Life Sciences Center

7 Saulėtekio av., LT-10257 Vilnius
Tel. 223 4435
E-mail

Director – Dr Gintaras Valinčius

 

 

STAFF

93 teachers (incl. 66 holding research degree), 326 research fellows (incl. 191 holding research degree), 145 doctoral students.

Institute of Biotechnology
Institute of Biochemistry
Institute of Biosciences

INSTITUTE OF BIOTECHNOLOGY

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4365
E-mail:
http://www.bti.vu.lt/
Director – Dr Vytautas Smirnovas

DEPARTMENTS OF THE INSTITUTE

Department of Protein - DNA Interactions
Department of Biological DNA Modification
Department of Eukaryote Gene Engineering
Sector of Microtechnologies
Department of Immunology and Cell Biology
Department of Biothermodynamics and Drug Design
Sector of Applied Biocatalysis
Department of Bioinformatics
Laboratory for Epigenomics Research

RESEARCH AREAS

Structural biology and bioinformatics
Genomics, biomolecules and biotechnologies: fundamental and applied research

DOCTORAL DISSERTATIONS DEFENDED IN 2021

Milda Mickutė. The application of animal Hen1 methyltransferases for labelling and sequencing of single-stranded RNA.
Inga Songailienė. Bacterial defense islands: CRISPR-Cas and toxin-antitoxin systems.
Robertas Galinis. Synthesis of DNA and magnesium pyrophosphate particles and their use for protein expression in vitro.
Agnė Janonienė. Exploration of carbonic anhydrase IX inhibitor influence on cancer cell migration and suitability to use in anticancer agent delivering nanosystems.
Martynas Simanavičius. The prevalence studies and diagnostics of hepatitis E virus.
Gediminas Drabavičius. Study and application of CRISPR-Cas systems.

DEPARTMENT OF PROTEIN - DNA INTERACTIONS

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4354
E-mail:
Head - Prof. Dr Virginijus Šikšnys

STAFF

Research professors: Prof. Dr V. Šikšnys, Dr S. Gražulis, Dr G. Sasnauskas, Dr M. Zaremba, Dr G. Tamulaitis.
Senior researchers: Dr G. Tamulaitienė, Dr E. Manakova, Dr G. Gasiūnas, Dr A. Šilanskas, D. T. Karvelis.
Researchers: Dr T. Šinkūnas, Dr P. Toliušis, Dr A. Merkys, Dr E. Zagorskaitė, Dr M. Skapas, Dr M. Tutkus, Dr I. Songailienė.
Junior researchers: G. Bigelytė, A. Vaitkus, E. Golovinas, A. Grybauskas.
Other researchers and technical staff: R. Žedaveinytė, D. Norkūnaitė, A. Tunevič.
Doctoral students: G. Bigelytė, E. Golovinas, I. Mogila, T. Urbaitis, D. Smalakytė, D. Dakinevičienė, J. Juozapaitis, M. Štitilytė, G. Druteika, A. Kopūstas.

RESEARCH INTERESTS

Structural and molecular mechanisms of restriction enzymes
Bacterial antivirus defence 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 2021

Karvelis, T. et al. Transposon-associated TnpB is a programmable RNA-guided DNA endo-nuclease. Nature. 2021, 599: 692–696.

Balderston, S. et al. Discrimination of single-point mutations in unamplified genomic DNA via Cas9 immobilized on a graphene field-effect transistor. Nat Biomed Eng. 2021, 5: 713–725.

Bigelyte, G. et al. Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modifi-cation in cells. Nat Commun. 2021, 12: 6191.

Manakova, E., Mikutenaite, M., Golovenko, D., Gražulis, S. & Tamulaitiene, G. Crystal structure of restriction endonuclease Kpn2I of CCGG-family. Biochimica et Biophysica Acta (BBA) - General Subjects. 2021, 1865: 129926.

Golovinas, E. et al. Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer. Sci Rep. 2021, 11: 4518.

PATENTS 2021

Applications:

Deschamps S., Šikšnys V., Young J. K., Zaremba M. Methods for the identification and characterization of double-strand break sites and compositions and uses thereof. US20210147909A1. Publication date: 20 May 2021.

Deschamps S., Šikšnys V., Young J. K., Zaremba M. Methods for the identification and characterization of double-strand break sites and compositions and uses thereof. EP3790993A1. Publication date: 17 March 2021.

Šikšnys V., Gasiūnas G., Karvelis T., Lubys A., Žaliauskienė J., Glemžaitė M., Smith A. RNA-directed DNA cleavage by the Cas9-crRNA complex. JP2021019617A. Publication date: 18 February 2021.

RESEARCH PROJECTS CARRIED OUT IN 2021

National Research Projects

Research Council of Lithuania/European Social Fund. Molecular Mechanisms of New Bacterial Antiviral Systems (No. 09.3.3-LMT-K-712-01-0126). Prof. Dr V. Šikšnys. 2018–2022.

Bacterial viruses, or bacteriophages, are bacterial parasites that employ the replication, transcription and translation machinery of the host cell to make new copies of the virus. They often kill bacteria when replication is completed. In order to survive bacteria built multiple defence barriers that interfere with nearly every step of virus life cycle. Different antiviral defence systems are clustered in the genome in the so-called “defence islands”. These defence islands, together with well-known antiviral defence systems, such as R-M and CRISPR-Cas systems, contain other putative antiviral defence systems of unknown molecular mechanism. The idea of the current project is that understanding of molecular mechanisms of novel antiviral defence systems in bacteria may pave the way for the development of new molecular technologies and tools. The major objective of the current project is to elucidate molecular mechanisms of two newly discovered bacterial antiviral defence systems, BREX and prokaryotic argonautes (pAgo). The major task of the project is to perform structural and functional characterization of protein components of the BREX and pAgo systems. We believe that the understanding of molecular mechanisms of these bacterial antiviral defence systems may pave the way the way for the development of new molecular tools.

Central Project Management Agency. Sequencing Center of DNA Double Stranded Breaks (No. 01.2.2-CPVA-K-703-02-0010). Dr M. Zaremba. 2018–2021.

The aim of the project is to develop and improve DNA double-strand break (DSB) detection technology. One of the most relevant applications of this method would be related to the genome (including human) editing and engineering, which is based on DSB introduction to the target site in the genome using programmable nucleases (homing endonuclease, ZF, TALE or CRISPR-Cas9 nucleases) and utilizing DNA repair systems of the cell. However, programmable nucleases are prone to cleave the DNA sites that are similar to the target sites, resulting in the chromosome rearrangements or mutations causing cell death or their transformation into cancer cells. In order to make genome editing technology safer it is crucial to utilize sensitive and reliable method for DSB detection to evaluate the specificity of a nuclease. Therefore, appropriate DSB detection technology allowing evaluation and selection of the most specific Cas9 or other nucleases for every particular case (including the gene therapy) will be developed during the project.

Research Council of Lithuania. Adaptation Mechanism in Class 2 CRISPR-Cas Systems (S-MIP-19-305). Dr G. Sasnauskas. 2019–2022.

Prokaryotes (bacteria and archaea) are the most abundant cellular life form in the biosphere. However, they are outnumbered by bacteriophages, i.e., viruses that infect bacterial or archaeal cells. To cope with the threat of bacteriophage infection, prokaryotes employ a variety of antiviral defence mechanisms, including the adaptive immune system CRISPR-Cas. Mechanistically, CRISPR-Cas function can be divided into three stages: (i) integration of short virus sequences as spacers in the cell's CRISPR locus to memorise the invading virus
(adaptation/immunization step), (ii) generation of short CRISPR RNA (crRNA) using spacers as templates, and (iii) crRNA-guided destruction of the invader's nucleic acid by an effector nuclease (interference/immunity step). The interference stage, at least for the Type II CRISPR-Cas systems, is well characterized, as exemplified by Cas9 effector nucleases that have revolutionized the field of genome editing. By contrast, the adaptation stage in many CRISPR-Cas systems remains poorly understood. The major goal of this project is to decipher
molecular and structural mechanisms of the adaptation stage in the Class 2 CRISPR-Cas systems. Specifically, we will focus on the roles of individual Cas proteins (Cas1, Cas2, Csn2, Cas9 and others) and their complexes in the processes of spacer capture, end processing and
integration. Our results will provide new insights into the mechanisms and evolution of different types of CRISPR-Cas systems.

Research Council of Lithuania. Structural and Functional Studies of Split Prokaryotic Argonaute Proteins (No. S-MIP-20-37). Dr M. Zaremba. 2020–2022.

Argonaute (Ago) proteins are found in all three domains of life (bacteria, archaea, and eukaryotes). The best characterized group is eukaryotic Ago (eAgo) proteins, which are the functional core of RNA interference, and are critical for regulation of gene expression, silencing of mobile genome elements and defense against viruses. The best understood prokaryotic Ago (pAgo) proteins are full-length pAgos. They are composed of 4 major structural/functional domains (N, PAZ, MID and PIWI) and thereby closely resemble eAgos. It is believed that full-length pAgos function as prokaryotic antiviral systems, with the PIWI domain performing cleavage of invading nucleic acids. Full-length pAgos have recently attracted attention as potential tools for various in vitro and in vivo applications, including genome engineering, and in near future some full-length pAgos may become a viable alternative to CRISPR-Cas9 technology, since unlike Cas9, pAgos have no requirement for a PAM sequence in the vicinity of the target site. However, the majority of identified pAgos are shorter and catalytically inactive (encode just MID and inactive PIWI domains), thus their function and reaction mechanism remain unknown. Interestingly, most short pAgos are found in operons together with other proteins of unknown function, suggesting that short pAgos might form functional complexes with these partner proteins. The major objective of this project is to elucidate the structure and mechanism of selected short pAgos and partner proteins. We will employ a combination of in vivo, biochemical and modern biophysical methods, including X-ray crystallography and single molecule techniques. We believe that our studies will disclose the true potential of short pAgos, and open new avenues for their practical applications in medicine and biotechnology.

Research Council of Lithuania. Search of Anti-CRISPR Proteins and Research of Their Action (No. S-MIP-20-39). Dr T. Šinkūnas. 2020–2022.

Constant evolutionary race between bacteria and bacteriophages (bacterial viruses) leads to the development of various defence and counter defence mechanisms. One such example is an adaptive defence system of bacteria, called CRISPR-Cas, and virus borne small proteins suppressing the CRISPR-Cas protection that are named anti-CRISPR (Acr) proteins. According to the composition of CRISPR-Cas effector complex and its mechanism, these systems are classified into 6 types, which are then divided into subtypes. Acr protein families are grouped according to the inhibited subtype of the CRISPR-Cas. Elucidation of the molecular mechanism of CRISPR-Cas has enabled to adapt it as a powerful molecular tool, which allows precise editing of target DNA sequences, while Acr proteins were recently applied for regulation of this editing machine. The divergence of Acr proteins limits their detection by standard bioinformatic approaches; furthermore, inhibition details are clear only for a fraction of annotated Acr families. The object of this project will be proteins of AcrIF group that suppress type I-F CRISPR-Cas systems (I-F). By using our model I-F system we will construct selection system, which will be used for the search of new AcrIF proteins in the metagenomic libraries. Biochemical assays will be used to reveal molecular mechanisms of uncharacterised AcrIF proteins, while by exploiting X-ray crystallography we will try to figure out the interplay between AcrIF and the I-F system at atomic level. Overall, we expect to expand diversity of the AcrIF group and assess approaches of the I-F inhibition by AcrIF proteins that might pave the way to development of new molecular tools.

Research Council of Lithuania. Chemical annotation in the Crystallography Open Database (COD) (No. S-MIP-20-21). Dr A. Merkys. 2020–2022.

Knowledge about structure and properties of chemical compounds is essential for many fields of research, including pharmacology, design of new materials and drugs, to name a few. The most accurate structural knowledge about molecules comes from X-ray crystallography analyses. However, to our knowledge, there are no collections of chemically
annotated small-molecule crystallographic data accessible under the FAIR (Findability, Accessibility, Interoperability and Reusability) principles. The field of small-molecule crystallographic databases is dominated by a few proprietary databases with restrictive licenses and the Crystallography Open Database (COD), which is a public domain database. It has been demonstrated that at least half of the COD (200k entries) contains sufficient information to derive chemical identifiers under the supervision of a trained chemist. The curation process, however, is slow, expensive and does not scale well due to its reliance
on the effort of an experienced human-operator. In this project we propose to develop a generalized automated method capable of annotating any set of crystallographic data with chemical information. The novelty of the proposed approach is the ability to automatically infer, extract and cross-validate information from various sources in order to produce
the most plausible chemical descriptions. If successful, the project will result in an open-access database of all chemical compounds found in the COD. Publication of such database on the Internet will give access to reliable chemical information for the whole world, enabling
enhancement of research capabilities in pharmaceutical science, bio- and cheminformatics, materials science. What is more, the FAIR nature of the database will allow to link data in the COD with chemical databases, such as PubChem, as well as general purpose online encyclopaedias, such as Wikipedia, as well as facilitate automated database mining.

Research Council of Lithuania. Characterization of Novel Cas12 Effectors for Targeted Genome Modification. (No. MIP). 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.

Research Council of Lithuania. Structural and Functional Studies of Thoeris Bacterial Antiphage Defence System (No. S-MIP-21-6). 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.

International Research Projects

Research Council of Lithuania. CRISPR Tools for the Study of Embryonic Development in Zebrafish (No. S-LL-18-7). Dr G. Tamulaitis. 2018–2021.

Due to practical and ethical reasons, RNA silencing (not DNA knock-outs) is the preferred method in the studies of early development. The aim of this project is to develop novel RNA-silencing methods using the RNA-targeting CRISPR-Csm nucleases in vertebrate models, such as fish. Our preliminary experiments demonstrated that Csm nuclease pre-loaded with suitable crRNA can be used to target maternally expressed EGFP transcripts. During the project we are going to explore the possibility to use this tool to target endogenous transcripts and will quantify off-target effects using RNA sequencing techniques. Our next goal is to develop new tools for small targeted screens of (maternal) transcripts involved in early development that are not feasible using morpholinos, the current tool for RNA knockdown in zebrafish. The studies will be performed in collaboration with project partners from the International Institute of Molecular and Cell Biology in Warsaw.

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

Thermo Fisher Scientific Baltics (Lithuania)
Bristol University (UK)
Leipzig University (Germany)
DANISCO (France)
DuPont (USA)

OTHER RESEARCH ACTIVITIES

Prof. Dr V. Šikšnys –

• member of the Lithuanian Academy of Sciences;
• member of EMBO;
• member of EMBL council;
• member of EMBC council.

DEPARTMENT OF BIOLOGICAL DNA MODIFICATION

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

STAFF

Research professors: Prof. Dr Habil. S. Klimašauskas, Dr G. Vilkaitis.
Senior researchers: Dr E. Kriukienė, Dr V. Stankevičius.
Researchers: Dr M. Tomkuvienė, Dr A. Osipenko, Dr R. Rakauskaitė, Dr S. Gasiulė, Dr R. Krasauskas, Dr M. Mickutė.
Junior researchers: G. Urbanavičiūtė, Z. Staševskij, J. Ličytė, P. Gibas, K. Kvederavičiūtė, M. Narmontė.
Other researchers and technical staff: A. Rukšėnaitė, R. Mineikaitė, V. Mikulėnaitė, O. Safinas, B. Balaišytė, R. Bendorys, D. Gedgaudienė, M. Rutkauskaitė, G. Jankauskaitė, V. Dundaitė, G. Tupikaitė, J. M. Rimšelis, A. Čečkauskas, G. Olendraitė.
Doctoral students: B. Masiulionytė, K Skardžiūtė.

RESEARCH INTERESTS

Nucleic acids modification enzymes
Epigenome profiling
Biosynthesis of selenoproteins
Enzyme engineering

SELECTED PUBLICATIONS 2021

Gordevicius, J., et al. Epigenetic inactivation of the autophagy–lysosomal system in appen-dix in Parkinson’s disease. Nat Commun. 2021, 12: 5134.

Mickutė, M., et al. Methyltransferase-directed orthogonal tagging and sequencing of miR-NAs and bacterial small RNAs. BMC Biology. 2021, 19: 129.

Narmontė, M., Gibas, P., Daniūnaitė, K., Gordevičius, J. & Kriukienė, E. Multiomics Analy-sis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations. Frontiers in Cell and Developmental Biology. 2021, 9: 2427.

Tesfahun, A. N., et al. Alleviation of C⋅C Mismatches in DNA by the Escherichia coli Fpg Protein. Frontiers in Microbiology. 2021, 12: 1544.

PATENTS 2021

Granted:

Klimašauskas, S., Vilkaitis, G., Mickutė, M. Analysis of single-stranded RNA. US11008605B2. Publication date: 18 May 2021.

RESEARCH PROJECTS CARRIED OUT IN 2021

National Research Projects

Research Council of Lithuania/European Social Fund. Single Molecule TOP-seq – an Innovative Technological Platform for Early Non-Invasive Diagnostics of Cancer and Other Epigenetic Disorders (No. 09.3.3-LMT-K-712-01-0041). Dr E. Kriukienė. 2018–2022.

Cancer-specific mortality from most types of solid tumours has barely decreased in decades, despite an exponential increase in our knowledge about cancer pathogenesis and significant investments in the development of effective treatments. Liquid biopsies are non-invasive blood tests that detect cell-free circulating DNA (cfDNA) fragments that are shed into the bloodstream from a primary tumour. We offer a novel strategy for non-invasive diagnostics of epigenetic disorders including cancer. It will combine the unique advantages offered by droplet microfluidics technology and targeted analysis of epigenetic DNA modification. The resulting integrated analytical platform for analysis of cfDNA at a single molecule level will lead to accurate determination of a malignant tissue in cfDNA.

Research Council of Lithuania. Analysis of 5`-capped RNAs and Its Modulating Proteins in E. coli and Probiotic Lactic Acid Bacteria (No. S- MIP-19-217). Dr G. Vilkaitis. 2019–2022.

Epitranscriptome - dynamic ensemble of >150 RNA modifications, regulates the turnover and function of different types of RNA. It was thought for a long time that the 5'-end of the prokaryotic RNAs does not bare a special structure and remains mono- or triphosphorylated. However, recently it was shown that it can be covalently linked to nicotinamide adenine dinucleotide (NAD) which in E. coli is usually found on small non-coding RNAs, sRNAs. Recent discovery of 5’-NAD-RNA in eukaryotes such as yeast and human revealed universality of this modification. Although in bacteria the 5'-NAD modification is presently associated only with the RNA protection from degradation, it is likely that the unique cap could serve to recruit specific proteins endowing RNA with new functionalities. Nudix hydrolase NudC is the only E. coli protein known to interact with and hydrolyse 5’-NAD-RNA. Because there is no data on how the function of NudC is regulated, we seek to identify the proteins interacting with E. coli NudC and to determine their effect on 5'-NAD- and unmodified RNAs. The expertise gained in 5’-NAD-RNA research from work with gram- bacteria will be used for the analysis of industrially important lactic acid bacteria (LAB).

Research Council of Lithuania. DNA Modification and Chromatin Dynamics during Growth and Differentiation of Healthy and Malignant Cells. (No. S-MIP-S-21-1). 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.

International Research Projects

ERC Advanced Grant. Epitrack - Single-Cell Temporal Tracking of Epigenetic DNA Marks (ERC-2016-ADG/742654). Prof. S. Klimašauskas. 2017–2022.

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.

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)
Stanford University (USA)
Universidad de Sevilla (Spain

OTHER RESEARCH ACTIVITIES

Prof. Dr Habil. S. Klimašauskas –

• member of the Lithuanian Academy of Sciences;
• fellow of the Royal Society of Chemistry;
• EMBO member;
• editorial advisory board member, Open Life Sciences, https://www.degruyter.com/view/j/biol;
• management committee member, COST action CA18127;
• evaluation panel member, Horizon 2020/ European Research Council.

DEPARTMENT OF EUKARYOTE GENE ENGINEERING

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4421
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 A. Ražanskienė, Dr G. Žvirblis, Dr E. Čiplys, Dr M. Juozapaitis, 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. Abraitienė, Dr J. Lazutka.
Research assistant: A. Avižinienė.
Other researchers and technical staff: E. Rudokienė, O. Jančevskaja, D. Jaskytė.
Doctoral students: J. Rainytė, 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
Cell signalling regulation in Arabidopsis
Functions of PP2C phosphatases
Heart regeneration
Developmental biology
Genome editing

SELECTED PUBLICATIONS 2021

Čiplys, E. et al. Mapping human calreticulin regions important for structural stability. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 2021, 1869: 140710.

Dudas, G. et al. Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Nat Commun. 2021, 12: 5769.

Jandrig, B. et al. Hamster Polyomavirus Research: Past, Present, and Future. Viruses. 2021, 13: 907.

Kubickova, B. et al. A broadly cross-reactive monoclonal antibody against hepatitis E virus capsid antigen. Appl Microbiol Biotechnol. 2021, 105: 4957–4973.

Ratautaite, V. et al. Molecularly Imprinted Polypyrrole based Sensor for the Detection of SARS-CoV-2 Spike Glycoprotein. Electrochimica Acta. 2021, 139581.

RESEARCH PROJECTS CARRIED OUT IN 2021

National Research Projects

Research Council of Lithuania/European Social Fund. New Technologies for Development of Recombinant Allergens (No. 01.2.2-LMT-K-718-01-0008). Dr G. Žvirblis. 2018–2022.

The project is in line with EU Smart Specialization program and its priority 2.1. Molecular technologies for medicine and biopharmaceutics. It is dedicated for development of advanced molecular technologies for allergy diagnosis, immunotherapy and universal platform of expression and purification of recombinant protein allergens. Final project goal is to prepare a open-access collection (bank) of recombinant allergens consisting of well-characterized recombinant allergens and their strains-producers adapted to the effective biosynthesis in the most relevant hosts such as bacteria, yeast, mammalian and plant cell cultures. The project is aimed to select optimal biosynthesis conditions for specific protein allergens, ensure their high level of expression, efficient purification, their proper antigenicity and similarity to the natural allergens.

Research Council of Lithuania/ European Social Fund. Genetic and Molecular Studies of the Role of Tbx5a in Heart Regeneration (No. 09.3.3-LMT-K-712-17-0014). 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 analyse 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.

Research Council of Lithuania/ European Social Fund. Screening for New Methods for Treatment of Neurodegenerative Diseases (No. 01.2.2-LMT-K-718-03-0021). 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.

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

Institute for Novel and Emerging Infectious Diseases (Germany)
Department of Virology, University of Freiburg (Germany)
Friedrich-Loeffler-Institut Bundesforschungsinstitut für Tiergesundheit, Federal Research Institute for Animal Health OIE Collaborating Centre for Zoonoses in Europe (Germany)
Max Planck Institute for Molecular Plant Physiology (Germany)
Robert Koch-Institut (Germany)
Institute of Virology, Slovak Academy of Sciences (Slovakia)
A.Kirchenstein Institute of Microbiology and Virology, Riga Stradins University (Latvia)
Department of Medical Research, Mackay Memorial Hospital (Taiwan)
Temple University (USA)
Max Planck Institute for Heart and Lung Research, Bad Nauheim (Germany)

OTHER RESEARCH ACTIVITIES

Prof. Dr Habil. K. Sasnauskas –

• member of the Lithuanian Academy of Sciences.

SECTOR OF MICROTECHNOLOGIES

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

Research professor: Dr L. Mažutis.
Researchers: Dr R. Žilionis, Dr S. Juzėnas.
Research assistant: V. Milkus.
Other researchers and technical staff: J. Ritmejeris, A. Želvytė, P. Šėporaitis, E. Pranauskaitė, B. Vasiliauskaitė.
Doctoral students: G. Leonavičienė, K. Goda, L. Camissi, J. Žvirblytė, D. Baronas.

RESEARCH INTERESTS

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

SELECTED PUBLICATIONS 2021

Chan, J. M. et al. Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer. Cancer Cell. 2021, 39: 1479–1496. e18.

Maroni, G. et al. Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer. Commun Biol. 2021, 4: 1–15.

Siwicki, M. et al. Resident Kupffer cells and neutrophils drive liver toxicity in cancer im-munotherapy. Science Immunology. 2021, 6: eabi7083.

Zheng, T. et al. Genome-wide analysis of 944 133 individuals provides insights into the eti-ology of haemorrhoidal disease. Gut. 2021, 70: 1538–1549.

