repressive complexes, PRCs). However, the factors defining how PRCs perform their function and how their perturbation leads to human pathogenesis remains elusive. Studies of these large complexes is obscured by the lack of adequate techniques that permit their analysis in the context of a vast abundance of unrelated proteins associated with other parts of the genome. To this end, a chemo-enzymatic strategy, mTAG, for CpG-specific covalent tagging of DNA opens new opportunities for selective enrichment of CGI-bound complexes. The aim of this project is to develop and implement a novel experimental platform that enables selective study of CGI-bound proteomes in mammalian cells. Two major objectives will be reached:
1. Develop approaches for CpG-specific covalent tagging of genomic DNA in chromatin to permit selective capture of CGI-bound protein complexes.
2. Determine the complete inventory of regulatory proteins bound to CGI promoters in a series of mouse genetic lineages and differentiation pathways.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Centre for Addiction and Mental Health (Canada)
University of Stavanger (Norway)
International Institute of Molecular and Cell Biology (Poland)
University of Southern California (USA)
Regensburg University (Germany)
Cardiff University (UK)
RIKEN Yokohama (Japan)
INRA (France)
Tartu University (Estonia)
Vilnius University Hospital Santaros Klinikos (Lithuania)
Stanford University (USA)

OTHER SCIENTIFIC ACTIVITIES
Prof. Habil. Dr S. Klimašauskas
• Membership of Scientific societies:
• EMBO, elected member, https://people.embo.org/profile/saulius-klimaauskas
• Royal Society of Chemistry, Fellow of the (FRSC), https://members.rsc.org/Application.asp?Mode=UPDATE&Session=IKLLHI/LFFJK;
• Lithuanian Academy of Sciences, elected Member, https://www.lma.lt/asmsv/intranetas/index.php?m=profile&user=2556;
• Member: American Chemical Society, International Union of Crystallography, Epigenetics Society, Lithuanian Society of Biochemistry, Lithuanian Biotechnology Association;
• Current Opinion in Biotechnology, Editorial Board member, https://www.sciencedirect.com/journal/current-opinion-in-biotechnology/about/editorial-board
• Open Life Sciences, Editorial Board member, https://www.degruyter.com/journal/key/biol/html#editorial;
• Proceedings of the Estonian Academy of Sciences, Editorial Board member, https://kirj.ee/proc-editorial-board/?v=c562607189d7
• management committee member, COST action CA18127; https://www.cost.eu/actions/CA18127/#tabs+Name:Management%20Committee
• ERC Synergy grant Evaluation panel member
Dr G. Vilkaitis
• management committee member, COST action CA20128, https://www.cost.eu/actions/CA20128/#tabs+Name:Working%20Groups%20and%20Membership
Dr E. Kriukienė
• Frontiers in Cell ir Developmental Biology, review editor
• Frontiers in Genetics, review editor

SELECTED PRESENTATIONS AT CONFERENCES ABROAD
Prof. Habil. Dr S. Klimašauskas - Oral/invited presentations:
1. NextGen Omics 2023, 2023.11.09-10, London, United Kingdom. Title of presentation: “Chemical Tracking Of Individual Epigenetic Writers in Mammalian Cells“.
2. Gordon Research Conference on Histone and DNA Modifications, 2023.06.11-16, Smithfield, USA. Title of presentation: “Chemical Tracking of Individual DNMT Writers during Cell State Transitions“.
3. COST International Nucleome Consortium Conference: The Genome in Space and Time, 2023.09.10-13, Corfu, Greece. Title of presentation: “Chemo-enzymatic tools for tracking epigenome dynamics in vitro and in live cells“.

NATIONAL AND INTERNATIONAL AWARDS
1. Prof. Habil.Dr Saulius Klimašauskas and Dr Miglė Tomkuvienė received Lithuanian Radio and Television Awards of the Year 2022, “Discovery of the Year” for “Discovering a new method of gene regulation”.
2. Dr Miglė Tomkuvienė received L´Oréal- UNESCO for Women In Science Young Talent Program Baltic Award for research in molecular basis of human epigenetic diseases.
3. Dr Vaidotas Stankevičius, Dr Povilas Gibas, Bernadeta Masiulionytė, Dr Liepa Gasiulė, Dr Viktoras Masevičius, prof. Habil. Dr Saulius Klimašauskas, Dr Giedrius Vilkaitis received Vilnius University‘s Rector‘s commemorative sign for significant scientific achievement for the best publication in the fields of nature, technology and medical and health sciences in 2022.

SELECTED PARTICIPATION IN WORKING GROUPS OR COMMISSIONS OF STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
Prof. Habil. Dr S. Klimašauskas
• Delegate at Rare Diseases Health Policy Group organized by Ministry of Health.
• Member of Vilnius university Senate.
• Member of the Promotions committee of State research Center for Physical Sciences and Technology .
• Advisory board member, Tagomics Ltd, UK.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. Several interviews and participation at National TV and Radio shows on the occasion of receiving the L’Oreal UNESCO prize - Dr M. Tomkuvienė (Delfi, Lrytas News portals, National broadcaster news website:
https://www.delfi.lt/mokslas/mokslas/tarptautini-pripazinima-pelniusi-mokslininke-dr-migle-tomkuviene-atlieka-svarbius-dnr-tyrimus-yra-budas-kaip-nugyventi-15-metu-ilgiau-94473551;
https://www.lrytas.lt/it/laboratorija/2023/09/08/news/lietuve-mokslininke-apie-musu-dnr-ir-ka-galime-padaryti-kad-genai-veiktu-harmoningai-28315778;
https://www.lrt.lt/naujienos/mokslas-ir-it/11/2070727/dvi-lietuves-mokslininkes-pagerbtos-prestiziniais-moterims-moksle-apdovanojimais
2. Estonian news portal Postimees (Interview about the L’Oreal UNESCO prize and epigenetics – Dr M. Tomkuvienė https://tervis.postimees.ee/7853928/geenide-orkestrit-saab-mojutada-epigeneetika-taktikepiga 2023.09.13)
3. Public discussion at the MO museum (Participant in the anniversary event- discussion of the museum “"Why does a healthy life need art?" – Dr M. Tomkuvienė https://mo.lt/ivykiai/mo5-jubiliejinis-sestadienis/, 2023.10.21)
4. Radio show "Persona Grata" (Participant of the show on the subject “How do genes affect our lives?” – Dr M. Tomkuvienė https://www.ziniuradijas.lt/laidos/persona-grata/kokia-itaka-musu-gyvenimui-daro-genai?video, 2023.10.24)
5. Radio show “Minties eksperimentai” (Participant of the show explained about epigenetics, nucleosomes and the research in this field – Dr M. Tomkuvienė https://www.lrt.lt/mediateka/irasas/2000254844/minties-eksperimentai-lietuviu-mokslininku-atradimas-dizainerio-nukleosoma-kokia-gyvybe-gebesime-konstruoti-ateityje, 2023.01.24)

DEPARTMENT OF EUKARYOTE GENETIC ENGINEERING

Saulėtekio al. 7, LT-10257 Vilnius
Tel. +370 5 223 4358
E-mail:
Head - Dr Rasa Petraitytė-Burneikienė

STAFF
Research professors: Dr A. Gedvilaitė, Dr R. Slibinskas, Dr D. Balčiūnas.
Senior researchers: Dr R. Petraitytė-Burneikienė, Dr G. Dudas, Dr A. Ražanskienė, Dr G. Žvirblis, Dr E. Čiplys, Dr A. Žiogas
Researchers: Dr R. Ražanskas, Dr D. Žiogienė, Dr A. Bulavaitė, Dr P.L. Tamošiūnas, Dr M. Norkienė, Dr M. Zaveckas, Dr A. Dr J. Lazutka, Dr A. Avižinienė.
Junior researchers: E. Bakūnaitė, E. Žitkus, A. Verbickaitė, J. Rainytė, L. Silimavičius, M. Kalvaitytė, E. Vasiliūnaitė, V. Dapkutė.
Other researchers and technical staff: O. Jančevskaja, D. Jaskytė, E. Lekavičius
Doctoral students: A. Verbickaitė, L. Silimavičius, M. Kalvaitytė, E. Vasiliūnaitė, V. Dapkutė, L. Čepulytė.
Affiliated: prof. emeritus K. Sasnauskas

