Life Sciences Center

7 Saulėtekio av., LT-10257 Vilnius
Tel. 223 4435
E-mail 
Director – Dr. Gintaras Valinčius

 

 

 

STAFF

89 teachers (incl. 68 holding research degree), 239 research fellows (incl. 152 holding research degree), 138 doctoral students.

Institute of Biotechnology
Institute of Biochemistry
Institute of Biosciences

INSTITUTE OF BIOTECHNOLOGY

7 Saulėtekio Ave, 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 of Medical Epigenomics

RESEARCH AREAS

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

DOCTORAL DISSERTATIONS DEFENDED IN 2020

Stasė Gasiulė. Functional analysis of canonical and mirtronic miRNAs in thoracic ascending aortic aneurysm tissues and digestive system tumours.
Juozas Nainys. High-throughput single-cell sequencing and analysis.
Inga Pečiulienė. Pre-mRNA splicing associated with oncological diseases: a study of splicing factors and hypoxic microenvironment.
Tomas Šneideris. Towards understanding amyloid fibril formation and self-replication.

 

DEPARTMENT OF PROTEIN - DNA INTERACTIONS

7 Saulėtekio Ave, 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.
Researchers: Dr T. Šinkūnas, Dr T. Karvelis, Dr P. Toliušis, Dr A. Merkys, Dr E. Zagorskaitė. Dr M. Skapas, Dr M. Tutkus.
Teaching assistants: I. Songailienė. A. Vaitkus, A. Grybauskas.
Other researchers and technical staff: A. Tunevič, K. Budrė, G. Druteika, J. Matulevič Ilinykh.
Doctoral students: G. Drabavičius, G. Bigelytė, E. Golovinas, I. Mogila, T Urbaitis, D. Smalakytė, D. Tuminauskaitė, J. Juozapaitis.

RESEARCH INTERESTS

Structural and molecular mechanisms of restriction enzymes
Bacterial antivirus defence systems
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 2020

Smalakyte, D., Kazlauskiene, M., Havelund, J. F. , Rukšėnaitė, A., Rimaite, A., Tamulaitiene, G., Færgeman, N. J., Tamulaitis, G., and Siksnys, V. Type III-A CRISPR-associated protein Csm6 degrades cyclic hexa-adenylate activator using both CARF and HEPN domains. Nucleic Acids Research gkaa634. 2020

Songailiene, I., Juozapaitis, J., Tamulaitiene, G., Ruksenaite, A., Šulčius, S., Sasnauskas, G., Venclovas, Č., and Siksnys, V. HEPN-MNT toxin-antitoxin system: The HEPN ribonuclease is neutralized by OligoAMPylation. Molecular Cell. 2020, 80: 955–970.e7.

Makarova, K.S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., Brouns, S. J. J., Charpentier, E., Cheng, D., Haft, D. H., Horvath, P., et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 2020,18: 67–83.

Karvelis, T., Bigelyte, G., Young, J. K., Hou, Z., Zedaveinyte, R., Budre, K., Paulraj, S., Djukanovic, V., Gasior, S., Silanskas, A., et al. PAM recognition by miniature CRISPR–Cas12f nucleases triggers programmable double-stranded DNA target cleavage. Nucleic Acids Research. 2020, 48: 5016–5023.

Tuminauskaite, D., Norkunaite, D., Fiodorovaite, M., Tumas, S., Songailiene, I., Tamulaitiene, G. and Sinkunas, T. (). DNA interference is controlled by R-loop length in a type I-F1 CRISPR-Cas system. BMC Biol. 2020, 18: 65.

PATENTS 2020

Granted:

Šikšnys V., Gasiūnas G., Karvelis T. RNA-directed DNA cleavage by the Cas9-crRNA complex. US10844378B2. Publication date: 24 November 2020.

Applications:

Šikšnys V., Kazlauskienė M., Tamulaitis G., Kostiuk G. Production of cyclic adenylates and their use as allosteric regulators. EP3630966A1. Publication date: 08 April 2020.

RESEARCH PROJECTS CARRIED OUT IN 2020

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. Research and Practical Applications of a Type I-F CRISPR-Cas System (No. S-MIP-17-47). Dr G. Tamulaitienė. 2017–2020.

Prokaryotes are the most abundant cellular life form that is able not only to adapt to a variety of the physical conditions of life but also to the biological predators, called bacteriophages. To cope with the rapidly evolving phages, prokaryotes use various anti-virus systems. One of these is recently discovered defence system called CRISPR-Cas. According to composition of CRISPR-Cas effector complex and its mechanism these systems are classified into 6 types, which are then divided into subtypes. Elucidation of the molecular machinery of type II effector complex Cas9-sgRNR has enabled to adapt it as a powerful molecular tool, which allows precise editing of target DNA sequences. A practical potential of other CRISPR-Cas is not fully disclosed yet and requires studies of their molecular mechanisms. The object of the project is type I-F CRISPR-Cas from A. actinomycetemcomitans (Aa) bacteria that cause parodontitis. Effector complex of type I systems consist of 2 separate components: Cascade complex and Cas3 protein. Investigations of type I-E effector complex revealed that Cascade recognizes foreign DNA and binds it, and it is a signal to Cas3, which destroys DNA intruder. The composition of Cascade complex is slightly different between different subtypes of type I, and their properties should also vary. In case of type I-F system, details of the molecular mechanism of DNA degradation has not been studied yet; therefore, using in vivo and in vitro biochemical methods, we will seek to determine how the Cascade recognizes foreign DNA and how Cas3 destroys it. Furthermore, we will investigate the effect of DNA modifications on the system activity. These studies could help to find/create bacteriophages resistant to our system that could be used as a preventive measure against parodontitis. Using X-ray crystallography, we will try to figure out the mechanism of the CRISPR-Cas system at atomic level. Finally, we aim to add this system to the CRISPR-Cas molecular toolbox.

Research Council of Lithuania. Surface Nano-Structures for Mechanistic Studies of DNA - Protein Interaction at the Single-Molecule Level  (No. S-MIP-17-59). Dr E. Manakova. 2017–2020.

Protein-nucleic acids (NA) interactions are playing a crucial role in the regulation of many cellular processes. Modern single-molecule fluorescence microscopy (SMFM) experimental approaches allow studying the real-time behaviour of individual protein molecules during interaction with NA. However, these methods are technically challenging and not always successful. Also, due to labelling or surface effects, often it is challenging to collect enough data to prove statistical significance of effects measured during SM experiments. “DNA curtains” is the next step in the development of the high-throughput SM methods. “DNA curtains” are glass surface immobilized and in a predefined way distributed NA fragments, which are aligned horizontally with respect to the surface using the flow of the buffer solution. The method allows us to avoid complicated procedure of protein labelling - it is sufficient to conjugate it with the quantum dot (QD). Such a system allows studying many individual protein-NA interactions in a massively parallel manner. Potential of this new method for studying of protein - NA interactions is huge and therefore it is currently under intensive development. The main goal of the project is to create the novel platform for protein-NA interaction studies using SMFM. The platform is such that NA fragments are immobilized onto the glass surface, prepared by the proposed method, in an NA fragment density and arrangement controllable way. It also allows direct monitoring of interaction of the labelled protein with the immobilized NA fragments using an SMFM. Initially, we aim to test our platform with the relatively well characterized NA interacting proteins and later on to apply it for studies of less characterized objects. We expect that in the near future our developed platform will be relevant and broadly applied in other research groups because it will allow revealing information (target search, interaction constants, etc.) on various protein - NA interactions, which is inaccessible or difficult to access in any other way.

Research Council of Lithuania. Structural and Functional Studies of Prokaryotic Argonaute Proteins (No. S-MIP-17-61). Dr M. Zaremba. 2017–2020.

Argonaute proteins (Agos) are widespread in all three domains of life (bacteria, archaea and eukaryotes). In eukaryotic organisms, Agos are the functional core of the RNA-silencing machinery, which is critical for regulation of gene expression, silencing of mobile genome elements and defence against viruses. Defects in RNA interference (RNAi) machinery are associated with numerous major human pathologies, from metabolic disorders and viral infections to carcinogenesis. RNAi also has a broad therapeutic potential for various human diseases, such as infections and cancers. Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic Agos, the biological function of bacterial and archaeal Agos remains elusive. The diversity of prokaryotic Agos structural organization and genomic context suggests a wide spectrum of functions and a variety of action mechanisms. For example, all eukaryotic Agos contain a PAZ domain responsible for binding of the 3’ end of the guide RNA strand, while bacterial and eukaryotic Agos are divided into two groups: with and without a PAZ domain. It is believed that most prokaryotic Agos containing a PAZ domain are active nucleases. In contrast, most PAZ-free Agos are found in operons with genes of putative nucleases or other effector proteins. It is therefore proposed that PAZ-free Agos might form functional complexes with these proteins. In the proposed project we plan to elucidate the mechanism of action for an archaeal PAZ-free Argonaute protein. To this end we will employ a combination of biochemical experiments, single molecule FRET techniques and X-ray crystallography.

Research Council of Lithuania. Adaptation Mechanism in Class 2 CRISPR-Cas Systems (S-MIP-19-32). 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 defence 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. Studies of Genome Editing Tools at the Single-Molecule Level (No. S-MIP-20-55). Dr M. Tutkus. 2020–2020.

Protein-nucleic acids interactions are playing a crucial role in the regulation of many cellular processes. Modern single-molecule fluorescence microscopy (SMFM) experimental approaches allow studying the behaviour of individual protein molecules during interaction with nucleic acids in real-time. Despite technical challenges, they allow accessing unique insights that are obscured in ensemble studies.
The main goal of this project is to investigate the targeting mechanisms utilized by a diverse family of genome editing tools called CRISPR-Cas (clustered regularly interspaced short palindromic repeats) system that evolved to target invading foreign DNA (i.e. phages, plasmids) at the SM level. Broad and continuously increasing interest in nucleic acids recognition mechanisms of these systems could be rationalized on the potential to adapt CRISPR-Cas for genome editing. We aim to perform in vitro experiments using our developed “soft” DNA Curtains platform, SMFM in living cells (in vivo), and other complementary biochemical ensemble methods of three different Cas protein types.
DNA Curtains is the most recent high-throughput SM platform – arrays of surface-immobilized NA fragments, which are aligned along the surface using the shear force of the buffer flow. The platform allows avoiding the complicated procedure of protein labelling – conjugation with a functionalized quantum dot is often sufficient. Also, it allows studying individual protein-NA interactions in a massively parallel manner. Our recent publication on “soft” DNA Curtains development brought attention from a broad field of researchers.
We expect that the proposed project will bring much attention due to the study objects of broad interest and applied novel methods. Proposed experiments can bring new insights into protein-DNA interaction mechanisms of Cas effectors at the single-molecule level that could result in high-impact publications.

International Research Projects

H2020 Framework programme: Sonic Drilling Coupled with Automated Mineralogy and Chemistry On-Line-On-Mine-Real-Time (SOLSA) (No. 689868). Dr S. Gražulis. 2016–2020.

The main goal of the SOLSA project is to create a novel system for identification of drill core characterisation using combined XRD, XRD and spectroscopic techniques. One of the main components of this new system are open databases of experimental structural data. The COD database will provide the collected open access descriptions of crystal structures that will enable rapid identification of sample composition in real time using the X-ray powder diffraction technique. The COD will also collect, preserve and disseminate data that will be determined by the SOLSA project. This data will be useful later for mineralogy, crystallography, geology and palaeontology, to name just a few areas of application. The SOLSA data will be unique since it will, for the first time, record comprehensive geospatial, stratigraphic, crystallographic and spectral information about the sample.

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

7 Saulėtekio Ave, 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, Dr V. Masevičius.
Senior researchers: Dr E. Kriukienė, Dr V. Stankevičius.
Researchers: Dr M. Tomkuvienė, Dr A. Osipenko, Dr R. Rakauskaitė, Dr S. Gasiulė.
Teaching assistants: G. Urbanavičiūtė, Z. Staševskij, J. Ličytė, M. Mickutė, P. Gibas, K. Kvederavičiūtė.
Other researchers and technical staff: A. Rukšėnaitė, D. Ikasalaitė, M. Malikėnas, M. Jazdauskaitė.
Doctoral students: M. Narmontė, B. Masiulionytė, K Skardžiūtė.

RESEARCH INTERESTS

Nucleic acids modification enzymes
Epigenome profiling
Biosynthesis of selenoproteins
Enzyme engineering

SELECTED PUBLICATIONS 2020

Rakauskaitė, R., Urbanavičiūtė, G., Simanavičius, M., Lasickienė, R., Vaitiekaitė, A., Petraitytė, G., Masevičius, V., Žvirblienė A. and Klimašauskas, S. Photocage-selective capture and light-controlled release of target proteins. iScience. 2020, 23(12): 101833.

Tomkuvienė, M., Ikasalaitė, D., Slyvka, A., Rukšėnaitė, A., Ravichandran, M., Jurkowski, T. P., Bochtler, M. and Klimašauskas, S. Enzymatic hydroxylation and excision of extended 5-methylcytosine analogues. J. Mol. Biol. 2020, 423(23): 6157–6167.

Gordevičius, J., Narmontė, M., Gibas, P., Kvederavičiūtė, K., Tomkutė, V., Paluoja, P., Krjutškov, K., Salumets A. and Kriukienė, E. Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing. Clin. Epigen. 2020, 12: 153.

Ličytė, J., Gibas, P., Skardžiūtė, K., Stankevičius, V., Rukšėnaitė A. and Kriukienė, E. A bisulfite-free approach for base-resolution analysis of genomic 5-carboxylcytosine. Cell Rep. 2020, 32(11): 108155.

Gibas, P., Narmontė, M., Staševskij, Z., Gordevičius, J., Klimašauskas, S. and Kriukienė, E. Precise genomic mapping of 5-hydroxymethylcytosine via covalent tether-directed sequencing. PLOS Biol. 2020, 18(4): e3000684.

PATENTS 2020

Applications:

Kriukienė E., Gordevičius J., Narmontė M., Gibas P. Methods and compositions for noninvasive prenatal diagnosis through targeted covalent labelling of genomic sites, PCT/IB2020/053011. 30 March 2020.

S. Klimašauskas, R. Rakauskaitė, G. Urbanavičiūtė, R. Lasickienė, M. Simanavičius, A. Žvirblienė. Antikūnai fotoaktyvių baltymų manipuliavimui. LT2020539. Filing date: 24 August 2020.

Granted:

Klimašauskas S., Vilkaitis G., Mickutė M. Analysis of single-stranded RNA. EP3271478B1. Publication date: 06 May 2020.

RESEARCH PROJECTS CARRIED OUT IN 2020

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. Photosensitive Handles for Selective Manipulations of Biosynthetic Proteins (No. S-MIP-17-57). Prof. S. Klimašauskas. 2017–2020.

Photochemical transformations enable exquisite spatio-temporal control over biochemical processes, however, methods for reliable site-selective modification of proteins with biocompatible photo-sensitive high affinity reporters are lacking. The objective of this project is to create a high affinity binder specific to biosynthetically incorporated chemically modified amino acid residues carrying a photolytically removable caging group. We will utilize genetically encoded incorporation and chemical modification to synthesize proteins with photocaged cysteine or selenocysteine residues for subsequent production in a murine system of monoclonal antibodies against the photoremovable 4,5-dimethoxy-2-nitrobenzyl (DMNB) tag. Employing the produced antibodies, a general method for light-controlled protein affinity enrichment of photocaged target proteins from complex biological mixtures will be developed.

Research Council of Lithuania. A Technology for Single-Cell Analysis of Genomic DNA Modification. Neuroblastoma Epigenetic Heterogeneity (No. S-MIP-17-58). Dr E. Kriukienė. 2017–2020.

Neuroblastoma is a malignancy of the developing nervous system that is characterized by extreme clinical heterogeneity. For high-risk neuroblastoma patients, the prospect of long-term survival is dismal despite intensive multimodal therapy. Varying cellular composition detected at the same stages of neuroblastoma tumours might influence unexpected disease progression which prevents accurate assessment of disease prognosis. DNA methylation and demethylation of cytosines (mC) in the context of CG sites is a major epigenetic regulatory mechanism implicated in tumorogenenesis. During cancer development and progression, two epigenetic abnormalities are commonly observed: global hypomethylation and localized hypermethylation of specific promoters. Due to high heterogeneity of neuroblastoma cells it is unclear how changes in DNA modification define the tumorigenicity of different neuroblastoma cell types. Within the time-frame of the project, we will develop a new method for single-cell analysis of genomic hmC/unmodified CG profiles. We will employ our recently elaborated unique and economical approach for targeted sequencing of covalently labelled unmodified CG sites, TOP-seq with the most recent advance in single-cell techniques, droplet microfluidics. The new technology will be used to explore the epigenetic heterogeneity of neuroblastoma.

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 humans, 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).

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 analogue-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, Toronto (Canada)
University of Stavanger, Stavanger (Norway)
International Institute of Molecular and Cell Biology, Warsaw (Poland)
University of Southern California, Los Angeles (USA)
Regensburg University (Germany)
Cardiff University (UK)
RIKEN Yokohama (Japan)
INRA (France)
Tartu University (Estonia)
Stanford University (USA)

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 GENETIC ENGINEERING

7 Saulėtekio Ave, 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.
Teaching assistants: R. Zinkevičiūtė, E. Bakūnaitė, E. Žitkus, A. Avižinienė, N. Macijauskaitė, J. Bielskis, T. Paulauskas.
Other researchers and technical staff: E. Rudokienė, O. Jančevskaja, D. Jaskytė, V. Rudokas, A. Kolytaitė, E. Lekavičius.
Doctoral students: J. Rainytė, A. Verbickaitė, L. Silimavičius, M. Kalvaitytė, E. Vasiliūnaitė, V. Dapkutė.
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 2020

Špakova, A., Dalgėdienė, I., Insodaitė, R., Sasnauskienė, A., Žvirblienė, A. and Petraitytė-Burneikienė, R. vB_EcoS_NBD2 bacteriophage-originated polytubes as a carrier for the presentation of foreign sequences. Virus Research. 2020, 290: 198194. 10.1016/j.virusres.2020.19819.