PATENTS 2021

Granted:

Weitz D. A., Klein, A. M., Akartuna I., Mažutis L., Kirschner M. W. Systems and methods for barcoding nucleic acids. JP6853667B2. Publication date: 31 March 2021.

Weitz D. A., Klein, A. M., Akartuna I., Mažutis L., Kirschner M. W. Systems and methods for barcoding nucleic acids. US11052368B2. Publication date: 06 July 2021.

RESEARCH PROJECTS CARRIED OUT IN 2021

National Research Projects

Research Council of Lithuania/European Social Fund. Microfluidic Technologies for Single-Cell Geno- and Fenotyping Research (No. 09.3.3-LMT-K-712-01-0056). Dr L. Mažutis 2018–2021.

There is no doubt that advances of genomics technologies over the last decade have fundamentally altered our understanding of human biology and keeps affecting all branches of life sciences. However, until very recently most of the techniques used in the biological research have utilized homogenized tissues or mixtures of cells thus resulting in an “average” genotype (or phenotype) that does not recapitulate the true diversity of cells or their biological differences. Cellular heterogeneity is particularly relevant in biological systems where individual cells show profound physiological differences such as immune system or cancer. By enabling the analysis of tens of thousands of single-cells in a massively parallel fashion droplet microfluidics technology has created a breakthrough in biological and biomedical sciences. In this project we will harness the latest advances in droplet microfluidics and will establish a platform enabling quantitative analysis of phenotype-genotype linkage at single-cell level and do so in a high-throughput manner. Most of our research efforts will be directed towards immune cells producing therapeutic antibodies (phenotype) and recovery of the antibody-encoding sequences at single-cell level. We will apply developed platform to better understand the generation of antibody diversity by immune system, while the platform itself will likely to find a myriad of application in cell biology research, early disease diagnostics or directed evolution amongst others.

Research Council of Lithuania/European Social Fund. Establishment of Single-Cell Transcriptomics/Genomics Research Parallel-Laboratory (No. 01.2.2-LMT-K-718-04-0002). Dr L. Mažutis. 2020–2023.

Every biological system be it human immune system or crucial organ is composed of variety of cells that react differently to external signals or stimulus. Treatment of complex human diseases also largely depends on the physiological response of the individual cells’, constituting given tissue or organ. It is single cells rather than their populations that are driving tumorigenesis, metastasis and other human diseases. 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 tumours. 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.

Research Council of Lithuania. Single Genome Amplification of Clinically Relevant Microorganisms Using Microfluidics Technology (No. 01.2.2-MITA-K-702). 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.

Research Council of Lithuania. Development of a Highly Sensitive Digital RT-PCR Method for Absolute Quantification of SARS-CoV-2 Virus (No. 01.2.2-LMT-K-718). 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. Low-sensitivity and poor-repeatability analytical methods are not only undesirable but can also have detrimental consequences. It is therefore important to apply the most sensitive tests and analyses possible. From 2020 over 500 million SARS-CoV-2 tests have been performed worldwide, and their need continues to grow with the emergence of new variants of the virus. Unfortunately, the widely used reverse transcription PCR (RT-PCR) test has a detection limit of 100–1000 viral genomes per reaction, which in turn results in widely varying clinical susceptibility (32–96%), which depends on sampling time and tissue, virus titer, inhibitors, and other factors. Given these shortcomings, this project will 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. 2018–2022.

Natural evolution is a powerful process that has given rise to the functionally diverse set of proteins present in all living systems. However, natural evolution has driven the optimisation of enzymes subjected to living functions of microorganisms, according to ill-defined and fluctuating external conditions and is not suitable for industrial processes since it lacks of control of selection pressure. In EVOdrops, we will use directed evolution to overcome these limitations. 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.

H2020 FRAMEWORK PROGRAMME: High-Throughput Droplet-Based Single-Cell Small RNA Sequencing Technology (H2020-MSCA-IF-2020 Grant agreement ID: 101030265). Recipient: Dr S. Juzėnas. 2021–2023.

Droplet-based single-cell RNA-sequencing (scRNA-seq) technologies have penetrated almost all branches of life sciences and have significantly advanced our understanding of cellular processes and organism development. However, despite their astonishing impact, most of the scRNA-seq technologies reported to date rely on poly(A) tail capture and thus are mainly restricted to the protein-coding RNAs, while neglecting a substantial proportion of the transcriptome, including small non-coding RNAs. As a result, very little is known about the non-coding RNA expression and function in individual cells, and especially their role in the establishment of cellular phenotypic diversity. Small RNAs contain a variety of classes, of which miRNAs are the most common and these act as regulatory molecules by suppressing translation of mRNAs. In addition, loss-of-function studies of miRNAs uncovered their involvement in development of nearly all tissues, including hematopoiesis. However, most studies exploring miRNA dynamics reported to date relied on bulk cell assays, thus disregarding the individual cell types and their heterogeneity. In the scope of this proposal, we aim to develop a high-throughput droplet-based single-cell small RNA-seq (droplet-small-seq) for simultaneous miRNA and mRNA capture and sequencing. We will apply this newly developed technique to investigate the regulatory roles of miRNAs in cell fate decision during hematopoietic development at a single-cell level.

Contractual Research

MTEP Thermo Fisher Scientific Baltics, Lithuania. L. Mažutis. 2021–2022.

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)
Helsinki University (Finland)
Institute of Clinical Molecular Biology Christian-Albrechts-University of Kiel (Germany)
Bigelow Institute (USA)

OTHER RESEARCH ACTIVITIES

Dr L. Mažutis –

• co-founder Droplet Genomics, Vilnius, LT;
• co-founder Platelet Biogenesis Inc. Boston, MA, USA;
• participant of Human Cell Atlas and Human Tumour Atlas international projects;
• invited expert for evaluation of international research proposals.

DEPARTMENT OF IMMUNOLOGY AND CELL BIOLOGY

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

STAFF

Research professors: Dr A. Žvirblienė, Dr M. Plečkaitytė.
Senior researchers: Dr I. Kučinskaitė-Kodzė, Dr A. Kanopka.
Researchers: Dr P. Stakėnas, Dr E. Jakubauskienė, Dr D. Stravinskienė, Dr I. Pečiulienė, Dr M. Simanavičius.
Research assistants: I. Dalgėdienė, L. Vilys, A. Lučiūnaitė.
Other researchers and technical staff: D. Bakonytė, L. Diglienė.
Doctoral students: A. Sližienė, K. Juškaitė, V. Rudokas, K. Mašalaitė.

RESEARCH INTERESTS

Monoclonal and recombinant antibodies
Molecular epidemiology of Mycobacterium tuberculosis
Cellular hypoxia and alternative splicing

SELECTED PUBLICATIONS 2021

Bulavaitė, A., Maier, T. & Pleckaityte, M. Discrimination of Gardnerella Species by Com-bining MALDI-TOF Protein Profile, Chaperonin cpn60 Sequences, and Phenotypic Charac-teristics. Pathogens. 2021, 10: 277.

Jakubauskienė, E. & Kanopka, A. Alternative Splicing and Hypoxia Puzzle in Alzheimer’s and Parkinson’s Diseases. Genes. 2021, 12: 1272.

Kučinskaitė-Kodzė, I., Simanavičius, M., Šimaitis, A. & Žvirblienė, A. Persistence of SARS-CoV-2-Specific Antibodies for 13 Months after Infection. Viruses. 2021, 13: 2313.

Plikusiene, I. et al. Evaluation of kinetics and thermodynamics of interaction between im-mobilized SARS-CoV-2 nucleoprotein and specific antibodies by total internal reflection ellipsometry. Journal of Colloid and Interface Science. 2021, 594: 195–203.

Yu, J. C. et al. Characterization of the GBoV1 Capsid and Its Antibody Interactions. Viruses. 2021, 13: 330.

RESEARCH PROJECTS CARRIED OUT IN 2021

National Research Projects

Research Council of Lithuania. Novel Affinity Binders for Immunodetection of Antibacterial Resistance (No. 01.2.2.-MITA-K-702-05-0003). Dr A. Žvirblienė. 2020–2023.

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 aims 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 will select a series of antibiotic resistance factors and will develop commercially exploitable bioaffinity binders against them. The project will be implemented with the Finnish industrial partner ArcDia and Lithuanian industrial partner UAB Imunodiagnostika. The partners will contribute to evaluating the commercial and diagnostic potential of the binders by testing them in different diagnostic platforms with real biological samples. The expected 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. The Impact of Viral Antigens on Immune Cells in the Context of Inflammaging (No. S-SEN-20-11). Dr I.Kučinskaitė-Kodzė. 2020–2021.

As Lithuanian population is getting older it is important to investigate factors of immunosenescence and understand the molecular mechanisms behind it. The processes of aging and major changes of innate immune system that accumulate in time are closely related and modify each other. Activated phagocytes can be responsible for the inflammation-induced aging processes. This project aims to explore the potential of virus-like particles (VLPs) and virus nucleocapsid (N) antigens as model systems to investigate aging-related processes that are closely entangled with inflammation. We intend to explore a range of recombinant human polyoma VLPs which represent latent viral antigens as well as recombinant measles and mumps virus N proteins which represent antigens of an acute infection. The objective of the study is to investigate how immune cells respond to these viral antigens. A particular interest is in the inflammatory response and the mechanism of inflammasome activation of phagocytic cells. Two signals are required for inflammasome activation. The first signal is dependent on alarmins such as LPS, TNFα, S100. We assume that VLPs and N can also provide the first signal by inducing inflammatory and cellular damage molecules. The second signal will be investigated more thoroughly as it contains multiple pathways. One of the mechanisms of activation is related to mitochondrial damage. Another mechanism is directly connected to phagocytosis-induced damage. Furthermore, the question of interaction between viral protein particles and membrane receptors will be investigated by using phagocytosis inhibitors. In all cases the inflammasome activation will be evaluated by caspase-1 activation, IL-1β release and ASC specks formation. Furthermore, the monoclonal antibodies against viral proteins will be used to modulate cell activation. The major part of experiments will be carried out with mouse in vitro model systems. The obtained results will be confirmed with human cell models. As a project outcome, we expect to establish a model system for investigation of the immune response at molecular level. We also expect that this study will provide new data on the ability of virus antigens to induce inflammatory response which will lead to recommendations for further research on immunosenescence mechanisms.

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 (No. 01.2.2-LMT-K-718-03-0036). 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 invasivemeningococcal 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, will be determined. The characterization of meningococcal carriage strains, as envisaged by the project, would allow predicting N.meningitidis transmission routes and provide the preventive measures for IMD, including vaccination strategy. Data on molecular characterization of meningococcal isolates will be submitted into an international open-access database and a new digital resource will be created for use by the international scientific community.

Research Council of Lithuania. Hypoxia as Cell Stress in mRNA Diversity and Aging (No. S-SEN-20-17). Dr A. Kanopka. 2020–2021.

All living organisms must respond to, and defend against, environmental stresses. These include temperature shock, oxygen shock (hypoxia), nutrient deprivation and DNA damage. Depending on its extent and severity, cells try to alter their metabolism, and adapt a new state. Fluctuations in environmental conditions occur frequently, and such stress disturbs cellular homeostasis, but in general, stresses, such as short hypoxia, are reversible. There is increasing evidence that regulation of gene expression in response to temporal stress happens post-transcriptionally in specialized subcellular membrane-less compartments called ribonucleoprotein (RNP) granules. Interestingly, many factors that regulate alternative splicing are RNA-binding proteins that contain low-complexity sequence domains (LCDs) and localize to stress-induced liquid-like compartments.
During alternative splicing from a single pre-mRNA several different mRNA isoforms can form that encode proteins with distinguished functions. RNA splicing is vital for the cell to survive under stress conditions and to adapt to environmental changes.
One of such changes is a short decrease in oxygen tension in the cellular environment (for example in case of solid tumours, lung disorders, etc.). During the lack of oxygen (hypoxia), cells undergo gene expression changes that help them to adapt to stress conditions. There are limited data how short hypoxia as cellular stress, influences mRNA isoform formation.
The proposed project is intended to investigate whether alternative splicing changes in the cells are dependent on cellular stress. Also, the influence of splicing factors on hypoxia stress-dependent alternative splicing regulation will be studied.
This new idea of the project proposal would complement the current knowledge about the changes in mRNA isoforms and changed protein expression in stressed cells and may indicate new approaches for treatment of cell stress-associated disease treatment.

Research Council of Lithuania. Development of SARS-CoV-2 Specific Antibodies for Diagnostic Applications (No. 01.2.2.-LMT-K-718). Dr A. Žvirblienė. 2021–2023.

The project will contribute to solving problems caused by the COVID-19 pandemic. It is proposed to develop new biotechnological products - SARS-CoV-2-specific antibodies of diagnostic and commercial value. Antibodies will be 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 will be used for antibody production. The use of chimeric VLPs will allow generation of antibodies of tailored specificity against the selected conserved sequences of S protein. The newly developed antibodies will be 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 will be implemented without partners. 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.

Agency for Science, Innovation and Technology. Development of the Protype Test for Detection of SARS-CoV-2 Neutralizing Antibodies (TPP-04-024). Dr M. Simanavičius. 2021–2023.

The project aims to develop the prototype test for detection of SARS-CoV-2 neutralizing antibodies. The test will be used for evaluation of human immune response and preparation for defence against SARS-CoV-2 infection after vaccination or before potential reinfection. Furthermore, this product could aid in assessment of convalescent blood plasma collected from SARS-CoV-2-infected and vaccinated individuals. Such plasma is used in treatment of severe cases of COVID-19. The test prototype will employ recombinant viral antigens. Pro-ject partner UAB Baltymas has developed spike proteins of different SARS-CoV-2 variants. The use of these proteins would enable to evaluate antibody potential to neutralize virus var-iants of concern. During COVID-19 pandemic, there is a high demand for high-quality SARS-CoV-2 diagnostic tools such as neutralizing antibody detection tests, which are ad-justed to the mutating virus.

International Research Projects

Research Council of Lithuania. Genomic Insights into the Mechanisms of Drug Resistance, Virulence, and Transmission of Mycobacterium tuberculosis Strains from Lithuania and Poland (No. S-LL-18-103). Dr P. Stakėnas. 2018–2021.

With over 10 million new cases and nearly 2 million deaths every year, tuberculosis (TB) continues to be a major health problem worldwide. The key purpose of the project is to provide a comprehensive characterization of the genetic composition of Mycobacterium tuberculosis strains, representing both drug-resistant and drug-susceptible phenotypes, circulating in Lithuania and Poland. This will be accomplished through a detailed description of strain genotypes, with their comparison to each other and to those circulating in Europe and worldwide (i); assessment of TB transmission both within and between the two countries (ii); identification of the genetic polymorphisms associated with drug resistance and possibly other phenotypes (transmissibility, virulence) with evaluation of their clinical impact to diagnostic outcome in patients (iii). The project presumes a collaborative action of several TB dispensaries and laboratories operating in Poland and Lithuania, and coordinated by the University of Warsaw, in consortium with the Warsaw Medical University, and the Vilnius University, on the Polish and Lithuanian side, respectively.

Contractual Research

Contract No. 52-1705/TPS-600000-974 with UAB Imunodiagnostika, Vilnius. Characterization of Protein Allergens and Development of Allergen-Specific Antibodies. Dr A. Žvirblienė. 2017–2021.

The aim of this project is to investigate the antigenic and immunogenic properties of allergen extracts and allergen components used for diagnostics and immunotherapy. Both natural and recombinant protein allergens are subjected to the study. A collection of allergen-specific polyclonal and monoclonal antibodies is developed as a tool for allergen quantitation and mapping of their antigenic sites.

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.

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

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

UAB Baltymas (Lithuania)
Friedrich-Loeffler Institute, Institute for Novel and Emerging Infectious Diseases (Germany)
Justus-Liebig University Giessen (Germany)
ArcDia (Finland)
British Society for Immunology (UK)
Bruker Daltonics GmbH (Germany)
Oslo University (Norway)

OTHER RESEARCH ACTIVITIES

Dr A. Žvirblienė –

• member of the Lithuanian Academy of Sciences;
• member of the EuroMabNet;
• member of the Vaccine Task Force of the European Federation of Immunological Societies (EFIS);
• vice-president of the Lithuanian Immunological Society;
• member of the COVID-19 vaccination work group at the Ministry of Health of the Republic of Lithuania;
• member of the Advisory Council at the President’s Office of the Republic of Lithuania;
• member of the Advisory Council at the Government of the Republic of Lithuania;

Dr D. Stravinskienė –

• member of the Young Immunologists Task Force at the European Federation of Immunological Societies (EFIS).

DEPARTMENT OF BIOTHERMODYNAMICS AND DRUG DESIGN

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4364
E-mail:
Head - Dr Daumantas Matulis

STAFF

Research professors: Dr D. Matulis, Dr V. Smirnovas.
Senior researchers: Dr A. Zubrienė, Dr V. Petrikaitė, Dr V. Petrauskas, Dr J. Matulienė, Dr V. Dudutienė, Dr L. Baranauskienė, Dr E. Čapkauskaitė.
Researchers: Dr E. Kazlauskas, Dr V. Juozapaitienė, Dr Š. Grincevičienė, Dr A. Smirnov, Dr Z. Toleikis, Dr J. Kazokaitė, Dr A. Janonienė.
Research assistants: V. Michailovienė, J. Jachno, A. Zakšauskas, Dr. A. Toleikis.
Other researchers and technical staff: J. Jachno, D. Lingė, L. Davidian, A. Mickevičiūtė.
Doctoral students: J. Smirnovienė, G. Skvarnavičius, M. Žiaunys, S. Daunys, A. Sakalauskas, A. Petrošiūtė, V. Paketurytė, M. Gedgaudas, G. Žvinys, A. Vaškevičius, K. Mikalauskaitė, I. Paterylo.

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 sulphonamide-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 crystallographic 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 2021

Janoniene, A., Mazutis, L., Matulis, D. & Petrikaite, V. Inhibition of Carbonic Anhydrase IX Suppresses Breast Cancer Cell Motility at the Single-Cell Level. International Journal of Molecular Sciences. 2021, 22: 11571.

Kirchhain, A. et al. Biphenyl substituted lysine derivatives as recognition elements for the matrix metalloproteinases MMP-2 and MMP-9. Bioorganic Chemistry. 2021, 115: 105155.

Sakalauskas, A., Ziaunys, M., Snieckute, R. & Smirnovas, V. Autoxidation Enhances Anti-Amyloid Potential of Flavone Derivatives. Antioxidants. 2021, 10: 1428.

Ziaunys, M., Mikalauskaite, K., Sakalauskas, A. & Smirnovas, V. Using lysozyme amyloid fibrils as a means of scavenging aggregation-inhibiting compounds. Biotechnology Journal. 2021, 16: 2100138.

RESEARCH PROJECTS CARRIED OUT IN 2021

National Research Projects

Research Council of Lithuania. 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). Dr D. Matulis. 2020–2023.

The aim 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 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.

Central Project Management Agency. Design of Pharmaceutical Compounds for the Treatment of Cancer and Neurodegenerative Diseases (No. 01.2.2-CPVA-K-703-03-0006). 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.

Research Council of Lithuania. Development of Visualization Systems for Tumour and Metastases Detection in Cancer Diagnostics and Optically-Guided Surgery Using CA IX Biomarker (No. S-SEN-20-10). Dr J. Matulienė. 2020–2021.

Oncological diseases are one of the main causes of life quality deterioration and mortality for elderly people. Surgery is one of the main ways of first-line cancer treatment. Unfortunately, due to late diagnostics, especially in elderly people, cancer is usually metastasized and it is difficult to remove all metastases and clearly distinguish healthy tissue from tumour during surgery in real time. The successful elimination of malignant tissue is essential for quality of life after surgery. Therefore precise identification of tumour margins is a significant issue. Thus, it is important to develop novel and precise detection methods employing new markers for tumour visualization during surgery. One of such markers could be human carbonic anhydrase IX (CA IX). There are 12 catalytically active CA isoforms in the human body that catalyse the reversible reaction of carbon dioxide hydration. Most of the isoforms perform vital functions in all human tissues. However, CA IX is exceptional because it nearly does not express in healthy tissues but is highly overexpressed in most hypoxic tumours. The goal of this project is to develop new methods for visualization of primary and secondary tumours with the help of the technologies enabling the detection of CA IX in living organisms. To reach this goal we will use CA IX-specific compounds conjugated with NIR fluorescent or positron-emitting (PET) probes. We have already synthesized compounds that selectively bind to CA IX with 20 pM affinity. Based on those compounds, novel conjugates will be made and applied in mice xenograft models and on human cancer surgery tissue material where the cancerous tissue can be distinguished from healthy by applying conventional immunohistochemical methods to validate the new technique. This project should help solve the issues of more accurate cancer detection, staging and prognosis, which, together with upgraded surgery procedures, may help improve the future of elderly people.

Research Council of Lithuania. Cross-Interactions in Amyloid Fibril Formation: from Mechanisms to Inhibition (No. S-SEN-20-3). Dr V. Smirnovas. 2020–2021.

Amyloids are associated with such diseases as 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. Moreover, amyloid cross-interactions may be one of the links between neuroinflammation and amyloid diseases.
Here we study mechanisms of cross-interactions between S100A9 and alpha-synuclein, and test if/how these interactions affect the efficiency of amyloid aggregation inhibitors. In parallel, we try to detect possible interactions between the major neurodegeneration-related amyloid proteins. This work will help to understand the role of cross-interactions in amyloid aggregation and may give new hints in development of anti-amyloid drugs.

Research Council of Lithuania. Design of Technological Prototype to Determine Compound Efficiency as Inhibitors of SARS CoV-2 Recombinant Viral Enzymes (No. 13.1.1-LMT-K-718-05-0001). Dr J. Matulienė. 2021–2023.

The goal of this project is to contribute to the worldwide effort in search of an 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 viral 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 moietes 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. If potentially applicable compounds are discovered, we plan to submit patent applications and out-license them to pharmaceutical companies for development as antiviral drugs.

International Research Projects

Lithuanian-Latvian-Taiwan Cooperation Programme. Development of Lead Inhibitor of Carbonic Anhydrase IX as Anticancer Drug (No. S-LLT-20-2). Dr D. Matulis. 2020–2022.

The objective of this project is to perform preclinical development of an inhibitor designed as an anticancer drug for the treatment of triple-negative breast and highly invasive pancreatic cancers. Combined efforts of the three teams in Latvia, Lithuania and Taiwan should yield an inhibitor with an improved affinity towards CA IX and also improved selectivity over vital CAs in the human body to avoid toxic side effects of the compound. The lead compound is planned to be developed in GLP conditions with the help of Taiwanese CRO companies towards an anticancer drug. Taiwanese team will search for Institution for PMDK and toxicological studies mainly for pre-GLP experiments, make contact and propose joint development of the lead compound. Also, the Taiwanese team will measure by ITC the binding of sulfonamide inhibitors and carbonic anhydrases. Structure-thermodynamics correlations will be analysed and all data will be used for further improvement of the drug design. Latvian team will synthesize, purify and characterize novel CA IX inhibitors containing different conjugated bulky groups. Results of ITC binding analysis will be used to guide further optimization of chemical structure. Lithuanian team will recombinantly clone, express in bacterial or mammalian cells and purify CA IX and other CA proteins. Together with compounds synthesized by Latvian team they will be used for measuring of Gibbs free energy of binding by fluorescent thermal shift assay. All three teams will analyse and summarize the data on the recognition energetics and the structure-activity relationships for the compound–target interaction for the several metallo-protein groups.

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)

OTHER RESEARCH ACTIVITIES

Dr D. Matulis –

• editorial board member of the international journal BMC Biophysics;
• editorial board member of European Biophysics Journal with Biophysics Letters;
• president-elect of the Lithuanian Biochemical Society.

Dr V. Smirnovas –

• topic editor of the International Journal of Molecular Sciences;
• associate editor of the Frontiers in Molecular Biosciences.

SECTOR OF APPLIED BIOCATALYSIS

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

STAFF

Senior researcher: Dr I. Matijošytė.
Researcher: Dr A. Kaunietis.
Other researchers and technical staff: D. Daunoraitė, R. Šiekštelė.
Doctoral students: J. Babinskas, J. Krutkevičius

RESEARCH INTERESTS

Biocatalysts and their application

SELECTED PUBLICATIONS 2021

Rotter, A. et al. The Essentials of Marine Biotechnology. Frontiers in Marine Science. 2021, 8: 158.