RESEARCH INTERESTS
• Synthesis of recombinant proteins
• Molecular tools for diagnostics
• Investigation and characterization of new polyomaviruses, parvoviruses, paramyxoviruses and hantaviruses
• Improvement of expression systems and yeast genetic background for efficient production of recombinant viral proteins in yeast cells
• Heart regeneration

SELECTED PUBLICATIONS 2023
1. Rainyte, J. et al. Immunological comparison of recombinant shrimp allergen Pen m 4, produced in Pichia pastoris and Escherichia coli. Journal of Biotechnology 369, 1–13 (2023).
2. Avižinienė, A. et al. Characterization of a Panel of Cross-Reactive Hantavirus Nucleocapsid Protein-Specific Monoclonal Antibodies. Viruses 15, 532 (2023).
3. Dudas, G. & Batson, J. Accumulated metagenomic studies reveal recent migration, whole genome evolution, and undiscovered diversity of orthomyxoviruses. Journal of Virology e01056-23 (2023).
4. Lučiūnaitė, A. et al. Immunogenic Properties and Antigenic Similarity of Virus-like Particles Derived from Human Polyomaviruses. International Journal of Molecular Sciences 24, 4907 (2023).
5. Gåsland, H. et al. Antibodies to expanded virus antigen panels show elevated diagnostic sensitivities in multiple sclerosis and optic neuritis. Immunology Letters 254, 54–64 (2023).

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
Genetic and molecular studies of the role of Tbx5a role in heart regeneration. (Project No. 09.3.3-LMT-K-712-17-0014). Research Council of Lithuania/ European Social Fund. Project leader Dr D. Balčiūnas, 2020-2023.
In humans, cardiac muscle damaged by myocardial infarction is replaced by permanent scar tissue, resulting in impaired heart function. In contrast, the zebrafish Danio rerio is able to regenerate injured myocardium: within one or two months after injury, cardiac ventricle regenerates fully and the injured heart becomes functionally indistinguishable from an uninjured one. During heart regeneration, existing cardiomyocytes de-differentiate, proliferate, migrate into the wounded area and re-differentiate. Our knowledge of transcriptional programs necessary to carry out these processes is insufficient. We have recently demonstrated that Tbx5a transcription factor is required for cardiac regeneration in the zebrafish. Over the course of this project, we will analyze the role of Tbx5a in heart regeneration, including detailed analysis of the tbx5a loss of function in adult heart and identification of genes regulated by Tbx5a during cardiac homeostasis and regeneration.

Screening for new methods for treatment of neurodegenerative diseases (Project No. 01.2.2-LMT-K-718-03-0021). Research Council of Lithuania/ European Social Fund. Project leader Dr E. Čiplys, 2020-2023.
A range of recombinant human endoplasmic reticulum (ER) chaperones, which inhibit aggregation of proteins involved in progression of neurodegenerative disorders (ND), will be tested in both in vitro and in vivo models of these diseases. This may lead to discovery of new tools and methods for treatment of such disorders. During the course of the project, we are going to test four recombinant human ER chaperones in molecular interaction models as potential inhibitors of amyloid-like fibril formation. Inhibition of aggregation will be assessed using several model proteins related to different ND including Alzheimer‘s and Parkinson‘s diseases, amyotrophic lateral sclerosis, prion related disorders and multiple sclerosis. Chaperones showing the most promise will be tested alone or in combination with each other in order to establish optimal molar ratio of a functional mixture of different chaperones. Ultimately, successful implementation of this project may introduce new, more effective therapies for neurodegenerative diseases.

International Research Projects
Characterising metagenomically discovered orthomyxovirus surface proteins. EMBO installation grant. Project leader Dr G. Dudas, 2023 - 2026
The main task of the proposed research programme is to functionally characterise the surface protein gp64 of the eight-segmented quaranjavirus clade we discovered (Batson et al, 2021) specifically, and of quaranjaviruses broadly. Within Orthomyxoviridae both thogoto- and quaranjaviruses use gp64 as their surface protein. Their gp64 proteins can enter both vertebrate and arthropod cells because they use Niemann-Pick C1 (NPC1) protein (Li et al, 2019), a highly conserved (Higaki et al, 2004) eukaryotic membrane protein involved in lipid transport, as their receptor. So a priori there are strong indications that virtually any quaranja- or thogotovirus should be able to at least enter, if not infect, vertebrate cells expressing NPC1. The dual function of gp64 - receptor binding and membrane fusion - makes its evolution much more interesting since either function can be tuned (Sinn et al, 2017) or even lost (e.g. Langereis et al, 2009) in response to changes in ecology (e.g. host shifts). This dual function also adds an interesting evolutionary dimension, since it can translate to phenotypic flexibility and/or evolutionary constraint during evolution. To begin making headway the EMBO Installation Grant will be used to answer specific questions about gp64 proteins of orthomyxoviruses - how efficiently do various orthomyxovirus gp64 proteins enter vertebrate cells? Do specific groups of orthomyxoviruses look like they are more of an immediate threat to vertebrates than others? Do all major orthomyxovirus gp64 clades use NPC1 as their receptors.

Contractual Research
Recombinant Viral Proteins. Abcam Ltd, London, UK. Dr G. Žvirblis, Dr R. Petraitytė-Burneikienė.

Recombinant Viral Proteins. Arc Dia International Oy Ltd, Finland. Dr R. Petraitytė-Burneikienė.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS

Friedrich-Loeffler-Institut Federal Research Institute for Animal Health (Germany)
Nature Research Centre (Lithuania)
Institute of Ecology and Evolution, University of Bern (Switzerland)
National Cancer Institute, Center for Cancer Research USA)
National Institute for Public Health and the Environment (Netherlands)
Institute of Tropical Medicine (Belgium)
Chan Zuckerberg Biohub (USA)
University of Alberta (Canada)
University of California San Diego (USA)
Statens Serum Institut (Denmark)
Rigshospitalet (Denmark)
University of Southern Denmark (Denmark)
Dalhousie University (Canada)

OTHER SCIENTIFIC ACTIVITIES
Prof. Habil. Dr K. Sasnauskas
• member of the Lithuanian Academy of Sciences, https://www.lma.lt/asmsv/intranetas/index.php?m=profile&user=2545

BEST REPORTS DELIVERED AT CONFERENCES ABROAD
1. Rimantas Slibinskas, oral presentation (invited speaker) „Topical application of calreticulin decreases vascular leakage in the mouse laser-induced choroidal neovascularization model“ at 14th International Calreticulin Workshop, May 9th – 12th, 2023 — Saint-Malo, France.
2. Evaldas Čiplys, oral presentation „Topical application of calreticulin decreases vascular leakage in the mouse laser-induced choroidal neovascularization model“ at 14th International Calreticulin Workshop, May 9th – 12th, 2023 — Saint-Malo, France.
3. Gytis Dudas oral presentation „Towards Genomic Epidemiology of Arthropod Viruses“ at Meeting of the EMBO Young Investigator Network on ecology and evolutionary biology of microbes, 5 – 7 October 2023, Warszawa, Poland.