Lazutka, J., Simutis, K., Matulis, P., Petraitytė-Burneikienė, R., Kučinskaitė-Kodzė, I., Simanavičius, M. and Tamošiunas, P. L. Antigenicity study of the yeast-generated human parvovirus 4 (PARV4) virus-like particles. Virus Research. 2020, 198236. 10.1016/j.virusres.2020.198236.

Starkevič, P., Ražanskienė, A., Starkevič, U., Kazanavičiūtė, V., Denkovskienė, E., Bendokas, V., Šikšnianas, T., Rugienius, R., Stanys, V. and Ražanskas, R. Isolation and analysis of anthocyanin pathway genes from Ribes Genus reveals MYB gene with potent anthocyanin-inducing capabilities. Plants. 20209, 1078. 10.3390/plants9091078.

Houen, G., Heiden, J., Trier, N. H., Draborg, A. H., Benros, M. E., Zinkevičiūtė, R., Petraitytė-Burneikienė, R., Ciplys, E., Slibinskas, R. and Frederiksen, J. L. Antibodies to Epstein-Barr virus and neurotropic viruses in multiple sclerosis and optic neuritis. Journal of Neuroimmunology. 2020, 346: 577314. 10.1016/j.jneuroim.2020.577314.

Vilmane, A., Terentjeva, A., Tamosiunas, P. L., Suna, N., Suna, I., Petraityte-Burneikiene, R., Murovska, M., Rasa-Dzelzkaleja, S. and Nora-Krukle, Z. Human parvoviruses may affect the development and clinical course of meningitis and meningoencephalitis. Brain Sciences. 2020, 10: 339. 10.3390/brainsci10060339.

RESEARCH PROJECTS CARRIED OUT IN 2020

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. Investigation of K.Lactis Mutations Conferring Enhanced Secretion Phenotype and Generation of Yeast Strains for Supersecretion of Recombinant Proteins (No. S-MIP-17-88). Dr A. Gedvilaitė. 2017–2020.

Yeast, especially Saccharomyces cerevisiae, serves as an important model eukaryote for many fundamental studies and as hosts for recombinant protein production. Kluyveromyces lactis, a close relative of S. cerevisiae, is very attractive for biotechnological processes as has the broader metabolic diversity and significant advantages in the production of certain secreted proteins than baker’s yeast. Through detailed knowledge of the secretion pathway - an essential process for living organisms - and engineering, it has become possible to improve the secretion yield and efficiency of some proteins in engineered S. cerevisiae. Yet despite all advantages, heterologous protein secretion in yeast, in many instances, is far from optimal. This can be explained by the complexity of protein processing and secretion pathways and needs for further studies. The aim of the project is identification and characterization of K. lactis gene and its mutation/s conferring the super-secretion phenotype and application of acquired knowledge for generation of new yeast super-secretion strains.

Research Council of Lithuania/ European Social Fund. Genetic and Molecular Studies of the Role of Tbx5a Role 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-Institute (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, Philadelphia (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

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

Research professor: Dr L. Mažutis.
Researchers: Dr R. Žilionis, Dr S. Juzėnas.
Teaching assistants: Dr J. Nainys, V. Milkus.
Other researchers and technical staff: J. Ritmejeris, R. Kisielius, E. Gegevičius, J. Žvirblytė, A. Želvytė.
Doctoral students: G. Stonytė, K. Goda, L. Camissi.

RESEARCH INTERESTS

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

SELECTED PUBLICATIONS 2020

Pfirschke, C., Engblom, C., Gungabeesoon, J., Lin, Y., Rickelt, S., Zilionis, R., Messemaker, M., Siwicki, M., Gerhard, G. M., Kohl, A., Meylan, E., Weissleder, R., Klein, A. M., Pittet, M. J., Pfirschke, C. et al. Tumor-promoting Ly-6G(+) siglecF(high) cells are mature and long-lived neutrophils. Cell Rep. 2020, 32: 108164.

Gegevicius, E., Goda, K., and Mazutis, L. Book chapter: Droplet Gene Analysis – Digital PCR. Droplet Microfluidics. 2020, pp. 89–121.

Leonaviciene, G., Leonavicius, K., Meskys R. and Mazutis, L. "Multi-step processing of single cells using semi-permeable capsules. Lab on a Chip. 2020, 20(21): 4052–4062.

PATENTS 2020

Granted:

Weitz D. A., Klein, A. M., Akartuna I., Mažutis L., Kirschner M. W. Systems and methods for barcoding nucleic acids. US10596541B2. Publication date: 24 March 2020.

Weitz D. A., Klein, A. M., Akartuna I., Mažutis L., Kirschner M. W. Systems and methods for barcoding nucleic acids. EP3299469B1. Publication date: 04 March 2020.

Italiano J., Mažutis L., Thon J. N., Weitz D. A. System and method for a biomimetic fluid processing. EP2941642B1. Publication date: 13 May 2020.

Italiano J., Mažutis L., Thon J. N., Weitz D. A. System and method for a biomimetic fluid processing. US10710073B2. Publication date: 14 August 2020.

Mažutis L., Stonytė G., Kiseliovas V., Žilionis R., Janulaitis A., Galinis R., Studer S., Hilvert D. System and method for synthesis of dna particles and use thereof. EP3402594B1. Publication date: 19 August 2020

Applications:

Italiano J., Mažutis L., Thon J. N., Weitz D. A. System and method for a biomimetic fluid processing. US20200316597A1. Publication date: 08 October 2020.

RESEARCH PROJECTS CARRIED OUT IN 2020

National Research Projects

Research Council of Lithuania/European Social Fund. Microfluidic Technologies for Single-Cell Geno- And Phenotyping 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. 2020–2024.

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.

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.

Contractual Research

MTEP Thermo Fisher Scientific Baltics, Lithuania. L. Mažutis. 2020–2021.

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)

OTHER RESEARCH ACTIVITIES

L. Mažutis –

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

 

DEPARTMENT OF IMMUNOLOGY AND CELL BIOLOGY

7 Saulėtekio Ave, 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.
Teaching assistants: I. Dalgėdienė, I. Pečiulienė, L. Vilys.
Other researchers and technical staff: D. Bakonytė, L. Diglienė.
Doctoral students: A. Lučiūnaitė, M. Simanavičius, A. Sližienė, K. Juškaitė, V. Rudokas.

RESEARCH INTERESTS

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

SELECTED PUBLICATIONS 2020

Kucinskaite-Kodze, I., Simanavicius, M., Dapkunas, J., Pleckaityte, M., Zvirbliene, A. Mapping of recognition sites of monoclonal antibodies responsible for the inhibition of mneumolysin functional activity. Biomolecules. 2020, 10(7): 1009. doi: 10.3390/biom10071009.

Stravinskiene, D., Sliziene, A., Baranauskiene, L., Petrikaite, V., Zvirbliene, A. Inhibitory monoclonal antibodies and their recombinant derivatives targeting surface-exposed carbonic anhydrase XII on cancer cells. Int J Mol Sci. 2020, 21(24): 9411. doi: 10. 3390/ijms21249411.

Bulavaitė, A., Dalgediene, I., Michailoviene, V., Pleckaityte, M. Type II restriction-modification system from Gardnerella vaginalis ATCC 14018. Pathogens. 2020, 9(9): 703. doi: 10.3390/pathogens9090703.

Pleckaityte, M. Cholesterol-dependent cytolysins produced by vaginal bacteria: certainties and controversies. Front Cell Infect Microbiol. 2020, 10(9): 452. doi: 10.3389/fcimb.2019.00452.

Rakauskaitė, R., Urbanavičiūtė, G., Simanavičius, M., Lasickienė, R., Vaitiekaitė, A., Petraitytė, G., Masevičius, V., Žvirblienė, A., Klimašauskas, S. Photocage-selective capture and light-controlled release of target proteins. iScience. 2020, 23(12): 101833. DOI: 10.1016/j.isci.2020.101833.

RESEARCH PROJECTS CARRIED OUT IN 2020

Projects Supported by University Budget

Development of Novel Antibodies and Testing of Their Properties. Dr A. Žvirblienė. 2016–2020.
We develop monoclonal and recombinant antibodies against different targets, mainly recombinant antigens of diagnostic relevance. Monoclonal antibodies are generated using traditional hybridoma-based technologies. For construction of recombinant antibodies, gene sequences encoding the variable parts of immunoglobulins are cloned from hybridoma cells producing antibodies against the target of interest. In 2017, large collections of monoclonal antibodies against recombinant viral antigens, including human parainfluenza virus 4 nucleocapsid protein, were generated and characterized.

National Research Projects

Research Council of Lithuania. The Prevalence and Distribution of Virulence Factors Among Subgroups of Vaginal Bacteria Gardnerella Vaginalis (No. S-MIP-17-49). Dr M. Plečkaitytė. 2017–2020.

Bacterial vaginosis (BV) is a microbial shift condition, characterized by the displacement of vaginal lactobacilli and the overgrowth of anaerobic bacterial populations. This projects aims to characterize the virulence features of Gardnerella vaginalis strains of different subgroups isolated from BV-negative and BV-positive women. It is also proposed to determine whether G.vaginalis secreted nucleases are related to virulence. Identification of phenotypic properties of G.vaginalis subgroups would advance our knowledge on human vaginal microbiota and promote new diagnostic and treatment options.

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 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.

Agency for Science, Innovation and Technology (MITA). Development of Labelled Antibodies for Allergy in vitro Diagnostics (No. TPP-03-031). Dr A. Žvirblienė. 2019–2020.

Allergy in vitro diagnostics is based on detection of allergen-specific IgE antibodies. Molecular allergology employs individual allergens instead of allergen extracts. The main component of molecular allergology tests is labelled secondary antibody against human IgE. Depending on the test type, the anti-IgE can be labelled either with enzymes or fluorescent dyes. In the current project, a panel of in-house produced monoclonal antibodies against human IgE were covalently coupled with different labels and tested as detection reagents for microarray-based allergy tests. The performance and stability of labelled anti-IgE were evaluated using recombinant allergens. The best conjugate was selected and tested with blood serum samples from atopic patients. The project was implemented in collaboration with an industrial partner UAB Immunodiagnostics that is in charge of developing microarray-based allergy tests for molecular allergology.

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 the 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 Centre for Disease Prevention and Control (ECDC), the incidence of IMD in Lithuania for unknown reasons is the highest in the EU/EEA and remains stable for more than a decade. This is a major public concern and the situation calls for active surveillance of IMD, which cannot be done without molecular epidemiology to predict IMD morbidity, disease outbreaks and vaccination strategies. So far, in Lithuania, the monitoring of IMD is passive, limited to the detection of disease cases. Meningococcal strains are not characterized by molecular methods that are used internationally. The aim of this project is to introduce modern methods of genotyping N.meningitidis strains and to identify potential virulence (invasiveness) molecular markers that would allow monitoring of circulating invasive meningococcal strains in Lithuania. It is not known how many asymptomatic individuals in Lithuania are N.menigitidis carriers and, thus potential transmitters of invasive meningococcal strains. Meningococcal transmission occurs via a human-to-human route from IMD sufferers or asymptomatic carriers. During the implementation of the project, the meningococcal carriage rate among asymptomatic subjects 19-25 years of age in the Vilnius region, where the highest incidence of IMD is observed, 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 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 adapt to stress conditions. How short hypoxia, as cell stress, influences mRNA isoform formation only limited data are available in the literature currently.
The proposed project is intended to investigate whether alternative splicing changes in the cells 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 our current knowledge about the changes in mRNA isoforms and changed protein expression in stressed cells and may indicate new cell stress associated disease treatment pathways.

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. 2017–2020.

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.

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

Karolinska Institute (Sweden)
Oslo University (Norway)
Friedrich-Loeffler Institute, Institute for Novel and Emerging Infectious Diseases (Germany)
Justus-Liebig University Giessen (Germany)
ArcDia (Finland)
Biomedical Research Center SAS, Bratislava (Slovakia)

OTHER RESEARCH ACTIVITIES

Dr A. Žvirblienė –

• 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 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

7 Saulėtekio Ave, 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.
Teaching assistants: V. Michailovienė, J. Jachno, A. Zakšauskas, Dr. T. Šneideris.
Other researchers and technical staff: A. Mickevičiūtė, D. Lingė, L. Davidian.
Doctoral students: A. Janonienė, J. Smirnovienė, G. Skvarnavičius, M. Žiaunys, S. Daunys, A. Sakalauskas, A. Petrošiūtė, V. Paketurytė, M. Gedgaudas, G. Žvinys, A. Vaškevičius.

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 2020

Zakšauskas, A., Čapkauskaitė, E., Jezepčikas, L., Linkuvienė, V., Paketurytė, V., Smirnov, A., Leitans, J., Kazaks, A., Dvinskis, E., Manakova, E. et al. Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms. European Journal of Medicinal Chemistry. 2020, 185: 111825.

Dudutienė, V., Zubrienė, A., Kairys, V., Smirnov, A., Smirnovienė, J., Leitans, J., Kazaks, A., Tars, K., Manakova, L., Gražulis, S. et al. Isoform-selective enzyme inhibitors by exploring pocket size according to the lock-and-key principle. Biophysical Journal. 2020, 119: 1513–1524.

Kazokaitė-Adomaitienė, J., Becker, H. M., Smirnovienė, J., Dubois, L. J. and Matulis, D. Experimental approaches to identify selective picomolar inhibitors for carbonic anhydrase IX. Curr Med Chem. 2020, 76 (9): 3159–3167.

Ziaunys, M., Sakalauskas, A. and Smirnovas, V. Identifying insulin fibril conformational differences by dhioflavin-T binding characteristics. Biomacromolecules. 2020, 21(12): 4989–4997. https://doi.org/10.1021/acs.biomac.0c01178.

Mikalauskaite, K., Ziaunys, M., Sneideris, T. and Smirnovas, V. Effect of ionic strength on thioflavin-T affinity to amyloid fibrils and its fluorescence intensity. International Journal of Molecular Sciences. 2020, 21: 8916.

RESEARCH PROJECTS CARRIED OUT IN 2020

National Research Projects

Research Council of Lithuania. The Mechanism of Inhibitor Recognition by Carbonic Anhydrases - Towards Anticancer Therapy (No. S-MIP-17-87). Dr D. Matulis. 2017–2020.

Despite more than 50 years of research into biomolecular recognition, we are still not able to predict the structure of a ligand that will bind tightly to a target protein. Gaining a better understanding of the physical forces which determine the underlying protein-ligand interactions would provide tools for the rational design of therapeutically active compounds.
There are 12 catalytically active carbonic anhydrase (CA) isoforms in human body. Their malfunction, overexpression causes numerous ailments including cancer. To tackle cancer, it is important to design inhibitors selective towards CA IX isoform and not inhibit vital isoforms, primarily CA I and CA II. However, since the active site environment in CAs is highly similar, it is a significant challenge to design isoform selective CA inhibitors. The goal of our project is to determine the factors which are important for the selectivity towards CAs and especially CAIX. A series of novel inhibitors will be designed and synthesized by organic synthesis methods and the compound binding to human recombinant CA catalytic domains will be evaluated by biophysical techniques including fluorescent thermal shift assay, isothermal titration calorimetry, enzymatic activity stopped flow assay, and surface plasmon resonance. The thermodynamic and kinetic parameters will be partitioned to the different structural interactions between the ligand and CA (Zn-sulphonamide bond and the contacts between the substituted benzene ring and CA). The studies with different metal substituents in the CA active site will reveal the contribution of the coordination bond and ligand substituent groups to the overall binding energetics. Thus, the project will provide deeper understanding not only of CA inhibitor interactions, but could be extended to other drug design projects where there are no high affinity ligands available yet.

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 to create new chemical compounds – lead drug candidates for cancer and neurodegenerative diseases. The current library of sulfonamide 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.

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. In addition, the Taiwanese team will measure by ITC the binding of sulphonamide 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.
  
  

SECTOR OF APPLIED BIOCATALYSIS

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

STAFF

Research professor: Dr I. Matijošytė.
Teaching assistant: R. Šiekštelė.
Other researchers: D. Daunoraitė, A. Veteikytė.
Postdoc researcher: A. Kaunietis.
Doctoral students: J. Babinskas, J. Krutkevičius.

RESEARCH INTERESTS

Biocatalysts and their application

SELECTED PUBLICATIONS 2020

Baliukynas, M., Veteikytė, A., Kairys, V., Matijošytė, I. The hydrolysis of indoxyl acetate: a versatile reaction to assay carbonic anhydrase activity by high-throughput screening. Enzyme Microb. Technol. 2020, 136: 109584.