Rotter, A., Barbier, M., Bertoni, F., Bones, A. M., Cancela, M. L., Carlsson, J., Carvalho, M. F., Cegłowska, M., Chirivella-Martorell, J., Conk Dalay, M., Cueto, M., Dailianis, T., Deniz, I., Díaz-Marrero, A. R., Drakulovic, D., Dubnika, A., Edwards, C., Einarsson, H., Erdogan, A., Eroldogan, O. T., Ezra, D., Fazi, S., FitzGerald, R. J., Gargan, L. M., Gaudêncio, S. P., Gligora Udovic, M., Ivoševic DeNardis, N., Jónsdóttir, R., Kataržyte, M., Klun, K., Kotta, J., Ktari, L., Ljubešic, Z., Lukic Bilela, L., Mandalakis, M., Massa-Gallucci, A., Matijošyte, I., Mazur-Marzec, H., Mehiri, M., Nielsen, S. L., Novoveská, L., Overlinge, D., Perale, G., Ra-masamy, P., Rebours, C., Reinsch, T., Reyes, F., Rinkevich, B., Robbens, J., Röttinger, E., Rudovica, V., Sabotic, J., Safarik, I., Talve, S., Tasdemir, D., Theodotou Schneider, X., Thomas, O. P., Torunska-Sitarz, A., Varese, G. C. and Vasquez, M. I. The Essentials of Ma-rine Biotechnology. Frontiers in Marine Science. 2021, 8: 158.

RESEARCH PROJECTS CARRIED OUT IN 2021

International Research Projects

Baltic Research Programme. Novel High-Performance Polymers from Lignocellulosic Feedstock (No. EMP426). Dr I. Matijošytė. 2020–2023.

This project will investigate novel sustainable platform chemicals from lignocellulosic biomass to produce bio-derived polymers for highly functionalized applications (e.g., automotive industry, coatings, packaging, etc.). A stream of wood sugars from forestry residues is used as raw material, so to promote an efficient use of resources and a circular economy perspective.

A key intermediate in polymer development is citric acid, a large volume product currently produced from raw materials of agricultural origin. The efficient route from lignocellulosic sugar streams to citric acid could further amplify its potentials.

The environmental benefits and possible adverse effects are analysed for enabling the optimization of the production process from a sustainability point of view, and the performance of the bio-based polymers will be benchmarked against conventional fossil-derived plastics.

Nordic Council of Ministers. Nordic-Baltic Collaboration to Boost Bio-and Circular Economy (Biobalt). Dr I. Matijošytė. 2021– 2023.
https://nordregioprojects.org/biobaltic/

The project aims at deepening Nordic-Baltic cooperation around bio-circular-economy. Key goals are: i) generate better understanding of the state of development of forms of bio- and circular-economy models; ii) peer-to-peer learning amongst key actors, (using the quintuple helix model); iii) capacity-building (including students, businesses, authorities and others); iv) exploring business opportunities. A bottom-up approach makes ‘Mobile Learning Hubs’ in each Baltic country responsible for desk and field-work and stakeholder mobilization. In Lithuania, Vilnius University, Vytautas Magnus University and Lithuanian Biotechnology Association is analysing the case “Industrial Symbiosis opportunities” in four selected Lithuanian municipalities, i.e. Marijampolė, Panevėžys, Tauragė and Telšiai municipalities. This work will build preliminary identifying favourable conditions for introducing circular economy models.

Collaboration and Research Agreements

Framework Agreement for Scientific Cooperation between UNIVERSITÀ di TORINO De-partment of Life Sciences and Systems Biology and Vilnius University (Sector of Applied Biocatalysis). Dr Inga Matijošytė. 2020–2025.

Cooperation on biotransformations of various lignocellulosic based biomass into added val-ue products. Latvian State Institute of Wood Chemistry, Cooperation Agreement, No. BS-15600-1341. 30 August 2018. Dr I. Matijošytė (open-ended).

Enzymes and Their Application in Detergents. SC Naujoji Ringuva, No. B1-560000-153. Dr I. Matijošytė (open-ended).

Research agreement Investigation of Tetrahydrofurans and Its Derivatives Synthesized in Yeasts MB Bioam Consulting, No. (1.57)15600-INS-168. Dr I. Matijošytė. 2021–2023.

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

University of Tartu (Estonia)
Norwegian 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)
JSC Genie Biotech EU (Lithuania)
JSC Fibenol (former Graanul Invest) (Estonia)
JSC Biorro (Lithuania)

OTHER RESEARCH ACTIVITIES

Dr I. Matijošytė -

• national representative in State Representative Group (SRG) at Bio-Based Industry Joint Undertaking;
• vice-president of Lithuanian Biotechnology Association;
• scientific member of European Society of Applied Biocatalysis (ESAB);
• steering committee member of Life Sciences Baltics 2021;
• member of EFIB2022 Advisory Board.

DEPARTMENT OF BIOINFORMATICS

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4368
E-mail:
Website: http://bioinformatics.lt
Head - Dr Česlovas Venclovas

STAFF

Research professor: Dr Č. Venclovas.
Senior researchers: Dr V. Kairys, Dr M. Margelevičius, Dr J. Dapkūnas, Dr D. Kazlauskas, Dr K. Olechnovič.
Researcher: Dr A. Timinskas.
Other researchers: K. Timinskas.
System administrator: R. Dičiūnas.
Doctoral student: L. Valančauskas.

RESEARCH INTERESTS

Protein three-dimensional (3D) structure modelling
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 2021

Olechnovič, K. & Venclovas, Č. VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures. Bioinformatics. 2021, 37: 4873–4875.

Igashov, I., Olechnovič, K., Kadukova, M., Venclovas, Č. & Grudinin, S. VoroCNN: deep convolutional neural network built on 3D Voronoi tessellation of protein structures. Bioinformatics. 2021, 37: 2332–2339.

Karvelis, T. et al. Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease. Nature. 2021, 599: 692–696.

Dapkūnas, J., Olechnovič, K. & Venclovas, Č. Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction. Proteins: Structure, Function, and Bioinformatics. 2021, 89: 1834–1843.

Lensink, M. F., Brysbaert, G., Mauri, T. et al. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins. 2021, 89: 1800–1823.

RESEARCH PROJECTS CARRIED OUT IN 2021

National Research Projects

Research Council of Lithuania/European Social Fund. Computational Study of Evolutionary Relationships, Genomic Distribution, Structural and Functional Properties of DNA Polymerases (No. 09.3.3-LMT-K-712-01-0080). Dr Č. Venclovas. 2018–2022.

The goal of this project is to significantly advance the knowledge regarding DNA polymerases at the same time improving scientific qualification of the members of research team. This goal will be achieved by carrying out research activities directed at enriching the scientific knowledge related to structures, interactions, functional properties and evolutionary relationships of DNA polymerases. The proposed research will encompass all three domains of life – eukaryotes, bacteria and archaea. We will perform the proposed research by analysing and integrating different types of publicly available biological data using cutting-edge methods of computational biology and bioinformatics. We will classify all of the identified DNA polymerases and will characterize in detail their structural and functional properties. We will also pursue the characterization of structural-functional assemblies involving DNA polymerases and the associations between DNA polymerases and recently discovered prokaryotic CRISPR-Cas immune systems. Furthermore, we will identify sets of DNA polymerases and their functional modules encoded in genomes of individual organisms. We will then try to understand whether and if so, how the nature of the polymerase set possessed by a given organism is linked to the global characteristics of both the organism and its living environment.

Research Council of Lithuania/European Social Fund. A System of RESTful Web Services for Protein Remote Homology Search in Real Time and Protein Modelling (No. 01.2.2-LMT-K-718-01-0028). Dr M. Margelevičius. 2018–2022.

Protein structure prediction from amino acid sequence is one of the most important problems in bioinformatics, the successful addressing of which would impact the entire field of biomedicine. The most reliable approach for predicting protein structure today is modelling by homology established by alignment of sequence families. The goal of the project is to increase the sensitivity of homology detection and alignment accuracy and develop convenient and fast computational tools allowing researchers to search for protein homologues in real time, perform evolutionary analysis, and predict protein structures. Achieving this goal includes the development of a general methodology for estimating the statistical significance of alignments between sequence families, a critical issue in homology search. Software implementing the methodology and a search engine developed using high-performance computing technologies will provide a means for extremely fast sensitive homology search, which will underlie protein evolutionary studies and structure modelling by alignment of sequence families on a new web service platform. New developments are expected to be useful for both evolutionary analysis of selected proteins and analysis performed on a large scale in a real-time environment, contributing to a deeper understanding of biological processes.

Research Council of Lithuania. Expanding the CRISPR Toolbox for Rapid Detection and Genomic Surveillance of SARS-CoV-2 Variants of Concern (No 13.1.1-LMT-K-718-05-0021). Dr D. Kazlauskas. 2021–2023.

SARS-CoV-2 emerged in Wuhan, China in December 2019 and soon after started spreading worldwide causing 3 million deaths and huge economic losses. Prompt reaction of pharmaceutical companies resulted in a development of vaccines against SARS-CoV-2. Recently, new SARS-CoV-2 variants of concern (VOCs) have emerged in Great Britain, South Africa and Brazil. These SARS-CoV-2 variants are dangerous because they have mutations in a spike gene, which results in a lower efficacy for current vaccines. Moreover, British VOC spreads faster and has increased absolute risk of death. Early detection of VOCs allows for rapid intervention and minimizes the risk of spreading the disease. Currently, 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 located 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 is aiming at expansion of the CRISPR toolbox for use in rapid detection and genomic surveillance of SARS-CoV-2 VOCs. We will use state-of-the-art sequence search methods to collect C2EPs and machine learning to select best candidates for experimental validation by our partner CasZyme.

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

Inria Grenoble – Rhone-Alpes Research Center (France)
Institut Pasteur, Département de Microbiologie (France)
National Center for Biotechnology Information (USA)
University of California, Davis (USA)
University of Cape Town (South Africa)

OTHER RESEARCH ACTIVITIES

Dr Č. Venclovas –

• editorial board member of Scientific Reports (Nature Publishing Group);
• member of the Lithuanian Academy of Sciences. 

LABORATORY FOR EPIGENOMICS RESEARCH

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

STAFF

Research professor: Dr A. Petronis.
Teaching assistant: K. Koncevičius.
Other researchers and technical staff: A. Kazlauskaitė, R. Reventas, R. Toleikienė.
Doctoral student: A. Kriščiūnas.

RESEARCH PROJECTS CARRIED OUT IN 2021

National Research Projects

Research Council of Lithuania. Daily Effects on Epigenetic Prediction of Individual’s Age (No. S-MIP-19-192). Dr A. Petronis. 2019–2021.

Estimation of individual’s biological age using molecular tools is an interesting and challenging task. Discrepancy between biological and chronological ages can help to identify individuals at disease risk and therefore is of major biomedical importance. Currently, the best methods for biological age prediction are based on epigenetic markers, known as epigenetic “clocks”. The accuracy of epigenetic “clocks” can be further refined and improved by taking into account the intra-individual epigenetic fluctuations. A significant proportion of such fluctuations are generated by the circadian regulation which has been investigated by our international Lithuanian - Canadian team. In this project, we will perform a comprehensive analysis of daily epigenetic DNA (cytosine) modification fluctuations using blood samples collected over 5 time intervals from 40 healthy individuals. We will develop computational tools and algorithms for epigenetic age estimates which take into account the peculiarities of sample collection time. Such effort should significantly improve the precision of the epigenetic “clock” and open new translational opportunities in disease prediction and precision medicine.

Research Council of Lithuania/European Social Fund. Identifying Chronoepigenetic Markers in Schizophrenia (No. 09.3.3.-LMT-K-712-17-0008). Dr A. Petronis. 2020–2023.

Schizophrenia (SCH) is a chronic mental illness that severely disturbs thoughts, feelings, behaviour. 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 analysed 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.

Research Council of Lithuania. Next Generation Epigenetic Markers for Accelerated Ageing in Colorectal Cancer (No. S-SEN-20-19). PI of Vilnius University: Dr A. Petronis. 2020–2021.

Ageing, a major risk factor in cancer, is accompanied by vast epigenetic rearrangements. In recent years “epigenetic ageing”, a measure of biological age based on DNA methylation patterns within the cell, received a large amount of attention. Intriguingly, epigenetic changes observed in cancer exhibit numerous similarities with the ageing epigenome. It has been shown that in nearly all types of cancer the malignant tissue, compared to its healthy counterpart, appears to be epigenetically older. On top of that our group has recently discovered a link between ageing and another universal biological phenomenon - circadian rhythms. While there are major efforts exploring ageing and circadian regulation in cancer, there has never been an attempt to study all of these phenomena simultaneously. We believe that age-related circadian fluctuations could help explain the increase in cancer risk with age and provide significant advances towards personalized cancer treatment.
The overall goal of this project is to understand why old age is a major risk factor for many human diseases. In this pilot project, we will use colorectal cancer as the proof of principle for identification of next generation epigenetic markers of accelerated ageing and malignancy. We will perform a comprehensive mapping of epigenetically oscillating cytosines in 10 cancer patients and 10 healthy controls. We will collect 8 peripheral blood samples from each individual over the course of 24 hours for a total of 160 samples. Neutrophils, the largest fraction of white blood cells, will be isolated, and their DNA modification status will be interrogated at over 850,000 distinct cytosine positions across the genome.
Circadian epigenetic studies are much more informative compared to the traditional cross-sectional studies. In addition to the identification of next generation epigenetic markers for ageing and old age disease, this project may lead to new mechanistic insights on their relationship.

SELECTED PUBLICATIONS 2021

Oh, E. S. & Petronis, A. Origins of human disease: the chrono-epigenetic perspective. Nat Rev Genet. 2021, 22: 533–546.

OTHER RESEARCH ACTIVITIES

Dr A. Petronis –

• member of Academia Europea.

 

INSTITUTE OF BIOCHEMISTRY

Saulėtekio al. 7, LT-10257
Tel. 223 4378
E-mail:
http://www.bchi.vu.lt
Director - Dr Kastis Krikštopaitis

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 2021

A. Krikštaponis. Investigation of the catabolism of 7-hydroxycoumarin in Pseudomonas mandelii 7HK4 bacteria.
E. Šimoliūnas. Study of molecular mechanisms induced by cell-scaffold interaction.

DEPARTMENT OF BIOANALYSIS

Saulėtekio al. 7, LT-10257
Tel. 223 4389
E-mail:
Head – Dr Marius Dagys

STAFF

Research professor: Dr J. Razumienė.
Senior researchers: Dr G. Bagdžiūnas, Dr M. Dagys, Dr R. Šimkus.
Researchers: Dr A. Laurynėnas, Dr T. Makaras, Dr D. Ratautas, Dr I. Šakinytė, Dr L. Tetianec.
Research assistants: I. Bratkovskaja, M. Butkevičius, I. Radveikienė.
Senior specialist: V. Gurevičienė.
Doctoral students: M. Katelynas, E. Ramonas, S. Serapinas.

RESEARCH INTERESTS

Investigation of charge and energy transfer in biomolecules, bioreactor design
Creation and investigation of biosensors and bioanalytical systems
Whole-cell biosensors, bacterial self-organization, biofilms

RESEARCH PROJECTS CARRIED OUT IN 2021

Project Supported by University Budget

Design and investigation of new systems for biocatalysis. Dr J. Razumienė.

In general, we specialise in application of the oxidoreductases for bioreactor applications and creation of mediatorless bio-anodes and bio-cathodes in bio-solar cells, bio-batteries and bio-fuel cells.

The development of artificial nanocatalysts, especially those incorporating the highly active biocatalysts (enzymes) present in nature, is a rapidly developing field in nanocatalysis and nanomaterials science. Dehydrogenases are exceptionally attractive, as they catalyze the oxidation of various cheap/common substrates to more expensive and desired products. Our continuing research in this regard is the design of unique nanomaterials composed of several redox enzymes (e.g., nonspecific glucose dehydrogenase and oxygen-reducing laccase) and nanoparticles. Properly wired enzymes through the nanoparticle surface experience direct electrochemical “communication” allowing electron transfer from one redox center to other. As a result, self-sufficient nanocatalysts are synthesized and shown to oxidize various carbohydrates directly with molecular oxygen. Such system usually exhibits reduced activity per mole, but they do not require any electron mediators, a feature very useful in bioreactor setups.

For the biocatalytic systems that do require redox mediator, recently new potential electron transfer mediators, 2-substituted 1,4-benzoquinone derivatives bearing an arylamino group with various substituents in o-, m- and p-positions of an aromatic ring were synthesised. In addition, our bioelectrocatalytic β-D-glucose sensor system was applied in fish holding tanks monitoring stress levels of Oncorhynchus mykiss juveniles by measuring nanomolar glucose concentrations.

Main publications:

Repečka, D., Jauniškis, V., Karpus, L., Rembeza, E., Rokaitis, I., Zrimec, J., Povilonienė, S., Laurynėnas, A., Viknander, S., Abuajwa, W., Savolainen, O., Meškys, R., Engqvist, M. K. M., Zelezniak, A. Expanding functional protein sequence spaces using generative adversarial networks. Nature Machine Intelligence. 2021, 3: 324–333.

Ramonas, E., Shafaat, A., Dagys, M., Ruzgas, T., Ratautas, D. Revising catalytic "acceleration" of enzymes on citrate-capped gold nanoparticles. Journal of Catalysis. 2021, 404: 570–578.

Javorskis, T., Jurys, A., Bagdžiūnas, G., Orentas, E. Synthesis of C- and N-substituted 1,5,2,6-dithiadiazocanes -electrophilic-nucleophilic thioamination (ENTA) reagents. Advanced Synthesis & Catalysis. 2021, 363(13): 3329.

Patent application:

Ramonas, E., Butkevičius, M., Dagys, M., Ratautas, D. Enzymatic self-calibrating biosensor for continuous pH monitoring. 2021, EP21203942.4.

National Research Projects

Research Council of Lithuania. Development of Non-Invasive Method Platform for Early Diagnostics and Prognosis of Acute Pancreatitis (No. 01.2.2-LMT-K-718-01-0025). Dr Julija Razumienė. Partner – Vilnius University Hospital Santaros Klinikos. 2018–2022.

Research Council of Lithuania. Biocatalytic Systems for Conversion of Non-Starch Poli- and Oligosaccharides (No. 01.2.2-LMT-K-718-01-0019). Dr Marius Dagys. 2018–2022.

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. 2020–2024.

Central Project Management Agency. 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.

International Research Projects

The European Joint Programme on Rare Diseases (EJP RD). Unveiling the Role of Glutamate in dopaminE traNspoTer deficiency syndrome (URGENT). Coordinator: Ris, Laurence (BE), LT partner – Dr Julija Razumiene. 2019–2022.

Contractual Research

Several contractual R&D works were done and ordered by UAB Bioanalizės sistemos.

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

Vilnius Gediminas Technical University (Lithuania)
Malmo University (Sweeden)
Lund University (Sweden)
UAB Bioanalizės sistemos (Lithuania)
UAB Ubique calculus (Lithuania)
UAB Laboratorija 1 (Lithuania) 

DEPARTMENTS OF XENOBIOTICS BIOCHEMISTRY

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4392
E-mail:
Head – Dr Habil. Narimantas Čėnas

STAFF

Research professor: Dr Habil. N. Čėnas.
Senior researchers: Dr Ž. Anusevičius, Dr K. Krikštopaitis, Dr J. Šarlauskas.
Researchers: Dr A. Marozienė, Dr L. Misevičienė, Dr B. Valiauga.
Research assistants: M. Lesanavičius, E. Polmickaitė-Smirnova.
Senior specialist: 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 activity and electronic properties on their cytotoxic and atiparasitic action
The studies of the catalytic mechanism of mamalian 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 2021

Project Supported by University Budget

Molecular Mechanisms of Enzymatic Activation, Detoxification, Biodegradation, and
Cytotoxicity of Redox Active Xenobiotics. Dr Habil. N. Čėnas. 2017–2021.

We detalized the catalysis mechanism of Rhodopseudomonas palustris ferredoxin:NADP+ reductase (RpFNR) demonstrating that it follows a ‚ping-pong‘ mechanism, and that there exists two typical Marcus‘ type dependences (log rate constant vs. single-electron reduction potential, E¹₇) for quinones and aromatic N-oxides, and for nitroaromatic compounds. The electron acceptors interact with the active centre containing both positively and negatively charged aminoacid residues. The standard redox potential of the FAD cofactor of enzyme, determined according to the kinetics of transhydrogenase reaction, is equal to -0.276 V. We continued the studies of neuronal NO synthase (nNOS), showing that the binding of calmodulin, irrespectively of possible change in redox potential of FMN, increases its solvent accessibility by 1-2 Å. We demonstrated that the heme cofactor of nNOs, namely Fe2+-NO complex, also participates in quinone reduction. It was shown that the specific permutation of positions of methyl and nitrogroups is required to ensure low sensitivity and high thermal stability of high energy nitrobenzimidazole compounds. We performed the molecular docking studies of several new generation o-quinones (naphthopyridine-5,6-diones) in the active center of NAD(P)H:quinone oxidoreductase (NQO1, PBD code 1KBQ) and obtained the most favourable configurations of their binding. Their calculated binding free energy changes varied between 7-11 kcal/mol. The mode of binding of the above compounds is similar to that of natural o-quinones β-lapachone and tanshinone.

Main publications:

Nemeikaitė-Čėnienė, A., Marozienė, A., Misevičienė, L., Tamulienė, J., Yantsevich, A. V., Čėnas, N. Flavoenzyme-catalyzed single-electron reduction of nitroaromatic antiandrogens: implications for their cytotoxicity. Free radical research. 2021, 55: 246–54.

Šarlauskas, J., Tamulienė, J., Bekešienė, S., Kravcov, A. Benzimidazole derivatives as energetic materials: a theoretical study. Materials. 2021, 14: 4112.

National Research Projects

Research Council of Lithuania: Redox Chemistry, Biochemistry and Cytotoxicity of Aromatic Nitrocompounds and N-Oxides: New Insighths (No. DOTSUT-34/09.33-LMT-K712-01-0058). Dr Habil. N. Čėnas. 2018–2022.

The aim of this project is to provide new insights on redox processes and cytotoxicity of aromatic nitrocompounds and N-oxides: i) a number of nitrobenzene derivatives (n=6) with mitochondriotropic and bioreductively activated leaving mustard groups was synthesized. It was shown that the leaving mustard group enhances the cytotoxicity of compounds in HCT-116 cells; ii) we derived tirapazamine-resistant MH22a cell subline and performed its proteomic analysis. It demonstrates downregulation of NADPH: cytochrome P-450 reductase and other single-electron transferring flavoenzymes, and upregulation of antioxidant enzymes carbonyl reductase and aldehyde dehydrogenase; and iii) using quantum mechanical calculations and enzymatic single-electron reduction data, we determined the E¹₇ values of a number of nitroheterocyclic drugs including nitazoxanide, tizoxanide, nifuroxazide and fexinidazole. The cytotoxicity of compounds in HCT-116 cells except nitazoxanide and tizoxanide correlated with their E¹₇ values and lipophilicity. Evidently, in this particular case, there exist other factors of cytotoxicity of nitrothiazoles in addition to the oxidative stress.

Main publication:

Čėnas, N., Nemeikaitė-Čėnienė, A., Kosychova, L. Single- and two-electron reduction of nitroaromatic compounds by flavoenzymes: mechanisms and implications for cytotoxicity. International Journal of Molecular Sciences. 2021, 22: 8534.

International Research Projects

Bilateral Lithuanian-French Programme Gilibert. Characterization of the Flavointeractome of the Antiplasmodial Agent Plasmodione and its Metabolites (No. S-LZ-19-4). Dr Habil. N. Čėnas. 2019–2021.

The initial studies of quinone- and nitroaromatic oxidant specificity for Plasmodium falciparum mitochondrial NADH:ubiquinone reductase (NDH2) were carried out, showing that this enzyme performs two-electron reduction of quinones, and possesses certain specificity towards plasmodione derivatives.

Main publication:

Cichocki, B. A., Donzel, M., Heimsch, K. C., Lesanavičius, M., Feng, L., Montagut, E. J., Becker, K., Aliverti, A., Elhabiri, M., Čėnas, N., Davioud-Charvet, E. Plasmodium falciparum ferredoxin-NADP⁺ reductase-catalyzed redox cycling of plasmodione generates both predicted key drug metabolites: implications for antimalarial drug development. ACS Infectious Diseases. 2021, 9: 1996–2012.