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
1. Justas Lazutka, a member of the evaluation committee responsible for granting the Ltd Linea Libera Scholarship to Vilnius University students for the execution of a technological research project.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. Annual science popularization seminar „Mokslas tau“ (A seminar about genomic epidemiology – Dr Gytis Dudas, https://www.mokslastau.lt/?page_id=1036, 2023.04.13)
2. EMBO podcast for EMBO community (A podcast about career development and current research – Dr G. Dudas, https://www.embo.org/podcasts/its-viruses-all-the-way-down-a-conversation-with-hsiao-han-chang-gytis-dudas-and-hedvig-tamman/, 2023.10.30)
3. Independent journalism platform “Nara” (An interview about the discovery of SARS-CoV-2 line B.1.620 – Dr G. Dudas, https://nara.lt/lt/articles-lt/gytis-dudas-pandemijos-pabaiga, 2023.11.30)
4. National TV and Radio show “Laba diena Lietuva” (Participant of the show explained about Wuhan mosquito virus 6 research conducted at VU LSC – Dr G. Dudas, https://www.lrt.lt/mediateka/irasas/2000304355/laba-diena-lietuva, 2023.11.10)

DEPARTMENT OF IMMUNOLOGY

Saulėtekio al. 7, LT-10257 Vilnius
Tel. +370 5 223 4360
E-mail:
Head - Dr Aurelija Žvirblienė

STAFF
Research professors: Dr A. Žvirblienė, Dr M. Plečkaitytė, Dr I. Kučinskaitė-Kodzė
Senior researchers: Dr A. Kanopka, Dr M. Simanavičius
Researchers: Dr D. Stravinskienė, Dr A. Lučiūnaitė, Dr A. Sližienė,
Junior researcher: I. Dalgėdienė
Technical staff: L. Diglienė
Doctoral students: K. Bielskė, A. Rimkutė, K. Mašalaitė, D. Gudas, V. Rudokas.

RESEARCH INTERESTS
• Monoclonal and recombinant antibodies
• Investigation of molecular mechanisms of macrophage activation
• Immunodiagnostics and prevalence studies of viral infections
• Molecular epidemiology of Neisseria meningitidis

SELECTED PUBLICATIONS 2023
1. Ivaškevičienė, I. et al. Molecular characteristics of Neisseria meningitidis carriage strains in university students in Lithuania. BMC Microbiology 23, 352 (2023).
2. Sereikaitė, E. et al. Molecular characterization of invasive Neisseria meningitidis isolates collected in Lithuania (2009-2019) and estimation of serogroup B meningococcal vaccine 4CMenB and MenB-Fhbp coverage. Frontiers in Cellular and Infection Microbiology 13, (2023).
3. Lučiūnaitė, A. et al. Immunogenic Properties and Antigenic Similarity of Virus-like Particles Derived from Human Polyomaviruses. International Journal of Molecular Sciences 24, 4907 (2023).
4. Sližienė, A. et al. Cross-reactive monoclonal antibodies against fish parvalbumins as a tool for studying antigenic similarity of different parvalbumins and analysis of fish extracts. Molecular Immunology 154, 80–95 (2023).
5. Avižinienė, A. et al. Characterization of a Panel of Cross-Reactive Hantavirus Nucleocapsid Protein-Specific Monoclonal Antibodies. Viruses 15, 532 (2023).

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
Novel afinity binders for immunodetection of antibacterial resistance (Project No. 01.2.2.-MITA-K-702-05-0003). Agency for Science, Innovation and Technology and Lithuanian Research Council. Project leader Dr A. Žvirblienė, 2021-2023.
Antimicrobial resistance is announced by the World Health Organisation (WHO) one of the greatest threats to global health in this century. New bacterial resistance mechanisms are emerging and spreading globally. According to WHO, greater innovations are required in research and development of new antimicrobial medicines and diagnostic tools. The current project aimed to develop novel bioaffinity binders – monoclonal and recombinant multimeric antibodies - against bacterial factors responsible for antibiotic resistance, thus providing new tools for a direct immunodetection of antibiotic-resistant bacteria. Immunoassays have many advantages over the microbiological, biochemical and genotyping assays currently used in clinical laboratories. The necessary components of immunoassays are highly specific antibodies against the target of interest. In this project, we selected a series of antibiotic resistance factors and developed commercially exploitable bioaffinity binders against them. The project was implemented in collaboration with the Finnish industrial partner ArcDia and Lithuanian industrial partner UAB Imunodiagnostika. The partners contributed to evaluating the commercial and diagnostic potential of the binders by testing them in different diagnostic platforms with real biological samples. The outcome of the project is a collection of novel well-characterized monoclonal and recombinant multimeric antibodies with high diagnostic and commercial potential.

Research Council of Lithuania/European Social Fund. Studies on the virulence potential of meningococcal isolates: implications for an improved molecular diagnostics of invasive meningococcal disease (Project No. 01.2.2-LMT-K-718-03-0036). Project leader Dr M. Plečkaitytė, 2020-2023.
Invasive meningococcal disease (IMD) is a serious and life-threatening infection caused by the bacterium Neisseria meningitidis, also known as meningococcal disease. IMD develops rapidly with bacteremia and/or meningitis. In Europe, the incidence of the disease is steadily declining. According to the European Center for Disease Prevention and Control (ECDC), the incidence of IMD in Lithuania for unknown reasons is the highest in the EU/EEA and remains stable for more than a decade. This is a major public concern and the situation calls for active surveillance of IMD, which cannot be done without molecular epidemiology to predict IMD morbidity, disease outbreaks and vaccination strategies. So far in Lithuania, the monitoring of IMD is passive, limited to the detection of disease cases. Meningococcal strains are not characterized by molecular methods that are used internationally. The aim of this project is to introduce modern methods of genotyping N.meningitidis strains and to identify potential virulence (invasiveness) molecular markers that would allow monitoring of circulating invasive meningococcal strains in Lithuania. It is not known how many asymptomatic individuals in Lithuania are N.menigitidis carriers and, thus potential transmitters of invasive meningococcal strains. Meningococcal transmission occurs via a human-to-human route from IMD sufferers or asymptomatic carriers. During the implementation of the project, the meningococcal carriage rate among asymptomatic subjects 19-25 years of age in the Vilnius region, where the highest incidence of IMD is observed, was determined. The characterization of meningococcal carriage strains is of great importance for predicting N.meningitidis transmission routes and provide the preventive measures for IMD, including vaccination strategy. Data on molecular characterization of meningococcal isolates were submitted into an international open-access database and published in two peer-reviewed papers.

Development of SARS-CoV-2 Specific Antibodies for Diagnostic Applications (Project No. 01.2.2.-LMT-K-718). Research Council of Lithuania. Project leader Dr A. Žvirblienė, 2021-2023.
The project contributed to solving problems caused by the COVID-19 pandemic. It aimed to develop new biotechnological products - SARS-CoV-2-specific antibodies of diagnostic and commercial value. Antibodies were raised against recombinant viral antigens - nucleocapsid (N) protein, spike (S) protein, and receptor-binding domain (RBD) as well as recombinant virus-like particles (VLPs) harbouring target epitopes of S protein. Antigens of both currently circulating and emerging variants of SARS-CoV-2 were used for antibody production. The use of chimeric VLPs allowed generation of antibodies of tailored specificity against the selected conserved sequences of S protein. The newly developed antibodies were characterized in detail and used to investigate the antigenic structure of SARS-CoV-2 proteins to obtain new scientific data on their immunodominant epitopes. These data are of great importance for the development of vaccines and diagnostic reagents. The project is consistent with Smart Specialization priority 2. Health technologies and biotechnologies and its thematic specificity 2.1. Molecular technologies for medicine and biopharmaceutics.
Development of advancing antibody-based tests for quantification of endoplasmic reticulum proteins (Project No. S-TPP-23-2). Research Council of Lithuania. Project leader Dr M. Simanavičius, 2023-2024.
The research project focuses on the development of enzyme-linked immunosorbent assay (ELISA) and antibody microarray technology-based methods for the quantification of key endoplasmic reticulum proteins, including calreticulin, ERp57, and BiP. These proteins play critical roles in protein folding, quality control, and stress response within the endoplasmic reticulum, a vital organelle in eukaryotic cells. Dysregulation of endoplasmic reticulum protein homeostasis has been implicated in various diseases, including neurodegenerative diseases, cancer, metabolic disorders, and autoimmune diseases. Measurement of these proteins in blood samples could serve as potential biomarkers for disease diagnosis, prognosis, and monitoring of treatment response. The project aims to provide reliable and sensitive methods for quantifying these endoplasmic reticulum proteins, intending to advance our understanding of their roles in disease pathogenesis and potentially facilitate the development of personalized medicine approaches. The research has the potential to contribute to the field of translational medicine by bridging basic research on endoplasmic reticulum proteostasis with clinical applications for disease management. The project is implemented with UAB Baltymas as a partner.