Rotter, A., Bacu, A., Barbier, M., Bertoni, F., Bones, A. M., Cancela, M. L., Carlsson, J., Carvalho, M. F., Cegłowska, M., Dalay, M. C., Dailianis, T., Deniz, I., Drakulovic, D., Dubnika, A., Einarsson, H., Erdoğan, A., Eroldoğan, O. T., Ezra, D., Fazi, S., FitzGerald, R. J., Gargan, L. M., Gaudêncio, S. P., Ivošević DeNardis, N., Joksimovic, D., Kataržytė, M., Kotta, J., Mandalakis, M., Matijošytė, I., Mazur-Marzec, H., Massa-Gallucci, A., Mehiri, M., Nielsen, S. L., Novoveská, L., Overlingė, D., Portman, M. E., Pyrc, K., Rebours, C., Reinsch, T., Reyes, F., Rinkevich, B., Robbens, J., Rudovica, V., Sabotič, J., Safarik, I., Talve, S., Tasdemir, D., Schneider, X. T., Thomas, O. P., Toruńska-Sitarz, A., Varese, G. C. and Vasquez, M. I. A new network for the advancement of marine biotechnology in Europe and beyond. Front. Mar. Sci. 2020, 7: 278. doi: 10.3389/fmars.2020.00278.

RESEARCH PROJECTS CARRIED OUT IN 2020

Projects Supported By University Budget

Development and Application of Biocatalysts and Biocatalytic Systems. Dr I. Matijošytė. 2018–2020.

The research was directed towards development of biocatalysts with novel activities by three common ways: screening of enzymes, development of biocatalyst and application of biocatalyst. In 2018, the research was focused on development of screening systems for targeted enzyme activities, development of protein expression systems for production of targeted enzymes and exploring carrier-free immobilization methods.

International Research Projects

Baltic Research Programme. Novel High-Performance Polymers from Lignocellulosic Feedstock (No. EMP426). Dr I. Matijošytė. 2020–2024.

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.

Collaboration Contracts

Scientific cooperation agreement with the Department of Life Sciences and Systems Biology of University of Torino in the disciplinary fields Treatment of Lignin by Fungal Laccases Provided by UniTO, Production of Enzymes, Degradation of Pollutants in Marine Environment, Fungal and Enzymatic Treatment of Plastic Material (Cooperation Agreement N° 1.79 E) SU-1051). 15 June 2020. I. Matijošytė.

Cooperation on Biotransformations of Various Lignocellulosic Based Biomass into Added Value Products. Latvian State Institute of Wood Chemistry, Cooperation Agreement N° BS-15600-1341. 30 August 2018. I. Matijošytė (open-ended).

Enzymes and Their Application in Detergents. SC Naujoji Ringuva, N° B1-560000-153. I. Matijošytė (open-ended).

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

University of Tartu (Estonia)
Norwegian University of Science and Technology (Norway)
Latvian State Institute of Wood Chemistry (Latvia)
University of Ljubljana (Slovenia)
National Institute of Biology (Slovenia)
University of Turin (Italy)

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.

 

DEPARTMENT OF BIOINFORMATICS

7 Saulėtekio Ave, 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: A. Nausėdas, 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 2020

Olechnovič, K. and Venclovas, Č. Contact area-based structural analysis of proteins and their complexes using CAD-score. Methods Mol Biol. 2020, 2112: 75–90. https://doi.org/10.1007/978-1-0716-0270-6_6.

Makarova, K. S. et al. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 2020, 18: 67–83. https://doi.org/10.1038/s41579-019-0299-x.

Makarova, K. S., Timinskas, A., Wolf, Y. I., Gussow, A. B., Siksnys, V., Venclovas, Č. and Koonin, E. V. Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defence. Nucleic Acids Res. 2020, 48: 8828–8847. https://doi.org/10.1093/nar/gkaa635.

Kazlauskas, D., Krupovic, M., Guglielmini, J., Forterre, P. and Venclovas, Č. Diversity and evolution of B-family DNA polymerases. Nucleic Acids Res. 2020, 48: 10142–10156. https://doi.org/10.1093/nar/gkaa760.

Margelevičius, M. COMER2: GPU-accelerated sensitive and specific homology searches. Bioinformatics. 2020, 36: 3570–3572. https://doi.org/10.1093/bioinformatics/btaa185.

RESEARCH PROJECTS CARRIED OUT IN 2020

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. Analysis and Prediction of Structural Features of Proteins and Protein Complexes Using Interatomic Contact Areas and Evolutionary Information (No. S-MIP-17-60). Dr Č. Venclovas. 2017–2020.

The knowledge of three-dimensional structure of proteins and protein complexes is critical for comprehensive understanding of their molecular function. However, experimental determination of protein structure is often tedious or unsuccessful. Currently, a feasible alternative to experiments is computational prediction of protein structure. Computational methods are also indispensable for the analysis of protein structure regardless of whether it is solved experimentally or derived using computational modelling. However, at present it is often difficult to estimate how accurate the computationally derived protein structural model is. The same is true for structural models of protein complexes. Better computational methods for the analysis and prediction of protein binding sites are also in high demand. In this project we are going to develop computational methods to estimate the accuracy of protein models, to assess the accuracy of protein-protein interfaces, to predict unknown binding sites in proteins and to improve analysis of protein-nucleic acids complexes.

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

Most departments at Vilnius University Institute of Biotechnology (Lithuania)
Inria Grenoble – Rhone-Alpes Research Centre (France)
Institute of Molecular and Cell Biology, University of Tartu (Estonia)
Institut Pasteur, Département de Microbiologie, Paris (France)
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

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

STAFF

Research professor: Dr A. Petronis.
Teaching assistant: K. Koncevičius.
Doctoral student: A. Kriščiūnas.

RESEARCH PROJECTS CARRIED OUT IN 2020

National Research Projects

Research Council of Lithuania. Daily Effects on Epigenetic Prediction of Individual’s Age (No. S-MIP-19-192). Dr A. Petronis. 2019–2022.

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 part 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 2020

Carlucci, M., Kriščiūnas, A., Li, H., Gibas, P., Koncevičius, K., Petronis, A. and Oh, G. DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity. Bioinformatics. 2020, 36: 1952–1954.

 

INSTITUTE OF BIOCHEMISTRY

7 Saulėtekio Ave, 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 2020

E. Balčiūnas. Development of bioactive scaffolds for tissue engineering applications.
M. Alksnė. Substrate-dependent fate of stem cells: insights into artificial bone fabrication.
N. Dreižė. Elucidation of the complexity of molecular mechanisms of cancer cell drug resistance to enhance treatment efficiency.
A. Laurynėnas. Investigation and modelling of complex biocatalytic and bioelectrocatalytic processes.
M. Sadauskas. Indigo-producing enzymes: selection and application.
M. Talaikis. Vibrational spectroscopy study of membrane anchoring monolayers and adsorbed biomolecules.
N. Urbelienė. Methods for the selection of hydrolases by applying E. coli uridine auxotrophic strain and synthetic nucleosides.
B. Valiauga. Investigation of the mechanism of quinone- and nitroreductase reactions by flavoenzymes dehydrogenases-transhydrogenases.
A. Vitkevičienė. Investigation of molecular mechanisms in human myeloid leukaemia cells using new epigenetic and metabolic regulators.

 

DEPARTMENT OF BIOANALYSIS

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

STAFF

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

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 2020

Project Supported by University Budget

Design and Investigation of New Systems for Biocatalysis. Dr. J. Razumienė. 2017–2020.

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 exhibit 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:

Ramašauskas, L., Meškys, R., Ratautas, D. Real-time glucose monitoring system containing enzymatic sensor and enzymatic reference electrodes. Biosensors and Bioelectronics. 2020, 164: 112338.

Gružauskaitė, J., Jasinskaitė, J., Meškys, R., Gaidamavičienė, G., Žalga, A., Laurynėnas, A., Tetianec, L., Dagys, M. Gold-coated magnetic nanocatalyst containing wired oxidoreductases for mediatorless catalysis of carbohydrate oxidation by oxygen. Catalysis Communications. 2020, 135: 105848.

Makaras, T., Razumienė, J., Gurevičienė, V., Šakinytė, I., Stankevičiūtė, M., Kazlauskienė, N. New approach of stress evaluation in fish using β-D-Glucose measurement in fish holding-water. Ecological Indicators. 2020, 109, 105829.

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. Efficiency and Substrate Specificity Research of Third-Type Biosensors Created by Using TRGO Fractions and Glucose Dehydrogenase (No. 09.3.3-LMT-K-712-16-0125). G. Rimkutė.

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.

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

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

 

DEPARTMENTS OF XENOBIOTICS BIOCHEMISTRY

7 Saulėtekio Ave, 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 L. Kosychova, Dr A. Marozienė, Dr L. Misevičienė.
Research assistants: E. Polmickaitė-Smirnova, Dr B. Valiauga.
Doctoral student: M. Lesanavičius.

RESEARCH INTEREST

SInvestigations 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 antiparasitic action
The studies of the catalytic mechanism of mammalian 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 2020

Project Supported by University Budget

Molecular Mechanisms of Enzymatic Activation, Detoxification, Biodegradation, and Cytotoxicity of Redox Active Xenobiotics. Dr Habil. N. Čėnas. 2017–2020.

We further detailed the catalysis mechanism of Plasmodium falciparum ferredoxin:NADP⁺ reductase (PfFNR) demonstrating the appearance of a transient FAD semiquinone (FADH.) during the turnover of quinone reductase reaction. This enzyme was used as a model system for the characterization of unknown E¹₇ values of aromatic N-oxides and nitrocompounds. We continued the studies of neuronal NO synthase (nNOS), examining the effects of ionic strength and calmodulin on reduction kinetics of nonphysiological electron acceptors. High ionic strength increases the reactivity of uncharged duroquinone and attenuates the stimulating effect of calmodulin. This shows that both factors are responsible for the conformational transition of nNOS, accelerating the reaction. In parallel, the charged electron acceptors interact with negatively charged domain of enzyme. We examined the kinetics of single-electron reduction of nitroaromatic antiandrogens nilutamide, flutamide and their derivatives by NADPH:cytochrome P-450 reductase (P-450R) and adrenodoxin reductase/adrenodoxin (ADR/ADX), showing that the reactivity of compounds is consistent with their E¹₇ values in the range of -0.41 - -0.37 V. We have shown that both FADH₂-NAD⁺ charge-transfer complex and FADH. are formed during the turnover of quinone reductase reaction of Thermotoga maritima thioredoxin reductase. The equilibrium of this enzyme with APAD⁺/APADH redox couple enabled to establish its E⁰₇ value, -0.23 V. Further, the studies of photodynamic inactivation (PDI) of Salmonella enterica cells exposed to 5-ALA were continued using different sensitization patterns. The comparative studies showed that the presence of endogenous porphyrins results in secondary sensitization of the cells, causing remarkably stronger photoinactivation effects when compared to their externally used porphyrin standards (coproporphyrin I or uroporphyrin I).

Main publications:

Benitez, D., Comini, M. A., Anusevičius, Ž., Šarlauskas, J., Miliukienė, V., Miliuvienė, E., Čėnas, N. 5-Vinylquinoline-substituted nitrofurans as inhibitors of trypanothione reductase and antitrypanosomal agents. Chemija. 2020, 31: 111–117.

Valiauga, B., Rouhier, N., Jacquot, J.-P., Čėnas, N., Characterization of redox properties of FAD cofactor of Thermotoga maritima thioredoxin reductase. Chemija. 2020, 31: 191–195.

Lesanavičius, M., Aliverti, A., Šarlauskas, J., Čėnas, N. Reactions of Plasmodium falciparum ferredoxin:NADP⁺ oxidoreductase with redox cycling xenobiotics: a mechanistic study. International Journal of Molecular Sciences. 2020, 21: 3234.

National Research Projects

Research Council of Lithuania: Redox Chemistry, Biochemistry and Cytotoxicity of Aromatic Nitrocompounds and N-oxides: New Insights (No. DOTSUT-34/09.33-LMT-K712-01-0058). Dr Habil. N. Čėnas. 2018–2021.

The aim of this project is to provide new insights on redox processes and cytotoxicity of aromatic nitrocompounds and N-oxides: i) the synthesis of 9 new aromatic N-oxides with varied reactivity towards NAD(P)H:quinone oxidoreductase (NQO1) and parallel studies of their single-electron reduction enabled to demonstrate the quantitative relationship between their reactivity towards NQO1 and cytotoxicity in MH22a and HCT116 cells; ii) we found that the reduction of quinones and aromatic N-oxides by PfFNR and nNOS follow the same dependence on their E¹₇ values; iii) it was shown that the cytotoxicity of nitrobenzenes, nitrofurans and nitrothiophenes in MH22a and HCT116 cells follow the same cytotoxicity vs. E¹₇ relationships. The protective action of antioxidants show that the main factor of cytotoxicity is redox cycling. Cytochromes P-450 enhance the cytotoxicity of above compounds, whereas NQO1 may either enhance or attenuate the cytotoxicity; iv) mammalian thioredoxin reductase and apoptosis induction factor reduced aromatic N-oxides with negligibly low rates, and v) further analysis of antibacterial action of aromatic N-oxides was performed using the molecular descriptors of compounds obtained by quantum mechanical calculations.

Main publications:

Nemeikaitė-Čėnienė, A., Šarlauskas, J., Misevičienė, L., Marozienė, A., Jonušienė, V., Lesanavičius, M., Čėnas, N. Aerobic cytotoxicity of aromatic N-oxides: the role of NAD(P)H:quinone oxidoreductase (NQO1). International Journal of Molecular Sciences. 2020, 21: 8754.Polmickaitė-Smirnova, E.,

Šarlauskas, J., Krikštopaitis, K., Lukšienė, Ž., Staniulytė, Z., Anusevičius, Ž. Preliminary investigation of the antibacterial activity of antitumor drug 3-amino-1,2,4-benzotriazine-1,4-dioxide (tirapazamine) and its derivatives. Applied Sciences. 2020, 10: 4062.

Nemeikaitė-Čėnienė, A., Šarlauskas, J., Jonušienė, V., Misevičienė, L., Marozienė, A., Yantsevich, A. V., Čėnas, N. QSARs in prooxidant mammalian cell cytotoxicity of nitroaromatic compounds: the roles of compound lipophilicity and cytochrome P-450- and DT-diaphorase-catalyzed reactions. Chemija. 2020, 31: 170–177.

International Research Projects

Bilateral Lithuanian-French programme Žiliberas. Characterization of the Flavointeractome of the Antiplasmodial Agent Plasmodione and Its Metabolites (No. S-LZ-19-4). Dr Habil. N. Čėnas. 2019–2020.

The studies of quinone-mediated ascorbate oxidation enabled to determine the E¹₇ values of 12 plasmodione derivatives in the range of -0.16 - -0.29 V. Due to higher lipophilicity, their reactivity towards PfFNR is typically higher than that of model benzo- and naphthoquinones.

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.

 

DEPARTMENT OF BIOELECTROCHEMISTRY AND BIOSPECTROSCOPY

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

STAFF

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

RESEARCH FIELDS

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

MAIN SCIENTIFIC ACHIEVEMENTS IN 2020

Dr R. Budvytytė - winner of L’Oréal Baltic-UNESCO Fellowship for Women in Science 2020.

Dr G. Valinčius - Commemorative Medal form the Prime Minister of Lithuania for fruitful collaboration 2016–2020;
Acknowledgement Certificate from the Prime Minister of Lithuania for Significant Contribution in Fight against COVID-19;
Acknowledgement Certificate and Medal from the Minister of Health of Lithuania for Significant Contribution in Efforts to Improve Public Health in Lithuania.

RESEARCH PROJECTS CARRIED OUT IN 2020

Project Supported by University Budget

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

Molecular anchors for tethered bilayer membranes. The effects of solvent polarity on the formation and properties of multi-component self-assembled monolayers (SAMs) for surface immobilization of tethered bilayer membranes (tBLMs) were studied. We found that the solvent polarity allows controlling the surface concentration of molecular anchors on a surface in the range from 9% to 57% while keeping constant adsorbate concentration in solution.
The electric potential-induced structural changes in mixed SAMs comprised of lipid-like WC14 molecules and surface backfiller 2-mercaptoethanol (ME-D4) were probed in-situ by isotope-edited electrochemical surface enhanced Raman spectroscopy (EC-SERS) coupled with first-principles calculations, reductive desorption voltammetry, and generalized two-dimensional correlation spectroscopy (G2DCS). We found that negative electrode polarization leads to lengthening of Au–S bond and reorganization of molecules in the headgroup region. We also demonstrated that clustering of WC14 molecules in membrane-anchoring monolayers leads to a formation of large WC14-free areas in which mercaptoethanol molecules are less constrained to engage in surface coordination through the hydroxyl group and Au–O linkage formation. These findings are important in analysis and interpretation of the function of biosensors and biotechnological processes based on tBLM.

New metal-oxide molecular anchors and possibilities to assemble phospholipid bilayer on metallurgical rust-free steel substrates were demonstrated. These finding may be of use in design of novel biomedical instruments for surgeries and in vitro bio-sensing devices.

Main publications:

Talaikis, M., Valinčius, G., Niaura G. Potential-induced structural alterations in the tethered bilayer lipid membrane-anchoring monolayers revealed by electrochemical surface-enhanced Raman spectroscopy. Journal of Physical Chemistry C. 2020, 124: 19033–19045.

Tumėnas, S., Ragaliauskas, T., Penkauskas, T., Valančiūtė, A., Ambrulevičius, F., Valinčius G. Solvent effects on composition and structure of thiolipid molecular anchors for tethering phospholipid bilayers. Applied Surface Scienc. 2020, 509: 145268.

Sabirovas, T., Valiūnienė, A., Gabriūnaitė, I., Valinčius G. Mixed hybrid bilayer lipid membranes on mechanically polished titanium surface. Biochimica et Biophysica Acta (BBA) – Biomembranes. 2020, 1862: 183232.