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

Universita degli Studi di Milano (Italy)
Universite de Paris Sud, Orsay (France)
Universite de Strasbourg (France)
Universite de Lorraine, Nancy (France)
Victoria University of Wellington (New Zealand)

OTHER RESEARCH ACTIVITIES

Dr Habil. N. Čėnas –

• Member of the Society for Redox Biology and Medicine, https://sfrbm.org/.

BEST REPORTS DELIVERED AT CONFERENCES ABROAD

• M. Lesanavičius, J.-L. Boucher, N. Čėnas. The "outer-sphere" electron-transfer reactions of nitric oxide synthase with prooxidant xenobiotics. 20th International Symposium on Flavins & Flavoproteins. Graz, 5–9 September 2021.
• Nemeikaitė-Čėnienė, V. Jonušienė, L. Misevičienė, A. Marozienė, N. Čėnas. The use of rate constants of flavoenzyme-catalyzed single-electron reduction of nitroaromatics in the analysis of their cytotoxicity mechanisms. 9th International Conference on radiation in Various Fields of Research. Herceg Novi, 14–18 June 2021.

DEPARTMENT OF BIOELECTROCHEMISTRY AND BIOSPECTROSCOPY

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4394
E-mail:
Head – Dr Gintaras Valinčius

STAFF

Research professors: Dr G. Valinčius, Dr Habil. G. Niaura (part-time).
Senior researcher: Dr G. Preta.
Researchers: Dr R. Budvytytė, Dr M. Jankunec, Dr B. Pavliukevičienė, Dr T. Ragaliauskas, Dr M. Talaikis.
Research assistant: I. Aleknavičienė.
Teaching assistant: T. Penkauskas.
Senior specialist: Dr A. Bulovas.
Doctoral students: F. Ambrulevičius, S. P. Arun, R. Bagdonaitė, E. Jankaitytė, S. Ganpule, R. Tamulytė.

RESEARCH FIELDS

Spectroelectrochemistry of proteins and biologically relevant redox species
Self-organization in lipid systems
Membranes/protein (peptide) interactions
Measurement techniques and experimenta data analysis

RESEARCH PROJECTS CARRIED OUT IN 2021

Project Supported by University Budget

Spectroelectrochemical Studies of Biological Systems and their Models. Dr G. Valinčius. 2019–2021.

Molecular anchors for tethered bilayer membranes on Silver Substrates. The assembly of functional tBLMs on silver substrates was accomplished for the first time. The suitability of mixed-component self-assembled monolayers (SAMs) for tBLM formation was further interrogated by electrochemical impedance spectroscopy (EIS) and vibrational spectroscopy. We found that using different-length backfiller molecules it is possible to control the orientation of anchor molecules WC14 on the surface thus ensuring control of the properties of tethered bilayer membranes. EIS attested the formation of well-insulating tBLMs if 3-mercapto-1-propanol (3M1P) is used as a backfiller. An increase in the length of the backfiller led to increased defectiveness of tBLMs, however, presumably proper adjustments of the SAM composition can improve properties of tBLMs when other backfillers are utilized. All tBLMs assembled on silver substrates responded to the pore-forming cholesterol-dependent cytolysin, vaginolysin in a manner consistent with the functional reconstitution of the toxin into phospholipid bilayer. Our experiments demonstrate the biological relevance of tBLMs assembled on silver surfaces and indicate their utility as biosensing elements for the detection of pore-forming toxins in liquid samples.

Main publications:

Aleknavičienė, I., Jankunec, M., Penkauskas, T., Valincius, G. Electrochemical properties of tethered lipid bilayers on thin film silver substrates. Electrochim. Acta. 2021, 389: 138726. https://doi.org/10.1016/j.electacta.2021.138726.

Aleknavičienė, I., Talaikis, M., Budvytyte, R., Valincius, G. The Impact of an Anchoring Layer on the Formation of Tethered Bilayer Lipid Membranes on Silver Substrates. Molecules. 2021, 26: 6878. https://doi.org/10.3390/molecules26226878.

Tethered lipid membranes for non-invasive bioanalysis of acute pancreatitis. When cells undergo stress in Acute Pancreatitis (AP), heat shock proteins (HSPs) response is activated. Our multidisciplinary study shows that the heat shock proteins HSP90 and HSP70 are expressed during the development of AP, which affects the course of AP. The understanding the disease development mechanisms involving HSPs interaction with cell membranes may provide new clues for the clinical prevention and therapy solutions in AP. Tethered bilayer lipid membranes (tBLMs) have been developed to investigate HSP’s interaction with membrane that can be probed by electrochemical impedance spectroscopy (EIS). The results revealed that HSP70 and HSP90 interact with the membrane via different mechanisms: HSP70 shows the damage of the membrane, while HSP90 increases the insulation properties of tBLM. Herein, we are presenting an alternative, simple electrochemical technique without any immunoprobes for monitoring HSPs action on tBLM. This project is a part of collaboration with Dr Julija Razumiene group from the Institute of Biochemistry at Life Science Center of Vilnius University. This study covers several research fields: Self-organization in lipid systems and Membranes/protein (peptide) interactions.

Main publication:

Budvytyte, R., Milasiute, A., Vitkus, D., Strupas, K., Gulla, A., Sakinyte, I., Razumiene, J. Tethered Lipid Membranes as a Nanoscale Arrangement towards Non-Invasive Analysis of Acute Pancreatitis. Biomedicines. 2021, 9: 755.

Molecular anchors for tethered bilayer membranes on metaloxide surfaces. New metal-oxide molecular anchors and possibilities to assemble phospholipid bilayer on metal oxide substrates were demonstrated. Two component silane-based self-assembled monolayrs were formed on fluorine doped tin oxide surface, and one component silane based molecular anchor was formed on mechanically polished aluminum surface. Both surfaces triggered vesicle fusion and formation of hybrid bilayers, yielding biomimetic, regenable electrodes suitable for probing protein/phospholipid interactions. In all cases, melittin (membrane damaging toxin) interaction with both funcionalised surfaces was observed, demonstrating biological relevance of these novel biomimetic surfaces. These finding may be of use in design of advanced in vitro bio-sensing devices.

Main publications:

Gabriūnaitė, I., Valiūnienė, A., Sabirovas, T., Valinčius, G. Mixed Silane-based Self-assembled Monolayers Deposited on Fluorine Doped Tin Oxide as Model System for Development of Biosensors for Toxin Detection. Electroanalysis. 2021, 33: 1315–1324. https://doi.org/10.1002/elan.202060578.

Sabirovas, T., Valiūnienė, A., Valinčius, G. Hybrid bilayer membranes on metallurgical polished aluminium. Scientific Reports. 2021, 11: 9648. https://doi.org/10.1038/s41598-021-89150-2.

Other topics. We also contributed through the collaborative initiatives to the research projects done at other departments of VU Life Sciences Center, Vilnius University Faculty of Chemistry and groups at the National Institute of Cancer, Center for Physical Science and Technology as well Lithuanian University of Health Sciences, as well as at Sapienza University, Department of Experimental Medicine, Rome, Italy. 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:

Garofalo, T., Misas, R., Preta, G. Editorial: Targeting lipid rafts as a strategy against infection and cancer. Frontiers in Cell and Developmental Biology. 2021, 9: 748905.

Golovinas, E., Rutkauskas, D., Manakova, E., Jankunec, M., Silanskas, A., Sasnauskas, G., Zaremba, M. Prokaryotic argonaute from archaeoglobus fulgidus interacts with DNA as a homodimer. Scientific Reports. 2021, 11(1): 4518.

Liustrovaitė, V., Valiūnienė, A., Valinčius, G., Ramanavičius, A. Electrochemical impedance spectroscopy based evaluation of chlorophyll A reconstitution within tethered bilayer lipid membrane. Journal of the Electrochemical Society. 2021, 168 (6): 066506.

National Research Council Projects

Research Council of Lithuania. Development of Non-Invasive Method Platform for Early Diagnostics and Prognosis of Acute Pancreatitis (No. 01.2.2-LMT-K-718-01-0025). Dr J. Razumienė. Partner – Vilnius University Hospital Santaros Klinikos. 2018–2022.

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. Dr R. Budvytytė. 2020–2022.

Research Council of Lithuania. Development of Drug Candidates for Alzheimer’S Disease Treatment, No. 01.2.2-LMT-K-718-03-0003. Dr D. Matulis. 2020–2023.

Research Council of Lithuania. Statins and Pleiotropic Effects: Interactions with Lipid Plasma Membranes, No. KD-19047. Dr. Giulio Preta. Doctoral candidate: S. Ganpule. 2019–2022.

Research Council of Lithuania. Student research projects (No. 09.3.3-LMT-K-712-22-0116). Dr. M. Jankunec, student M. Rakauskaitė.

Research Council of Lithuania. Student Research Projects, No. 09.3.3-LMT-K-712-22-0219. Dr. R. Budvytyte, student E. Jankaitytė.

Central Project Management Agency. Development of Biosensor Research and Engineering Competence and Technology Transfer Centre (BIOSENSE), No. 01.2.2-CPVA-K-703-03-0010. Dr. M. Dagys. 2020–2023.

Project Funded by Vilnius University

Surface Modification of Functional Eletrodeposited Mos2 Surfaces with Self-Assembled Monolayers and Phospholipid Bilayers. Dr T. Sabirovas. 2021–2022.

International Research Projects

Cost Action – CA18133. European Research Network on Signal Transduction (ERNEST). MS Member Dr R. Budvytytė, MC Substitute Dr M. Jankunec. 2020–2023.

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

Faculty of Mathematics and Informatics, Vilnius University (Lithuania)
Faculty of Chemistry, Vilnius University (Lithuania)
National Institute of Cancer (Lithuania)
UAB Lipidohms (Lithuania)
Institute of Neurosciences, Lithuanian University of Health Sciences (Lithuania)
Institute of Chemistry, Center for Physical Sciences and Technology (Lithuania)
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)
Institute of Lifescience, Swansea University (United Kingdom)
Sapienza University, Department of Experimental Medicine, Rome (Italy)

OTHER RESEARCH ACTIVITIES

Dr G. Valinčius –

• editorial board member of the journal Chemija, Redkolegija.pdf (lmaleidykla.lt);
• member of the Lithuanian Biophysical Society, (20+) Lietuvos biofizikų draugija / Lithuanian Biophysical Society | Facebook;
• member of the Lithuanian Biochemical Society, LBD | Lietuvos Biochemikų Draugija (biochemistry.lt);
• member of International Society of Electrochemistry, International Society of Electrochemistry (ise-online.org);
• expert of Research and Higher Education Monitoring and Analysis Centre (STRATA), STRATA - News.

Dr Habil. G. Niaura –

• member of the Lithuanian Academy of Sciences, Home - Lietuvos mokslų akademija (lma.lt);
• editorial board member of the journal Chemija, Redkolegija.pdf (lmaleidykla.lt;)
• member of the International Society of Electrochemistry, International Society of Electrochemistry (ise-online.org).

Dr R. Budvytytė –

• member of the American Biophysical Society.

MOST IMPORTANT NATIONAL AND INTERNATIONAL AWARDS RECEIVED FOR R&D ACTIVITIES

• Prof. G. Niaura: 2020 Lithuanian national science prize for Studies of Molecular Structure and Functionality of Materials by Vibrational Spectroscopy Methods (together with prof. A. Malinauskas).

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES

• Prof. G. Valinčius: member of STRATA expert group “On the effectiveness of the Lithuanian Research Council” (Group leader Prof. R. Jankauskas); member of expert group member at Science Development Program (led by Z. Duchovskiene) for the National Progress Plan at the Ministry of Education Science and Sports (2020–2021).

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES

Prof. G. Valinčius –

• Expert opinion at Lithuanian Parlament Comittte for Economics meeting, 08 December 2021. Topic On possibilieties to increase budgetary allocation for R&D and on the future of Science and Innovations in Lithuanian (resp. MP Lukas Savickas)
• Raporteur at the online workshop “Science for policymaking in Lithuania” organised by the European Commission’s Joint Research Centre (JRC) and Lithuania’s Government Strategic Analysis Center STRATA, 23 November 2021.
• Speaker at „Invest Lithuania “„Lithuanian-Taiwan collaboration meeting, Radissson Blue, Vilnius 27 October 2021.
• Consultation presentation to Lihuanian economic ataches and commercial diplomats on Increasing Lithuania’s visbility. Online meeting 17 June 2021 (organized by Lithuanian Government Chancelor Office, resp. Egle Kudzmanienė);
• Consultation to the Minister of Education Dr. J. Šiugždiniene, Science and Sports on European Molecular Biology Laboratory ahead of the meeting with the Director General of EMBL Prof. E. Heardt, 04 June 2021 (resp. A. Žalys).

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

Dr R. Budyvytė –

• Lectures for school children – schools belonging to UNESCO list: „Paprastas užmarštumas ar prasidėjęs Alzhaimeris? (Simple oblivion or the onset of Alzheimer’s )“
• Cycle of lectures at the National student`s academy: Membranų sudėtis ir savybės. Lipidiniai membranų modeliai. Lipidiniai biosensoriai. Alzhaimerio ligos mechanizmas. (Composition and properties of membranes. Lipid membrane models. Lipid biosensors. Mechanism of Alzheimer’s disease).
• IQ journal. A day with a scientist. Searching for invisible diseases.
• Delfi TV Show: Sentient. "Neurodegenerative diseases: what risk factors can you control"

Prof. G. Valinčius -

• Radio interview on Covid situation in Lithuania (interviewer D. Matas, 19 August 1921). 

DEPARTMENT OF BIOLOGICAL MODELS

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4408
E-mail:
Head – Dr Virginija Bukelskienė

STAFF

Research professors: Dr A. Burokas, E. B.-M. Daliri.
Senior researchers: Dr V. Bukelskienė, Dr D. Baltriukienė.
Researchers: Dr M. Alksnė, E. Šimoliūnas.
Research assistant: I. Rinkūnaitė.
Doctoral students: E. Baltrukonytė, V. Baranauskas, P. Barasa, M. Grubliauskaitė, M. Iešmantaitė, A. Kunevičius, A. Megur, E. M. Meškytė, J. Mingaila, 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 2021

Project Supported by University Budget

Development of the Cell Technologies for Regenerative Medicine and Their Evaluation on Biological Models. Dr V. Bukelskienė.

Improvement and biodecoration of the scaffolds. The purpose of this study was to evaluate the new bone formation in vivo effect of 3D-printed PLA/HA scaffolds, enhanced with DPSC or the extracellular matrix (ECM) they produce. The decellularisation procedure used in the current study was sufficient, and an evenly dispersed ECM network remained on the PLA/HA ECM scaffolds. PLA/HA ECM group showed better bone regeneration results when compared to cellularised PLA/HA scaffolds. Gender specific differences were observed in all experimental groups and a statistically significant difference between cellularised PLA/HA and PLA/HA ECM groups in female rats was detected.

Main publication:

Gendvilienė, I., Šimoliūnas, E., Alksnė, M., Dibart, S., Jasiūnienė, E., Cicėnas, V., Jacobs, R., Bukelskienė, V., Rutkūnas, V. Effect of extracellular matrix and dental pulp stem cells on bone regeneration with 3D printed PLA/HA composite scaffolds. European Cells & Materials. 2021, 41: 204–215.

The impact of extracellular environment on cell fate. Oxidative stress (OS) induced by reactive oxygen and nitrogen species is involved in various pathologic processes and plays a crucial role in stem cell death processes during cell therapy applications. We have shown that the sensitivity of gingival MSCs (GMSCs) sensitivity to OS depends on the stiffness of the surface, on which the cells are grown. Furthermore, the activity and expression of mitogen activated protein kinases ERK, JNK, and p38 were surface stiffness dependent. GMSCs isolated from intermediate/stiff gingiva tissue (~20 kPa) have shown the best proliferative and survival properties, then grown on the stiffest tissues mimicking polyacrylamide hydrogels (40 kPa). Therefore, the source of MSCs might determine their sensitivity to OS in different stiffness environments and should be considered when developing a treatment strategy.

Main publication:

Šimoliūnas, E., Ivanauskienė, I., Bagdzevičiūtė, L., Rinkūnaitė, I., Alksnė, M., Baltriukienė, D. Surface stiffness depended gingival mesenchymal stem cell sensitivity to oxidative stress. Free Radical Biology and Medicine. 2021, 169: 62–73.

Development of DNA-DAPI interaction-based method for cell counting in 3D. Effective cell number monitoring throughout the three-dimensional (3D) scaffold is a key factor in tissue engineering, however, the methods developed for cell number evaluation in 2D environments are often encounter limitations in 3D. For this purpose, we developed a method for cell quantification by measuring the DNA content. This method can be applied to various cells types grown in 2D, 2.5D, and 3D environments. Since this DAPI-based method analyzes cellular DNA content, its accuracy is not affected by changes in cell metabolism due to differentiation or other biological processes. This method uses simple buffers and a common DNA binding dye, DAPI, which can be combined with different assays where signal standardization to the cell number is required.

Main publication:

Šimoliūnas, E., Kantakevičius, P., Kalvaitytė, M., Bagdzevičiūtė, L., Alksnė, M., Baltriukienė, D. DNA-DAPI Interaction-Based Method for Cell Proliferation Rate Evaluation in 3D Structures. Current Issues in Molecular Biology. 2021, 43(1): 251–263.

National Research Council Projects

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 aims to identify a possible biomarker of the gut microbiota in order to create a method for early diagnosis of the disease, which would enable doctors to start treatment much earlier. Preliminary data conformed the potential of microbiota for new biomarkers.

Main publications:

Megur, A., Baltriukienė, D., Bukelskienė, V., Burokas, A. The microbiota-gut-brain axis and Alzheimer's disease: neuroinflammation is to blame? Nutrients. 2021, 13(1): 37.

Arnoriaga-Rodríguez, M., Mayneris-Perxachs, J., Contreras-Rodríguez, O., Burokas, A., Ortega-Sanchez, J. A., Blasco, G., Coll, C., Biarnés, C., Castells-Nobau, A., Puig, J., Garre, J., Ramos, R., Pedraza, S., Brugada, R., Vilanova, J., Serena, J., Barretina, J., Gich, J., Pérez-Brocal, V., Moya, A., Fernández-Real, X., Ramió-Torrentà, L., Pamplona, R., Sol, J., Jové, M., Ricart, W., Portero-Otin, M., Maldonado, R., Fernández-Real, J. M. Obesity-associated deficits in inhibitory control are phenocopied to mice through gut microbiota changes in one-carbon and aromatic amino acids metabolic pathways. Gut. 2021, 70(12): 2283–2296.

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.

Our project aims to investigate the faecal microbiota transfer therapy in children with autism spectrum disorder and to identify possible biomarkers-targets of the gut microbiota in this pathology in order to create a system allowing regulating biomarkers-those targets. As a result, that would be a big breakthrough in a development of therapy for symptoms of autism spectrum disorder.

Research Council of Lithuania. Artificial Urethra for the Treatment of Hypospadias and Urethral Strictures, No. 01.2.2-LMT-K-718-01-0087. Dr V. Bukelskienė. Partner – Vilnius University Hospital Santaros Klinikos. 2020–2023.

The aim of the research is to eliminate urethral stricture defects. For this purpose, artificial structures for the formation of artificial urethral tissue have already been prepared using 3D bioprinting. They will be refined to obtain a construct with appropriate physical properties.
In addition, in the model system, urethral strictures of the animal were induced using laboratory rabbits. The obtained results show that strictures, surgically induced by us, have formed successfully and this model can be further used in the next stages of the work.

Research Council of Lithuania. Healthy Microbiota - Healthy Brain Aging, No. SEN-S-20-9. Dr A. Burokas. 2020–2021.

Neuroinflammation characterized by activation of microglia cells is involved in various brain disorders and could be one of main target of treating them. Meanwhile, ageing increases neuroinflammation while some microbiota-derived metabolites can reduce it. Therefore, the microbiota-gut-brain axis seems to be an interesting candidate for modulation of neuroinflammation diminishing negative ageing related consequence. The obtained data confirmed that microglia showed a decline in functionality and increase of ROS in aged animals when compared to young animals in phagocytosis. Neuroinflammation is also evident in obese animals when compared to lean ones.

Central project management angency. Center for Genetic Modeling of Animals, No. 01.2.2-CPVA-K-703-03-0032. Dr D. Baltriukienė. 2020–2023.

The project aims to develop rodent models for the study of neuroinflammation, heart failure, and regulation of cancer growth. Molecular tools have been prepared for the development of these models.

International Research Projects

COST Action CA16119. In vitro 3-D Total Cell Guidance and Fitness (CellFit). Dr D. Baltriukienė. 2017–2021.

European Innovative Research & Technological Development Project in Nanomedicine (EURONANOMED3). A Liquid Corneal Glue-Filler as an Alternative to Transplantation in High Risk Patients. Dr. M. Griffith (Canada); Partner – Vilnius University, Life Sciences Center, Institute of Biochemistry; Dr V. Bukelskienė. 2019–2021.

A model system for evaluating the effectiveness of a liquid corneal filler has been developed. For this purpose, a corneal defect was formed in the eyes of laboratory rabbits, then the eyes were infected with the virus, and the lesions were further treated with liquid corneal samples prepared by the partners. The healing process of the eye was analyzed, and animal tears were collected. The results are being processed.

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.

Contractual Research

Evaluation of FX Series Compounds Using Type I Diabetes Mouse Model. Cureline Baltic, UAB. Dr A. Burokas

Assessment of changes in induced inflammatory indices in rats treated with chestnut seed extract. Švenčionių vaistažolės, UAB. Dr V. Bukelskienė.

Evaluation of the treatment of induced ischemic stroke in rats using stem cells. Aksada, UAB. Dr V. Bukelskienė.

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

Uppsala University (Sweden)
Center for physical sciences and technology (FTMC) (Lithuania)
The Dairy Research Institute of Asturias (IPLA-CSIC) (Spain)
University Pompeu Fabra, Barcelona (Spain)
Vilnius University, Faculty of Physics, Laser Research Centre (Lithuania)
Vilnius University, Faculty of Medicine (Lithuania)
Vilnius University, Faculty of Medicine, Institute of Odontology (Lithuania)
Vilnius University Hospital Santaros Klinikos (Lithuania)
Vilnius University Children’s Hospital (Lithuania)
UAB Prodentum (Lithuania)
UAB Experimentica (Lithuania)

OTHER RESEARCH ACTIVITIES

Dr D. Baltriukienė –

• President of Baltic Laboratory Animal Science Association, http://www.baltlasa.lt;
• Board member of the FELASA (Federation of European Laboratory Animal Science Associations), http://www.felasa.eu/;
• Board member of the Lithuanian stem cell researchers association, http://www.stemcell.lt/;
• member of the Lithuanian Biochemical Society, LBD | Lietuvos Biochemikų Draugija (biochemistry.lt);
• scientific supervisor of the section of Bioshemistry and Biology at the National Academy of Schoolchildren, https://nmakademija.lt/mokomieji-dalykai/.

Dr V. Bukelskienė –

• Board member of Baltic Laboratory Animal Sciensce Association, http://www.baltlasa.lt;
• Board member of FELASA (Federation of European Laboratory Animal Science Associations), http://www.felasa.eu/.

BEST REPORTS DELIVERED AT CONFERENCES ABROAD

• Burokas A. Targeting the microbiota-gut-brain axis in Alzheimer’s disease. Virtual FENS Regional Meeting 2021. 25–27 August. Organiser: Polish Neuroscience Society.
• Alksne M., Kalvaityte M., Simoliunas E., Rinkunaite I., Barasa P, Gendviliene I., Baltriukiene D., Rutkunas V, Bukelskiene V. In vitro comparison of 3D printed polylactic acid/hydroxyapatite and polylactic acid/bioactive glass composite scaffolds designed for bone regeneration. COST Action CA16119 CellFit Final Conference. 8–10 September 2021, Alghero, Italy.
• Vijaya A. K., Kuras S., Rinkūnaitė I., Šimoliūnas E., Mingaila J., Baltriukienė D., Burokas A. Impact of diet on microglia functions in ageing mice, Best Poster: 2^nd prize. XIII International Conference of the Lithuanian Neuroscience Association Consciousness - 2021, 26 November 2021, Kaunas (virtually).