Contractual Research
Collaboration Contract with Abcam Ltd, UK. Dr A. Žvirblienė (open-ended). Contract on the supply of monoclonal antibodies against different targets.

Collaboration Contract with Santa Cruz Biotechnology Inc., US. Dr A. Žvirblienė (open-ended). Contract on the supply of monoclonal antibodies against different targets.

Collaboration Contract with Kalon Biological/Clin-Tech Ltd, UK. Dr A. Žvirblienė (open-ended). Contract on the supply of virus-specific monoclonal antibodies.

Collaboration Contract with UAB Baltymas, Vilnius. Dr A. Žvirblienė (open-ended). Contract on the supply of virus-specific monoclonal antibodies.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Friedrich-Loeffler Institute (Germany)
Justus-Liebig University Giessen (Germany)
ArcDia (Finland)
Tartu University (Estonia)
Vilnius University Hospital Santaros Klinikos (Lithuania)
UAB Immunodiagnostika (Lithuania)

OTHER RESEARCH ACTIVITIES
Dr A. Žvirblienė
• member of the Lithuanian Academy of Sciences;
• member of the EuroMabNet;
• president of the Lithuanian Society for Immunology;
• member of the Vaccine Task Force of the European Federation of Immunological Societies (EFIS)
• chair of COVID-19 comission at the Lithuanian Academy of Sciences;
• member of Vilnius University Council;
• member of the National Cancer institute Council;
• chair of Vilnius University PhD committee on Chemical engineeting;
• member of Vilnius University Study committee on Molecular Biotechnology;
• member of the Board of the Lithuanian Biochemical Society;
• member of Lithuanian Science prize comission at the Lithuanian Academy of Sciences;
• member of the Comission on L'Oreal Women in Science prizes.
Dr D. Stravinskienė
• Member of the Young Immunologists Task Force at the European Federation of Immunological Societies (EFIS);
• secretary of the Lithuanian Society for Immunology.
V. Rudokas and A. Sližienė
• Members of the European Academy of Allergy and Clinical Immunology (EAACI)
Dr M. Simanavičius and I. Dalgėdienė
• Members of the board of the Lithuanian Society for Immunology.
Dr M. Plečkaitytė and Dr Indrė Kučinskaitė-Kodzė
• Members of Vilnius University PhD committee on Chemical engineeting
Dr A. Kanopka
• Member of academic ethics commission at Vilnius University Life Sciences center

BEST REPORTS DELIVERED AT CONFERENCES ABROAD
1. Dr M. Plečkaitytė, oral presentation “Predicted coverage by 4CMenB and MenB-Fhbp vaccine against invasive serogroup B Neisseria meningitidis isolated from 2017 to 2019 in Lithuania” at the 4th Edition of World Congress of Infectious Diseases (Italy, Rome, 21-06-2023)
https://infectiouscongress.com/uploads/pdfs/infection-abstract-book.pdf
2. Dr A. Lučiūnaitė, oral presentation “Investigation of inflammatory response in macrophages activated by immune complexes” at the ABC7: Autoimmunity, B cells and Complement summer school (Tallinn, Estonia, 14-16/6/2023) https://abc7.ee
3. Dr A. Sližienė, poster presentation „Epitope mapping of monoclonal antibodies raised against fish parvalbumins and their reactivity with different fish extracts” at the EAACI Congress 2023 (Hamburg, Germany, 9-11/06/2023)
https://eaaci.org/events_congress/eaaci-congress-2023/

MOST IMPORTANT NATIONAL AND INTERNATIONAL AWARDS RECEIVED FOR R&D ACTIVITIES
1. K. Mašalaitė received the Doctoral scholarship for study results from Research Council of Lithuania;
2. A. Rimkutė received the award ((2nd place) for the best poster presentation in the Immunology category at "The Coins 2023" conference

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
Dr A. Žvirblienė
• member of the COVID-19 vaccination work group at the Ministry of Health of the Republic of Lithuania;
• member of the group of independent experts on the National immunoprophylaxis program 2019-2023 organized by the Ministry of Health of the Republic of Lithuania.
• member of work group dedicated to consider issues of extreme health situations preparedness and response to them organized by Ministry of Health of the Republic of Lithuania;
• member of work group for COVID-19 medicines organized by Ministry of Health of the Republic of Lithuania;
• member of the Advisory Council at the President’s Office of the Republic of Lithuania;

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES
Dr A. Žvirblienė
• Participated in the meeting of Health Committee of the Lithuanian Parliament (Seimas) on the preparedness for seasonal respiratory infections, 13-09-2023:
https://www.lrt.lt/naujienos/sveikata/682/2076332/prof-zvirbliene-medicinine-kauke-nuo-dabar-vyraujanciu-covid-19-atmainu-neapsaugos
• Provided information on the adapted COVID-19 vaccines at the press-conference organized by the Ministry of Health, 25-09-2023:
https://www.lrt.lt/mediateka/irasas/2000295613/nuo-spalio-5-d-vieno-vizito-metu-bus-galima-pasiskiepyti-ir-nuo-gripo-ir-nuo-covid-19

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
Dr M. Simanavičius
• Interview at lrt.lt portal about human virome 22-01-2023:
• https://www.lrt.lt/naujienos/mokslas-ir-it/11/1871504/dvi-paros-po-gimimo-ir-jau-esame-kolonizuoti-ka-veikia-390-trilijonu-zmogaus-organizme-gyvenanciu-virusu
• Several interviews at national radio, BNS, Lrytas TV news, LNK TV news about COVID-19 seroepidemiologic study:
https://www.lrt.lt/mediateka/irasas/2000264293/ryto-garsai-lietuvoje-pradedamas-covid-19-imuniteto-tyrimas
https://www.lrt.lt/mediateka/irasas/2000268016/ryto-garsai-mokslininkai-aiskinasi-ar-lietuvos-gyventojai-yra-igije-imuniteta-nuo-covid-19
https://sc.bns.lt/view/item/458347
https://lnk.lt/zinios/lietuvoje/194372
https://tv.lrytas.lt/zinios/lietuvos-diena/2023/03/26/news/imsis-veiksmu-identifikuojant-covid-19-paliktus-pedsakus-bus-tiriamas-tautieciu-imunitetas-koranavirusui-26544828
https://www.lrt.lt/mediateka/irasas/2000268016/ryto-garsai-mokslininkai-aiskinasi-ar-lietuvos-gyventojai-yra-igije-imuniteta-nuo-covid-19
Dr A.Žvirblienė
• Interview at national radio and Vilnius University news about the parallels between the pandemic and the war, 09-03-2023:
https://www.lrt.lt/mediateka/irasas/2000261413/mokslas-be-pamokslu-kas-sieja-kara-ir-pandemija
• Several interviews at national radio, national TV, Žinių radijas, lrt.lt, 15min.lt, Kauno diena, Delfi.lt, TV3.lt about the pandemic and COVID-19 vaccines
https://www.tv3.lt/naujiena/lietuva/ar-koronaviruso-pandemija-jau-isties-baigta-ekspertai-perspejo-koks-scenarijus-labiausiai-kelia-nerima-n1209444
https://www.lrt.lt/naujienos/sveikata/682/1859242/zvirbliene-apie-teorijas-jog-skiepai-nuo-covid-19-silpnina-imuniteta-jei-naudojami-tinkamai-jokiu-problemu-zmonems-nebuna
https://www.lrt.lt/mediateka/irasas/2000257062
https://www.lrt.lt/mediateka/irasas/2000252942/sveikata-kiek-lietuvai-pavojinga-naujoji-koronaviruso-atmaina-ir-ka-reikia-zinoti-pries-neriant-i-ekete-ziema
https://www.lrt.lt/mediateka/irasas/2000257062
https://www.ziniuradijas.lt/laidos/dienos-klausimas/ar-rudeni-sugris-covid-19?video=1
https://www.delfi.lt/sveikata/sveikatos-naujienos/nauja-vakcina-nuo-covid-19-jau-pakeliui-bet-esminis-klausimas-dar-neatsakytas-situacija-kardinaliai-pasikeitusi-94457299
https://www.tv3.lt/naujiena/lietuva/ne-tik-covid-19-ar-gripas-nerima-del-nauju-epidemiju-mokslininkams-kelia-tirpstantys-ledynai-ir-klimato-kaita-n1279266
https://kauno.diena.lt/naujienos/sveikata/sveikata/covid-19-nauja-banga-ar-tik-bangele-1140562
https://www.lrytas.lt/sveikata/medicinos-zinios/2023/09/08/news/nauju-duomenu-apie-covid-19-pazerusi-profesore-a-zvirbliene-tai-kardinaliai-keicia-situacija-28316900
https://www.15min.lt/gyvenimas/naujiena/sveikata/prof-a-zvirbliene-apie-skiepus-nuo-gripo-ir-kovido-siemet-turime-aiskia-rekomendacija-1028-2118610?utm_medium=copied
• Interview at Lrytas.lt about the discoveries awarded in 2023 by the Nobel prize in Physiology or Medicine, 02-10-2023:
https://www.lrytas.lt/sveikata/medicinos-zinios/2023/10/02/news/profesore-a-zvirbliene-apie-nobeli-pelniusi-medicinos-atradima-atrode-kad-tos-technologijos-nebus-imanoma-panaudoti--28577770