Effect of statins on properties of phospholipid membranes. Using a combined approach based on biophysical (electrochemical impedance spectroscopy on tethered bilayer lipid membranes) and biological methods (hemolysis on erythrocytes and immunocytochemistry on tumour cell lines), we demonstrate that lipophilic, but not hydrophilic statins are capable of reducing the damage caused by cholesterol-dependent cytolysins, by clustering lipid rafts.

Main publications:

Penkauskas, T., Zentelytė, A, Ganpule, S., Valinčius. G., Preta G. Pleiotropic effects of statins via interaction with the lipid bilayer: A combined approach. Biochimica et Biophysica Acta (BBA) – Biomembranes. 2020, 1862: 183306.

Preta, G. New insights into targeting membrane lipids for cancer therapy. Frontiers in Cell and Developmental Biology. 2020, 8: 571237.

Electrochemical Tools for Structural Studies of Phospholipid Bilayers. In collaboration with the Faculty of Mathematics and Informatics at Vilnius University (Prof. T. Meškauskas) we continued developing mathematical analysis tools for the electrochemical impedance response from tethered bilayer membranes. Specifically, we explored possibilities to detect clusters of the pore-forming proteins in biological membranes by EIS. By invoking the Voronoi tessellation concept we demonstrate the possibility to distinguish between random and sparsely clustered patterns both in computer generated and real-world systems of membrane defects using one single parameter σ, the standard deviation of the normalized Voronoi sector areas distribution. For random systems, σ ≈ 0.54, for sparsely clustered patterns σ > 0.54. We also proposed the EIS spectra-derived metric ζ to be a diagnostic parameter that allows assessment of the distribution type (homogeneous, random or clustered) of defects at nanometre level.

Main publication:

Raila, T., Ambrulevičius, F., Penkauskas, T., Jankunec, M., Meškauskas, T., Vanderah, D. J., Valinčius, G. Clusters of protein pores in phospholipid bilayer membranes can be identified and characterized by electrochemical impedance spectroscopy. Electrochimica Acta. 2020, 364: 137179.

Other research topics covered biospectroscopy of amyloid assemblies, and spectroscopy of live yeast cells. We also contributed through the collaborative initiatives to the research projects done at groups at National Institute of Cancer, Physical Technology and Science Centre as well Lithuanian University of Health Sciences.

Main publications:

Golubewa, L., Rehman, H., Kulahava, T., Karpicz, R., Baah, M., Kaplas, T., Shah, A., Malykhin, S., Obraztsov, A., Rutkauskas, D., Jankunec, M., Matulaitienė, I., Selskis, A., Denisov, A., Svirko, Y., Kuzhir, P. Macro-, micro- and nano-roughness of carbon-based interface with the living cells: towards a versatile bio-sensing platform. Sensors. 2020, 20: 5028.

Talaikis, M., Strazdaitė, S., Žiaunys, M. Niaura, G. Far-off resonance: multiwavelength Raman spectroscopy probing amide bands of amyloid-beta-(37-42) peptide. Molecules. 2020, 25: 3556.

Zaleskis, G., Garberytė, S., Pavliukevičienė, B., Valinčius, G., Characiejus, D., Mauricas, M., Krasko, J. A., Žilionytė, K., Žvirblė, M., Pašukonienė, V. Doxorubicin uptake in ascitic lymphoma model: resistance or curability is governed by tumor cell density and prolonged drug retention. Journal of Cancer. 2020, 11: 6497–6506.

National Research Council Projects

Research Council of Lithuania. Project QAPHOMEDA (No. P-MIP-19-394).

The detailed study of all stages of the protein reconstitution into the phospholipid membranes and pore formation in parallel to the biological tests in cell cultures is undertaken to provide molecular level information on the mechanisms of the cell membrane damage. The project will take advantage of the tethered phospholipid bilayer membrane technology developed in the proposing group as well as the multidisciplinary approach, which involves integration of the biophysical and biological research techniques with the mathematical modelling of the membrane damage processes. By establishing major factors affecting membrane susceptibility we expect developing fast screening tests for the toxic activities, that allows detection of the pathogens at or below lytic concentrations. 4 peer-reviewed research papers will be published in this project. The results of the project will be disseminated at the international research conferences and in the science popular media.

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. Participants - R. Budvytytė, M. Jankunec, T. Ragaliauskas, T. Penkauskas.

The mortality rate of the patient in the first phase of severe acute pancreatitis has declined significantly over the past two decades due to significant improvements of the processes in the intense care. Thus, the mortality rate of patients in the late phases of disease remains high. This project aims to develop non-invasive methods that can be used to determine the initial severity of disease and individualize timely treatment. Within the project framework, two activities are planned: 1) identification of specific proteins in cell membrane damage mechanisms in severe acute pancreatitis and 2) development of non-invasive prognosis and diagnostic methods using selected biomarkers, enzymes and metabolites. Project results: i) a scientific publication will cover the mechanism of action of determined specific proteins; ii) a patent application submitted to European Patent Office will cover the developed non-invasive method for prognosis and diagnosis of acute pancreatitis.

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 Rima Budvytytė.

Main focus of the proposed research project is to find out possible factors that may be related to the molecular level biochemical and biophysical events triggering or promoting neurodegenerative diseases. The project will focus on one of the important group of these events: the interaction between the misfolded aggregates of proteins implicated in neurodegeneration and the phospholipid membranes. The innovative tool to reach this result is to use a unique lipid platform – tethered bilayer lipid membranes (tBLMs). The geometry and stability of tBLMs allows us to use a number unique of surface composition and structure sensitive techniques for misfolded protein aggregates-membrane interaction study. Those include electrochemical impedance spectroscopy (EIS), surface plasmon resonance (SPR). In parallel with the damage of the membrane, a possible link between the binding strength and aggregate size, morphology and structural changes will be targeted. It is expected that 1 peer-reviewed research paper (1 quartile (Q1) by the Thomson Reuters Web of Knowledge), will be published in this project.

Research Council of Lithuania. Statins and Pleiotropic Effects: Interactions with Lipid Plasma Membranes (No. KD-19047). Supervisor - Dr Giulio Preta. PhD st. Shamish Ganpule. 2019–2022.

Using a combined approach based on biophysical (electrochemical impedance spectroscopy on tethered bilayer lipid membranes) and biological methods (haemolysis on erythrocytes and immunocytochemistry on tumour cell lines), we demonstrate that lipophilic, but not hydrophilic statins are capable of reducing the damage caused by cholesterol-dependent cytolysins, by clustering lipid rafts.

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

Antimicrobial substances are becoming one of the most promising alternatives to traditional antibiotics. The substances with antimicrobial activity are likely to be discovered on a daily basis, but their application in practice (in the treatment process) still lacks an understanding of their action not only in bacterial but also in host cell metabolism. The project is focused on registration of topographical and nanomechanical properties of bacteria surface before and after exposure to bacteriocin. This toxin is known as not peptidoglycan degrading enzyme.

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

Alzheimer’s disease (AL) is the most common form of senile dementia. Increased production of s100A9 and Abeta peptides is a critical factor in the development of Alzheimer’s disease. s100A9 (like Abeta) proteins spontaneously tend to aggregate into coexisting multiple physical forms: oligomers, protofibrils, fibrils. In the course of the project, the aggregation of s100A9 proteins will be studied under various oligomerization conditions. The s100A9 protein derivatives will be characterized by the dynamic light scattering (DLS) method, and the morphology of the aggregates will be assessed by high-resolution atomic force microscopy (AFM). The electrochemical impedance spectroscopy (EIS) method will be used to study the s100A9 protein interaction.

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.

Medical diagnostic tools – biosensors – are devices that allow the rapid and sccurate detection and concentration measurements of compouds considered as biomarkers, and thus the monitoring or diagnosis of specific diseases. The aim of this project is to promote the activities of a joint research and engineering center of excellence, where diagnostic biotechnologies (amperometric enzymatic and membrane biosensors) adapted for biomarker detection, early disease diagnosis, monitoring and production of new antibacterial preparations would be developed. The planned results of this project include three patent applications to the European Patent Office (EPO) and prototypes of new technologies ready for further commercialization.

International Research Projects

Cost Action – CA18133. European Research Network on Signal Transduction (ERNEST). Management Committee (MC) Member Dr Rima Budvytytė, MC Substitute Dr Marija Jankunec. 2020–2023.

The main scientific objective of the Acrion is to develop a common, comprehensive and holistic map of signal transduction that will advance development of pathway-specific chemical modulators. This unique and innovative goal will be realised by linking of diverse group of researchers in the field through the networking activities funded by COST.

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

Faculty of Mathematics and Informatics, Vilnius University (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 Life Science, Swansea University (United Kingdom)

OTHER RESEARCH ACTIVITIES

Dr G. Valinčius –

• editorial board member of the journal Chemija;
• member of the Lithuanian Biophysical Society;
• member of the Lithuanian Biochemical Society;
• member of International Society of Electrochemistry;
• expert of Research and Higher Education Monitoring and Analysis Centre (STRATA);
• public advisor to the Minister of Education, Science and Sports.

Dr Habil. G. Niaura –

• member of the Lithuanian Academy of Sciences;
• member of the editorial Board of the scientific journal Chemija;
• member of the International Society of Electrochemistry.

Dr R. Budvytytė –

• member of the American Biophysical Society.

Dr M. Jankunec –

• guest topic editor of Biosensors (MDPI).

Dr G. Preta –

• guest associated editor for Membrane Traffic in Cell and Developmental Biology;
• topic editor in Life (MDPI);
• topic editor in Pharmaceutics (MDPI).

 

DEPARTMENT OF BIOLOGICAL MODELS

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

STAFF

Senior researchers: Dr V. Bukelskienė, Dr D. Baltriukienė, Dr A. Burokas.
Researcher: Dr M. Alksnė.
Research assistant: E. Šimoliūnas.
Doctoral students: V. Baranauskas, P. Barasa, I. Rinkūnaitė, M. Grubliauskaitė, A. Kunevičius, E. M. Meškytė, S. Samulėnaitė, A. K. Vijaya.
Veterinary doctor: A. Ščerbavičienė.
Assistants: E. Baltrukonytė, J. Kernagytė, R. Balsienė, D. Danilevičius.

RESEARCH INTERESTS

Laboratory animals, cell culture, stem cells, tissues engineering, microbiota-gut-brain axis

RESEARCH PROJECTS CARRIED OUT IN 2020

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. To promote spontaneous stem cell osteogenic differentiation and to improve osteoinductivity of the scaffolds, as well as to disguise the negative effects of PLA degradation, we created PLA composites with 10 % of hydroxyapatite (HA) or 10 % of bioglass (BG) filaments, which were used for scaffold production. It was observed that PLA+HA composite was more suitable for stem cell attachment and proliferation, PLA+BG composites promoted the earliest and strongest osteogenesis of the stem cells as well as PLA surface coated with stem cell-derived extracellular matrix network significantly improved the osteoinductive properties of the surface.

Main publications:

Alksnė, M., Kalvaitytė, M., Šimoliūnas, E., Rinkūnaitė, I., Gendvilienė I., Locs, J., Rutkūnas V., Bukelskienė, V. In vitro comparison of 3D printed polylactic acid/hydroxyapatite and polylactic acid/bioglass composite scaffolds: Insights into materials for bone regeneration. Journal of the Mechanical Behavior of Biomedical Materials. 2020, 104: 103641.

Gendvilienė I., Šimoliūnas, E., Rekstytė, S., Malinauskas, M., Zaleckas, L., Jegelevičius, D., Bukelskienė, V., Rutkūnas, V. Assessment of the morphology and dimensional accuracy of 3D printed PLA and PLA/HAp scaffolds. Journal of the Mechanical Behavior of Biomedical Materials. 2020, 104:103616.

Han, Y., Baltriukienė, D., Kozlova, E. Effect of scaffold properties on adhesion and maintenance of boundary cap neural crest stem cells in vitro. Journal of Biomedical Materials Research Part A. 2020, 108: 1274–1280.

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 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.

Main publications:

Arnoriaga-Rodrıguez, M., Mayneris-Perxachs, J., Burokas, A. et al. Obesity impairs short-term and working memory through gut microbial metabolism of aromatic amino acids. Cell Metabolism. 2020, 32: 548–560.

Arnoriaga-Rodriguez, M., Mayneris-Perxachs, J., Burokas, A. et al. Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile. Microbiome. 2020, 8: 59.

Mayneris-Perxachs, J., Arnoriaga-Rodriguez, M., Luque-Cordoba, D., Priego-Capote, F., Perez-Brocal, V., Moya A., Burokas, A., et al. Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status. Microbiome. 2020, 8: 136.

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. To this end, the conditions for growing primary urethral stricture cells in vitro were optimized, and a methodology for the cultivation of cocultures (mesenchymal cells and myofibroblasts) for the determination of cell-derived collagen types was developed.

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 and diminish negative ageing related consequence.

Central Project Management Agency. Centre for Genetic Modelling 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.

CellFit is a European network of excellence with competence on all levels within fundamental biology, bio-engineering as well as clinical research. CellFit aims to translate the present basic knowledge in cell control, cell repair and regeneration from the laboratory bench to the clinical application.

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. Bukelskiene. 2019–2021.

The project is aimed to confirm the possibility that corneal defects can be corrected using the patching method. This possibility will be confirmed using experimental animals.

The EU Joint Programme – Neurodegenerative Disease Research (JPND). Multicellular Organoids: Modelling, Mechanisms and Therapy Development for C9ORF72-Associated Neurodegeneration. The coordinator – the University of Sheffield; Partner - Vilnius University, Life Sciences Center, Institute of Biochemistry; Dr D. Baltriukienė.

The project is aimed at generating 3D in vitro multicellular organoids for drug- and gene-based therapeutic screening.

Contractual Research - to assess the chronic toxicity of sodium oxamate by using experimental mice. UAB Curaltus. Dr V. Bukelskienė.

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

Upsala University (Sweden)
Center for Physical Sciences and Technology (FTMC), Vilnius (Lithuania)
The Dairy Research Institute of Asturias (IPLA-CSIC), Asturias (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)
UAB Curaltus (Lithuania)

OTHER RESEARCH ACTIVITIES

Dr D. Baltriukienė –

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

 
DEPARTMENT OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

7 Saulėtekio Ave, 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 L. Truncaitė, Dr J. Urbonavičius (part-time).
Researchers: Dr A. Aučynaitė, Dr R. Gasparavičiūtė, Dr V. Petkevičius, Dr S. Povilonienė, Dr R. Rutkienė, Dr J. Stankevičiūtė, Dr R. Stanislauskienė, Dr E. Šimoliūnas, Dr A. Zajančkauskaitė.
Research assistants: R. Meškienė, J. Vaitekūnas, Dr M. Sadauskas, Dr N. Urbelienė.
Doctoral students: R. Jamontas, M. Kaplūnaitė, A. Krupeckaitė, A. Krikštaponis, A. Noreika, V. Preitakaitė, 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 2020

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 oxygenases active towards indole and pyridine as a primary substrate have been characterized. Screening for novel enzymes is also carried out by applying metagenomic techniques – effective selection systems combined with tailored substrates.

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 N⁴-acetylcytosine derivatives are well understood, but the catabolism or salvage of those compounds is only scarcely studied. For the first time, we show that in E. coli the ASCH domain-containing protein YqfB, which has a unique Thr-Lys-Glu catalytic triad, catalyses the hydrolysis of N4-acetylcytidine.

Main publications:

Sadauskas, M., Statkevičiūtė, R., Vaitekūnas, J., Petkevičius, V., Časaitė, V., Gasparavičiūtė, R., Meškys, R. Enzymatic synthesis of novel water-soluble indigoid compounds. Dyes Pigm. 2020, 173: 107882.

Stanislauskienė, R., Laurynėnas, A., Rutkienė, R., Aučynaitė, A., Tauraitė, D., Meškienė, R., Urbelienė, N., Kaupinis, A., Valius, M., Kaliniene, L., Meškys, R. YqfB protein from Escherichia coli: an atypical amidohydrolase active towards N ⁴-acylcytosine derivatives. Sci. Rep. 2020, 10: 788.

Sadauskas, M., Statkevičiūtė, R., Vaitekūnas, J., Meškys, R. Bioconversion of biologically active indole derivatives with indole-3-acetic acid-degrading enzymes from Caballeronia glathei DSM50014. Biomolecules. 2020, 10: 663.

Urbelienė, N., Meškienė, R., Tiškus, M., Stanislauskienė, R., Aučynaitė, A., Laurynėnas, A., Meškys, R. A rapid method for the selection of amidohydrolases from metagenomic libraries by applying synthetic nucleosides and a uridine auxotrophic host. Catalysts. 2020, 10: 445.

Science Promotion Fund of Vilnius University. Synthesis of Aromatic N-Oxides by Biocatalytic Methods (No. MSF-JM-16). Dr J. Stankevičiūtė. 2019–2020.

Main publications:

Petkevičius, V., Vaitekūnas, J., Tauraitė, D., Stankevičiūtė, J., Vaitkus, D., Šarlauskas, J., Čėnas, N., Meškys, R. Whole-cell biocatalysis using PmlABCDEF monooxygenase and its mutants: a versatile toolkit for selective synthesis of aromatic N-oxides. Applied Biocatalysis: The Chemist's Enzyme Toolkit. John Wiley & Sons. 2020, 528–534. Book chapter.