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 of the Committee of Experts on Genetically Modified Organisms under the Ministry of the Environment, Lithuania; member of the Advisory Committee for the Registration of Plant Protection Products under the Ministry of Agriculture, Lithuania.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Dr Baltriukienė. Science, Innovation and Technology Agency. From laboratory to market: pre-clinical and clinical trials. Lecture “Preclinical research models - their advantages and disadvantages”.
• Dr A Burokas. How brain activity depends on intestinal bacteria; www.15min.lt , www.valstietis.lt; How do intestinal bacteria" communicate "with our brains? Žinių radijas, radio show “The future belongs to them”; public lecture "Microbiotics and brain" conversations ", lecture series "Scientists in your room”; lecture for students of the School of Young Biochemists: “Microbiota-intestinal-brain axis”; Science, Innovation and Technology Agency: Life Sciences Xmas: Trends & Spells. Public lecture “Don't forget your microscopic friends at the Christmas table”.

DEPARTMENT OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4386
E-mail:
Head – Dr Rolandas Meškys

STAFF

Research professor: Dr R. Meškys.
Senior researchers: Dr V. Časaitė, Dr L. Kalinienė, Dr D. Tauraitė, Dr J. Stankevičiūtė, Dr L. Truncaitė.
Researchers: 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.
Research assistants: A. Noreika, J. Vaitekūnas.
Senior specialist: R. Meškienė.
Doctoral students: R. Jamontas, M. Kaplūnaitė, A. Krupeckaitė, G. Plakys, V. Preitakaitė, R. Statkevičiūtė, M. Šimoliūnienė, E. Žukauskienė.

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2021

Project Supported by University Budget

Investigation of Genetic and Biochemical Diversity of Bacteriophages and Microorganisms Dr R. Meškys.

Both genetic and biochemical microbial diversity is an immense source of different proteins and biocatalysts. The analysis and exploration of said diversity is one of the main aims of our group. Unique oxidoreductases active towards coumarins and heterocycles as a primary substrate have been characterized and applied for synthesis of target compounds. Screening for novel enzymes is also carried out by applying metagenomic techniques – effective selection systems combined with tailored substrates. In addition, deep-learning systems have been applied to generated novel functionally active variants of enzymes.

More than 160 of differently modified nucleotides play a crucial role in various biological processes. Also, various modified nucleotides are used as promising building blocks for programmable changes of nucleic acids. The biosynthetic pathways of many modified nucleotides including thionucleotides are well understood, but the catabolism or salvage of those compounds is only scarcely studied. For the first time, the structural features of the TudS enzyme have been identified and a mechanism of desulphuration of thiouridines has been proposed.

Main publications:

Petkevicius, V., Vaitekunas, J., Tauraitė, D., Stankevičiūtė, J., Vaitkus, D., Šarlauskas, J., Čėnas, N., Meškys, R. 13.4 Whole-Cell Biocatalysis Using PmlABCDEF Monooxygenase and Its Mutants: A Versatile Toolkit for Selective Synthesis of Aromatic N-Oxides.In: Applied Biocatalysis: The Chemist’s Enzyme Toolbox. Editor(s): John Whittall Peter W. Sutton. 2021, 528–533.

Zhou, J., Pecqueur, L., Aučynaitė, A., Fuchs, J., Rutkienė, R., Vaitekūnas, J., Meškys, R., Boll, M., Fontecave, M., Urbonavičius, J., Golinelli-Pimpaneau, B. Structural evidence for a [4Fe-5S] intermediate in the non-redox desulfuration of thiouracil. Angew. Chem. Int. Ed. 2021, 60: 424–431. 15.

Repecka, D., Jauniskis, V., Karpus, L., Rembeza, E., Rokaitis, I., Zrimec, J. Poviloniene, S., Laurynenas, A., Viknander, S., Abuajwa, W., Savolainen, O., Meskys, R., Engqvist, M. K. M., Zelezniak, A. Expanding functional protein sequence spaces using generative adversarial networks. Nat Mach Intell. 2021, 3: 324–333.

National Research Projects

Research Council of Lithuania. Phage Proteins for Targeted Nanomedicine, No. P-SEN-20-34. Dr V. Časaitė. 2020–2021.

New nanocarrier platforms based on natural biological building blocks have become an emerging type of nanocarriers for targeted drug delivery. One of the main limitations in the practical use of such molecular tools is the clearance mediated by phagocytes. The functional activity of aged macrophages and other phagocytes is reduced, resulting in the accumulation of unphagocytosed debris, chronic sterile inflammation, and exacerbation of tissue aging and damage. In this project, we investigated the interaction of nanotubes formed from self-assembled bacteriophage tail sheath proteins with the primary phagocytes both from young adult and aged animals. The approach of this project offers unique features for the creation of novel tubular nanoparticles applicable as drug delivery systems.

Main publication:

Labutytė, G., Povilonienė, S., Šimoliūnas, E., Gabrielaitis, D., Skapas, M., Noreika, A., Meškys, R., Časaitė, V. Functionalized protein nanotubes based on the bacteriophage vB_KleM-RaK2 tail sheath protein. Nanomaterials. 2021, 11: 3031.

Research Council of Lithuania. Molecular Mechanisms of Adaptation of Low-Temperature Phages to the Mesophilic Host, No. S-MIP-19-58. Dr L. Kalinienė. 2019–2022.

By using proteomic analysis and genetic methods, we aim to determine which functions encoded by both the host cells and the virus ensure the ability of selected phages to multiply in mesophilic cells at low temperatures and in the non-dividing cells. The results obtained during this study are important not only in terms of fundamental virology but also can be useful for the development of novel antibacterial systems that would function at low-temperature (food storage, disinfectants) and would allow elimination of stationary-phase cells as well (destruction of biofilms on medical equipment).

Main publications:

Zajančkauskaitė, A., Noreika, A., Rutkienė, R., Meškys, R., Kaliniene, L. Low-temperature virus vB_EcoM_VR26 shows potential in biocontrol of STEC O26 : H11. Foods. 2021, 10: 1500.

Kaliniene, L., Noreika, A., Kaupinis, A., Valius, M., Jurgelaitis, E., Lazutka, J., Meškienė, R., Meškys, R. Analysis of a novel bacteriophage vB_AchrS_AchV4 highlights the diversity of Achromobacter viruses. Viruses. 2021, 13: 374.

Research Council of Lithuania. Enzyme Toolkit for the Synthesis of Fucosylated Oligosaccharides, No. 01.2.2-LMT-K-718-03-0045. Dr J. Stankevičiūtė. 2020–2023.

The aim of this world-class R&D project is development of the enzyme toolkit for the synthesis of high-value fucosylated oligosaccharides. To achieve this aim, a high-throughput regioselective fucosidase selection method will be established, unique fucosidases suitable for the synthesis of modified oligosaccharides will be selected, and a model of bioconversion system for high-value fucosylated oligosaccharide synthesis will be constructed. The efficient fucosylation method created in this project will scale up the production of available human milk oligosaccharides and related functional food components.

Research Council of Lithuania. Diversity and Distribution of Viruses Infecting Sulfur Metabolising Bacteria, No. S-MIP-20-38. Dr E. Šimoliūnas. 2020–2022.

In this project, we investigate the diversity, taxonomic composition and dynamics of viruses infecting sulfur metabolizing bacteria from the unique gypsum karst lake ecosystems in Lithuania. The objective of this study is to better understand the role of viruses in biological cycling of sulfur, and, therefore, the functioning of microbial food web in sulfidic oxygen minimum habitats. By using standard molecular biology and microbial cultivation methods in combination with modern cultivation-independent (metagenomics, metatranscriptomics, single cell genomics) approaches supported by sequence-based computational tools, we aim to better understanding of how viral infections and lysis affects the dynamics and fate of sulfur in the aquatic environments.

Main publication:

Šulčius, S., Alzbutas, G., Juknevičiūtė, V., Šimoliūnas, E., Venckus, P., Šimoliūnienė, M., Paškauskas, R. Exploring viral diversity in a gypsum karst lake ecosystem using targeted single-cell genomics. Genes. 2021, 12: 886.

Research Council of Lithuania. Selective Enzymatic System for Prodrug Activation, No. 01.2.2-LMT-K-718-03-0082. Dr R. Meškys. 2020–2023.

A prodrug is a modified form of the active drug, designed specifically to improve its pharmacokinetic profile: the drug's activity is “locked” and can only be restored by bioconversion which occurs in the human body. Although very promising, the development of enzyme-targeted drugs faces several limitations, such as the lack of appropriate enzyme variants or the limited choice of chemical bonds to be activated. One possible solution to this problem would be to develop a prodrug that, ideally, would not be activated by human or its microbiota enzymes, and only be targeted by the specifically engineered variants of recombinant enzymes. To reach the main goal of this project, an enzymatic toolkit for the selective activation of the prodrugs needs to be developed. The enzyme toolkit will consist of a set of enzyme variants that de-modify modified cytidines and cytosines. Together, the enzyme toolkit and the modified nucleosides or heterocyclic bases can be used to develop a prototype of the selective enzymatic prodrug activation system.

Central Project Management Agency. Center for Engineering of the Next-Generation Enzymes, No. 01.2.2-CPVA-K-703-03-0023. Dr R. Meškys. 2020–2023.

The main goal of the project is to develop an integrated system for the selection of high-performance stable proteins. This integrated system consists of three complementary parts: 1) selection of stable proteins based on auxotrophic microorganisms, 2) selection of thermostable proteins by emulsion polymerase chain reaction (ePGR), and 3) selection of stable proteins based on microencapsulation. The main advantage of a composite, integrated system is the wide range of enzyme classes to be covered.

Contractual Research

Identification of Biocatalysts using in vivo and in vitro Screening Systems. UAB Biomatter Designs, Lithuania, Dr R. Meškys.

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

Center for Physical Sciences and Technology (Lithuania)
Nature Research Centre (Lithuania)
Biomatter Design (Lithuania)

BEST REPORTS DELIVERED AT CONFERENCES ABROAD

• Stanislauskienė R, Noreika A, Grigaitytė K, Meškys R, Stankevičiūtė J. Characterization of a Bacterial α-L-Fucosidase from the Metagenome of the Curonian Lagoon. EMBO | EMBL Symposium: New Approaches and Concepts in Microbiology. 2021, virtually.
• Stankevičiūtė J, Vitėnaitė R, Vaitekūnas J, Beniušis L, Meškys R, Čėnas N. Purification and characterization of NADH:FMN reductase from Arthrobacter sp. PY22. 20th International Symposium on Flavins & Flavoproteins, 2021 Graz, Austria.
• Šimoliūnienė M, Petrikonytė P, Šulčius S, Meškys R, Šimoliūnas E. Diversity of bacteriophages from sulfate-type gypsum karst lake of Northern Lithuania. 11th International Bacteriophage Meeting Phages 2021, 07–08 September 2021, Oxford, UK, virtual (Poster).

MOST IMPORTANT PARTICIPATION CASES OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS, ORGANISATIONS, BUSINESS ENTITIES

• Prof. Dr R. Meškys: member of the Committee of Experts on Genetically Modified Organisms under the Ministry of the Environment, Lithuania; member of the Advisory Committee for the Registration of Plant Protection Products under the Ministry of Agriculture, Lithuania.

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES

• Prof. Dr R. Meškys. Consultations provided to Biomatter Designs Co Ltd regarding the enzymatic production of the modified nucleotides.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Dr R. Stanislauskienė: organiser of International Microorganisms Day 2021 (in Lithuania).
• Dr V. Petkevičius: Microorganisms: diversity, adaptation, and application, LGMOA Biology Association (BioSa14), 05 February 2021.
• Dr J. Stankevičiūtė: Lecture to the public during the festival "Spacecraft Earth": "Microorganisms - a valuable source of enzymes", 2021, Vilnius; scientific consultant at the School of Young Biochemists. Lecture for students “Successful Research. Idea. Results. Conclusions”, 2021, Vilnius; event for schoolchildren “Fair of Ideas”. The expert of scientific ideas, 2021, Vilnius.

DEPARTMENT OF MOLECULAR CELL BIOLOGY

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4409
E-mail:
Head – Prof. Dr Rūta Navakauskienė

STAFF

Research professor: Prof. Dr R. Navakauskienė.
Senior researchwea: Dr V. V. Borutinskaitė, Dr A. Kalvelytė.
Researchers: Dr A. Imbrasaitė, Dr N. Krestnikova, Dr G. Valiulienė, Dr A. Vitkevičienė.
Research assistants: A. Stulpinas, E. Valatkaitė, A. Zentelytė.
Doctoral students: R. Baušytė, G. Skliutė, A. Stulpinas, B. Vaigauskaitė, D. Žukauskaitė.

RESEARCH INTERESTS

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 tumours

RESEARCH PROJECTS CARRIED OUT IN 2021

Project Supported by University Budget

Studies of Regulatory Mechanisms of Cancer and Stem Cell for New Technologies of Personalized Medicine. Prof. R. Navakauskienė. 2019–2023.

Assessement of gene expression changes in stem and cancer cells. Human cancer cells (acute myeloid leukaemia and lung cancer) as well as stem cells isolated from human perinatal derivatives and reproduction system are used to study cell functioning and regulation.

Main publication:

Zentelytė, A., Žukauskaitė, D., Jacerytė, I., Borutinskaitė, V., Navakauskienė, R. Small Molecule Treatments Improve Differentiation Potential of Human Amniotic Fluid Stem Cells. Front Bioeng Biotechnol. 2021 Feb 22, 9: 623886. doi: 10.3389/fbioe.2021.623886. eCollection 2021.

International Research Project

The 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.

Main publication:

Valatkaitė, E., Baušytė, R., Vitkevičienė, A., Ramašauskaitė, D., Navakauskienė, R. Decidualization Potency and Epigenetic Changes in Human Endometrial Origin Stem Cells during Propagation. Front Cell Dev Biol. 2021 Nov 19, 9: 765265. doi: 10.3389/fcell.2021.765265. eCollection 2021.

National Research Projects

Research Council of Lithuania. The National Research Programme Healthy Ageing project: Development of Innovative Targeted Therapies and Prognostic Tools for Chemotherapy-Resistant Acute Myeloid Leukaemias. Prof. R. Navakauskienė. 2020–2021.

Acute myeloid leukaemia (AML) is the most common blood cancer in elderly people, fast-growing and deadliest. Project objective is to develop an innovative and precise treatment method and treatment prognostic test for chemotherapy-resistant/refractory AML patients. During the project, we compare R/R AML patients’ blasts response to selected innovative treatments in ex vivo, in vitro systems and in in vivo samples by using metabolomics, genomic/epigenomic and proteomic analysis. The research results can lead to innovative personalized therapy, expanding and prolonging the well-being of patients.

Main publication:

Valiulienė, G., Vitkevičienė, A., Skliutė, G., Borutinskaitė, V., Navakauskienė, R. Pharmaceutical Drug Metformin and MCL1 Inhibitor S63845 Exhibit Anticancer Activity in Myeloid Leukemia Cells via Redox Remodeling. Molecules. 2021 Apr 15, 26(8): 2303. doi: 10.3390/molecules26082303.

Research Council of Lithuania. Targeted Research in Smart Specialization Areas. 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. 2018–2022.

Non-genetic resistance of cells to cancer drugs is increasingly recognized. At this stage of the project in 2021, we investigated the cross-talk and feedback mechanisms between of PI3K / Akt and MEK / ERK signaling pathways during therapeutic treatment using a panel of phenotypically and genotypically different lung cancer cell lines. Studies have highlighted the potential role of cell state.

In addition, modeling studies of different cell states - adherent cells, single-suspension cells, and cell aggregates - showed an opposite dependence of MAP kinases JNK and p38 basal phosphorylation on substrate loss compared to Akt kinase. However, abnormal activation of ERK1/2 in lung cancer A549 cells, in contrast to decrease in ERK1/2 phosphorylation in other cell lines studied, was observed in anchorage-independent state. The opposite dependence of members of the same signaling pathway, transcription factor cJun and kinase JNK, on cell-cell contacts was also shown.

Main publication:

Stulpinas, A., Užusienis, T., Imbrasaitė, A., Krestnikova, N., Ungurytė, A., Kalvelytė, A. V. Cell-cell and cell-substratum contacts in the regulation of MAPK and Akt signalling: Importance in therapy, biopharmacy and bioproduction. Cellular Signalling. 2021, 84: 110034.

Science Promotion Fund of Vilnius University. Investigation of Exosomes Derived from Mesenchymal Stem Cells for Drug Treatment Resistant Depression Therapy, No. MSF-LMT-3/2020. Dr G. Valiulienė. 2020–2023.

Main publication:

Valiulienė, G., Zentelytė, A., Beržanskytė, E., Navakauskienė, R. Metabolic Profile and Neurogenic Potential of Human Amniotic Fluid Stem Cells from Normal vs. Fetus-Affected Gestations. Front Cell Dev Biol. 2021, 16(9): 700634.

Science Promotion Fund of Vilnius University. Exploring the Physiological Traits and Dynamics of Treatment Resistant Depression: A Biomarker Analysis, No. MSF-LMT-6. Dr G. Valiulienė. 2019–2022.

In these studies we aim to investigate the neurogenic potential of human amniotic fluid stem cells (hAFSCs), as well as the applicability of hAFSCs’ derived exosomes for treatment resistant depression (TRD) therapy. In addition, our research enrolls systematical analysis of the physiology of TRD by studying markers, related to pathology manifestation, and brain stimulation therapy induced reorganization of the brain.

Main publication:

Valiuliene, G., Valiulis, V., Dapsys, K., Vitkeviciene, A., Gerulskis, G., Navakauskiene, R., Germanavicius, A. Brain stimulation effects on serum BDNF, VEGF, and TNFα in treatment-resistant psychiatric disorders. Eur J Neurosci. 2021, 53(11): 3791–3802.

International Research Projects

COST Action CA17116 International Network for Translating Research on Perinatal Derivatives into into Therapeutic Approaches (SPRINT). Prof. R. Navakauskienė & Dr V. Borutinskaitė. 2018–2022.

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

Linkoping University (Sweden)
Nice University (France)
Milan University (Italy)
Malta University (Malta)
Northwestern University (USA)

OTHER RESEARCH ACTIVITIES

Prof. R. Navakauskienė -

• member of American Society for Cell Biology, The American Society for Cell Biology | A Global Cell Biology Community | ASCB;
• member of Lithuanian Stem Cell Researchers Association, Lietuvos kamieninių ląstelių tyrėjų asociacija (stemcell.lt);
• member of Federation of European Biochemical Society, FEBS | Home;
• member of Perinatal Stem Cell Society, Perinatal Stem Cell Society - Perinatal Tissue Donation & Info.

Dr A. V. Kalvelytė –

• member of Lithuanian Stem Cell Researchers Association, Lietuvos kamieninių ląstelių tyrėjų asociacija (stemcell.lt);
• member of Federation of European Biochemical Society, FEBS | Home.

Dr V. Borutinskaitė -

• member of Lithuanian Stem Cell Researchers Association, Lietuvos kamieninių ląstelių tyrėjų asociacija (stemcell.lt);
• member of Federation of European Biochemical Society, FEBS | Home. 

LABORATORY OF BIOORGANIC COMPOUNDS CHEMISTRY

Mokslininkų g. 12A, LT-08412 Vilnius
Tel. 272 9058
E-mail:
Head – Dr Regina Jančienė

STAFF

Senior researcher: Dr R. Jančienė.
Researchers: Dr M. Jonušis, Dr Z. Staniulytė.
Senior specialists: Dr A. Klimavičius, J. Meškauskas, R. Rozenbergas, S. Palaikienė, D. Podėnienė, Dr R. Sirutkaitis.

RESEARCH INTERESTS

Synthesis of heterocyclic, amino acid and polyether derivatives, design and development of technology of chemical processes, custom synthesis

RESEARCH PROJECTS CARRIED OUT IN 2021

Project Supported by University Budget

Investigation of the Synthesis and Structure of Modulators and Catalysts of Biological Processes. Dr R. Jančienė.

Synthesis of model tetraethylene glycol (PEG) derivatives bearing different α- and ω-substituents. High chemical and oligomer purity polyethylene glycol derivatives (PEG) are applied in a broad range of research and industrial sectors – biotechnology, nanotechnology, pharmacology. Typical commercial PEG is a polydispersion of PEG oligomers. It is difficult to achieve monodisperse product in polymerisation reactions. Therefore, the investigation of synthesis methods leading to high purity PEG oligomers is relevant. The aim of our permanent studies in this field is to synthesize pure monodisperse di- and monoprotected PEG (n=4÷10) derivatives which can be used for the preparation of longer PEG. On the basis of model triethyleneglycol, di- and monomesylation, di- and monobenzylation reactions were developed and methods for purification of obtained products were established. Moreover, possibilities and conditions of scale up of these reactions were tested. The use of substituted triethylene glycol derivatives for chain extension and synthesis of longer monodisperse PEG derivatives was investigated.

Investigation of the synthesis of disubstituted s-tetrazine derivatives. Studies of synthesis of new potential electron transfer mediators, 2-substituted 1,4-benzoquinone derivatives were continued.

Investigation and optimization of synthesis methods of indole derivatives. In continuation of our search for new inhibitors among heterocyclic derivatives, synthesis of tricyclic imidazo-1,5-benzodiazepine systems was investigated. Imidazo-1,4-benzodiazepine derivatives are specific antagonists of benzodiazepine receptors and are used as an antidote in the treatment of benzodiazepine overdoses. We investigated the synthesis of imidazo[1,5-a][1,5]benzodiazepines employing Wittig-Horner methodology. Generally, the imidazo-annulation at amido group of hetero-ring is accomplished via the activation of the amido function to an imino phosphate in the presence of KOtBu and its cyclocondensation with the anion generated from isocyanoalkanoic esters. The accepted mechanism for the formation of C=C bond by standard Wittig reactions proceeds via a four membered intermediate, generated by the attack of phosphorus-oxygen anion to the C=O group of amides. This common synthetic route was utilized for our study. 5-Substituted 1,5-benzodiazepines were successively treated with KOtBu, diphenyl- or diethylchloro phosphate and α-metalated ethyl isocyanoacetate and gave basically sole product, that is ethyl 5-[2-(R {2-[(diphenoxyphosphoryl)amino]phenyl}amino)ethyl]-1,3-oxazole-4-carboxylates. Only 5-benzyl substituted benzodiazepinones led to expected imidazobenzodiazepines which were isolated in small yields. The structure of new1,3-oxazole derivatives was established on the basis of IR, NMR, MS spectra and X-ray structural analysis. Such unexpected transformation of 1,5-benzodiazepine derivatives under conditions of Wittig-Horner reaction is not described so far, the rearrangement mechanism is studied by the DFT method using the B3LYP functional and 6-31+G(d, p) basis set.

Main publication:

Voitechovič, E., Stankevičiūtė, J., Vektarienė, A., Vektaris, G., Jančienė, R., Kuisienė, N. Razumienė, J., Meškys, R. Bioamperometric Systems with Fructose Dehydrogenase from Gluconobacter japonicus for D-Tagatose Monitoring. Electroanalysis. 2021, 33(6): 1393–1397.

Contractual Research

Optimization of Synthesis Technology for Pantetine-4‘,4‘-diphosphate. Contract with UAB Thermo Fisher Scientific Baltics. Dr R. Jančienė.

Investigation of Regeneration Conditions of Butylacetate and Negative Developer and Manufacturing of their Experimental Batches. Contract with UAB Vilniaus Ventos puslaidininkiai. Dr A. Klimavičius.

Research in Development of New Methods for Making Monobenzyl Poliethylene Glycol. Contract with Ramidus AB (Sweden). 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.

Efficacy Study of Immobilized Lipases. Contract with UAB Ekorama. Dr R. Jančienė.

Study of the Synthesis of Tetrazine Derivatives. Contract with UAB Sanobiotech, UAB Sanobiotech R&D, UAB Sanobiotech Novus. Dr R. Jančienė.

Study of Optimization of DAPI Synthesis Scheme and Synthesis of Experimental Batches of DAPI Dichloride. Contract with UAB Certumtech. Dr R. Jančienė.

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.

Optimization of Used Oil Refining Technology. Contract with UAB Nagenus. Dr M. Jonušis.

Development of Glycerol Phenyl Butyrate Synthesis Scheme. Contract with UAB Curaltus. Dr M. Jonušis.

Investigation of the Maceration Process of Plant Raw Material. Contract with UAB Kosmetikos tyrimo centras. Dr M. Jonušis.