DEPARTMENT OF SINGLE CELL ANALYTICS

Saulėtekio al. 7, LT-10257 Vilnius
Tel. +370 5 223 4356
E-mail:
Head - Dr Linas Mažutis

STAFF

Research professor: Dr L. Mažutis.
Senior researchers: Dr R. Žilionis, Dr S. Juzėnas.
Researchers: Dr G. Leonavičienė
Research assistants: K. Goda, L. Camisi, V. Milkus, D. Baronas, J. Žvirblytė, D. Murza, S. Norvaišis, V. Mikulėnaitė
Other researchers and technical staff: E. Pranauskaitė, S. Kim, M. Sinis, I. Čiutaitė
Doctoral students:, L. Camissi, J. Žvirblytė, D. Baronas, D. Murza, S. Norvaišis, V. Mikulėnaitė.

RESEARCH INTERESTS
• Single-cell transcriptomics, genomics and epigenomics
• Droplet microfluidics
• Directed evolution of enzymes
• Antibody screening

SELECTED PUBLICATIONS 2023
1. Glasner, A. et al. Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies. Nat Immunol 24, 1020–1035 (2023).
2. Leonaviciene, G. & Mazutis, L. RNA cytometry of single-cells using semi-permeable microcapsules. Nucleic Acids Research 51, e2 (2023).
3. Burdziak, C. et al. Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis. Science 380, eadd5327 (2023).
4. Kanai, M. et al. A second update on mapping the human genetic architecture of COVID-19. Nature 621, E7–E26 (2023).
5. Jung, E. S. et al. Genome-wide association analysis reveals the associations of NPHP4, TYW1-AUTS2 and SEMA6D for Behçet’s disease and HLA-B*46:01 for its intestinal involvement. Digestive and Liver Disease (2023).

PATENTS 2023
Granted:
1. Thon, J. N., Italiano, J. E., Mazutis, L. & Weitz, D. A. Systems and methods for biomimetic fluid processing. US11566214B2 (2023).
2. Systems and methods for encapsulation and multi-step processing of biological samples (WO/2020/255108)
Applications:
1. Italiano, J., Mazutis, L., Thon, J. N. & Weitz, D. A. System and method for a biomimetic fluid processing. US20230009208A1 (2023).
2. A microcapsule and methods of making and using same (WO/2023/117364).
3. Microcapsules comprising biological samples, and methods for use of same (WO/2023/099661).
4. Barcoding nucleic acid molecules derived from individual cells (WO/2023/099662).
5. Methods for processing and barcoding nucleic acids (WO/2023/099667).

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
Establishment of single-cell transcriptomics/genomics research parallel-laboratory (Project No. 01.2.2-LMT-K-718-04-0002). Research Council of Lithuania/European Social Fund. Project leader Dr L. Mažutis, 2020-2024.
Considering growing importance of single-cell biology field and huge opportunities offered by genomics technologies, this project will seek to realize two objectives: 1) Develop microfluidics technology for processing clinical samples and 2) Establish a computational biology parallel laboratory for analysis of single-cell transcriptomics/genomics data. Accomplishing these two objectives we will build single-cell atlas(es) of human pathologies whilst focusing our efforts on liver and blood tumors. Analysis of gene expression landscape will enable us to differentiate cells according to their physiological state and possibly provide a better understanding of the biological mechanisms underlying the pathology. Such efforts are likely to lead to identification of novel diagnostic markers and possibly offer alternative treatment strategies.

Single Genome Amplification of Clinically Relevant Microorganisms Using Microfluidics Technology. (Project No. 01.2.2-MITA-K-702). MITA. Project leader Dr L. Mažutis, 2021–2023.
The goal of this project is to develop a droplet microfluidics-based platform for single bacterial cell analysis and sequencing. Unbiased sample capture and preparation, faithful capture of the individual genomes, improved genes recovery and other functionalities improving the characterization of single-cell genomics will be part of this effort. In the field of clinical microbiology the need for new and improved types of single-cells assays is steadily growing and this project fulfil this demand by developing a system for a single genome amplification (SAG) assay. Among different SAGs assays available today, only microfluidic approaches can provide the much-needed throughput and sensitivity.

Development of a Highly Sensitive Digital RT-PCR Method for Absolute Quantification of SARS-CoV-2 Virus. (Project No. 01.2.2-LMT-K-718). Research Council of Lithuania. Project leader Dr R. Žilionis 2021–2024.
High-sensitivity tests to accurately assess the prevalence of the virus in a population are one of the essential tools for both identifying new foci of SARS-CoV-2 and managing pandemic prevalence. Depending on the test results, important socio-economic decisions are made that determine people’s life constraints. This project aims to develop an ultra-sensitive digital RT-PCR method for the absolute detection of genetic information in a sample. The project idea is based on droplet microfluidic technology and its advantages: absolute quantification of the analyte, greater resistance to factors that inhibit analytical reactions, such as excess background DNA or polymerase inhibitors. The developed ultra-sensitive method will expand the current testing capabilities. For example, it will be possible to test larger groups by the pooling method or to detect extremely small amounts of viral DNA in environmental samples. By selecting different DNA primers, it will be possible to simultaneously detect both wild-type and mutant viruses.

International Research Projects
H2020 FRAMEWORK PROGRAMME: Directed EVOlution in DROPS (H2020-MSCA-ITN-2018 Grant agreement ID: 813786). Dr L. Mažutis, 2018–2023.
In EVOdrops, we use directed evolution to overcome limitations set by Nature. It is a synthetic, man-made approach of evolution, aiming at improving living systems based on predefined needs, controlling the external selection pressure. While natural evolution took billions of years to optimise macromolecules, directed evolution – to be efficient in an industrial process – requires both the generation of genetic diversity and ultra-high throughput screening capabilities to recover the variants of interest. We will develop and optimise these tools using the ground-breaking potential of droplet-based microfluidics for high-throughput experimentation and the fine control of gene library construction. EVOdrops, a European training network, will bring together the leading research scientists, laboratories and industries in Europe with outstanding expertise in protein engineering and microfluidics.