Vaitekūnas, J., Gasparavičiūtė, R., Stankevičiūtė, J., Urbelis, G., Meškys, R. Biochemical and genetic analysis of 4-hydroxypyridine catabolism in Arthrobacter sp. Strain IN13. Microorganisms. 2020, 8: 888. https://doi.org/10.3390/microorganisms8060888.

Science Promotion Fund of Vilnius University. Ecogenomics and Potential Biogeochemical Impacts of Viruses in the Gypsum Karst Lake Ecosystems (No. MSF-LMT-2). Dr E. Šimoliūnas. 2019–2020.

In this study, a number of bacteria and bacteriophages were isolated from water samples of the unique sulfate-type gypsum karst lakes Kirkilai and Ramunėlis located near Biržai, Lithuania. The data presented here will not only expand our knowledge of the diversity of bacteriophages but will also lead to a better understanding of almost unexplored communities of bacteria and viruses in the sulfate-type gypsum karst lakes.

Main publication:

Šimoliūnienė, M., Tumėnas, D., Kvederavičiūtė, K., Meškys, R., Šulčius, S., Šimoliūnas E. Complete genome sequence of Bacillus cereus bacteriophage vB_BceS_KLEB30-3S. Microbiol Resour Announc. 2020, 9(20): e00348-20. DOI: 10.1128/MRA.00348-20.

National Research Projects

Research Council of Lithuania. The Role of Atmospheric Nitrogen Fixation in the Largest Eutroficated European Lagoon (No. S-MIP-17-7). Dr M. Žilius (Klaipėda University), work package leader Dr R. Stanislauskienė. 2017–2020.

Seasonally nitrogen-limited and phosphorus-replete temperate coastal waters generally host dense and diverse diazotrophic communities. Despite numerous studies in marine systems, little is known about diazotrophs and their functioning in oligohaline estuarine environments. We applied a combination of nifH transcript and metagenomic shotgun sequencing approaches to investigate temporal shifts in taxonomic composition and nifH activity of size-fractionated diazotrophic communities in a shallow and mostly freshwater coastal lagoon. Patterns in active nifH phylotypes exhibited a clear seasonal succession, which reflected their different tolerances to temperature change and nitrogen availability. The results contribute to a better understanding of the realized genetic potential of pelagic N2 fixation and its seasonal dynamics in oligohaline estuarine ecosystems, which are natural coastal biogeochemical reactors.

Main publication:

Zilius, M., Samuiloviene, A., Stanislauskienė, R., Broman E., Bonaglia S., Meškys R., Zaiko A. Depicting temporal, functional, and phylogenetic patterns in estuarine diazotrophic communities from environmental DNA and RNA. Microb. Ecol. 2020. https://doi.org/10.1007/s00248-020-01562-1

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 plan to investigate 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.

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).

Research Council of Lithuania. Diversity and Distribution of Viruses Infecting Sulphur 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 sulphur 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 sulphur, 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 sulphur in the aquatic environments.

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. 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.

Main publication:

Koplūnaitė, M., Butkutė, K., Meškys, R., Tauraitė, D. Synthesis of pyrimidine nucleoside and amino acid conjugates. Tetrahedron Lett. 2020, 61: 152598.

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

Detection of Metabolites in Yeast Cultures. UAB Neurostrain, Lithuania, Dr R. Meškys.

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

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

 

DEPARTMENT OF MOLECULAR CELL BIOLOGY

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

STAFF

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

RESEARCH INTERESTS

Evaluation of proliferation, differentiation and apoptosis signalling 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 signalling molecules in chemotherapeutic drugs-induced pathway for establishment of new strategies for targeted anti-cancer treatment of many tumours

RESEARCH PROJECTS CARRIED OUT IN 2020

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.

Assessment 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 publications:

Gasiūnienė, M., Valatkaitė, E., Navakauskienė, R. Long-term cultivation of human amniotic fluid stem cells: The impact on proliferative capacity and differentiation potential. J Cell Biochem. 2020, 121(7): 3491–3501.

Zentelytė, A., Gasiūnienė, M., Treigytė, G., Baronaitė, S., Savickienė, J., Borutinskaitė, V., Navakauskienė, R. Epigenetic regulation of amniotic fluid mesenchymal stem cell differentiation to the mesodermal lineages at normal and fetus-diseased gestation. J Cell Biochem. 2020, 121(2): 1811–1822.

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., Navakauskienė, R. The epigenetic treatment remodel genome-wide histone H4 hyper-acetylation patterns and affect signaling pathways in acute promyelocytic leukemia cells. Eur J Pharmacol. 2020, 9, 889: 173641.

Research Council of Lithuania. Targeted Research in Smart Specialization Areas. Project Designing of the Patient-Specific, Heterogeneous Lung Cell ex vivo Model System for Drug Efficiency Prediction in Personalized Oncotherapy (No. 01.2.2-LMT-K-718-01-0072). Dr A. Kalvelytė. 2018–2022.

During the implementation of the project in 2020, by using a panel of phenotypically and genotypically different lung cancer and stem cell lines, we have studied dependency of the intracellular signalling molecules on extracellular contacts. Modelling different cellular states adherent, single-cell suspension, and aggregated cells were compared in respect of cellular signalling. The studies revealed cell state-dependent changes in the phosphorylation of protein kinases studied, pointed out differences in ERK1/2 activation between the cell lines under detachment conditions, highlighted the different dependency of molecules of the same signalling pathway, JNK and c-jun, on cell-cell contacts. Within the frame of the project, as a chapter of the book, we have published an overview of current ex vivo tumour cell models and clinically relevant platforms to functionally test drug combinations for cancer treatment prediction in individual patients, encompassing the phenotypic cell heterogeneity and solving the problem of cancer resistance.

Main publication:

Stulpinas, A., Imbrasaitė, A., Krestnikova, N., Kalvelytė, A.V. Chapter 7. Recent Approaches Encompassing the Phenotypic Cell Heterogeneity for Anticancer Drug Efficacy Evaluation. IntechOpen Tumour Progression and Metastasis. 2020; ISBN: 978-1-78985-350-6.

Science Promotion Fund of Vilnius University. Neurogenic Differentiation of Human Amniotic Fluid Mesenchymal Stem Cells (No. MSF-JM-4). Dr G. Valiulienė. 2019–2020.

Human amniotic fluid is a very attractive source of stem cells, as human amniotic fluid mesenchymal stem cells (hAF-MSCs) possess intermediate characteristics between embryonic and adult stem cells and have the broader differentiation potential compared to mesenchymal stem cells obtained from other sources (e. g. bone marrow). Although much research is performed in order to evaluate the possible applicability of hAF-MSCs in the clinical practice, more thorough and concise investigation of hAF-MSCs neurogenic potential is still lacking. Therefore, in this study we investigated the neurogenic and neurotrophic potential of hAF-MSCs, obtained from normal foetus unaffected gestations.

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.

According to the World Health Organization, annually around 350 million people suffer from depression worldwide. It has been estimated that only less than one third of depression patients reach remission after 12 weeks of initial antidepressant treatment, while another 30% of major depressive disorder patients are eventually diagnosed with drug treatment resistant depression. Therefore, aim of this project is to systematically explore the physiology of drug resistant depression by studying markers related to pathology manifestation and therapy-induced reorganization of brain.

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.

Research indicates a third of depressive patients to develop a treatment resistant depression (TRD). Thus the further investigation and development of novel more effective therapies, particularly those designed for TRD, are of great importance. Therefore, in the study we aim to investigate the applicability of mesenchymal stem cell (MSC) derived exosomes for cell-free TRD therapy.

International Research Projects

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

The European Cooperation in Science and Technology Action brings together for cooperation of young researchers and scientists from 37 different countries. The main aim of collaboration - understanding and exploitation of the mechanisms and therapeutic actions of perinatal derivatives. This COST Action covers academic, clinical, and industry expertise to enhance both basic understanding and translational potential of perinatal derivatives.

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;
• member of Lithuanian Stem Cell Researchers Association;
• member of Federation of European Biochemical Society;
• member of International Perinatal Stem Cell Society.

Dr A. V. Kalvelytė –

• member of Lithuanian Stem Cell Researchers Association;
• member of Federation of European Biochemical Society.

Dr V. Borutinskaitė –

• member of Lithuanian Stem Cell Researchers Association;
• member of Federation of European Biochemical Society.
   

LABORATORY OF BIOORGANIC COMPOUNDS CHEMISTRY

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

STAFF

Senior researcher: Dr R. Jančienė.
Researcher: 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 2020

Project Supported by University Budget

Investigation of the Synthesis and Structure of Modulators and Catalysts of Biological Processes. Dr R. Jančienė. 2017–2020.

• Synthesis of model tetraethylene glycol (PEG) derivatives bearing different α- and ω-substituents.
• Investigation of the synthesis of disubstituted s-tetrazine derivatives.
• Investigation and optimization of synthesis methods of indole derivatives.

The possibility to synthesize branched chain polyethylene glycol derivatives was studied. Reaction of mono- and diaminosubstituted ethylene glycols with dimesylethylene glycol derivatives was investigated. Mono-aminotetraethylene glycol was used as starting compound for this investigation. Mono-aminotetraethylene glycol was prepared via a sequence of 3 reactions: (1) synthesis of monomesyl-TEG, (2) synthesis of TEG monoazide, (3) reduction of azide group with triphenylphosphine to amino group. By analogy, diaminosubstituted TEG derivative was synthesized from dimesyltetraethylene glycol. Further treatment with dimesylpolyethylene glycols of various length led to the branched polyethylene glycol derivatives. Optimal reaction conditions for the synthesis of disubstituted amino derivatives were established in various volumes. Results of these studies were used for the synthesis of branched chain ethylene glycol derivatives of varying degrees of polymerization (n 4÷18) of both the amino-containing component and the dimesylated derivatives.

The synthesis of dimethyl 1,2,4,5-tetrazine-3,6-dicarboxylate was investigated and multistep synthesis scheme was created. The synthesis of dimethyl 1,2,4,5-tetrazine-3,6-dicarboxylate was performed in 4 steps. After optimization of each step, the total yield of disubstituted tetrazine derivative was 40%.

DAPI (4′,6-diamidino-2-phenylindole) is a fluorescent dye which exhibits several binding modes to DNA and it has been widely utilized as a DNA specific probe for flow cytometry, chromosome staining, DNA visualization and quantitation, and has become now an important tool in molecular biology. The DAPI structure has been modified by replacing the phenyl group with substituted phenyl or heteroaryl rings. DAPI synthesis scheme we developed was adapted for preparation of 2-(4-amidino-3-methylphenyl)-1H-indole-6-amidine. Optimal reaction conditions were determined after a series of experiments.

Main publications:

Voitechovič, E., Vektarienė, A., Vektaris, G., Jančienė, R., Razumienė, J., Gurevičienė V. 1,4-benzoquinone derivatives for enhanced bioelectrocatalysis by fructose dehydrogenase from Gluconobacter Japonicus: towards promising D-fructose biosensor development. Electroanalysis. 2020, 32(5): 1005–1016.

Polmickaite-Smirnova, E., Šarlauskas, J., Krikštopaitis, K., Staniulyte, Z., Anusevičius, Z. Preliminary investigation of the antibacterial activity of antitumor drug 3-amino-1,2,4-benzotriazine-1,4-dioxide (Tirapazamine) and its derivatives. Applied Sciences (Switzerland). 2020, 10(12): 4062.

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 Triethylene Glycol. Contract with Ramidus AB (Sweden). Dr R. Jančienė.

Development of Viable Methods for the Synthesis of Various Organic Compounds and Preparation of Their Experimental Batches. Contract with Synthon Chemicals GmbH (Germany). Dr R. Jančienė.

Studies on Polymeric Encapsulation of Bacteria and Their Enzymes. Contract with UAB Ekorama. Dr R. Jančienė.

Study of the Synthesis of Tetrazine Derivatives. Contract with UAB Sanobiotech. 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 Experimental Samples of DAPI Dihydrochloride. Contract with UAB Elymus. Dr R. Jančienė.

Optimization of Used Oil Refining Technology. Contract with UAB Nagenus. Dr R. Jančienė.

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)

 

PROTEOMICS CENTRE

7 Saulėtekio Ave, 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 A. Kaupinis, Dr M. Ger, Dr N. Dreižė.
Doctoral students: S. Urnikytė, E. Žalytė, G. Karzaitė, I. Meškinytė, J. Žukas.

RESEARCH AREAS

High throughput proteomics analysis of cell signalling
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 2020

Project Supported by University Budget

New Technologies for Tumour Diagnosis and Treatment Based on Nano-Materials and Proteomics. Dr M. Valius. 2014–2020.

National Research Projects

Research Council of Lithuania. Development of Novel Proteomics-based Drug Selection Approach for Pancreatic Cancer Individualized Therapy (No. S-SEN-20-16). Project manager prof. P. Schemmer, work package manager Dr M. Valius, 2020–2021.

In this project, we seek to develop a new drug selection approach for patients with PDAC based on differential high-throughput proteomic analysis, phosphoproteomics and kinomics using surgically removed patient tumor samples and primary cell lines derived from the same tumors. Novel bioinformatic methods of proteins database analysis will enable us to predict the list of promising anticancer agents and to evaluate their efficiency in vitro using tumor-derived patient cell lines. Moreover, in case of conventional treatment, our approach will be correlated with the treatment outcome in clinic. In addition, we will continue the search for predictive treatment protein markers in the urine and blood, which will be correlated with patients’ treatment follow up and with the in vitro data of cell lines. All this will allow us to validate our method and will enable the discovery of new drugs and their combinations for further clinical trials for PDAC treatment.

Main publication:

Peterman, E., Valius, M., Prekeris, R. CLIC4 is a cytokinetic cleavage furrow protein that regulates cortical cytoskeleton stability during cell division. J Cell Sci. 2020, 14, 133(9): jcs241117.

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

University of Colorado, Denver (USA)
Swiss Institute of Bioinformatics, Geneva (Switzerland)
Aargus University, Aargus (Denmark)
University of North Carolina School of Medicine, Department of Pharmacology, Chapel Hill (USA)
National Cancer Institute, Vilnius (Lithuania)
Vilnius University Hospital Santaros Klinikos, Vilnius (Lithuania)
State Pathology Center, Vilnius (Lithuania)
Lithuanian University of Health Sciences, Institute of Cardiology, Kaunas (Lithuania)

OTHER RESEARCH ACTIVITIES

Dr M. Valius –

• guest editor of Cells (Research on Cancer Proteomics);
• editorial board member of the journal MAP Kinases.

Dr J. Cicėnas –

• collection editor (Kinases and cancer) of Cancers.

 

INSTITUTE OF BIOSCIENCES

7 Saulėtekio Ave, LT-10257 Vilnius
Tel. 239 8210
E-mail:
www http://www.gf.vu.lt
Director – Prof. Dr Habil. Juozas Lazutka
Director – Assoc. Prof. Dr Eglė Lastauskienė (since January 2021)

DEPARTMENTS OF THE INSTITUTE

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

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 2020

R. Mončiunskaitė. The influence of oral contraceptives on female cognitive functions and affective processing.
L. Baliulytė. Quantum chemical investigations of the simplest biological molecules and their processes.
R. Dulinskas. Effect of acute and chronic alcohol consumption and withdrawal to visual evoked potentials of rat’s visual system.
I. Lapeikaitė. Effect of amino acids and NMDA on electrical signalling parameters of Charophyte Nitellopsis obtuse.
E. Pipinis. Evaluation of electrical brain responses to linear chirp-modulated tones: effect of task and changes in neuropsychiatric disorders.
A. Kamarauskaitė. The habitat preferences of Common Buzzard (Buteo buteo) and interaction with other birds of prey.
R. Krasauskas. The role of Acinetobacter baumannii BfmRS system in environmental fitness and inter-bacterial competition.
A. Skerbedytė. Salinomycin and dicjloroacetate synergistically inhibit cancer cells in vitro and in vivo.
R. Petkauskaitė. Screening, characterization and functionality analysis of heteropolysaccharide degrading enzymes.
R. Bandariavičiūtė. Gene expression research in prostate adenocarcinoma tissues.
K. Stuopelytė. Research of organism fluids RNR for prostate cancer diagnostics and prognosis of the course of the disease.

MAIN CONFERENCES ORGANIZED IN 2020

Conference dedicated to the 120th birth anniversary of professor Antanas Minkevičius, 10 December 2020.
12th conference of the Lithuanian Neuroscience Association (LNA), 6 November 2020.
2nd Baltic Biophysics Conference – Open Lectures, 15 October 2020.

 

DEPARTMENT OF BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

STAFF

Professors: Dr S. Serva, Dr E. Sužiedėlienė, Dr V. Starkuvienė (part-time), Dr K. Sužiedėlis (part-time).
Associate professors: Dr V. Jonušienė, Dr D. Labeikytė, Dr A. Markuckas, Dr A. Sasnauskienė, Dr A. Zimkus.
Assistant professors: Dr A. Konovalovas, Dr A. Mikalkėnas, Dr J. Skerniškytė.
Teaching assistants: L. Aitmanaitė, N. Daugelavičienė, Dr. R. Krasauskas.
Lecturer: Z. Žitkus.
Senior researcher: Dr J. Armalytė.
Researchers: Dr V. Jonušienė, Dr A. Konovalovas, Dr D. Labeikytė, Dr A. Sasnauskienė, Dr A. Zimkus.
Research assistants: L. Aitmanaitė, N. Daugelavičienė, Dr R. Krasauskas, Dr J. Skerniškytė.
Doctoral students: E. Celitan, L. Klimkaitė, L. Kunigėnas, T. Liveikis, R. Prokarenkaitė, V. Žitkutė.