Investigation of Synthesis of Sodium 2-[2-[2-[2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethoxy]ethansulphonate and Development of Preparative Technology. Contract with UAB Thermo Fisher Scientific Baltics. Dr M. Jonušis.

Optimization of the Synthesis of Methyl 6-propyl-2-hydroxy-4-oxo-cyclohex-2-ene-1-Carboxylate. Contract with UAB Sanobiotech, UAB Sanobiotech R&D, UAB Sanobiotech Novus. Dr. M. Jonušis.

MAIN R&D&I (RESEARCH, DEVELOPMENT AND INNOVATION) 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 (Lithuania)
UAB Sanobiotech R&D (Lithuania)
UAB Sanobiotech Novus (Lithuania)
UAB Elymus (Lithuania) 

PROTEOMICS CENTRE

Saulėtekio al. 7, LT-10257, Vilnius
Tel. 223 4410
E-mail:
Head – Dr Mindaugas Valius

STAFF

Research professor: Dr M. Valius.
Senior researcher: Dr J. Cicėnas.
Researchers: Dr N. Dreižė, Dr M. Ger, Dr A. Kaupinis.
Research assistant: S. Urnikytė.
Doctoral students: I. Lagunavičienė, J. Žukas.

RESEARCH AREAS

High throughput proteomics analysis of cell signaling
Investigation of mechanisms of cancer cell resistance to chemotherapy
Elucidation of artificial microstructures and nano particles on cell functioning
Biomarkers for cancer diagnostics and treatment

RESEARCH PROJECTS CARRIED OUT IN 2021

Project Supported by University Budget

New Technologies for Tumour Diagnosis and Treatment Based on Nano-Materials and Proteomics. Dr M. Valius. 2019–2023.

National Research Projects

Research Council of Lithuania. Development of Novel Proteomics-Based Drug Selection Approach for Pancreatic Cancer Individualized Therapy, No. SEN-16041. Project manager Prof. P. Shemmer, work package manager Dr M. Valius. 2020–2021.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive oncological diseases, characterized by late diagnosis, high metastatic potential, and most importantly, a lack of effective therapy. In this study we identified prognostic PDAC treatment biomarkers in the blood serum and urine samples of PDAC patients. CEACAM6 protein was validated as the prognostic protein biomarker in a large set of blood serum samples from PDAC patients. The larger concentration of CEACAM6 correlates with a lack of response to adjuvant chemotherapy. Proteomic analysis of urine samples revealed several potential diagnostic and prognostic biomarkers applicable for noninvasive diagnostics. We also developed a novel drug prediction technology for PDAC therapy based on the using proteome, phosphoproteome, and kinome analysis, as well as patient-derived cell lines. We identified a number of drugs whose anti-cancer effects were confirmed in tumour-derived cells from PDAC patients. Some of these drugs are already used to treat tumours of other localizations; this will facilitate the implementation of these drugs into practice.

Main publications:

Linklater, E. S., Duncan, E. D., Han, K.-H., Kaupinis, A., Valius, M., Lyons, T. R., Prekeris, R. Rab40–Cullin5 complex regulates EPLIN and actin cytoskeleton dynamics during cell migration. J.Cell Biol. 2021, 220(7): e202008060.

Voronovic, E., Skripka, A., Jarockyte, G., Ger, M., Kuciauskas, D., Kaupinis, A., Valius, M., Rotomskis, R., Vetrone, F., Karabanovas, V. Uptake of Upconverting Nanoparticles by Breast Cancer Cells: Surface Coating versus the Protein Corona. ACS Applied Materials & Interfaces. 2021, 13(33): 39076–39087.

Kurlinkus, B., Ger, M., Kaupinis, A., Jasiunas, E., Valius, M., Sileikis, A. CEACAM6’s Role as a Chemoresistance and Prognostic Biomarker for Pancreatic Cancer: A Comparison of CEACAM6’s Diagnostic and Prognostic Capabilities with Those of CA19-9 and CEA. Life. 2021, 11(6): 542.

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

University of Colorado, Denver (USA)
Swiss Institute of Bioinformatics, Geneva (Switzerland)
Lithuania National Cancer Center (Lithuania)
Vilnius University Hospital Santariskiu Klinikos (Lithuania)

OTHER RESEARCH ACTIVITIES

Dr M. Valius -

• guest editor of Cells (Research on Cancer Proteomics), Cells | Special Issues (mdpi.com);
• editorial board member of the journal MAP Kinases, Editorial Board | MAP Kinase (pagepressjournals.org).

Dr J. Cicėnas –

• editor-in-Chief, Editorial Board | MAP Kinase (pagepressjournals.org);
• collection editor (Kinases and cancer) of Cancers, Cancers | Special Issues (mdpi.com).

 

INSTITUTE OF BIOSCIENCES

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 239 8210
E-mail:
www http://www.gf.vu.lt
Director – 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
Center of Ecology and Environmental Research

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

DOCTORAL DISSERTATIONS MAINTAINED IN 2021

D. Dapkutė. Response of mesenchymal stem and cancer cells to teranostatic nanoparticles - a reference for cell therapy
A. Nesterenkaitė. Immune response assessment in colorectal cancer microenvironment by digital pathology analytics
L. Aitmanaitė. Virus compatibility in Saccharomyces cerevisiae LA and M virus systems
R. Kubiliūtė. Diagnostic and prognostic DNA methylation biomarkers of renal clear cell carcinoma

MAIN CONFERENCES ORGANIZED IN 2021

13^th conference of the Lithuanian Neuroscience Association, 26 November 2021, online.
Virtual FENS Regional meeting, 25–27 August 2021.
2nd Baltic Biophysics Conference – Open Lectures, 03 February and 23 March 2021.
Co-organizer of EQIPD consortium (the Enhancing Quality in Preclinical Data; originally called European Quality in Preclinical Data) virtual workshop “Rigor, reproducibility and data management in non­clinical research”, 21 April 2021, University of Helsinki, Finland. 

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.
Teaching assistants: E. Žalytė, V. Žitkutė.
Lecturer: Z. Žitkus.
Senior researchers: Dr J. Armalytė, Dr A. Sasnauskienė.
Researchers: Dr D. Dabkevičienė, Dr V. Jonušienė, Dr A. Konovalovas, Dr D. Labeikytė, Dr A. Zimkus.
Research assistants: Dr L. Aitmanaitė, E. Žalytė, V. Žitkutė.
Doctoral students: E. Celitan, L. Klimkaitė, L. Kunigėnas, T. Liveikis, R. Prokarenkaitė, G. Skinderytė, V. Žitkutė.

RESEARCH INTERESTS

Bacterial stress responses, pathogenesis, antibiotic resistance
Molecular virology: mechanisms, applications, antivirals
Molecular mechanisms of chemoresistance

RESEARCH PROJECTS CARRIED OUT IN 2021

Projects Supported by University Budget

Investigation of Mechanisms of Cellular Homeostasis and Their Clinical and Biotechnological Application. Dr J. Armalytė, Prof. Dr S. Serva, Dr A. Sasnauskienė.
Investigation of biochemical mechanisms and components conferring resistance of viruses, bacterial and eukaryotic cells against antiviral, antibacterial compounds and anticancer treatment: 1) cellular response to anti-cancer treatment, cellular and molecular mechanisms of acquired chemoresistance and carcinogenesis; 2) molecular mechanisms of antibiotic resistance and microbial pathogenesis of gram-negative bacterial pathogens with the emphasis on the novel antibacterial targets and bacterial toxin-antitoxin systems, development of molecular techniques for detection of antibiotic resistant bacteria; 3)research on yeast dsRNA viruses and nucleoside/nucleotide based antivirals for retroviruses.

Main publications:

Aitmanaitė, L., Konovalovas, A., Medvedevas, P., Servienė, E., Serva, S. Specificity Determination in Saccharomyces cerevisiae Killer Virus Systems. Microorganisms. 2021, 9(2): 236. doi: 10.3390/microorganisms9020236.

Skerniškytė, J., Karazijaitė, E., Lučiūnaitė, A., Sužiedėlienė, E. OmpA Protein-Deficient Acinetobacter baumannii Outer Membrane Vesicles Trigger Reduced Inflammatory Response. Pathogens. 2021, 10(4): 407. doi: 10.3390/pathogens10040407.

Daugelaviciene, N., Grigaitis, P., Gasiule, L., Dabkeviciene, D., Neniskyte, U., Sasnauskiene, A. Lysosome-targeted photodynamic treatment induces primary keratinocyte differentiation. J Photochem Photobiol B, 2021, 218: 112183. doi: 10.1016/j.jphotobiol.2021.112183.

Science promotion fund of Vilnius University project Application of CRISPR-Cas13 Technology in Studying Mechanisms of Chemoresistance (No. MSF-JM-2/2021). Project leader – V. Žitkutė. 2021–2022.

This project aims to apply CRISPR-Cas13 technology for downregulation of serpin B5 expression in chemoresistant colorectal cancer cells and to determine the effect of serpin B5 on chemoresistance.

Science promotion fund of Vilnius University project Synergistic Antibiotic-Photodynamic Therapy Combination in Inactivation of Opportunistic Pathogen Stenotrophomonas maltophilia (No. MSF-JM-3/2021). Project participant – L. Klimkaitė. 2021–2022.

Due to its innate resistance to antibiotics, new strategies are needed to control the infections and detrimental effects of multidrug resistant opportunistic pathogen Stenotrophomonas maltophilia. Antimicrobial photodynamic therapy is a biophotonic technology, which can be used as an alternative to antibiotics or in combination with them. This project aims to investigate the synergistic effects of antibiotics and photodynamic therapy and their ability to inactivate pathogen S. maltophilia.

National Research Projects

Research Council of Lithuania. National research program “Healthy ageing” project Development of Virus-Like Particles-Based Vaccine against Acinetobacter baumannii (No. S-SEN20-1). Project leader - J. Armalytė. 2020–2021.

The objective of the project is to investigate the conserved Blp protein of the opportunistic pathogen A. baumannii as a possible vaccination target. During the second year of the project (2021), A. baumannii Blp protein fragments were expressed and purified. To increase the immunogenic properties of the Blp peptides, they were also displayed on virus-like particles (VLPs). The fusions with best properties are being immunized to laboratory animals to check their ability to counteract infection.

Research Council of Lithuania. Redox Chemistry, Biochemistry and Cytotoxicity of Aromatic Nitrocompounds and N-oxides: a New Look (No. DOTSUT-34/09.33-LMT-K712-01-0058). Participant - V. Jonušienė. 2018–2021.

Research Council of Lithuania. National research program “Healthy ageing” project Self-assembling Phage Proteins for Targeted Nanomedicine (No. S-SEN 20-4). Participants - A. Sasnauskienė, V. Žitkutė. 2020–2021.

The ability of bacteriophage-derived nanotubes to enter human colorectal cancer cells was tested and their localisation to organelles of endocytic system was analysed.

Contractual Research

Ministry of Education, Science and Sports. Short-term research in health and education project System for Virus Spread Control and Extreme Situation Management during COVID-19 Epidemics (No. S-DNR-20-2). Project leader - S. Serva, participants - A. Konovalovas, A. Mikalkėnas, L. Aitmanaitė, E. Celitan, G. Skinderytė. 2021.

The idea of the project is knowledge-based use of safe yeast Saccharomyces cerevisiae viral system in selection of the COVID-19 pathogen-inactivating compounds. Addressing the tasks of the project resulted in formulation of new, safe to use products and defined methods and practical recommendations, enabling the control of COVID-19 pathogen spread in pharmacies and general management of extreme situations.

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)
Heidelberg University (Germany)
Universite Libre de Brussels (Belgium)
Université Paris-Saclay (France)

OTHER RESEARCH ACTIVITIES

Prof. S. Serva –

• CEO of Association Futura Scientia;
• Secretary of the Lithuanian Biochemical Society;
• 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.
• member of management committee of 2020–2022 European Cooperation in Science and Technology (COST) activity CA17103: “Delivery of antisense RNA therapeutics (DARTER)”.

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 V. Morkūnas (part-time), Dr R. Šiukšta (part-time), Dr K. Daniūnaitė (part-time), Dr V. Dedonytė (part-time).
Assistant professors: Dr I. Prigodina Lukošienė (part-time), Dr M. Rasimavičius (part-time), Dr R. Rimgailė-Voicik (part-time).
Teaching assistant: A. Stapulionytė,
Lecturers: S. Juzėnas, A. Meldžiukienė, P. Venckus.
Researchers: Dr V. Dedonytė (part-time), Dr J. Mierauskienė, Dr V. Morkūnas (part-time), Dr D. Naugžemys, Dr J. Patamsytė, Dr V. Vaitkūnienė, Dr J. Butkuvienė, Dr R. Šiukšta (part-time), Dr K. Daniūnaitė (part-time), Dr R. Rimgailė-Voicik, Dr. K. Šnipaitienė.
Research assistants: Dr. M. Rasimavičius, Dr T. Arslanova.
Senior biologists: Dr J. Rukšėnienė, Dr J. Tupčiauskaitė (part-time), Dr. V. Kleizaitė, E. Semaškaitė (part-time), J. Mačiulaitis (part-time)
Doctoral students: G. Radžiuvienė, L. Šiaulienė, D. Žalimas, D. Žilovič, I. Vincerževskienė, M. Babonaitė, J. Gaiževska, R. Maleckaitė, A. Šeštokaitė, B. Buragaitė-Staponkienė, K. Žukauskaitė, I. Vaicekauskaitė, E. Semaškaitė, V. Pukenytė, V. Mensonas.

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
Analysis of epigenetic changes in 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 historical fungal, algae, lichen and plant collections, maintained in the Herbarium of Vilnius University; study of the history of botany in Lithuania

RESEARCH PROJECTS CARRIED OUT IN 2021

Projects Supported by 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 (epi)genetic characterization of various human tumours (prostate, kidney, berast, lung, etc.). Epigenetic changes in other diseases were studied as well.

Main publications:

Kubiliute, R., Jarmalaite, S. Epigenetic Biomarkers of Renal Cell Carcinoma for Liquid Biopsy Tests. International Journal of Molecular Sciences. 2021, 22: 8846. doi: 10.3390/ijms22168846.

Narmonte, M., Gibas, P., Daniunaite, K., Gordevicius, J., Kriukiene, E. Multiomics Analysis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations. Front Cell Dev Biol. 2021. https://doi.org/10.3389/fcell.2021.727353.

Daniunaite, K., Bakavicius, A., Zukauskaite, K., Rauluseviciute, I., Lazutka, J. R., Ulys, A., Jankevicius, F., Jarmalaite, S. Promoter Methylation of PRKCB, ADAMTS12, and NAALAD2 Is Specific to Prostate Cancer and Predicts Biochemical Disease Recurrence. Int J Mol Sci. 2021, 22(11): 6091. doi: 10.3390/ijms22116091.

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. Our study aimed to evaluate the genetic diversity of Phragmites australis populations in the natural and modified Lithuanian watercourses. Like in many other parts of the world, Phragmites australis distribution and abundance are changing in Lithuania because of the impact of human activities on aquatic habitats. We examined P. australis genetic diversity patterns and the effect of hydro-graphic modifications, introduced in the mid-late twentieth century with great impact on Lithuanian landscape. The genetic diversity was studied using chloroplast DNA sequences and nuclear microsatellite markers in natural and straightened river stretches for water regulation. We found haplotypes M and L and their variants in the studied populations. The analysis of microsatellites revealed high genetic diversity within populations and significant structure both at the population and river level. Our results revealed that anthropogenic river modifications have had an impact on the genetic diversity of P. australis populations; however, disturbance is not the only factor that affects genetic diversity recruitment and dynamics in new P. australis stands.

Barley developmental mutants tweaky spike (tw) with disturbed auxin pathways possess a unique feature of an increased level of mouldy germinating grains (MGG), which serves as a convenient model to investigate the effects of plant immunity-related substances. The effects of the auxin 2,4-dichlorophenoxyacetic acid (2,4-D), auxin inhibitors, salicylic acid (SA), and trans-cinnamic acid (TCA) were studied using the tw-WT system in surface-sterilized and unsterilized germinating grains under high rates of natural infection. Significant differences among the allelic tw mutants were revealed at the natural MGG level and in response to 2,4-D, SA, and TCA. The tw mutations influenced variations in the seed-borne fungal spectra, decreasing the frequency of Bipolaris sorokiniana and increasing Fusarium spp. The study also revealed that auxin pathway disturbances specific for pleiotropic tw mutants are generally restricted to organogenesis but not to germination events

Main publications:

Šiukšta, R., Vaitkūnienė, V., Mačkinaitė, R., Rančelis, V. Application of barley tweaky spike mutants for the study of effects of plant immunity-related substances. Agronomy. 2021, 11: 2180. https://doi.org/10.3390/agronomy11112180.

Naugžemys, D., Lambertini, C., Patamsytė, J., Butkuvienė, J., Khasdan, V., Žvingila, D. Genetic diversity patterns in Phragmites australis populations in straightened and in natural river sites in Lithuania. Hydrobiologia. 2021, 848: 3317–3330. doi: https://doi.org/10.1007/s10750-021-04606-w.

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. Changes in climate, environment and the traditional management of various habitats over the last decades have triggered changes in the composition and distribution of species, stimulated an introduction of alien species and increased interest in understanding the processes of biodiversity change and maintenance. Studies on biology, ecology, distribution, conservation status and threats of protected in Lithuania plant, fungi and lichen species were summarised and published in the Red Data Book of Lithuania.
The use of native species is often desired in revegetation projects. However, there is a paucity of information about hydroseeding native species in Northern areas of Europe. Therefore, a total of 40 native plant species in Lithuania were sowed using hydroseeding and regular seeding. The results show a relatively small and short positive effect of hydroseeding on plant cover formation. A comparison of species composition revealed significant differences between the sowing treatments that were more associated with species abundance than species diversity. Overall, our findings emphasize that legume species that display more competitive growth traits should be included in the seed mixture in lower proportions when hydroseeding is applied.
Rosa rugosa is among the most invasive species in Europe, and it is considered a severe threat to the diversity and stability of coastal habitats. In Lithuania, it is a widespread invasive species occurring in coastal and inland areas. We studied the variation in R. rugosa hip and sepal parameters within and among sites from coastal and inland areas, and assessed the effects of environmental factors on the hip and sepal sizes.

Main publications:

Gudyniene, V., Juzenas, S., Stukonis, V., Norkeviciene, E. Sowing mixtures of native plant species: are there any differences between hydroseeding and regular seeding? Plants. 2021, 10(11): 2507. https://doi.org/10.3390/plants10112507.

Gudžinskas, Z., Rasimavičius, M. Variation in hip and sepal parameters of invasive Rosa rugosa between sites and years . Botanica. 2021, 27(1): 1–12. https://doi.org/10.2478/botlit-2021-0001.

Venckus, P., Cicchi, B., Chini Zittelli, G. Effects of medium salinity on growth and biochemical composition of the green microalga Tetraselmis suecica. Journal of Applied Phycology. 2021, 33: 3555–3563. https://doi.org/10.1007/s10811-021-02560-7.

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)
Prostate Cancer Research Centre, University of Tampere (Finland)
Department of Pathology, University of Helsinki (Finland)
HUSLAB, Helsinki University Hospital (Finland)
University of Bologna (Italy)
Papanin Institute for Inland Water Biology (Russia)
Lithuanian Research Centre for Agriculture and Forestry (Lithuania)
University of Greifswald (Germany)
University of Tartu (Estonia)

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.

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.

Dr I. Arslanova –

• member of Lithuanian Mycological Society.

Prof. E. Kutorga –

• editor of the journal Botanica;
• editorial board member of the journal Folia Cryptogamica Estonica;
• editorial board member of multivolume edition Lietuvos grybai (Mycota Lithuaniae);
• chairman of the Council of Lithuanian Mycological Society;
• reviewer of journals Acta Baltica Historiae, Biologia (Springer).

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.

MOST IMPORTANT NATIONAL AND INTERNATIONAL AWARDS RECEIVED FOR R&D ACTIVITIES

• Prof. E. Kutorga. The State Commission of the Lithuanian Language award sculpture „Sraigė“ and diploma “For the prepared and published book “Inoperkuliniai diskomicetai (Discomycetes inoperculatae)” of multi-volume edition Lietuvos grybai (Mycota Lithuaniae), Vol. 3, Book 6 (http://www.lma.lt/news/1203/38/Apdovanoti-lietuviu-kalbos-kurejai-ir-puoseletojai)

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

• 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).
• Dr. I.Prigodina Lukošienė - member of the Scientific Council of the Nature Research Center.
• Dr. Kristina Daniūnaitė - member of the workgroup for the preparation of the Regulation for the verification of the entirety of laboratory tests for detection of SARS-CoV-2 (2019-nCoV) RNA by real-time PCR (Ministry of Health).
• Dr M. Rasimavičius - member of the sub-commission on Terminology of The State Commission of the Lithuanian Language (as expert in Botany).

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES

• Dr Kristina Daniūnaitė. The Temporary Diagnostic Laboratory for SARS-CoV-2 testing (TDL) was established in 2020, during the COVID-19 pandemic, to increase the testing capacities in Lithuania. In addition to the routine testing of clinical samples (individual and pooled), identification of variant-specific mutations was performed. At the beginning of the year, the methodology for the viral RNA detection on environmental surfaces was developed and later validated performing thorough screening-based testing at several institutions. In April, the methodology was approved by the Ministry of Health and has been applied as a preventive measure to detect pre-symptomatic infection cases in pre-school and pre-primary educational institutions nationwide since then. Until September, TDL was the only laboratory conducting surface sample testing for viral traces in Lithuania.
• Dr. J. Butkuvienė. Cooperation with Eufitas Public Institution in evaluating the effectiveness of renaturalization measures for renaturalized river sections. 2019–2022.
• Dr. J. Butkuvienė. Cooperation with MB Scientia Practica in the assessment of the status of populations and habitats in Pavilniai and Verkiai regional parks. 2021–2022.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Butkuvienė J. Augalų bendrijos upėse. Kaip šias bendrijas išsaugoti? Ar dar ilgai džiaugsimės kurklėmis [Plant communities in rivers. How to preserve these communities? Will we be happy with the water-crowfoots for a long time ?]. Žaliasis pasaulis, Nr. 35(1241):7.
• Butkuvienė J. Report at the Protected Areas Service: Investigations of the habitat of Ranunculus sect. Batrachium in some rivers of Lithuania” 2021.
• Daniūnaitė K. – video interview for TV3 and publication in TV3.lt website: “Pradėjo tirti darželių paviršius dėl COVID-19: kaip tai atrodo”; 16 April 2021.
• Maleckaitė R. – interview for LRT, publication in LRT.lt website: “Į pagalbą kovojant su koronavirusu stojusi genetikė: nesitikėjau, kad pandemija taip pakeis mūsų gyvenimus ir tęsis tiek ilgai”; 26 Feb 2021.
• Kutorga E.: articles (https://www.vle.lt/straipsnis/gudukas/ ; https://www.vle.lt/straipsnis/raudonvirsis/ ; https://www.vle.lt/straipsnis/voveraite/ ), interviews (https://www.lrt.lt/mediateka/irasas/2000165978/mikologas-prof-kutorga-primena-grybavimo-etiketa-nereikia-stengtis-surinkti-visu-grybu ; https://www.tv3.lt/naujiena/video/tokiu-grybu-net-nebandykite-liesti-specialistas-ivardijo-pagrindine-taisykle-n1115003 ; https://www.melc.lt/lt/2021-metu-gimtoji-kalba/734-gimtoji-kalba-nr-6-pdf-formatu ; https://fb.watch/8wpV_vqubk/ ; https://www.manokrastas.lt/straipsnis/taip-kuriami-lietuviski-grybu-vardai ; https://www.youtube.com/watch?v=ofFBqeAEd9E ).
• Melžiukienė A.: National Science festival „Erdvėlaivis Žemė“ [‘Spaceship Earth’] – four excursions “Recognize the Plants”, 16 September 2021 ( https://www.mokslofestivalis.eu/renginiu-archyvas/2021/page/7/).
• Rasimavičius M.: project “Mokymasis tyrinėjant [Learning by exploring]”, Nr. 09.2.1-ESFA-K-728-03-0041. The aim of the project is to improve achievements in the natural sciences (physics, chemistry and biology) of 8th grade students. https://www.varenossc.lt/projektas-mokymasis-tyrinejant/ ; interviews (https://www.lrt.lt/mediateka/irasas/2000164216/magijos-mokslas-odisejas-ir-kiaules ; https://www.lrt.lt/mediateka/irasas/2000164311/magijos-mokslas-skraidancios-raganos ; https://www.lrt.lt/mediateka/irasas/2000157161/atspindziai-paveldo-kolekcija-jurgis-ambraziejus-pabreza-kunigas-vienuolis-ir-zolininkas-kurio-surinktu-augalu-yra-islike-iki-siu-dienu; https://www.lrt.lt/mediateka/irasas/2000159225/10-12-grybu-dvaro-seimininkas-dvaras-ne-vien-pastatai).
• Rimgailė-Voicik R.: cooperation with Hugo Scheu museum in Šilutė (https://www.silaineskrastas.lt/kultura/paparteliu-paieskos-vakaru-lietuvoje-vingiuoja-pirmtaku-keliais/); publication (https://naujienos.vu.lt/vu-gmc-botanike-kaip-augalai-gali-padeti-aptikti-bombas-ir-dingusius-zmones/ ); lecture for teachers, 2021-04-08, „Aklumas augalams: kaip mokysime pastebėti ir pažinti augalus ateityje?“; report “Aklumas augalams” in festival of Panevėžys schools „O mes kitokie“, 2021-06-01 (https://www.svietimonaujienos.lt/o-mes-kitokie/); interviews (https://www.ziniuradijas.lt/laidos/ateitis-priklauso-tiems/mokslininke-jei-ne-karas-lietuva-botanikos-moksle-pirmautu-pasaulyje?video=1; https://www.lrt.lt/mediateka/irasas/2000174862/mokslas-be-pamokslu-kaip-augalai-gali-padeti-aptikti-bombas-ir-dingusius-zmones).
• Semaškaitė E.: Virtual lesson for children “Meeting with Naturalist” organized by Anykščiai Regional Park and Anykščiai Education Assistance Authority. 