Micro-capsules for versatile multiplexed cytometry. (Project No. CA278392-01). National Institutes of Health (NIH), Project co-PI Dr L. Mažutis, 2023-2026.
Here, we leverage the recent innovation in capsule technology to enable gene expression analysis in 10-100k single-cells rapidly and cost efficiently, without relying on sequencing, and we further multiplex it with protein expression analysis. The capsules enable rapid cell phenotyping at unprecedented scale, and provide a flexibility of targeting any useful marker gene, with lower noise profiles associated with FC rather than scRNA-Seq. Importantly, as we develop these tools, we will set the stage for many other capsule-based single-cell assays, including other multi-omic assays, for development in future work.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Harvard Medical School (USA)
Harvard University, School of Engineering and Applied Sciences (USA)
Memorial Sloan Kettering Cancer Center (USA)
ETH Zurich (Switzerland)
Paris ESPCI (France)
Christian-Albrechts-University of Kiel, Institute of Clinical Molecular Biology (Germany)
Columbia University (USA)
California Institute of Technology (USA)
Bigelow Institute (USA)

OTHER RESEARCH ACTIVITIES
Dr L. Mažutis
• Editorial board member of the Current Opinion in Biotechnlogy.
• Co-founder “Droplet Genomics”, Vilnius, LT;
• Co-founder “Platelet Biogenesis” Inc. Boston, MA, USA;
• Invited expert for evaluation of international research proposals

SECTOR OF APPLIED BIOCATALYSIS

Saulėtekio al. 7, LT-10257 Vilnius
Tel. +370 5 223 4371
E-mail:
Head - Dr Inga Matijošytė

STAFF
Senior researcher: Dr I. Matijošytė.
Researchers: Dr Z. Toleikis.
Research assistants: J. Krutkevičius, D. Daunoraitė, J. Babinskas.
Other researchers and technical staff: R. Šiekštelė, I. Ožiūnaitė.
Doctoral students: J. Krutkevičius, D. Daunoraitė, J. Babinskas.

RESEARCH INTERESTS
• Development of biocatalysts and their application systems
• Exploring Industrial symbiosis approach
• Precision fermentation and alternative proteins

SELECTED PUBLICATIONS 2023
1. L.L. Bilela, I. Matijošytė, J. Krutkevičius, D.A.M. Alexandrino, I. Safarik, J. Burlakovs, S.P. Gaudêncio, M.F. Carvalho. Impact of per- and polyfluorinated alkyl substances (PFAS) on the marine environment: Raising awareness, challenges, legislation, and mitigation approaches under the One Health concept. Marine Pollution Bulletin. 2023, 194 (A) 115309.
2. J. Babinskas, J. Sabotič, I. Matijošytė. Synthesis and application of a phenazine class substrate for high-throughput screening of laccase activity. Applied Microbiology and Biotechnology. 2024, 108, 1-12.

RESEARCH PROJECTS CARRIED OUT IN 2023
International Research Projects
Project “BIOCONNECT: Developing the Action Plan to Foster Baltic Region Innovation Ecosystem in Biotechnology and Synthetic Biology”
Project leader of VU: Dr Inga Matijošytė
VU executors: Dr Paulina Martusevičė, Ieva Ožiūnaitė, Justinas Babinskas, Jokūbas Krutkevičius
Funding source: HORIZON-EIE-2023-CONNECT-01 (Type of Action: CSA)
Other Project partners: Tallinn University of Technology, University of Tartu, Biocatalyst Foundation, Latvian Institute of Organic Synthesis, Association LithuaniaBIO, Synbio Powerlabs.
Project duration: December 2023- December 2024
The BIOCONNECT project aims to address this challenge by developing an integrated innovation action plan for a more interconnected Baltic biotechnology ecosystem, facilitating new intra-regional links through initiatives targeting students, researchers, startups, industry, capital, and policymakers. The consortium has been designed to involve diverse quadruple helix actors through a system of networks of the consortium’s members, while tapping into the best practices of innovation leaders represented by Finland - and applying them in the Baltic States. The overarching goal is to set the stage for an integrated Baltic-Nordic biotechnology cluster.

Project "Novel high-performance polymers from lignocellulosic feedstock”
Project leader of VU: Dr Inga Matijošytė
VU executors: Dovilė Daunoraitė, Rimantas Šiekštelė, Justinas Babinskas
Funding source: Baltic Science programme (Estonian Call)
Other Project partners: Institute of Technology, University of Tartu; Department of Energy and Process Engineering, Norwegian University of Science and Technology (NTNU), company Fibenol (Estonia)
Project duration: 2020-2024
This project develops new sustainable platform for novel bio-derived polymers used in applications with strict demands for properties (e.g. automotive industry, coatings, packaging, etc). As a raw material, a stream of wood sugars, which very recently became available and is derived from low quality wood residues, is used. Importantly, the environmental benefits and possible adverse effects are fully analyzed throughout the project, enabling the optimization from the sustainability point of view. The environmental sustainability profile of the bio-based polymers studied will be benchmarked against the conventional fossil-derived plastics

Project “BioBaltic: Nordic-Baltic collaboration to boost bio- and circular- economy”
Project leader of VU: Dr Inga Matijošytė
VU executors: Ieva Ožiūnaitė, Jokūbas Krutkevičius
Project website: https://nordregioprojects.org/biobaltic
Funding source: Nordic Council of Ministers and NordRegio
Other Project partners: the formed Mobile Learning Hubs in Estonia, Latvia, and Lithuania
Project duration: 2021-2023
In the course of the BioBaltic project implementation, the Mobile Learning Hub in Lithuania was developed and the network of local stakeholders for boosting circular bioeconomy was gathered. In total, over one hundred agri-food business enterprises in five Lithuanian municipalities were engaged in the industrial symbiosis study. The obtained results were presented and discussed involving participating municipalities and other Lithuanian stakeholders. Meanwhile, experience exchange with the Nordics took place during the Lithuanian delegation visit to Sotenäs Symbiosis Centre in the last month of the project.

COST Action CA18238 "European transdisciplinary networking platform for marine biotechnology"
Project leader of VU: Dr Inga Matijošytė
VU executors: Dovilė Daunoraitė, Jokūbas Krutkevičius, Justinas Babinskas
Project website: https://www.ocean4biotech.eu/
Project duration: 2019-2024
The overall aim of Ocean4Biotech is to bring together experts in the field of marine biotechnology, to provide a platform for sharing experience, knowledge and technologies, and to design a roadmap for a more efficient and rapid development of marine biotechnology research in Europe and beyond.

COST CA20137 “Action Making Early Career Researchers' Voices Heard for Gender Equality”
Project leader of VU: Dr Inga Matijošytė
VU executors: Dovilė Daunoraitė
Project website: https://gendervoices.eu/
Project duration: 2021-2025
Sector of Applied Biocatalysis is involved in WG2 activities. This Working Group seeks to gather best practices that work towards an integration of Young Researchers and Innovators (YRIs) in decision-making bodies and the consideration of their specific challenges, from a gender perspective, by institutional leaders.

The project "The Center for Engineering of Next Generation Industrial Enzymes (TVIRTAS)"
NO 01.2.2-CPVA-K-703-03-0023 under the programme Promoting the activity of centers of excellence, innovation technologies and transfer centers funded by Central project management Agency.
Project leader of VU: prof. Rolandas Meškys
VU executor of Sector of Applied Biocatalysis: Dr Inga Matijošytė
Project duration: 2020-2023

COLLABORATION CONTRACTS
1. Framework Agreement for Scientific Cooperation between BLUE ECOTECH LTD and Vilnius University (Sector of Applied Biocatalysis). Dr Inga Matijošytė. 2023.09.01 – 2028.09.01
2. Cooperation on biotransformations of various lignocellulosic based biomass into added value products. Latvian State Institute of Wood Chemistry, Cooperation Agreement N° BS-15600-1341 (2018-07-30, I. Matijošytė (open-ended).
3. Enzymes and their application in detergents. SC Naujoji Ringuva, N° B1-560000-153, I. Matijošytė (open-ended).

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
University of Tartu (Estonia)
Norvegian University of Science and Technology (Norway)
National Institute of Biology (Slovenia)
University of Torino (Italy)
Vytautas Magnus University (Lithuania)
Latvian State Institute of Wood Chemistry (Latvia)
National Council of Ministers Office (Lithuania)
Aarhus University (Denmark)
Jožef Stefan Institute (Slovenia)
Tallinn University of Estonia (Estonia)
JSC Genie Biotech EU (Lithuania)
JSC Fibenol (Estonia)
JSC Blue Ecotech LTD (Malta)
JSC Probiosanus (Lithuania)
JSC Biorro (Lithuania)

BEST REPORTS DELIVERED AT CONFERENCES ABROAD
1. Discovery of biocatalysts and the paths for their identification. The International Conference of Biochemists and Molecular Biologists – ABMBBIH Conference 2023. 17-20 May 2023, Sarajevo, Bosnia & Herzegovina. Dr Matijošytė, invited lecture.
2. Dr Inga Matijošytė presentation "The boost of bio- and circular-economy: the quintuple helix model in practise" at the session Transfer in Sustainability: Circular Economy Approaches at Arqus Pilot Training Programme/Arqus Transfer Skills. 6th June 2023.