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2020

Projects Supported by University Budget

Investigation of Mechanisms of Cellular Homeostasis and Their Clinical and Biotechnological Application. Prof. Dr E. Sužiedėlienė, Prof. Dr S. Serva, Assoc. Prof. A. Sasnauskienė.

Investigation of biochemical mechanisms and components conferring resistance of viruses, bacterial and eukaryotic cells against antiviral, antibacterial and anticancer compounds: 1) cellular response to anti-cancer treatment, cellular and molecular mechanisms of acquired chemoresistance - the role of autophagy and immunoregulatory molecules; 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:

Klimkaitė, L., Armalytė, J., Skerniškytė, J., Sužiedėlienė, E. The toxin-antitoxin systems of the opportunistic pathogen Stenotrophomonas maltophilia of environmental and clinical origin. Toxins (Basel). 2020, 12(10): E635. doi:10.3390/toxins12100635.

Krasauskas, R., Skerniškytė, J., Martinkus, J., Armalytė, J., Sužiedėlienė, E. Capsule protects Acinetobacter baumannii from inter-bacterial competition mediated by CdiA toxin. Frontiers in Microbiology. 2020, 11: 1493. doi:10.3389/fmicb.2020.01493.

Sauliutė, G., Markuckas, A., Stankevičiūtė, M. Response patterns of biomarkers in omnivorous and carnivorous fish species exposed to multicomponent metal (Cd, Cr, Cu, Ni, Pb and Zn) mixture. Part III. Ecotoxicology. 2020, 29(3): 258–274. doi:10.1007/s10646-020-02170-y.

Kunigėnas, L., Stankevičius, V., Dulskas, A., Budginaitė, E., Alzbutas, G., Stratilatovas, E., Cordes, N., Sužiedėlis, K. 3D cell culture-based global miRNA expression analysis reveals miR-142-5p as a theranostic biomarker of rectal cancer following neoadjuvant long-course treatment. Biomolecules. 2020, 10(4): 613. doi:10.3390/biom10040613.

Projects Supported by University Budget

Genome and Transcriptome Analysis in Pathogenesis Studies of Rare Genetic Disorders (MSF-JM-2/2020). Participant - A. Sasnauskienė, 2020.

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 first year of the project (2020), bioinformatics analysis of the C-terminal domain (located on the outside of the bacterium) of A. baumannii Blp protein was performed. The most conserved C-terminal part of Blp was shown to consist of several predicted domains, which were divided into shorter peptides based on their predicted structure. Four fusion constructs for protein purification were created, two more are being verified. To increase the immunogenic properties of the Blp peptides, they were also displayed on virus-like particles (VLPs).

Research Council of Lithuania. National research program “Sustainability of agro, forest and water ecosystems” project The Influence of Intensive Fish Farming on Aquatic Microbiome and Resistome (No. S-SIT-20-6). Participant - J. Armalytė. 2020–2021.

Programme for the European Union Funds Investments in Lithuania measure ”Targeted Research in Smart Specialisation Areas” project Individualized Analysis of Upper Respiratory Tract Microbiome – a Novel Diagnostic and Healthcare Tool (No. 01.2.2-LMT-K-718-03-0079). Participant (project coordinator for Vilnius University) - J. Armalytė. 2020–2023.

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). Participant - A. Sasnauskienė. 2020–2021.

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. E. Sužiedėlienė –

• member of Research Council of Lithuania.

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.

DEPARTMENT OF BOTANY AND GENETICS

7 Saulėtekio Ave, 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 Habil. V. Rančelis (emeritus), Dr D. Žvingila.
Associate professors: Dr T. Čėsnienė, Dr J. Kostkevičienė, Dr V. Morkūnas (part-time), Dr R. Šiukšta (part-time), Dr K. Daniūnaitė (part-time), Dr V. Dedonytė (part-time).
Assistant professor: Dr I. Prigodina Lukošienė.
Teaching assistants: A. Stapulionytė, K. Šnipaitienė.
Lecturers: S. Juzėnas, A. Meldžiukienė, P. Venckus.
Senior researcher: Dr V. Kleizaitė.
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.
Research assistant: M. Rasimavičius.
Senior biologists: Dr J. Rukšėnienė, Dr J. Tupčiauskaitė.
Doctoral students: A. Nestarenkaitė, G. Radžiuvienė, Ž. Kapustina, R. Kubiliūtė, D. Strepetkaitė, L. Šiaulienė, D. Žalimas, D, Uljanionok, J. Sejonienė, I. Vincerževskienė, M. Babonaitė, J. Gaiževska, R. Maleckaitė, A. Šeštokaitė, B. Buragaitė-Staponkienė.

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 malignancies
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 2020

Projects Supported by University Budget

Function, Variability and Genome Structure in Higher Eukaryotes. Prof. J. R. Lazutka, Prof. S. Jarmalaitė. 2018–2022.

Recent genome-scale analyses have provided novel insights into the genomic and epigenomic landscape of various cancers, 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.). By evaluation of whole blood circulating androgen receptor transcripts we showed that they can serve as blood based biomarkers for identification of the primary resistance to abiraterone acetate and the tool to monitor de novo resistance development during abiraterone acetate treatment. Epigenetic analyses were used to identify mechanisms of lung carcinogenesis. The investigation of molecular mechanisms of combined action of dichloroacetate and salinomycin for the development of novel solutions in cancer therapy was carried out.

Main publications:

Stuopelytė, K., Sabaliauskaitė, R., Bakavičius, A., Haflidadóttir, B. S., Visakorpi, T., Väänänen, R.-M., Patel, C., Danila, D. C., Lilja, H., Lazutka, J. R., Ulys, A., Jankevičius, F., Jarmalaitė, S. Analysis of AR-FL and AR-V1 in whole blood of patients with castration resistant prostate cancer as a tool for predicting response to abiraterone acetate. The Journal of Urology. 2020, 204(1) 71–78.

Daniūnaitė, K., Šeštokaitė, A., Kubiliūtė, R., Stuopelytė, K., Kettunen, E., Husgafvel-Pursiainen, K., Jarmalaitė, S. Frequent DNA methylation changes in cancerous and noncancerous lung tissues from smokers with non-small cell lung cancer. Mutagenesis. 2020, geaa022, 1–7.

Skeberdytė, A., Sarapinienė, I., Krasko, J. A., Barakauskienė, A., Žilionytė, K., Prokarenkaitė, R., Sužiedėlis, K., Bukelskienė, V., Jarmalaitė, S. Salinomycin and dichloroacetate synergistically inhibit Lewis lung carcinoma cell proliferation, tumor growth and metastasis. Biochemical and Biophysical Research Communications. 2020, 523(4): 874–879.

Plant Polymorphism, Genome Stability and its Changing Factors. Prof. Emeritus V. Rančelis, Prof. D. Žvingila. 2016–2020.

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 Nuphar lutea individuals growing in the Lithuanian watercourses. The populations were studied in the river catchments of Lithuania: the Nemunas, the Venta and the Lielupė. The genetic structure of the populations was evaluated at six SSR (simple sequence repeats) loci. Our results indicate that anthropogenic land use activity in surrounding areas may have an effect on genetic diversity pattern of macrophyte species. Studies were carried out in collaboration with colleagues from other Lithuanian research institutions and abroad.

Besides, in vitro screening of aluminum tolerance in the collection of Lithuanian barley varieties was revived since barley is among the most acidic soil-sensitive crops. To screen the most sensitive markers of aluminum tolerance, the experiments were performed in hydroponic cultures using a bouquet of morphometric, biochemical (oxidative stress) and genetic markers in comparison to histochemical staining technique, and the most tolerant barley genotypes were selected. The analysis of aluminum tolerance was performed in cooperation with the Lithuanian Research Centre for Agriculture and Forestry.

Main publications:

Vyšniauskienė, R., Rančelienė, V., Naugžemys, D. Rudaitytė-Lukošienė, E., Patamsytė, J., Butkauskas, D., Kupčinskienė, E., Žvingila, D. Genetic diversity of Nuphar lutea in Lithuanian river populations. Aquatic Botany. 2020, 161: UNSP 103173.

Butkuvienė, J., Sinkevičienė, Z., Naugžemys, D., Žvingila, D., Skridaila, A., Bobrov, A. A. Genetic diversity of aquatic Ranunculus ( Batrachium, Ranunculaceae) in one river basin caused by hybridization. Plants. Basel. 2020, 9(11): 1455.

National Research Projects

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 Scientific Competence of Scientists, Other Researchers, Students through Practical Scientific Activity” “Development of Students' Abilities through Research during Semesters (2020–2021) 09.3.3-LMT-K-712-22-0119 Genetic Characterisation of Barley Pleiotropic Flower/Inflorescence Developmental Mutant tweaky spike Using Comparative Genomics. Assoc. Prof. Dr Raimondas Šiukšta, student Vėjūnė Pukenytė.

The genetic characterisation of barley pleiotropic flower/inflorescence developmental tweaky spike was performed using comparative genomics methods.

The Structure, Functioning in Ecosystems and Conservation of Vegetation, Algobiota and Mycobiota. Prof. E. Kutorga. 2019–2021.

Studies of species diversity, distribution and ecology of inoperculate discomycetes in Lithuania were summarised. In total, 381 species from 119 genera and 29 families have been recorded in Lithuania. A retrospective study of scientific legacy of professor Povilas Snarskis has been undertaken. The study presents a brief biography of prof. P. Snarskis, and discusses the importance of his work for Lithuanian botany. The study of the collection of the Poaceae specimens collected by P. Snarskis mainly from eastern Lithuania in 1943–1960 provided new data on abnormal growth forms of common Lithuanian grasses and the distribution of rare and endangered Poaceae species in Lithuania. The virtual conference dedicated to the 120th birth anniversary of prof. A. Minkevičius took place on December 10 2020. The participants overviewed his outstanding contributions in the development of botany, mycology and phytopathology in Lithuania was discussed.

Main publications:

Kutorga, E. Lietuvos grybai (Mycota Lithuaniae), Volume 3, Book 6: Inoperkuliniai diskomicetai (Discomycetes inoperculatae). Vilnius: Vilnius University Press, 2020. ISBN 978-609-07-0390-8.

Skujienė, G., Kuznecova, V., Jukonis, B., Juzėnas, S. New records of rare Vertiginidae (Mollusca: Gastropoda) in Lithuania. Bulletin of the Lithuanian Entomological Society. 2020, 4(32): 132–140.

Tupčiauskaitė, J., Rimgailė-Voicik, R. Professor Povilas Snarskis – life dedicated to the research of Lithuanian flora. Botanica. 2020, 26(1): 101–108.

Tupčiauskaitė, J., Rimgailė-Voicik, R., Rasimavičius, M. Newly discovered Poaceae specimens in the Herbarium of Vilnius University collected by Povilas Snarskis (1889–1969). Botanica. 2020, 26(2): 138–149.

National Research Projects

Research Council of Lithuania. Book Lithuanian fungi: Helotiales and Rhytismatales- final preparation and publishing (No. S-LIP-19-24). Prof. E. Kutorga.

The main result of the project was the final preparation of the book „Lietuvos grybai (Mycota Lithuaniae), Volume 3, Book 6: Inoperkuliniai diskomicetai (Discomycetes inoperculatae)”. The monograph provides: general information about inoperculate discomycetes and their research history in the world and in Lithuania, descriptions of 381 species from 119 genera, 29 families, 8 orders and 4 classes (structure, ecology, distribution in Lithuania and in the world, notes), nomenclature of scientific and Lithuanian names, identification keys to fungal genera and species, abstracts in Lithuanian and English, bibliographic references, glossary of used terms, and indexes of Latin and Lithuanian names of organisms. The book is illustrated with black and white line drawings, and color photographs of fungi.

Main publication:

Kutorga E. Lietuvos grybai (Mycota Lithuaniae), Volume 3, Book 6: Inoperkuliniai diskomicetai (Discomycetes inoperculatae). Vilnius, Vilnius University Press. 2020, 398 p.

Research Council of Lithuania. Modern Technologies to Resolve a Complex Structure of Tumour (No. P-MIP-17-189). Prof. S. Jarmalaitė, R. Kubiliūtė. 2017–2020.

The main objective of the present study is to investigate the intrinsic and extrinsic complexity of renal and pulmonary tumors for improved understanding of molecular mechanisms of cancer development and progression. Genomic profile cellular subclones from the same renal tumour were analyzed in order to resolve intratumoral and extratumoral heterogeneity of cancer and understand clinical consequences of genetic complexity of tumour.

Ministry of Environment of Republic of Lithuania. Preparation of the Edition Red Data Book of Lithuania. Participants from VU: Dr E. Kutorga, Dr Habil. J.R. Naujalis, Dr I. Prigodina Lukošienė, Dr M. Rasimavičius.

The proof of a forthcoming new edition of the Red Data Book of Lithuania was reviewed and updated during the project in 2019.

Research Council of Lithuania. Modern Technologies to Resolve a Complex Structure of Tumour (No. P-MIP-17-189). Prof. S. Jarmalaitė. 2017–2020.

The main objective of the present study is to investigate the intrinsic and extrinsic complexity of renal and pulmonary tumours for improved understanding of molecular mechanisms of cancer development and progression. Genomic profile cellular subclones from the same renal tumour has been analysed in order to resolve intratumoral and extratumoral heterogeneity of cancer and understand clinical consequences of genetic complexity of tumour.

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

Nature Research Centre (Lithuania)
Vytautas Magnus University (Lithuania)
National Cancer Institute (Lithuania)
Institute for Ecosystem Studies (Florence, Italy)
Prostate Cancer Research Centre, University of Tampere (Finland)
Department of Pathology, University of Helsinki
HUSLAB, Helsinki University Hospital (Finland)
University of Bologna (Italy)
Papanin Institute for Inland Water Biology (Russia)

OTHER RESEARCH ACTIVITIES

Prof. V. Rančelis –

• editorial board member of the journal Ecological Genetics (Russian Academy of Sciences);
• member of the Lithuanian Academy of Sciences.

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;
• member of the Sub-commission on Terminology of The State Commission of the Lithuanian Language (as expert in Mycology);
• Chairman of the Organizing Committee of the conference dedicated to the 120th birth anniversary of professor Antanas Minkevičius.

Dr M. Rasimavičius –

• member of the International Equisetological Association (IEA);
• member of the sub-commission on Terminology of The State Commission of the Lithuanian Language (as expert in Botany).

Prof. J. R. Lazutka –

• editor of the journal Open Life Sciences.

Assist. Prof. I. Prigodina Lukošienė –

• member of the Scientific Council of the Nature Research Centre.

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

• Dr Kristina Daniūnaitė - Medal of the Order of the Grand Duke of Lithuania Gediminas for the contribution to the fight against the coronavirus pandemic;
  The Minister of Health medal "For significant contribution to the health of the Lithuanian people".

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

• Ernestas 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.

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES

• Dr Kristina Daniūnaitė. SARS-CoV-2 Termporary Diagnostic Laboratory (TDL) was established in 2020, during COVID19 pandemic, to increase the testing capacities in Lithuania. In addition to testing, the identificatin of the SARS-CoV-2 in the wastewater sludge and surface samples was performed. As a project of Lithuanian government the Pooled-sample testing metodology was developed in the TDL.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Butkuvienė J. – articles, interviews in mass dedia: Grožis reikalauja aukų: ar natūralios vandens augalų bendrijos išliks tvarios? ["Beauty requires sacrifices: will natural aquatic plant communities remain sustainable?]. – Sodo spalvos, Nr. 11 (287): 42–43; Interview on LRT.lt portal, Science and IT topic. 09 October 2020.
• Kutorga E. – participation in the LRT radio programme “10-12”, 30 January 2020; interview for the BNS, publication in “Delfi.lt” site, 14 February 2020; Interview at TV programme “Žinios” (LNK), 26 March 2020.
• Rasimavičius M. – artciles in national and regional press; participation in LTV programmes.

DEPARTMENT OF MICROBIOLOGY AND BIOTECHNOLOGY

7 Saulėtekio Ave, LT-10257 Vilnius
Tel. 239 8205
E-mail:
Head: Prof. Dr Lilija Kalėdienė

STAFF

Professors: Dr L. Kalėdienė, Dr N. Kuisienė, I. Girkontaitė (part-time).
Associate professors: Dr E. Lastauskienė, Dr V.Kašėta (part-time).
Assistants: Dr A. Gegeckas, Dr R.Gudiukaitė, Dr R. Kananavičiūtė, Dr R. Petkauskaitė, Dr A. Gricajeva.
Lecturers: Dr J. Raugalas, J. Lebedeva, J. Jurgelevičiūtė, Dr R.Ražanskas (part-time), Ž. Dapkunas (part-time).
Researcher: Dr A. Kaunietis.
Specialists: J. Lekavičiūtė, R. Jurkevičienė.
Doctoral 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 2020

Projects Supported by University Budget

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

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 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 substances or aromatic 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 a 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. Antibacterial compounds, eukaryotic microorganisms’ β-glucans, a diverse group of polysaccharides, exhibiting immunostimulating activity, are among the research group’s topics. 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 publications:

Buchovec, I., Gricajeva, A., Kalėdienė, L., Vitta, P. Antimicrobial photoinactivation approach based on natural agents for control of bacteria biofilms in spacecraft. International Journal of Molecular Sciences. 2020, 21(18): 6932. DOI: 10.3390/ijms21186932.

Kumar, A., Gudiukaitė, R., Gricajeva, A., Sadauskas, M., Malūnavičius, V., Kamyab, H., Sharma, S., Sharma, T., Pant, D. Microbial lipolytic enzymes - promising energy-efficient biocatalysts in bioremediation. Energy. 2020, 192: 116674. DOI: 10.1016/j.energy.2019.116674.