DEPARTMENT OF MICROBIOLOGY AND BIOTECHNOLOGY

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 239 8213
E-mail:
Head – Prof. Dr Nomeda Kuisienė

STAFF

Professors: Dr N. Kuisienė, Dr E. Lastauskienė, Dr L. Kalėdienė, I. Girkontaitė (part-time).
Associate professors: Dr R.Gudiukaitė, Dr V.Kašėta (part-time).
Assistants: Dr A. Gegeckas, Dr R. Kananavičiūtė, Dr R. Petkauskaitė, Dr A. Gricajeva.
Lecturers: Dr J. Raugalas, Dr R.Ražanskas (part-time), Ž. Dapkunas (part-time).
Researcher: Dr A. Kaunietis.
Specialists: J. Lekavičiūtė, R. Jurkevičienė, V. Dzekevičienė
PhD students: R. Bikmurzinas, T. Kirtiklienė, J. Jurgelevičiūtė, K. Čekuolytė, V. Malūnavičius, R. Povilavičiūtė, R. Mažylytė, A. Slavinska.

RESEARCH INTERESTS

Genomics 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

Molecular taxonomy of prokaryotes
Microbial culture collections
Bioactive compounds of microorganisms
Electroporation and magnetoporation methods for the biocontrol of the skin colonizing microorganisms
Yeast prions
Microbial enzymes
Microbial biotechnologies
Bioremediation, biodegradation, waste treatment

RESEARCH PROJECTS CARRIED OUT IN 2021

Projects Supported by University Budget

Selection and Research of Microorganisms for Innovative Biotechnology Creation. Prof. Dr L. Kalėdienė. 2021.

Although the potential for microbial degradation is ubiquitous, many organic contaminants are not or often only poorly transformed in natural environmental conditions, thus, organic and other waste treatment and recycling (bioremediation of polluted environments) is an important topic of the research group. Through exploitation of advances of conventional and molecular biology techniques, search, identification and characterization of microbial enzymes (lipases and esterases) active towards fatty acid esters, aromatic 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. The research group is also participating in research regarding safe bacterial biofilm control method development for European Space Agency (ESA). In collaboration with the Institute of Photonics and Nanotechnology, Faculty of Physics (Vilnius University), a novel natural photosensitizers-based antimicrobial photoinactivation (API) technology that is safe for the use in the confined, closed-loop systems such as spacecraft is being developed. The group is currently adapting the API technology and creating the prototype that could be used for the destruction of phytopathogenic microorganisms infecting strawberries. The project is being implemented under the project of Lithuanian Agency for Science, Innovation and Technology. 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, which are identified, characterized and analysed by our research group, are attractive both, biotechnologically and in basic research.

Main publication:

Gricajeva, A., Kumar, A., Gudiukaitė, R. Insights into polyester plastic biodegradation by carboxyl ester hydrolases. Journal of Chemical Technology and Biotechnology. 2021. doi: https://doi.org/10.1002/jctb.6745.

Molecular Microbiology of Prokaryotes for Modern Biotechnology and Biopharmacy. Prof. Dr N. Kuisienė. 2021.

The aim is the development of the new products for biotechnology and biopharmacy using modern methods of molecular microbiology of prokaryotes. Molecular approach was used to study epidemiology of multidrug-resistant Acinetobacter baumannii isolated from clinical samples. The results of the study showed the genetic relatedness of the different A. baumannii isolates as well as a possible circulation of resistance genes or profiles during the different years of the study.

In order to contribute to the development of novel antimicrobial compounds, genome mining for bacteriocins, polyketide synthases, and nonribosomal peptide synthetases in the genomes of mesophilic endospore forming strains of the genus Paenibacillus was performed. Both strains were isolated from the deep oligotrophic Krubera-Voronja Cave and were found to be highly active against both Gram-positive and Gram-negative bacteria. Most biosynthetic gene clusters in the genomes of the cave strains showed a low similarity with the reference pathways and were predicted to represent novel biosynthetic pathways. In order to reveal the potential of uncultivated prokaryotes to produce bioactive compounds, the type II polyketide synthases ketosynthases α and β and the adenylation domains of nonribosomal peptide synthetases were investigated using a metagenomic approach. Only three putative metabolites could be predicted: an angucycline group polyketide, a massetolide A-like cyclic lipopeptide and a surfactin-like lipopeptide. The absolute majority of polyketide synthase and nonribosomal peptide synthetase sequences showed low similarity with the sequences of the reference biosynthetic pathways, suggesting that these sequences could be involved in the production of novel secondary metabolites.

Main publications:

Kirtikliene, T., Mierauskaitė, A., Razmienė, I., Kuisiene, N. Multidrug-Resistant Acinetobacter baumannii Genetic Characterization and Spread in Lithuania in 2014, 2016, and 2018. Life (Basel). 2021, 11(2):151. doi: 10.3390/life11020151.

Lebedeva, J., Jukneviciute, G., Čepaitė, R., Vickackaite, V., Pranckutė, R., Kuisiene, N. Genome Mining and Characterization of Biosynthetic Gene Clusters in Two Cave Strains of Paenibacillus sp. Front Microbiol. 2021, 11: 612483. doi: 10.3389/fmicb.2020.612483.

Lukoseviciute, L., Lebedeva, J., Kuisiene, N. Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave. Microb Ecol. 2021, 81(1): 110–121. doi: 10.1007/s00248-020-01554-1.

Strategies in Antimicrobial Therapy and Protein Engineering. Prof. Dr E. Lastauskienė. 2021.

The aim is screening 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; construction of the novel proteins with the potential application in biotechnology and biopharmacy.
Recently the new microbial producents synthesizing active compounds against pathogenic Candida yeasts and Fusarium spp. were discovered as well as the active compounds against pathogenic Pseudomonas, Staphylococcus, Streptococcus strains.

By using direct evolution strategies, we improved microbial lipolytic enzymes, constructed the new fused lipolytic proteins and analyzed of them application in the ester synthesis. Lipolytic enzymes as biocatalysts can be used in organic synthesis reactions to produce precursors of drug and bioactive compounds, biofuels production and polyester wastes degradation.

Main publications:

Gudiukaite, R., Kumar Nadda, A., Gricajeva, A., Shanmugam, S., Duc Nguyen, D., Lam, S. S. Bioprocesses for the recovery of bioenergy and value-added products from wastewater: A review. J Environ Manage. 2021, 300: 113831. doi.org/10.1016/j.jenvman.2021.113831.

Gricajeva, A., Kumar Nadda, A., Gudiukaite, R. Insights into polyester plastic biodegradation by carboxyl ester hydrolases. J Chem Technol Biotechnol. 2021. doi: 10.1002/JCTB.6745.

Lastauskienė, E., Valskys, V., Stankevičiūtė, J., Kalcienė, V., Gėgžna, V., Kavoliūnas, J., Ružauskas, M., Armalytė, J. The impact of intensive fish farming on pond sediment microbiome and antibiotic resistance gene composition. Frontiers in Veterinary Science. 2021, 8: 673756. doi: 10.3389/fvets.2021.673756.

International Research Projects

European Space Agency (ESA). Fifth call under the plan for European cooperating states (PECS) in Lithuania Antimicrobial Photoinactivation Approach Based on Natural Agents for Control of Bacteria Biofilms in Spacecraft (Feasibility Study (LT5_1). Head of the project - Dr Lilija Kalėdienė. 2020–2021.

During the current project, effects and applications of antimicrobial photoinactivation technology (API) on the planktonic bacteria and formed biofilms, their integrity, and vitality were investigated. API based technology showed some prominent advantages over the chlorhexidine and UV irradiation that are used in spacecraft. But the limiting factor of the applicability of API is a necessity of rather high illumination doses and application (spread) of PS solution on surfaces in microgravity conditions. The feasibility to develop an effective, safe and bacteria-resistance-free technology for future applications in spacecraft and long-term space missions were evaluated. The goal was achieved by performing the comprehensive literature analysis, experimental trials, and elaborating the possible solutions. It was shown that API had a bacteriocidic effect (in vitro) on all tested bacteria in both planktonic and biofilm states. On the other hand, the spreading of PS solution on a wide area in microgravity conditions and ensuring the relatively high illumination doses of (deep blue-violet) light are the limiting factors and need more in-depth investigation and development.

National Research Projects

Research Council of Lithuania. National research programme “Sustainability of agro-, forest and water ecosystems” project The Influence of Intensive Fish Farming on Aquatic Microbiome and Resistome (No. S-SIT-20-6). Head of the project - Dr Eglė Lastauskienė. 2020–2021.

Sediment sample, fish gut samples and fish skin samples were gathered from control area, fishery ponds and one lake with the connection to the fishery ponds. Evaluation of the heavy metal concentrations was performed in the sediment samples. We detected contamination with the Co and Cr. The detection of the antibiotic residues revealed that no detectable amount of antibiotics was found in the sediments. Metagenome sequencing analysis showed the dominance of 10 main phylum of bacteria: Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, Nitrospirae, Verrucomicroba, Ignavibacteriae. The analysis of antibiotic resistance genes revealed that from 1 to 6 different resistance genes conferring resistance to up to 4 different classes of antibiotics are detected in the samples.

Main publications:

Lastauskienė, E., Valskys, V., Stankevičiūtė, J., Kalcienė, V., Gėgžna, V., Kavoliūnas, J., Ružauskas, M., Armalytė, J. The impact of intensive fish farming on pond sediment microbiome and antibiotic resistance gene composition. Frontiers in Veterinary Science. 2021, 8: 673756. doi: 10.3389/fvets.2021.673756.

Ruzauskas, M., Armalytė, J., Lastauskienė, E., Šiugždinienė, R., Klimienė, I., Mockeliūnas, R., Bartkienė, E. Microbial and antimicrobial resistance profiles of microbiota in common carps (Cyprinus carpio) from aquacultured and wild fish population. Animals. 2021, 11(4): 929. doi: 10.3390/ani11040929.

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. 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 - Dr 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.

Project under measure No. 09.3.3-LMT-K-712 “Development of students' abilities to carry out R&D activities” of the activity “Development of students' scientific competence through practical scientific activities” “Development of students' abilities through research during semesters”, Grant No. 09.3.3-LMT-K-712-22-0074, Project Functionality Research of Microbial Cutinases. Leader - Dr R. Gudiukaitė, participant - Microbiology MSc student A. Savickaitė. 03 November 2020–30 April 2021.

This project focuses on the synthetic cutinase obtained from Streptomyces scabie, its mutagenesis and characterization. In this project Streptomyces scabie cutinase was analysed and will be one of the model enzymes for PoEs degradation and further protein engineering experiments in the future.

Project under measure No. 09.3.3-LMT-K-712 “Development of students' abilities to carry out R&D activities” of the activity “Development of students' scientific competence through practical scientific activities”, Grant no. 09.3.3.-LMT-K-712-24-0002, project Activity Analysis of Recombinant Bacterial Cutinases and Application for Polyesters Degradation. Leader - Dr R. Gudiukaitė, participant - Microbiology MSc student A. Savickaitė. 01 July 2021–31 August 2021.

This project is focused on developing detection systems for polycaprolactones degradation and characterization of new cutinases produced by Arthrobacter sp. bacteria.

Project under measure No. 09.3.3-LMT-K-712 “Development of students' abilities to carry out R&D activities” of the activity “Development of students' scientific competence through practical scientific activities” “Development of students' abilities through research during semesters”, Grant No. 09.3.3-LMT-K-712-25-0030, project Research of Fused Biocatalysts Containing GDEst-95, GD-95 and Kut-SP Domains. Leader - Dr R. Gudiukaitė, participant - Microbiology MSc student A. Savickaitė. 01 Septemer 2021–31 March 2022.

This project is focused on synthesis improvement of recombinant Streptomyces scabie cutinase (Kut-SP) through it fusion with GD-95 lipase and GDEst-95 esterase.

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

Nature Research Centre (Lithuania)
Vilnius Gediminas Technical University (Lithuania)
State Research Institute Centre for Innovative Medicine (Lithuania)
Center for Physical Sciences and Technology (Lithuania)
National Public Health Laboratory (Lithuania)
Thompson Rivers University (Canada)
Latvias University (Latvia)
University of Milan (Italy)
University of Ljubljana (Slovenia)
National Institute of Chemical Physics and Biophysics (Estonia)
NTNU (Norway)
ŽŪK Baltmilk (Lithuania)
UAB RhoNano (Lithuania)
UAB Alresta (Lithuania)

OTHER RESEARCH ACTIVITIES

Prof. Dr L. Kalėdienė –

• member of Lithuania’s Genetically Modified Organisms Experts Committee.

Prof. Dr N. Kuisienė –

• member of the board of Lithuanian Microbiological Society.

Prof. Dr E. Lastauskienė -

• Head of FEMS education group of Lithuanian Microbiological Society.

Assist. Dr A. Gegeckas -

• FEMS delegate of Lithuanian Microbiological Society.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• National Science festival „Erdvėlaivis Žemė“ [“Spaceship Earth”] - International Microorganisms Day, whole day event for the education in microbiology.
• Eglė Lastauskienė – interview for LTV, “Science soup”, “Microplastic particles in the environment”; Visit to Molėtai gymnasium with the lecture: “Microbes – friends or enemies”
• Renata Gudiukaitė – contributed to the international conference The (Extra)ordinary COINS 2021; lecture for School of Young Biochemists; interview: https://naujienos.vu.lt/mikrobiologu-tyrimu-lauke-plika-akimi-nematomipasauliai/; project “Hygiene of smartphone”: https://www.lrt.lt/mediateka/irasas/2000157898/ismaniuju-higienos-tyrimas-privertesusirupinti-
  ant-telefono-gali-buti-daugiau-bakteriju-nei-ant-viesojo-tualeto-klozetodangcio
  https://www.lrytas.lt/it/laboratorija/2021/06/30/news/pirmasis-lietuvoje-ismaniujuhigienos-
  tyrimas-nustebino-bakteriju-ant-telefono-daugiau-nei-lifte-19926317/ https://www.youtube.com/watch?v=phBnbV3ZLDk; lectures for National Student Academy; presentation “Microbiology today: from enzyme engineering to bacteria found on the screen of smartphones” at VU Innovation Day; interview: https://www.15min.lt/verslas/naujiena/mokslas-it/mokslininke-istyre-pastomatu-pavirsius-perspeja-kad-didzioji-ju-dalis-perpildyta-mikrobais-1290-1601424
• Alisa Gricajeva – practical activities and lectures for gymnasium pupils; several comments and interview articles for the Lithuanian news portals.

DEPARTMENT OF NEUROBIOLOGY AND BIOPHYSICS

Saulėtekio al. 7, 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.
Assoc. professors: Dr R. Grikšienė, Dr V. Kisnierienė, Dr M. Mitkus, Dr G. Svirskis (part-time), Dr M. Korostenskaja (part-time).
Lecturers: Dr R. Buišas, Dr U. Neniškytė, V. Gėgžna, I. Lapeikaitė, E. Pipinis, V. Survilienė, V. Pupkis, D. Šimkutė.
Senior researcher: Dr M. Mitkus, Dr V. Kisnierienė, Dr U. Neniškytė
Researchers: Dr R. Guzulaitis, Dr A. Šoliūnas, Dr Avinash Parimisetty.
Research assistants: I. Lapeikaitė, A. Voicikas, Pipinis.
Doctoral students: D. Dankin, A. Šlėktaitė, E. Janėnaitė, A. Kalnaitytė, S. Mėlynytė, T. Paulauskas, V. Parčiauskaitė, V. Survilienė, A. Grabauskaitė, D. Dapkutė, J. Kišonas, G. Jarockytė, D. Šimkutė, P. Tarailis, L. Saveikytė, V. Rafanavičius, V. Pupkis, D. Gabrielaitis, R. Gaižauskaitė, W. Liang, M. Plečkaitis, E. Voronovič, I. Zelionkaitė, D. Pamedytytė, K. Šveistytė, U. Kuliešiūtė, G. Urbonaitė, K. Mickevičius, A. Shelest

RESEARCH INTERESTS

Functional organization and realization of information coding/processing and cognitive functions in human and animal nervous system and plant model
Behavioural pharmacology and animal models for psychiatric disorders, electrical signalling in plant and animal cells

RESEARCH PROJECTS CARRIED OUT IN 2021

Projects Supported by University Budget

Science Promotion Fund of Vilnius University. The Impact of Mothers’ Metabolic Status to Offspring Neurodevelopment: Identification of Early Behavioral Aberrations through Ultrasonic Vocalizations. Leader - U. Neniškytė. 2020–2021.

Recent studies revealed that elevated inflammatory state in the mother during the pregnancy leads to pathological activation of immune system in the brain of the offspring, thus causing disordered brain development resulting in long term deficits. A common condition that causes mother’s chronic inflammation is obesity together with metabolic syndrome and type II diabetes. This is a worrying in developed countries currently experiencing the epidemic of obesity, which is diagnosed in young patients as well. We hypothesize that under the influence of obesogenic diet mother’s metabolic status is misbalanced and can elevate inflammation both directly and through the diet-induced microbiome changes. Such inflammatory environment during pregnancy interferes with normal neurodevelopment of the offspring. The aim of this project is to apply the analysis of ultrasonic vocalizations to evaluate the behavior of very young mouse pups to assess their neurodevelopment. We evaluate the changes of vocalizations in the context of morphological and molecular changes in the brains of the offspring of mothers with diet-induced chronic inflammation.

Science Promotion Fund of Vilnius University. 40 Hz Auditory Steady-State Responses: Dependence on Stimulus Duration. Leader - E. Pipinis. 2020–2021.

Auditory steady-state responses (ASSR) are brain responses recorded with electroencephalography or magnetoencephalography when brain reacts to periodic constant frequency auditory stimulation. One of the main parameters that have received very limited attention is the stimulus duration for elicitation of 40Hz ASSRs. The potential effects of the stimulus duration cannot be neglected as existing data points to divergent effects observed in schizophrenia when stimuli of different duration are used. We aimed to compare 40Hz ASSRs to stimulation of different duration. It may be possible, that currently widely used stimulation settings are suboptimal to estimate the ability of the brain to generate and support synchronous activity.

Science Promotion Fund of Vilnius University. Diet-Microbiota-Nervous System: the Impact of Maternal High Fat Diet for Offspring Neurodevelopment. Leader - G. Urbonaite. 2021–2022.

Maternal metabolic abnormalities, induced by high fat diet, interfere with the neurodevelopment of the offspring both through through placental dysfunction and directly. The changes in maternal microbiota caused by a high fat diet can alter the levels of pro-inflammatory and anti-inflammatory cytokines that disturb the metabolic environment during pregnancy. Both microbial changes and inflammatory cytokines during pregnancy disrupt the development of the brain of the offspring, such as neuron network formation, synaptic plasticity, myelination, leading to aberrant cognitive function, social behavior, and memory formation. In collaboration with Dr. Agne Knyzeliene from the Preclinical Imaging Facility (University of Edinburgh, UK) and Dr. Guoda Laurinaviciute from the Department of Medicine (VU) we are researching the link between maternal obesity and neurodevelopmental pathologies by assessing behavioral aberrations, altered brain structure and connectivity, microglial inflammation and synaptic deficits in both male and female offspring to define their molecular and circuit mechanisms paving new paths for the development on novel interventions. First we investigate high fat diet-induced changes in microbiota both in mothers and in their offspring. Then we evaluate the impact of maternal high fat diet to the structure and connectivity of offspring brain as well as microglial inflammatory activation in brain regions of interest. Finally, we assess how maternal obesity affects the morphology of offspring retinas aiming to identify the hotspots in the central nervous system that can be used to evaluate neuroinflammation by non-invasive methods.

Science Promotion Fund of Vilnius University. Electrophysiological Manifestations of Subjective Perception of Resting Stat. 2021–2022. Leader - P. Tarailis.

The resting-state paradigm is frequently applied in electroencephalography (EEG) research; however, it is associated with the inability to control participants’ thoughts. We aim to develop a paradigm to modulate certain aspects of resting state and test effect on EEG.

Science Promotion Fund of Vilnius University. Temporary Principles of Coding of Stable Image (No. MSF-LMT-3). Participant from the Department - Dr A. Šoliūnas. 2019–2022.

National Research Projects

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. Project leader - Dr Aurelijus Burokas (VU BchI). (EU Funds Investment Action Program 2014–2020, Brain Attraction and Reintegration (SMART) Program). Participants from the Department Dr Rokas Buišas, Gintarė Urbonaitė. 2019–2023.

Project under measure No. 09.3.3-LMT-K-712 “Development of students' abilities to carry out R&D activities” of the activity “Development of students' scientific competence through practical scientific activities” (No. 09.3.3.-LMT-K-712-24-0038), Auditory Steady-State Response Dependence on Sex Hormones. Dr Robertas Guzulaitis, Neurobiology MSc student. 2021.

Auditory Steady-State response (ASSR) was recorded in awake mice. ASSR was continuously measured throughout estrous cycle and assessed during its different phases (proestrus, estrus, metestrus and diestrus).

Project under measure No. 09.3.3-LMT-K-712 “Development of students’ abilities to carry out R&D activities” of the activity “Development of students' scientific competence through practical scientific activities” “Development of students' abilities through research during semesters” No. 09.3.3.-LMT-K-712-25-0057. Sex Differences of Auditory Steady-State Response. Dr Robertas Guzulaitis. 2021–2022.

Auditory Steady-State response (ASSR) was measured in both male and female mice. Sex differences of ASSR were assessed.

Yeast Metabolic Engineering for the Biocatalytic Synthesis of Active Substances or Organic Compounds, Nr. 01.2.1-LVPA-K-856-01-0222. EU fund. Head of project - Prof. O. Rukšėnas. 2020–2023.

Developed protocol for pilot experiment, aiming to find out which dose of test compunds is the most efficient and whether there are any sex differences in response to test compounds.

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.

Research Council of Lithuania within the framework of National Programme “Welfare Society”. Determinants of Quality of Life in Lithuanian Students: Problematic Usage of the Internet and Neuropsychological Profile. Head of VU part - I. Griškova-Bulanova. 2020–2022.

Research Council of Lithuania. Screening for Treatment of Neurodegenerative Disorders (No. 01.2.2-LMT-K-718-03-0021). Head of project: Dr Evaldas Čiplys (GMC, BTI). SMART program. Participants: Dr Rokas Buišas, Prof. Valentina Vengelienė, Prof. Osvaldas Rukšėnas, Tomas Paulauskas, Ieva Pocevičiūtė, Lina Saveikytė, Dovydas Gabrielaitis. 2020–2023.