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES
Dr I. Matijošytė (in 2023):
• ASSOCIATION LITHUANIABIO / Board member & vice president
• EUROPEAN SOCIETY OF APPLIED BIOCATALYSIS / Member of the Scientific Committee
• SMK HIGH SCHOOL / Member of the Board
• EUROPABIO BIOMANUFACTURING PLATFORM / member of the working group
• EUROPEAN BIOTECHNOLOGY FEDERATION / member
• LITHUANIAN SOCIETY OF BIOCHEMISTS/ member
• MOLECULAR BIOTECHNOLOGY MASTER STUDY PROGRAM/ chair of the programme
• LITHUANIAN CLEANTECH CLUSTER / Board member
• LIFE SCIENCES BALTICS 2023/ member of the scientific committee
• COORDINATION COMMISSION OF IMPLEMENTATION OF BALTIC SEA REGION STRATEGY IN LITHUNIA/MEMBER / commission member

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. Innovation club discussion Science solutions 360 °C: Climate change and Circular Economy. Presentation about Industrial symbiosis by Dr Inga Matijošytė. 11th December 2023. https://www.youtube.com/watch?v=IDjopu2KD3w&list=PLB-vpWIIonyhfGDWZhe9JIPiMjxFXCw5B&index=11&t=9s
2. The interview about industrial symbiosis model implementation for indutry and society with regards to BioBaltic project results. 14th November 2023. https://naujienos.vu.lt/industrine-simbioze-atliekoms-virstant-zaliavomis-atsiveria-naujos-tvarumo-perspektyvos/
3. The lecture “BioBaltic project: analysis of technological feasibility” by I. Matijošytė at the event Agricultural Sciences for Business: Challenges and Opportunities for the Green Deal, 31st March 2023, Kaunas.
4. The lecture "Innovation-based experiential learning in university studies" by Dr I. Matijošytė at the international conference "Experiential education: challenges, experiences, discoveries" organized by Linkuva gymnasium, 28 April 2023

CHRONOEPIGENETICS LABORATORY

Saulėtekio al. 7, LT-10257 Vilnius
E-mail: ,
Head -Dr Artūras Petronis

STAFF

Research professor: Dr A. Petronis.
Researchers: Dr L. Vilys.
Junior researchers: K. Koncevičius, A. Kriščiūnas, Martynas Želnys, Viltė Čereškaitė, Julija Radevičiūtė, Rokas Reventas.
Other researchers and technical staff: Auksė Kazlauskaitė, Aušrinė Šveikauskaitė.
Doctoral students: A. Kriščiūnas.

RESEARCH INTERESTS
• The temporal dimension of the epigenome, referred to as the 'chrono' dimension, offers a promising avenue for integrating epigenetic, environmental, and genetic studies of diseases (Oh and Petronis, 2021). The ultimate objective of chrono-epigenetics is to predict disease risk and the age of disease onset based on individual-specific temporal dynamics of epigenomes.

SELECTED PUBLICATIONS 2023
1. Carlucci, M. et al. Diurnal oscillations of MRI metrics in the brains of male participants. Nat Commun 14, 7044 (2023).
2. Carlucci, M. et al. Scikick: A sidekick for workflow clarity and reproducibility during extensive data analysis. PLOS ONE 18, e0289171 (2023).

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
Identifying chronoepigenetic markers in schizophrenia (Project No. 09.3.3.-LMT-K-712-17-0008). Research Council of Lithuania/ European Social Fund. Project leader Dr A. Petronis, 2020– 2023.
Schizophrenia (SCH) is a chronic mental illness that severely disturbs thoughts, feelings, behavior. SCH affects one out of ~100 individuals, and thus the identification of molecular mechanisms and biomarkers of SCH is a significant biomedical, social, and economical priority. Chronoepigenetics provides new opportunities and new hope for individualized diagnostics and treatment of SCH. Chronoepigenetics investigates temporal dynamics in epigenetic regulation within the same individual to find “time-sensitive” regions in the human epigenome. Based on our recent discoveries, we hypothesize that these time-sensitive parts are susceptible to errors, and that these errors gradually accumulate and eventually perturb cellular functions to result in disease.
In this project, we will investigate time-sensitive epigenetic variation in white blood cells collected from SCH patients and controls at 2 hour intervals over a 12 hour period. In doing so, we will generate individual-specific temporal epigenetic profiles based on 100,000 cytosine modifications, and such profiles will be analyzed to identify chronoepigenetic biomarkers of SCH. The innovative step and the major strength of our approach is the emphasis on individual patient epigenomics rather than the traditional group-wise comparison of patients and controls. Chronoepigenetic markers could become the first biomarkers for SCH, and may open new diagnostic, therapeutic, and prognostic opportunities in precision psychiatry.
This highly original project will mark the beginning of large-scale molecular biology research of psychiatric diseases in Lithuania. This effort will become an epicentre for the formation of a new research team and contribute to training psychiatrists, molecular biologists, and bioinformaticians. Research strategies developed in this project may become useful for various other diseases further benefiting research and development in Lithuania and EU.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
University of Toronto (Canada)
Center for Addiction and Mental Health (Canada)

OTHER RESEARCH ACTIVITIES
Prof. A. Petronis
• Epigenetics, editorial board member https://www.tandfonline.com/action/journalInformation?show=editorialBoard&journalCode=kepi20

MOST IMPORTANT NATIONAL AND INTERNATIONAL AWARDS RECEIVED FOR R&D ACTIVITIES
1. Art Petronis group received the University Excellence Initiative Programme of the Ministry of Education, Science and Sports of Lithuania grant (Measure No. 12-001-01-01-01).

SECTOR OF CRYSTALOGRAPHY AND CHEMICAL INFORMATICS

Saulėtekio al. 7, LT-10257 Vilnius
E-mail: ,
Head - Dr S. Gražulis

STAFF
Research professor: Dr S. Gražulis
Researchers: Dr A. Merkys
Research assistants: A. Vaitkus, A. Grybauskas

RESEARCH INTERESTS
• Crystallography
• Scientific Databases
• DataManagement
Cheminformatics
• Scientific Software Development

SELECTED PUBLICATIONS 2023
1. Grybauskas, A. & Gražulis, S. Building protein structure-specific rotamer libraries. Bioinformatics 39, btad429 (2023).
2. Lingė, D. et al. PLBD: protein–ligand binding database of thermodynamic and kinetic intrinsic parameters. Database 2023, baad040 (2023).
3. Merkys, A. et al. Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions. Journal of Cheminformatics 15, 25 (2023).
4. Vaitkus, A. et al. A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database. Journal of Cheminformatics 15, 123 (2023).
5. Manakova, E. et al. Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein. Sci Rep 13, 6123 (2023).