Molecular Microbiology of Prokaryotes for Modern Biotechnology and Biopharmacy. Prof. Dr N. Kuisienė. 2020.

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 Gram-negative pathogenic bacteria in Lithuanian hospitals. Our study revealed intensive inter- and intrahospital spread of these pathogenic bacteria usually carrying 1–7 genes conferring β-lactam resistance. In order to contribute to the development of novel antimicrobial compounds against these drug-resistant bacteria, screening for polyketide synthases and nonribosomal peptide synthetases genes was carried out in bacterial strains isolated from Krubera-Voronja Cave. Mining for bacteriocins, polyketide synthases, and nonribosomal peptide synthetases in the genomes of both thermophilic (Geobacillus) and mesophilic (Paenibacillus) endospore forming bacteria was also performed.

Main publication:

Kananavičiūtė, R., Kvederavičiūtė, K., Dabkevičienė, D., Mackevičius, G., Kuisienė, N. Collagen-like sequences encoded by extremophilic and extremotolerant bacteria. Genomics. 2020, 112(3): 2271–2281.

Strategies in Antimicrobial Therapy and Protein Engineering. Assoc. Prof. E. Lastauskienė. 2020.

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 enzyme and constructed the new fused lipolytic protein and analyzed his application in the ester synthesis. Lipases as biocatalysts can be used in organic synthesis reactions to produce precursors of drug and bioactive compounds against microorganisms related to skin infections.

Main publication:

Savickaitė, A., Druteika, G., Sadauskas, M., Malūnavičius, V., Lastauskienė, E., Gudiukaitė, R. Study of individual domains' functionality in fused lipolytic biocatalysts based on Geobacillus lipases and esterases. International Jurnal of Biological Macromolecules. 2021, 168: 261–271. DOI:10.1016/j.ijbiomac.2020.12.026.

Druteika, G., Sadauskas, M., Malūnavičius, V., Lastauskienė, E., Taujenis, L., Gegeckas, A., Gudiukaitė, R. Development of a new Geobacillus lipase variant GDlip43 via directed evolution leading to identification of new activity-regulating amino acids. International Journal of Biological Macromolecules. 2020, 151: 1194–1204. DOI: 10.1016/j.ijbiomac.2019.10.163.

Kumar, A., Gudiukaitė, R., Gricajeva, A., Sadauskas, M., Malūnavičius, V., Kamyab, H., Sharma, S., Sharma, T., Pant, D. Microbial lipolytic enzymes - promising energy-efficient biocatalysts in bioremediation. Energy. 2020, 192: 116674. DOI: 10.1016/j.energy.2019.116674.

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.

During the current project, the effects and applications of antimicrobial photoinactivation technology (API) on the planktonic bacteria and formed biofilms, their integrity, and vitality were investigated. API based technology has some prominent advantages over the chlorhexidine and UV irradiation. But the limiting factor of the applicability is a necessity of rather high illumination doses and application (spread) of PS solution on surfaces in microgravity conditions. The main focus was on the environment, health, and safety-friendly natural agents (photosensitizer (PS)), which could be applied in closed-loop systems. The feasibility to develop an effective, safe for humans 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.

Main publication:

Buchovec, I., Gricajeva, A., Kalėdienė, L., Vitta, P. Antimicrobial photoinactivation approach based on natural agents for control of bacteria biofilms in spacecraft. Int. J. Mol. Sci. 2020, 21: 6932.. https://doi.org/10.3390/ijms21186932.

National Research Projects

Research Council of Lithuania. Discovery of Novel Bioactive Microbial Compounds in the Unique Environment: an Investigation of the Diversity, Prevalence and Expression (No. S-MIP-17-21). Project leader - Dr Nomeda Kuisienė. 2017–2020.

The objective of the project Bioaktibiomas is the evaluation of the diversity, prevalence and expression of bioactive compounds biosynthesis genes in both culturable and unculturable bacteria of the deepest Earth’s cave – Krubera-Voronja cave.

It was determined that 79.1% of the all studied strains have polyketide synthase (PKS) and/or nonribosomal peptide synthetase (NRPS) biosynthetic genes. Although more PCR products of the PKS and NRPS genes were detected in the case of the phenotypically active strains (88.9% of such strains), most strains (72.2%) without phenotypic antibacterial activity also gave PCR products of the correct size. Similarity of the identified PKS and NRPS sequences with those in the public databases varied and was in the range of 74-99%. Putative products (polyketides and nonribosomal peptides) of the identified PKS and NRPS were also determined. They were spinosad, bacillibactin, and surfactin. Antibacterial, insecticidal, antifungal, anticancer, antiviral, antimycoplasmic, and thrombolytic bioactivities have been reported for these compounds. Most products (nonribosomal peptides) of the identified NRPS are unknown.

Qualitative expression analysis showed that the identified biosynthetic genes can be not expressed at all, can be expressed constitutively, or their expression can depend on the culture growth phase. From one to four constitutively expressed biosynthetic genes were determined in all tested strains irrespective of their bioactivity. Quantitative expression analysis revealed that constitutively expressed biosynthetic genes can be differently expressed – their expression can depend on the availability of the nutrients as well the culture growth phase.

During metagenomics studies of the Krubera-Voronja Cave samples, it was determined that absolute majority of the identified PKS and NRPS genes encode enzymes involved in the biosynthesis of the novel, previously unknown bioactive compounds. Despite clustering of ketosynthase  (KS) and ketosynthase β (KSβ) sequences from our study with ketosynthases from the reference pathways, sequence similarity was low. Therefore, polyketides that could be produced by these enzymes, were not predicted. The only exceptions were two OTU of KS, that were predicted to participate in biosynthesis of angucycline group antibiotics. Similarly, adenylation domains of NRPS from our study clustered with adenylation domains from the reference pathways, but sequence similarity was low, and the substrate amino acid differed. Good correlation between phylogenetic analysis, sequence similarity and substrate amino acid analyses was found only for three OTUs. Two of these OTUs were predicted to participate in biosynthesis of massetolide A, while was predicted to be involved in biosynthesis of surfactin. Taxonomic diversity analysis showed that most PKS sequences could be attributed to actinobacteria Streptomyces – 41.7% of KSα and 91.3% of KSβ sequences. NRPS sequences instead were diverse and were assigned to Actinobacteria, Cyanobacteria, Firmicutes, Chloroflexi, Planctomycetes, Deinococcus-Thermus, Verrucomicrobia, and other bacterial phyla.

Main publications:

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.

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, vol. 81(1), 110-121.

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 E. 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 phyla 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.

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 E. 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.

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.

Assoc. Prof. Dr E. Lastauskienė -

• Head of FEMS education group of Lithuanian Microbiological Society.

Asisst. Dr A. Gegeckas -

• FEMS delegate of Lithuanian Microbiological Society.

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

• Dr Eglė Lastauskienė - Presidential award of the Medal of the Order of the Grand Duke of Lithuania Gediminas for the contribution to the fight against the coronavirus pandemic;
  The Minister of Health medal "For significant contribution to the health of the Lithuanian people".

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES

• Dr Eglė Lastauskienė. SARS-CoV-2 Termporary Diagnostic Laboratory (TDL) was established in 2020, during COVID19 pandemic, to increase the testing capacities in Lithuania. In addition to testing, the identificatin of the SARS-CoV-2 in the wastewater sludge and surface samples was performed. As a project of Lithuanian government the Pooled-sample testing metodology was developed in the TDL.

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 – interviewsfor LTV; public lecture at Cafe Scientifique: Human and microbiota: who controls whom?
• Renata Gudiukaitė – interview for LTV; contributed to the international conference The COINS 2020; workshop for high school students 2020; lecture for School of Young Biochemists.

 
DEPARTMENT OF NEUROBIOLOGY AND BIOPHYSICS

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

STAFF

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

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2020

Projects Supported by University Budget

Theoretical, Electrophysiological and Psychophysical Investigation of Information Coding and Processing. Prof. O. Rukšėnas., Prof. A. Alaburda, Dr. I. Griškova-Bulanova, Dr. V. Kisnierienė. 2016–2020.

We investigated hemispheric asymmetry of foreign language and visual working memory (VWM) processing by assessing participants’ behavioral metrics (response accuracy, reaction time, laterality index), evaluating links between language and VWM processing, and the effect of handedness. 83 volunteers (28 men, age 23 ±2 years) performed the translingual lexical decision task (TLDT), VWM task and completed the Edinburgh Handedness Inventory. Our study showed that the left hemisphere is dominant for foreign language and VWM processing. There was no direct correlation between laterality indices of language detection and working memory tasks, indicating that the left hemisphere advantage in visual working memory is independent from the left hemisphere language dominance.

The phase-locking and strength of slow gamma-band responses at 40Hz and at the individual peak (range 35–51 Hz, mean at 41 Hz) show positive correlation to the performance time on complex cognitive tasks for problem solving and planning in healthy young adults.

The phase plots were introduced for the qualitative analysis of the behavior of synaptic potentiation model. Based on the analysis results, we proposed the modification model to fulfil the requirements for bistability:
1) nitric monoxide dependent release of glutamate is described by Michaelis-Menten kinetics based member; 2) decay of nitric monoxide is described by two separate processes – linear and Michaelis-Menten kinetics based one.

Effect of different potassium channel inhibitors on electrical parameters of cytoplasmic droplets of Nitellopsis obtusa (Characeaen) and electrical signalling of intact single cells were investigated using glass-microelectrode technique in patch clamp, current-clamp and voltage-clamp modes. The effect of Cs⁺, Ba²⁺, TEA ions and agitoxin on the single channels of Nitellopsis obtusa cells and on parameters of action potentials as well as current transients during excitation was evaluated.

It was found that Cs⁺ in a concentration- and voltage-dependent way blocks 72 pS ion channels in the tonoplast of Nitellopsis obtusa by causing rapid channel flickering; the conductance of the 72 pS ion channels in the tonoplast of Nitellopsis obtusa depends on the concentration of K⁺ ions. The potential-dependent decrease of ion channel conductance was attributed to fast ion channel flickering induced by Cs⁺ ions rapidly associating and dissociating from the channel pore. We also tested the action of slow K⁺ ion channel blocker Ba²⁺ and confirmed that its effect is dissimilar to that of Cs⁺. Classical potassium channel inhibitor TEA diminished open probabilities of potassium channels in positive voltages. 2 open and 3 closed states of registered channels were confirmed. Agitoxin increases the amplitudes of currents of 75 pS conductivity channels at negative voltages (V≤-80 mV), presumably by attenuating rapid channel opening, but does not affecti the probability of opening and conductance.

Cs⁺ ions more than Cl^- ions increase the duration of the action potentials of N. obtusa and elicit a characteristic change of their shape. Another K⁺ channel blocker TEA caused the same effect as Cs⁺ on AP parametters. Cs⁺ ions more than Cl^- ions increase the amplitude of current transients during excitation of Nitellopsis obtusa.

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

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. Temporary Principles of Coding of Stable Image (No. MSF-LMT-3). 2019–2022. Participant from department: Dr A. Šoliūnas.
Two psychophysical experiments were performed:
1) The influence of eye movements on the disappearance and recovery of the stabilized image on retina using two types of stimuli, real and illusory figures.
2) The influence of eye movements on the disappearance and recovery of stabilized real figures on retina when stimuli are presented in different places in space in respect of fixation point.
It was found that eye movements increase before the figure recovers and decrease before the figure disappears. Eye blinks are also involved in the process of perceptual recovery, but their effect is smaller. The disappearance of visual illusion before the fading of real object suggests that eye movements suppression affects inference of perceived world in two stages. First as most probable object perception and second as real object perception. Eye movements are likely to promote the likelihood of perceptual guessing.
New method of evaluation of all possible eye movements is proposed: the calculation of the standard deviation of the gaze displacement from the fixation point in the selected time interval.

VU Science Fund grant Nr. MSF-JM-5/2020 40Hz Auditory Steady-State Response: Dependence on Stimulation Duration. Leader - E. Pipinis. 2020.
Alongside the onset processes, the steady-state development, and actual steady-state phases of the reponse were extracted. The actual steady-state phase is observed only with stimulation durations over 500ms.

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). 2019–2023. Project leader - Dr A. Burokas (VU BchI). (EU Funds Investment Action Program 2014-2020, Brain Attraction and Reintegration (SMART) Program). Participants: Dr R. Buišas, PhD student R. Dulinskas, G. Urbonaitė.

Behavioral experiments with mice were performed. Different types of behavioral tests were used to study mice sensory-motor functions, memory, learning and anxiety-like behavior and experimental data analyzed.

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” (Student research III call (2019–2020) 09.3.3.-LMT-K-712-16-0235 Changes in Electrophysiological Properties of Hippocampal Pyramidal Neurons during Postnatal Development in Wild-Type Mice. Leader - Dr A. Alaburda, participant - Neurobiology MSc student K. Vitkutė.

During the project the student implemented and optimized the technique for electrophysiological registration from acute mouse brain slices. A transgenic line of mice with knockout Xkr8 scramblase was bred.

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 Scientific Competence of Scientists, Other Researchers, Students through Practical Scientific Activity” Development of Students' Abilities through Research During Semesters. 2020–2021. Leader - Dr A. Alaburda, participant - Neurobiology MSc student K. Vitkutė.

During the project the synaptic activity and intrinsic firing properties of postnatal mouse hippocampal pyramidal CA1 neurons were recorded and evaluated. Substantial developmental changes following distinct timelines were found both in terms of synaptic maturation and firing properties, suggesting a close interdependency of these neuronal characteristics during development.

Research Council of Lithuania. Lateralization of Cerebral Hemispheres in Foreign Language and Working Memory Processing (code 09.3.3.-LMT-K-712-22-0170). November 2020–April 2021. Project leader R. Grikšienė, student I. Pretkelytė.

The aim of the project was to evaluate brain functional lateralization in a processing of foreign language (English) and working memory. During the first part of the project, 99 participants performed a translingual lexical decision task (language lateralization) and a change detection task (working memory lateralization). The preliminary results show that performance of both tasks was better when stimuli were presented in the right visual hemi-field and processed in the left hemisphere.

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 rofile. Head of VU part I. Griškova-Bulanova. 2020–2022.

In 2020, University students in Lithuania filled in questioinaries regarding their Internet usage and experienced psychopathology and participated in electrophysiological assessment of brain activity. The importance of the inclusion of impulsivity factor in the studies analyzing longitudinal effects of PIU on mental distress during COVID-19 pandemic was shown.

Research Council of Lithuania. Screening for Treatment of Neurodegenerative Disorders (No. 01.2.2-LMT-K-718-03-0021). 2020–2023. Head of project: Dr Evaldas Čiplys (GMC, BTI). Participants: Dr R. Buišas, Dr V. Vengelienė, T. Paulauskas.

Experimental setup for future experiments with rodents was developed with focus on designing new experimental equipment for behavioral studies.

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

Experimental setup for future behavioral experiments with mice was developed and new behavioral tests were adapted.

International Research Projects

Marie Sklodowska Curie Actions Individual Fellowship. 2018–2022. Dr U. Neniškytė.

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 act 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.

Lithuania - Poland research project. Long-Distance Electrical Signaling Systems in Plants – Adaptation to the Change from Water to Terrestrial Environment. 01 October 2018–30 September 2021. LT leader Dr V. Kisnierienė.

Electrophysiological research has been conducted in order to evaluate the effect of TPC channel blockers on electrophysiological parameter of macroalgae Nitellopsis obtusa. Two-electrode voltage clamp technique enabled recording of alterations of excitation current transients, while current clamp technique was employed to register changes in membrane resting potential as well as parameters of action potentials after exposure to a particular bioactive compound. It was found that known drugs trans-Ned 19, verapamil and tetrandrine, used for therapy because of their action as Ca2+ channel blockers, affect electrophysiological parameters of Nitellopsis obtusa.

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

In 2020, EEG data from musicians perfroming a simple musical piece with intended emotion was collected.The data is being analysed for a subsequenct implementation to the BCMI system.

The Processing of Highly Salient and Biologically Relevant Emotional Stimuli: Gender Differences and Relationship to Sex Steroids. AGREEMENT NO. 2020/7 Baltic-German University Liaison Office is supported by the German Academic Exchange Service (DAAD) with funds from the Foreign Office of the Federal Republic Germany. June–December 2020. Project leader R. Griksienė.

The aim of the project was to strengthened cooperation and share knowledge between project partners from Vilnius University (Lithuania), University of Tübingen (Germany), and Estonia, University of Tartu (Estonia). The project laid a strong foundation for future international collaboration in the field of emotion research and psychoneuroendocrinology. During the project a study for emotion perception and regulation was designed and was started to perform at Vilnius University. In addition, several events were organized: the starting meeting, the webinar „From emotion perception to emotion regulation: workshop on socio-emotional functioning“, presentations in the Conference of Lithuanian Neurosciences Association.

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

In 2020, EEG data was collected for identification of individual gamma peaks and search of associations with behavioural performance.

Marie Sklodowska Curie Actions Individual Fellowship. 2020–2022. Dr U. Neniškytė, Dr A. Parimisetty.

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 act 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.

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

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

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.

Assoc. Prof. 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.

Assoc. Prof. R. Grikšienė –

• member of the Lithuanian Neurosciences Association;
• member of the International Society for Brain Electromagnetic Topography.

Assoc. Prof. V. Kisnierienė –

• member of the Lithuanian Biophysical society;
• 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);
• member of the Biophysical Society (USA).