Research Council of Lithuania. Biomarkers of the Gut Microbiota in Autistic Spectrum Disorders (No. 01.2.2-LMT-K-718- -03-0099). Head of project - Dr Aurelijus Burokas (GMC, BChI) („Žarnyno mikrobiotos žymenys, sergant autizmo spektro ligomis “) SMART program. Participant Dr Rokas Buišas. 2020–2023.

Center for Genetic Modeling of Animals Nr. 01.2.2-CPVA-K-703-03-0032. Head of project - Dr Daiva Baltriukienė. Participants: Prof. Osvaldas Rukšėnas, Prof. Valentina Vengelienė. 2020–2023.

Research Council of Lithuania. Mechanotransductive L-Type Calcium Channels as a Therapeauticla Target Affecting Metabolic Processes in Osteortritic Cartilage, code 09.3.3-LMT-K-712-01-0157. Head of project - Dr Ali Mubasheri (Centre for Innovative Medicine), Vilnius. Participant from VU Dr Aidas Alaburda. 2017–2021.

Self-assembling Phage Proteins for Targeted Nanomedicine (P-SEN-20-34). Participants: Lina Saveikytė, Dovydas Gabrielaitis. 2020–2021.

EMBL Partnership Institute (01.2.2-CPVA-V-716-01-0001). Participant: U. Neniškytė. 2021–2023.

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.

International Research Projects

Marie Sklodowska Curie Actions Individual Fellowship LIPSYNING. Project leader - Dr Urtė Neniškytė. 2018–2021.

The development of the nervous system is associated with the generation of excess neuronal synapses that is followed by their tightly controlled removal, a process known as synaptic pruning. In the primate cortex, for example, 70% of connections are selectively lost during circuit refinement within the first six months of life. Brain imaging and post-mortem studies suggest that insufficient or excessive synaptic pruning might be the cause of deficits in neurodevelopmental disorders such as autism and schizophrenia. The aim of this project is to define the role of PtdSer in synapse-microglia interaction during development and to assess the morphological, circuit maturation and behavioural effects of impaired PtdSer exposure in phospholipid scramblase-deficient brains. We propose to use novel custom-made tool to observe PtdSer exposure without interfering with PtdSer-dependent cellular interactions and mouse models with disrupted PtdSer exposure to thoroughly investigate the role of PtdSer in neural circuit maturation in mice at different functional levels. Morphological analysis of the brains of mice with impared PtdSer exposure revealed changes in scramblase-deficient neurons both in pre-synaptic and post-synaptic compartment, including increased spine density, enlarged axonal boutons, and increased density of vesicular markers. We will further used these mice to demonstrate how scramblase-deficiency changes local PtdSer exposure on synapses, affects synapse-microglia interactions and described electrophysiological phenotype observed in these mice.

Lithuania - Poland research project. Long-Distance Electrical Signaling Systems in Plants – Adaptation to the Change from Water to Terrestrial Environment. LT leader Dr - Vilma Kisnierienė. 2018–2021.

Low-cost plant-based platform to examine the effectiveness of different drugs on two pore channels (SV/TPC) and other transport systems shaping the action potentials in plants was tested. The impact of inhibitors of human two-pore channels (TPC1 and TPC2) verapamil, tetrandrine, and NED-19 on action potentials (APs) and vacuolar channel activity was examined in the aquatic characean algae Nitellopsis obtusa. The results indicate effect of TPC channel blockers on Ca2+ -permeable channels governing plant excitation.

Research Council of Lithuania and Ministry of Science and Technology Taiwan. Brain-Computer Music Interfacing for Embodied Musical Interaction LLT-19-3. Partners: National Sun Yat-sen University (Taiwan) and Jāzeps Vītols Latvian Academy of Music (Latvia). Head of VU part I. Griškova-Bulanova. 2019–2021.

The estimation of EEG markers that differ between several emotional playing conditions was performed. The EEG markers are better suited to differentiated areousal-related aspects of emotional music playing. 

Research Council of Lithuania within the framework of collaboration with Japan. Individual Gamma Frequency-Based Neurofeedback: Development and Implementation Study P-LJB-20-4. Project leader - I. Griškova-Bulanova. 2020–2022.

In this project the neurofeedback system based on individual gamma frequency is developed ant tested in a sample of yound subjects, and results are associated with individual cognitive abilities.

Polish National Science Centre. Steady-state EEG Response to Gamma-range Auditory Stimulation: Effects of Brain Arousal, no. 2018/31/b/hs6/03920. Participants from VU: I. Griskova-Bulanova, E. Pipinis. 2020–2022.

Charles University Grant Agency (GA UK). Anti-psychotic-like Potential of Halogenated Cannabidiol (CBD) Derivatives in Animal Model of Psychosis: an EEG Study. Participant from VU - I. Griskova-Bulanova. 2021–2023.

Marie Sklodowska Curie Actions Individual Fellowship. Dr Urtė Neniškytė, Dr Avinash Parimisetty. 2020–2022.

Effective neuron-microglial communication is a prerequisite to achieve the final connectome. It is mediated by both the formation of new synapses and selective removal of unnecessary connections through synaptic pruning. Recent evidences suggest that superfluous connections are eliminated by microglia. Almost 70% of the connections are lost in a primate cortex within six months of life. But what drives this selective elimination of so many synapses is a million-euro question. Identifying neuronal signals that differentiate weak synapses from the strong ones is an emerging frontier in cellular neuroscience. Several eat-me signals in synaptic pruning have been identified, but spare-me signals that limit phagocytic elimination of synapses are yet to be explored. Sialic acids on neuronal glycocalyx acts as spare-me signal and prevents microglial phagocytosis through Siglec receptors. Aberrant regulation of sialic acid caused neuronal loss and embryonic lethality. It is also becoming evident that sialic acid plays a key role in neurodevelopment, but the cellular and molecular mechanisms by which it regulates neurodevelopment is yet to be explored. This makes sialic acid an ideal candidate to evaluate its role in neurodevelopment. Hence, we aim to interrogate whether sialidases, glycocalyx recognizing proteins are developmentally regulated and also to define sialic acid’s role in synaptic pruning during neurodevelopment. We propose to implement gene, protein expression and metabolic profiling studies to investigate whether sialidases and glycocalyx recognizing proteins are developmentally regulated. Also, we will use fluorescent azido sugars in ex vivo cultures to visualise how sialic acid regulates synaptic pruning during neurodevelopment using superresolution STED microscopy. This paves a path to identify cellular and molecular mechanisms by which glycocalyx composition defines neuron-microglia interactions and thus circuit refinement through synaptic pruning.

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.

IBRO-PERC InEurope Short Stay Grant Gliocobiology of Glioblastoma Multiforme. Project leader - U. Kuliešiūtė. 2020–2021.

The project was aimed at transferring the knowledge of maintaining human organotypic brain cultures from surgically resected cortical tissue samples. U. Kuliesiute has learned relevant methodology at the University of Freiburg (Germany) and has subsequently successfully established the technique at Vilnius University.

IBRO-PERC InEurope Short Stay Grant Evaluation of Electrical Brain Activity of the Resting State:
Relation with Subjective Experience. Project leader P. Tarailis. 2021.

We aimed to estimate associations between subjective experiences and resting-state microstates of EEG. Several associations between Comfort, Self and Somatic Awareness domains and temporal properties of neuroelectric microstates were revealed. Our study indicates the relevance of assessments of spontaneous thought occurring during the resting-state for the understanding of the intrinsic brain activity reflected in microstates.

Alliance4Life_ACTIONS, H2020 project. Participant from VU prof. O. Rukšėnas. 2021–2023.

International Research Networks

Lithuanian representative for COST action The Neural Architecture of Consciousness. Dr I. Griškova-Bulanova, E. Pipinis, P. Tarailis. 2019–2023.

Lithuanian representative for COST action European network for problematic internet usage. Dr I. Griškova-Bulanova, D. Šimkutė. 2018–2022.

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

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

OTHER RESEARCH ACTIVITIES

• Prof. A. Alaburda –
  board member of the Lithuanian Neurosciences Association;
• board member of Lithuanian Biophysical Society;
• European Commission expert.

Dr R. Buišas –

• member of the Lithuanian Neurosciences Association.

Dr I. Griškova-Bulanova –

• Vice-president of the Lithuanian Neurosciences Association;
• board member of International Brain Research Organization (IBRO);
• member of the DANA Alliance for Brain Initiatives;
• member of European Dana Alliance for the Brain;
• member of Australasian Society for Psychophysiology;
• member of the International Society for Brain Electromagnetic Topography;
• Scientific Committee member of 27^th European Congress of Psychiatry, Warsaw, Poland.
• Scientific Committee member of FENS Regional meeting 2021.

Assoc. Prof. R. Grikšienė –

• member of the Lithuanian Neurosciences Association;
• member of the International Society for Brain Electromagnetic Topography;
• Organized symposium „Female brain as a target of sex hormones“ in the virtual FENS Regional Meeting, 25–27 August, 2021.
• external referee and member of the defense committee. University of Salzburg (Paris-Lodron-Universität Salzburg), Austria. Phd student TiAnni Harris, Title: Sex differences in Navigation: A multi-method approach. 2021.

Assoc. Prof. V. Kisnierienė –

• member of the Lithuanian Biophysical society;
• member of the Lithuanian Neurosciences Association;
• member of the European Biophysical Societies’ Association (EBSA).

Dr I. Lapeikaitė –

• member of the Lithuanian Neurosciences Association;
• member of the Lithuanian Biophysical Society;
• member of the European Biophysical Societies’ Association (EBSA).

V. Pupkis –

• member of the Lithuanian Neurosciences Association;
• member of the Lithuanian Biophysical Society;
• member of the European Biophysical Societies’ Association (EBSA).

Dr M. Mitkus –

• member of the Lithuanian Neurosciences Association;
• member of European Ornithologists’ Union;
• member of International Society for Neuroethology;
• member of Lithuanian Ornithological Society;
• Lithuanian representative in the Committee on Animals in Research (CARE) by Federation of European Neuroscience Societies (FENS).

Prof. O. Rukšėnas –

• President of the Lithuanian Neurosciences Association;
• board member of the Baltic Laboratory Animal Science Association (Balt-LASA);
• Vice-president of the Lithuanian Laboratory Animal Science Association (Lith-LASA)
• editorial board member of the journal Laboratorinė medicina (Laboratory Medicine);
• editorial board member of the journal Current Issues of Mass Communication;
• advisory editorial board member of the journal Sensory Systems;
• European Commission expert;
• member of Federation of European Neuroscience Societies (FENS) governing board;
• organizing committee and scientific committee member of FENS Regional meeting 2021;
• member of the DANA Alliance for Brain Initiatives;
• member of European Dana Alliance for the Brain.

Dr A. Šoliūnas –

• member of the Lithuanian Neurosciences Association.

Prof. V. Vengelienė –

• member of Partnership for Assessment and Accreditation of Scientific Practice (PAASP);
• member of Federation of European Neuroscience Societies (FENS);
• member of Lithuanian Neuroscience Association (LNA);
• organizer and chair for the Symposium “Advances in the treatment of alcohol use disorder”, The FENS Regional Meeting 2021, Krakow, Polan
• Associate editor for Frontiers in Pharmacology, Translational Pharmacology.

Dr U. Neniškytė –

• member of the Young IBRO Committee;
• member of the Board of Lithuanian Neurosciences Association;
• member of the Biochemical Society;
• member of Lithuanian Biochemical Society;
• member of Society for Neuroscience;
• member of editorial board of the journal Frontiers in Cellular Neuroscience.

Dr A. Voickas –

• member of the Lithuanian Neurosciences Association.

Dr R. Guzulaitis –

• member of the Lithuanian Neurosciences Association
• member of Federation of European Neuroscience Societies (FENS);
• member of Society for Neuroscience (SfN).

Dr E. Pipinis –

• member of the Lithuanian Neurosciences Association.

MOST IMPORTANT CASES OF THE PARTICIPATION OF RESEARCHERS IN WORKING GROUPS OR COMMISSIONS SET UP BY STATE AUTHORITIES, STATE AND MUNICIPAL INSTITUTIONS AND ORGANISATIONS, AND BUSINESS ENTITIES

• Prof. O. Rukšėnas – expert for European Research Council (ERC) (Marie Skłodowska-Curie Actions (MSCA).
• Prof. A. Alaburda – national expert for European Research Council (ERC) (Future and Emerging Technologies (FET) and Marie Skłodowska-Curie Actions (MSCA).
• Dr U. Neniškytė - Board member of the Research Council of Lithuania.
• Dr I. Griskova-Bulanova – expert of Medical Research Council (UK).

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Dr. U. Neniškytė: two appearances on a TV program for secondary school pupils “Interesting lectures”; appearances on a TV program “The School of Creativity”; a lecture for school teachers at the training program organized by “The School of Creativity”; appearance on a TV program “Radical Curiosity”; podcasts with Justas Tertelis and Ugne Karalaite; a meeting hosted by European Commission at the public library of Lazdijai; meetings with high school teachers, pupils and their parents; autism month presentation on women autism at the conference organized by “Lietaus vaikai”.
• Dr. I. Griskova-Bulanova: two radio appearances on LRT Klasika, lecture at the public conference “Psychosis in Modern Society: an Interdisciplinary Approach”
  https://www.lrt.lt/mediateka/irasas/2000180734/teramuzika-koki-poveiki-muzika-daro-musu-smegenims
• Assoc. Prof. Grikšienė R.: Science popularizing fproject on Facebook platform “Mokslininkai tavo kambaryje”, multiple interviews on the topic of hormonal contraception (15min.lt, mieloji.lt); Radio appearance on Žinių radijo, appearance on TV “Radikalus smalsumas”:
  https://www.facebook.com/mokslastau;
  https://www.15min.lt/gyvenimas/naujiena/sveikata/lietuvoje-tiriama-kaip-hormonine-kontracepcija-veikia-smegenis-slopina-ne-tik-lytinius-hormonus-1028-1558008?
  https://mieloji.lt/moters-kunas-smegenys-hormonai-kaip-veikia-si-grandine/
• Prof. Vengelienė V.: appearances on TV (LRT.lt, delfi.lt) on the topic of alcohol effects on the brain and addiction
  https://www.lrt.lt/naujienos/mokslas-ir-it/11/1437682/atsako-mokslininkai-kodel-padauginus-alkoholio-skauda-galva-ir-kur-dingsta-atmintis
  https://www.delfi.lt/video/laidos/radikalus-smalsumas/radikalus-smalsumas-neuromokslininke-vengeliene-apie-tai-kodel-priklausomybe-alkoholiui-vis-dar-nepagydoma.d?id=87214221
• Dr M. Mitkus: radio appearance on Extra FM, open virtual lecture about bird vision and research organized by Lithuanian Ornithological Society
• V. Kisnierienė: Video interview on media channel Žinių radijas about sensory systems in plants, lecture on Aluminium toxicity.
  https://www.ziniuradijas.lt/laidos/ateitis-priklauso-tiems/augalu-reakcijos-i-garsa-kvapa-ir-sviesa-ar-augalai-turi-prota?video=1
• Prof. O. Rukšėnas: multiple lecture on neuroscience for National academy of schoolchildren, Busines leaders club, Lithuanian Biotechnology Association, Darbuotojų saugos ir sveikatos Vadovų klubas. Appearance on LRT „Sindromas“, „Smalsumo genas“, Delfi TV program Sentience, National radio program „Paraštės“
  https://www.lrt.lt/mediateka/irasas/2000175172/sindromas-priklausomybes-sindromo-neurobiologija-kaip-smegenyse-formuojasi-priklausomybe
  https://www.youtube.com/watch?v=GLnYdakh3LU.

BEST REPORTS DELIVERED AT CONFERENCES ABROAD

• Zelionkaitė, R. Gaižauskaitė, S. Upadhyaya, ‪H. Uusberg, A. Uusberg, B. Derntl, R. Grikšienė. Women’s ability to regulate emotions: relationship with personality, sex steroids and hormonal contraceptives. 46th Annual Conference Psychology and the Brain. Tübingen (virtual), 2021‬‬‬‬. ‬‬‬‬
• V. Vengeliene. Research quality from the perspective of academia, The FENS Regional Meeting 2021, Krakow, Poland.

MOST IMPORTANT NATIONAL AND INTERNATIONAL AWARDS RECEIVED FOR R&D ACTIVITIES

• Dr M. Mitkus – fellowship for academic work in Lithuania for researchers with a PhD diploma from a university abroad; Marius Jakulis Jason foundation.
• Dr Robertas Guzulaitis - IBRO Return Home Fellowship (2020–2022); MJJ (Marius Jakulis Jason) fellowship (2021–2023).

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES

• Prof. Valentina Vengelienė - Consultant for PAASP GmbH (Partnership for Assessment and Accreditation of Scientific Practice), Heidelberg, Germany.

DEPARTMENT OF ZOOLOGY

Saulėtekio al. 7, LT-10257 Vilnius
Tel. 223 4430
E-mail: .
Head – Prof. Dr Virginija Podėnienė

STAFF

Professors: Dr V. Podėnienė, Dr S. Podėnas, Dr K. Arbačiauskas (part-time).
Associate professors: Dr E. Bukelskis, Dr J. Turčinavičienė, Dr V. Sruoga (part-time), Dr A. Petrašiūnas.
Assistants: Dr G. Skujienė, Dr R. Aukštikalnienė.
Junior assistant: A. Lekoveckaite.
Lecturers: Dr M. Biteniekytė, S. Skuja.
Senior researchers: Dr J. Havelka, Dr V. Sruoga (part-time). Dr. M. F. Torres Jimenez.
Junior researcher: I. Gorban.
Doctoral students: A. Lekoveckaite, L. Stasiukynas. G. Mockevičienė, B. Masoit.

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)

RESEARCH PROJECTS CARRIED OUT IN 2020

Projects Supported by University Budget

Animal Biodiversity, Ecology and Population Structure. Prof. Dr V. Podėnienė, Prof. Dr S. Podėnas. 2018–2022.

The relationships between aphid species of the family Adelgidae (Hemiptera: Adelgoidea) and their endosymbiotic bacteria were determined. The study of ecological and mitochondrial COI diversity of Pauesia species (Hymenoptera: Braconidae: Aphidiinae) attacking Eulachnini aphids (Hemiptera: Aphididae: Lachninae) on coniferous plants in Lithuania was accomplished. Initial investigation of the invasive species American Eastern cherry fruit flies Rhagoletis cingulata was performed. Taxonomic studies of the Korean Tipula (Vestiplex) crane flies (Diptera: Tipulidae) and East Palaearctic Elliptera crane flies (Diptera: Limoniidae) were performed. Diversity of oak canopy insects is investigated. New genus of crane flies (Diptera: Limoniidae) from Burmese amber is described. Analysis of the biodiversity of spiders and dipterous insects of Lithuania continued. Investigation of the control methods of the invasive slug species Arion vulgaris continued. Monitoring of fish communities in Lithuanian lakes was continued. Monitoring of black storks, birds of prey and owls in forests of northern, eastern and southern Lithuania continued. Taxonomic studies of Elachsitinae (Lepidoptera, Elachistidae) of China and Nepal performed.

Main publications:

Havelka, J., Kaliuzhna, M., Danilov, J., Rakauskas, R. Pauesia species (Hymenoptera: Braconidae: Aphidiinae) attacking Eulachnini aphids (Hemiptera: Aphididae: Lachninae) on coniferous plants in Lithuania: ecological and mitochondrial COI diversity. Organisms Diversity & Evolution. 2021, 21 (3): 561–573. https://doi.org/10.1007/s13127-021-00512-0.

Sruoga, V. A new species of Elachista Treitschke, 1833 (Lepidoptera, Elachistidae, Elachistinae) from China, with identification keys to the Asian species of the Elachista saccharella species group. ZooKeys. 2021, 1068: 41–50. doi: 10.3897/zookeys.1068.70807.

Podeniene, V., Podenas, S., Park, S.-J., Kim, A.-Y., Kim, J.A., Gelhaus, J. K. Review of East Palaearctic Elliptera (Diptera, Limoniidae) immatures with description of a new species. European Journal of Taxonomy. 2021, 735: 110–132. https://doi.org/10.5852/ejt.2021.735.1245.

National Research Projects

Inventory and Research of Molluscs in the Whole Territory of the Curonian Spit National Park, No. (1.57) 15600-INS-49//BS-13(1.36))/21. Dr G. Skujienė, V. Kuznecova, students B. Jukonis, S. Skuja. 2021.

The Curonian Spit formed approximately 5,000 years ago. Sandy soils of this narrow peninsula are very young, which is conditioned by relatively recent formation of the area and still ongoing eolian processes. The main task of this project is to compare diversity of mollusc of peninsula to the continental mollusc diversity.

Development of an Action Plan for the Regulation of the Population Abundance of the Invasive Species (Arion lusitanicus) (No.1.55)15600-INS-56). Dr G. Skujienė, M. Adomaitis, S. Juzėnas, student A. Jucevičiūtė. 2021.

The invasive species Arion vulgaris first time in Lithuania was detected in environs of Kaunas city in 2008. In twelve years, it has spread into the whole territory of Lithuania and now is known already from 164 localities. In some settlements and even in some nature reserves the abundance of slugs has reached up to 80–120 ind./m2. Control strategies for this invasive species in settlements with high density of slugs was prepared based on our results and data from other scientists.

International Research Projects

National Institute of Biological Resources (South Korea). Korean Fauna (No NIBR2021021111). Prof. S. Podėnas, Prof. V. Podėnienė. Assist. R. Aukštikalnienė.

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.

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. Dr G. Skujienė, S. Skuja, Dr E. Budrys, Dr M. Biteniekytė, V. Kuznecova, students J. J. Valiulis, T. Laurinaitis. 2021–2025.

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)

OTHER RESCEARCH ACTIVITIES

Prof. V. Podėnienė –

• assoc. researcher of the Academy of Natural Sciences of Drexel University, Philadelphia, PA (USA);
• expert of Lithuanian Business Support Agency.

Prof. S. Podėnas –

• 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. E. Bukelskis –

• chairman of the Fisheries Council of the Republic of Lithuania of the Ministers of Agriculture and Environment of the Republic of Lithuania;
• member of the International Council for Game and Wildlife Conservation (CIC);
• member of the Council of the Lithuanian Hydrobiological Society.

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 Supervision Committee of Genetically Modified Organisms, http://gmo.am.lt/page?page=itemList&entity=biosafetyExpert;
• 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.

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.

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES

• 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.
• 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.
• 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
• 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

• Prof. assoc. A. Petrašiūnas – interviews for LRT programmes; lecture “When will it be too hot for bumblebees in Lithuania?” etc.
• Prof. assoc. A. Petrašiūnas – video-interview for LRT Plus about Forensic entomology https://www.lrt.lt/mediateka/irasas/2000183619/smalsumo-genas-kur-slypi-augalu-sekmes-saknys-ir-kaip-vabzdziai-padeda-kriminalistams
• Prof. V. Podėnienė – video-interview for LNK program „Good evening, Lithuania“ biting insects - https://www.facebook.com/watch/?v=837350283833452
• Prof. V. Podėnienė – audio-interview for LRT program “Ryto garsai” about new Red Book of Lithuania and problems of biodiversity protection, https://www.lrt.lt/mediateka/irasas/2000172653/ryto-garsai-ar-lietuva-pasiruosusi-galimoms-provokacijoms-prasidedanciu-rusijos-ir-baltarusijos-kariniu-pratybu-zapad-metu
• Dr G. Skujienė –In 2021, the Curonian Spit announced as a Year of Molluscs, and related events: video- interview and its dissemination on websites and in the press, cycle of lectures; for example, https://www.facebook.com/kursiu.parkas/posts/3993288930720178/
• Dr G. Skujienė – public consultations on the control of invasive slugs, https://www.birzai.lt/doclib/qknop9omtfe7jacxwmxmq5gnch713utc.

Museum of Zoology

• Accredited for international volunteering 2021–2027. Quality label application No. 2020-1-LT02-ESC52-007347 by The European Solidarity Corps. Funding is provided in the form of grants to organizations through call for proposals.
• Taking part in annual National Science festival „Erdvėlaivis Žemė“ [“Spaceship Earth”]. 16 September 2021: I-II-III parts “Mysterious Hunters” Dr G. Skujienė, Dr M.Biteniekytė, M. Adomaitis, S. Skuja, V. Kuznecova.
• Cooperation agreement and acceptance of the scientific butterfly collection from the new patron Giedrius Švitra.
• Acceptance of the scientific sea shells collection from the new patron Dr I. Palanevienė.