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
Chemical data engineering in the Crystallography Open Database (COD) (Project No. S-MIP-23-87). Research Council of Lithuania. Project leader Dr A. Merkys, 2023-2026.
Reliable knowledge about structure and properties of chemical compounds is essential for pharmacology, food safety, environment preservation, design of new materials and understanding of functions of small molecules in living organisms. The soon-to-be-finished project "Chemical annotation in the Crystallography Open Database (COD)" (CODCHEM, funded by the Research Council of Lithuania, ends on 2022-12-31) has successfully connected structural knowledge about small-molecule compounds in the Crystallography Open Database (COD) with their chemical descriptions, enabling studies of the fused dataset. While the CODCHEM project has achieved its main goal, it also highlighted certain aspects that would greatly benefit from further research and improvement. The current project proposes four interconnected objectives that address data validity and availability issues as well as enhance software accessibility and usability. Firstly, the detection of chemical bonds in crystal structure descriptions could be improved by deriving a high-quality interatomic covalent radii table from open data using a novel automated approach and applying it to the chemical information derivation pipeline. Secondly, an open-source tool capable of deriving IUPAC chemical names from chemical descriptions could be created to further enhance the fused dataset. Thirdly, the chemical annotation comparison system could be improved by reducing the prevalence of false-positive results and creating software capable of automatically resolving unambiguous data discrepancies. Finally, an online system which would allow to easily run open-source validation programs as well as construct custom computational pipelines could be developed. Successful implementation of these objectives would greatly improve the quality of the fused dataset, create new open-source cheminformatics tools for the scientific community and provide improved access to existing chemical data validation software.

International Research Projects
Geometric deep learning for crystal structure and properties predictions (Project No. S-LZ-23-3). Lithuanian-French Programme Gilibert. Project leader Dr S. Gražulis, 2023-2024.

There has been tremendous progress in the development of machine learning, and particularly deep-learning methods and their applications to image and speech recognition in the last decade. More recently, this progress has been transferred to physical, chemical and biological applications. In this project, we will explore predicting of crystal forms and molecular properties of small molecules from several artificial intelligence perspectives. More concretely, we will apply graph and geometric learning to infinite (cyclic) molecular graphs for crystal structure and properties prediction.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Centre Européen de Calcul Atomique et Moléculaire Switzerland)
Universidad de Granada (Spain)
National Center for Biotechnology Information (USA)
Université Grenoble Alpes, CNRS (France)

OTHER RESEARCH ACTIVITIES
Dr S. Gražulis
• Data, editorial board member, https://www.mdpi.com/journal/data/editors;
• member of Raman Open Database Advisory Board, https://solsa.crystallography.net/rod/
Dr S. Gražulis, Dr A. Merkys, Dr A. Vaitkus
• members of Crystallography Open Database (COD) Advisory Board, https://www.crystallography.net/cod/;
• members of Open Databases Integration for Materials Design (OPTIMADE) consortium, https://www.optimade.org/contributors.

SECTOR OF AMYLOID RESEARCH

Saulėtekio al. 7, LT-10257 Vilnius
Tel. +370 5 223 4354, +370 670 69929
E-mail:
Head – Dr Vytautas Smirnovas

STAFF
Research professor: Dr V. Smirnovas
Researchers: Dr D. Šulskis, Dr M. Žiaunys, Dr A. Sakalauskas, Dr A. Janonienė
Doctoral students: K. Mikalauskaitė, R. Sniečkutė, D. Veiveris, L. Krasauskas
RESEARCH INTERESTS
Protein misfolding and amyloid fibril formation
Prions and proteinaceous infectivity
Protein liquid-liquid phase separation

SELECTED PUBLICATIONS 2023
1. Šulskis, D., Šneiderienė, G., Žiaunys, M. & Smirnovas, V. The seeding barrier between human and Syrian hamster prion protein amyloid fibrils is determined by β2-α2 loop sequence elements. International Journal of Biological Macromolecules 238, 124038 (2023).
2. Sakalauskas, A. et al. The Major Components of Cerebrospinal Fluid Dictate the Characteristics of Inhibitors against Amyloid-Beta Aggregation. International Journal of Molecular Sciences 24, 5991 (2023).

3. Ziaunys, M., Mikalauskaite, K., Krasauskas, L. & Smirnovas, V. Conformation-Specific Association of Prion Protein Amyloid Aggregates with Tau Protein Monomers. International Journal of Molecular Sciences 24, 9277 (2023).
4. Pampuscenko, K. et al. Extracellular tau stimulates phagocytosis of living neurons by activated microglia via Toll-like 4 receptor–NLRP3 inflammasome–caspase-1 signalling axis. Sci Rep 13, 10813 (2023).
5. Ziaunys, M., Mikalauskaite, K., Sakalauskas, A. & Smirnovas, V. Investigating Lysozyme Amyloid Fibril Formation and Structural Variability Dependence on its Initial Folding State Under Different pH Conditions. Protein Science e4888 (2023).

RESEARCH PROJECTS CARRIED OUT IN 2023
National Research Projects
Cross-interactions in amyloid fibril formation: the role of pro-inflammatory S100A9 protein (Project No. S-MIP-22-34). Research Council of Lithuania. Project leader Dr V. Smirnovas, 2022-2025.
Amyloids are associated with multiple diseases including well-known Alzheimer’s and Parkinson’s (AD and PD), as well as infectious prion diseases. Prion-like self-replication of fibrils in vitro (termed “seeding”) is a common feature for many amyloid-forming proteins and there is growing evidence of prion-like spreading of amyloids in vivo. Moreover, emerging data suggests that cross-seeding and other cross-interactions between different amyloid-forming proteins may play an important role in the progress of amyloid-related diseases. Inability to account for these interactions during development of anti-amyloid drugs may be one of the reasons for failed clinical trials.
Some cases of amyloid cross-interactions are related to neuroinflammation. The pro-inflammatory protein S100A9 can form amyloid fibrils and accelerate amyloid formation of amyloid beta peptide (related to AD) and alpha-synuclein (related to PD). Recent data suggests that a S100A9-driven amyloid-neuroinflammatory cascade may serve as a mechanistic link between traumatic brain injury and AD. Similar links are also highly probable in case of PD. It suggests that amyloid cross-interactions may be one of the links between neuroinflammation and amyloid diseases. However, the information about S100A9 interactions with other brain-localized amyloid proteins is absent
Here we propose to study mechanisms of cross-interactions between S100A9 and major neurodegeneration-related amyloid proteins: Prion protein (PrP), and Tau protein (Tau), as well as of superoxide dismutase-1 (SOD1), which is related to Amyotrophic lateral sclerosis; and test if/how these interactions affect the efficiency of amyloid aggregation inhibitors. Absorbance and fluorescence spectroscopies will be used to follow kinetics of aggregation. Global fitting of the kinetic data will be employed to test possible mechanisms of aggregation and inhibition. FTIR will give insight into secondary structure of aggregates, and AFM will reveal the morphology of fibrils. Cell viability assay will be used to test toxicity of amyloid aggregates and efficiency of inhibitors.
This work will help to understand the links between neuroinflammation and amyloid diseases and may give new hints in development of anti-amyloid drugs.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) PARTNERS
Lithuanian University of Health Sciences (Lithuania)
Umea University (Sweden)
Latvian institute of Organic Synthesis (Latvia)
Institute of Atomic and Molecular Sciences, Academia Sinica (Taiwan)
Aarhus University (Denmark)

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES
1. National TV and Radio show “Laba diena, Lietuva” (Participant of the show on the subject “Explanation about the cause of Alzheimer's disease and prospects of curing it“ – Dr A. Sakalauskas, https://www.lrt.lt/mediateka/irasas/2000271059/alzheimerio-ligos-tyrimai-vu-mokslininkai-bando-issiaiskinti-kas-stabdo-ligos-progresavima. 2023.03.22)
2. National TV and Radio newspaper article (Interview, explaining about the medicaments of Alzheimer's disease – Dr A. Sakalauskas, Dr D. Šulskis, https://www.lrt.lt/naujienos/mokslas-ir-it/11/2060546/du-naujai-patvirtinti-vaistai-ir-kuriamos-vakcinos-nuo-alzheimerio-ar-laukia-kokybiskesne-senatve. 2023.08.26)
3. Public TV news LNK (Interview explaining about the medicaments of Alzheimer's disease – Dr A. Sakalauskas, Dr D. Šulskis, https://lnk.lt/zinios/211530. 2023.09.03)
4. National TV and Radio show "Kaip Jautiesi" (Participants of the show on the subject “Explanation about the cause of Alzheimer's disease and prospects of curing it“ – Dr A. Sakalauskas, Dr D. Šulskis, https://www.youtube.com/watch?v=EmC66J2pxO4&ab_channel=Lietuvosnacionalinisradijasirtelevizija. 2023.10.05)