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.

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 member of FENS Regional meeting;
• 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).

Dr U. Neniškytė –

• member of the Young IBRO Committee;
• member of the Lithuanian Neurosciences Association;
• member of the Biochemical Society;
• member of Lithuanian Biochemical Society;
• member of Society for Neuroscience.

Dr A. Voickas –

• member of the Lithuanian Neurosciences Association.

Dr R. Guzulaitis –

• member of the Lithuanian Neurosciences Association.

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.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Neniškytė U. – meetings with secondary school pupils; interview for TV on autism: myths and reality; lectures for secondary school teachers; presentation at the LOGIN conference on brain-machine interface developments; virtual meeting with high school students at Jurbarkas A. A. Giedraicio gymnasium; presentation at the AKADE forum on brain development and learning.
• Rukšėnas O. – lectures “Neuroscience news”, “Evolution of nervous system” and others, interviews.
• Grikšienė R., Mončiunskaitė R. – lectures, articles on emotions, stereotypes etc.
• Šimkutė D. – Webpage www.bernardinai.lt „Wellbeing of students in Lithuania – under the magnifying glass: a broad research is ongoing“; online program Science Soup.
• Mitkus M. – meeting with the secondary school pupil in Kaisiadorys; popular science article “Where do birds look and what do they see?” in nature magazine the Birds (Paukščiai).

 

DEPARTMENT OF ZOOLOGY

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

STAFF

Professors: Dr S. Podėnas, Dr Habil. R. Rakauskas, Dr K. Arbačiauskas (part-time).
Associate professors: Dr E. Bukelskis, Dr J. Turčinavičienė, Dr V. Podėnienė, Dr V. Sruoga (part-time), Dr A. Petrašiūnas.
Assistants: Dr G. Skujienė, Dr R. Aukštikalnienė.
Lecturers: Dr M. Biteniekytė, S. Skuja.
Senior researchers: Dr J. Havelka, Dr V. Sruoga (part-time).
Doctoral students: M. Adomaitis, I. Gorban, A. Lekoveckaite, L. Stasiukynas.

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
Biosystematic studies in insects (Coleoptera, Hemiptera, Sternorrhycha: Aphididae, Diptera), spiders (Araneae), snails and slugs (Mollusca: Gastropoda).

RESEARCH PROJECTS CARRIED OUT IN 2020

Projects Supported by University Budget

Animal Biodiversity, Ecology and Population Structure. Prof. Dr Habil. R. Rakauskas, Prof. Dr S. Podėnas. 2018–2022.

Distribution, host specificity and molecular (mitochondrial COI and nuclear EF-1α) diversity of Eulachnini aphids (Hemiptera: Aphididae: Lachninae) on coniferous plants in Lithuania was accomplished. A list of winter gnat (Diptera, Trichoceridae) fauna of Italy was compiled. Taxonomic studies of the Korean Elephantomyia and Atypophthalmus crane flies (Diptera: Limoniidae) performed. Analysis of the biodiversity of spiders and dipterous insects of Lithuania continued. The invasive slugs’ (species Arion lusitanicus) investigation of control studies performed. Distribution analysis of Vertigo geyeri (a snail of EU interest) in North-East and South-East Lithuania performed. 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.

Main publications:

Havelka, J., Havelka, J., Starý, P. Cinara splendens (Hemiptera: Aphididae: Lachninae) – First Record in Palaearctic Region. Forests. 2020, 11: 911. doi: 10.3390/f11090911.

Turčinavičienė, J., Petrašiūnas, A., Bernotienė, R., Masiulis, M., Jonušaitis, V. The contribution of insects to African swine fever virus dispersal: data from domestic pig farms in Lithuania. Medical and Veterinary Entomology. 2020. https://doi.org/10.1111/mve.12499.

Adomaitis, M., & Skujienė, G. Lethal Doses of Saponins from Quillaja saponaria for invasive slug Arion vulgaris and non-target organism Enchytraeus albidus (Olygochaeta: Enchytraeidae). Insects. 2020, 11(11): 738. https://doi.org/10.3390/insects11110738.

National Research Projects

Research Council of Lithuania. Biodiversity and Ecological Pecularities of Aphid Species (Hemiptera: Adelgidae, Lachnidae) Inhabiting Coniferous Host Plants In Central Europe (No. P-MIP-17-365). Prof. R. Rakauskas. 2017–2020.

Twenty seven aphid species of the tribe Eulachnini (Hemiptera, Aphidoidea: Aphididae: Lachninae) and 14 aphid species of the family Adelgidae (Hemiptera, Adelgoidea) were recorded on coniferous plants in Lithuania. Thirteen aphid species were detected in Lithuania for the first time. Nearctic species C. splendens was recorded in the Palearctic region for the first time, information on its bionomy in Central Europe was also provided. Ten species of aphid parasitoids of the genus Pauesia (Hymenoptera: Braconidae: Aphidiinae) reared from 14 out of 27 available Eulachnini species are listed for Lithuanian fauna, 7 species being recorded for the first time. A complete development cycle was proved for the populations of Cinara piniphila in Lithuania. Oviparous females and males of this species were described for the first time. In addition to currently recognized taxa of Adelgidae endosymbionts, gamma-proteobacterial Sodalis-allied symbionts were detected in Adelges (Aphrastasia) pectinatae and Pineus cembrae for the first time. Adelges (Cholodkovskya) viridana endosymbionts were detected for the first time and they were the most similar to ‘Candidatus Profftia japonica’ and ‘Candidatus Vallotia japonica’. Partial COI sequences of eight aphid parasitoid species of the genus Pauesia deposited in the GenBank for the first time, the same as Buchnera aphidicola sequences of GroEL and TrpB fragments from the 15 aphid host species genus Cinara.

International Research Projects

National Institute of Biological Resources (South Korea). Korean Indigenous Species Project (No NIBR202020108). Prof. S. Podėnas, Assoc. Prof. V. Podėnienė.

The aim of the Indigenous species 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. Two PhD students visited Vilnius University in the few last years, they both decided to chose crane flies for their research because of our suggestions and advices. Our goal is taxonomy, ecology and development of selected groups of organisms and evaluation of influence of climate change, agriculture, deforestation and fragmentation of habitats on distribution and abundance of separate species.

MAIN 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)
Institute of Zoology, 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)

OTHER RESCEARCH ACTIVITIES

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.

Prof. S. Podėnas –

• assoc. researcher of the Academy of Natural Sciences, Philadelphia, PA (USA);
• expert of the National Centre for Quality Assessment in Higher Education (Lithuania);
• Director of Nature Research Centre (Lithuania).

Prof. R. Rakauskas –

• expert of the Research Council of Lithuanial;
• 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.

Assoc. Prof. V. Podėnienė –

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

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 2014–2020 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

• 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 Grita Skujienė-lecturer – 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” (LIFE-IP PAF-NATURALIT).
• Dr Grita Skujienė – moderator of practical events for teachers (biology) Public Institution “Educational Forum”, project “Development and testing of general education content and organization models in general education”, project code 09.2.1-ESFA-V-726-04-0001.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Petrašiūnas A. – interviews for LRT programmes; lecture “When will it be too hot for bumblebees in Lithuania?” etc.
• Dr. Skujienė G. – video- inteview and its dissemination on websites and in the press; the world news: https://theworldnews.net/lt-news/ypatingos-sraigytes-musu-gamtos-sveikatos-matuoklis-video; video-interviews about invasive slugs as well as article in the press; recomendations how to fight invasive slugs http://sbmozaika.lt/2020/10/06/rekomendacijos-del-invaziniu-sliuzu/ https://zolininkas.lt/patarimai/invaziniu-sliuzu-naikinimas/.

Museum of Zoology

• Taking part in annual National Science festival „Erdvėlaivis Žemė“ [“Spaceship Earth”]. 16 September 2020: I-II-III parts “Mysterious Hunters” Dr G. Skujienė, Dr M.Biteniekytė, doct. students M. Adomaitis, S. Skuja, V. Kuznecova.

 

CENTRE FOR ECOLOGY AND ENVIRONMENTAL RESEARCH

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

STAFF

Professor: Dr A. Ulevičius.
Associate professors: Dr G. Ignatavičius, Dr J. Satkūnas (part-time), Dr V. Oškinis.
Assistant professors: Dr V. Kalcienė, Dr I. Nedveckytė, Dr A. Samas, Dr V. Valskys, Dr G. Trakimas (part-time).
Researcher: Dr G. Trakimas (part-time).
Doctoral students: M. H. Ünsal, H. R. Hassan, L. Galinskaitė.

RESEARCH INTERESTS

Pollution of natural ecosystem components and anthropogenical environmental impact assessment
Ecology of the key-stone species of ecosystems: population dynamics and structure and environmental affects
Toxic impacts of environmental pollutants to ecosystems using tests of luminescent microorganisms and biomarkers
Infochemical interactions and behaviour of organisms

RESEARCH PROJECTS CARRIED OUT IN 2020

Projects Supported by University Budget

Vehicle-Animal Collisions and Their Natural and Anthropogenic Factors. Dr G.Ignatavičius, Dr A. Ulevičius, Dr V.Valskys, Dr G.Trakimas, L. Galinskaitė.

Wildlife-vehicle collisions (WVC) are of socioeconomic and ecological importance. We develop spatially explicit and other models how to predict and prevent WVC in anthropogenized landscape. Wildlife-vehicle collisions are analysed using GIS, spatial and temporal modelling. Roe deer (Capreolus capreolus) behavior can change hourly, daily, weekly, annually and throughout an individual’s life. Therefore, understanding the temporal behavioral patterns of roe deer is important when investigating the number of vehicle collisions with these animals. Similar aspects of roe deer – vehicle collisions (RDVC) are well documented in other European countries usually characterized by high density of roads and intensive traffics. Lithuania, on the contrary, has a relatively low density of total road network and especially low motorway network density among other countries of European lowlands. We examine whether the time dependent patterns of document roe deer-vehicle collisions (RDVC) under conditions of low density road network demonstrate the similar tendencies as elsewhere in Europe.

Main publication:

Ignatavicius, G., Ulevicius, A., Valskys, V., Trakimas, G., Galinskaite, L., Busher, P. E. Temporal patterns of ungulate-vehicle collisions in a sparsely populated country. European Journal of Wildlife Research. 2020, 66(4): 58. DOI: 10.1007/s10344-020-01396-9.

Ecotoxic Effects of Landfill Leachate and Cyanobacterial Biomass on Aquatic Organisms. Dr V. Kalcienė.

Assessment of the pollution of ecosystems requires reliable markers. We test the toxic impacts of the environmental pollutants on ecosystems using tests of luminescent microorganisms and biomarkers. The effect of landfill leachate and cyanoHAB biomass on test organisms was concentration- and trophic-level-dependent, and in the case of fish, development stage–dependent. The secondary consumer Oncorhynchus mykiss and larvae of the Danio rerio proved to be most sensitive to LL additions, while Scenedesmus quadricauda, representing primary producers, to cyanoHAB exposure. The overall ecotoxic effect of both mixtures on the tested organisms varied from low (Class II) to high (Class IV). This study highlights complex and unambiguous effects of LL and cyanoHAB biomass on aquatic organisms. We suggest that the use of multiple tests on organisms belonging to different trophic levels for the assessment of the ecotoxicological risk of these mixtures may provide a better understanding of how anthropogenic pollution affects food web functioning.

Main publication:

Montvydienė, D., Šulčius, S., Jurgelėnė, Ž., Makaras, T., Kalcienė, V., Taraškevičius, R., Kazlauskas, M., Kazlauskienė, N. Contrasting ecotoxic effects of landfill leachate and cyanobacterial biomass on aquatic organisms. Water Air and Soil Pollution. 2020, 231(7): 323. https://doi.org/10.1007/s11270-020-04684-x.

Chemoreception of Phytophagous Insects and Plant Allelopathy and Materials Cycling. Dr I. Nedveckytė, Dr G. Trakimas.

An introduction of alien species provokes new info chemical interactions and changes in the behaviour of organisms, which leads to a reorganization of the functional groups within an impacted ecosystem. Allelopathic properties of the Solidago canadensis and its interactions with other plants have been investigated. The elemental composition of organisms belongs to a suite of functional traits that change during development in response to environmental conditions. However, associations between adaptive variations in developmental speed and elemental body composition are not well understood. We compared body mass, elemental body composition, food uptake and fat metabolism of Drosophila melanogaster male fruit flies in relation to their larval development speed. The amount of triacylglycerides was highest in the flies with intermediate developmental speed which optimizes development under many climatic conditions. Although low food intake slows down developmental speed and the accumulation of body fat reserves in slowly developing flies, their phenotype conceivably facilitates survival under higher stochasticity of their environments. Rapidly developing flies grew with less emphasis on storage buildup. Overall, this study showed that a combination of bet-hedging, adaptive tracking and developmental plasticity enables fruit flies to respond adaptively to environmental uncertainty.

Main publication:

Krams, I. A., Krams, R., Jõers, P., Munkevics, M., Trakimas, G., Luoto, S., Eichler, S., Butler, D. M., Merivee, E., Must, A., Rantala M. J., Contreras-Garduño, J., Krama, T. Developmental speed affects ecological stoichiometry and adult fat reserves in Drosophila melanogaster. Animal Biology. 2020, published online: 2020/8/10 https://doi.org/10.1163/15707563-bja10043.

Winter Survival of Subordinate Group Members of Egalitarian Mixed-Species Bird Groups in High-Quality Forests. Dr G.Trakimas.

Birds often live in hierarchically organized mixed-species groups (MSGs), in which heterospecific individuals are considered to substitute for conspecifics as protection against predators at a significantly reduced competition cost. Crested tits and willow tits form MSGs during the non-reproductive season that typically exhibit a nearly linear (‘despotic’) dominance hierarchy in which the highest ranking male willow tit is fourth in the overall hierarchy. Much less frequently, ‘egalitarian’ dominance structures occur in which the adult willow tits rank second and the hierarchy is less steep, or linear. A comparison of individuals in the despotic MSGs revealed a strong negative correlation between subcutaneous fat stores and dominance rank in the interspecific dominance hierarchy. Egalitarian groups exhibited markedly less within-group aggression and improved winter survival in both tit species. However, winter survival of birds in egalitarian groups was impaired relative to despotic groups in forests recently affected by industrial forestry. This suggests that the more egalitarian bird societies may best be adapted to less-disturbed environments.

Main publication:

Krams, I. A., Luoto, S., Krama, T., Krams, R., Sieving, K., Trakimas, G., Elferts, D., Rantala, M. J., Goodale, E. Egalitarian mixed-species bird groups enhance winter survival of subordinate group members but only in high-quality forests. Scientific Reports. 2020, 10(1): 4005. DOI: 10.1038/s41598-020-60144-w.

Food Caching Behaviour of the Eurasian Beaver in Northern Europe. Dr A.Ulevičius, Dr A. Samas.
We studied the food caching behavior of the Eurasian beaver in three northern European countries (Sweden, Norway, and Lithuania). Construction of caches began as early as late September (week 39/40) in Sweden and Lithuania and by mid October (week 42) in Norway. We observed plasticity in timing of cache initiation. Declining air temperature and mean minimum temperatures of 0°C or below were associated with cache initiation. Caches in Lithuania were larger than in Sweden and Norway, which may be associated with colder winter temperatures.

Main publication:

Busher, P. E., Mayer, M., Ulevičius, A., Samas, A., Hartman, G., Rosell, F. Food caching behavior of the Eurasian beaver in northern Europe. Wildlife Biology. 2020, 3: wlb.00734.

Genetic Diversity and Structure of the Eurasian Beaver. Dr A.Ulevičius.

In collaboration with the Natural Resources Institute, Finland (Luke), genetic structure of reintroduced Eurasian beaver Castor fiber was assessed. Results discover very different genetic structure and diversity among Scandinavian and other European beaver populations suggesting specific means of conservation.

Main publication:

Iso-Touru, T., Huitu, O., Tapio, M., Kucinskiene, J., Ulevicius, A., Bukelskis, E., Tirronen, K., Fyodorov, F., Panchenko, D., Saarma, U. Low genetic polymorphism in the re-introduced Eurasian beaver (Castor fiber) population in Finland: implications for conservation. Mammal Research. 2020, 65(2): 331–338.

National Research Projects

Research Council of Lithuania. Assessment of cumulative toxicity impact in the aquatic organisms induced by different types of stressors, ACTIS. 2017–2020. Dr Virginija Kalcienė – research group member.

Synergistic Effects of Heavy Metal and Antibiotic Pollution on Communities of Microorganisms in Bottom Sediments of Fish Culture Ponds. VU Science Promotion Fund. 2019–2020. Dr V.Valskys - head, Dr V. Kalcienė, Prof. A. Ulevičius.

The greatest effects of pollutants on surface water ecosystems are observed in aquaculture bodies, especially in intensive fishing ponds. The influx of antibiotics into these ecosystems is unavoidable due to the high density of cultivated populations and the consequent growing threat of pathological microbial diseases. This shows the urgency of the problem of antibiotic contamination. During this project sediments of Simnas fishing ponds have been analysed for the first time including ecotoxicity, heavy metals and antibiotics.

National Research Programme “Sustainability of Agro-, Forest, and Water Ecosystems. P-SIT-20-6.” The Influence of Intensive Fish Farming on Aquatic Microbiome and Resistome (OMICS). 2020–2021. Dr V. Valskys, Dr V. Kalcienė – research group members.

Research Council of Lithuania. Seasonal Features of School Air Pollution and Its Impact on the Incidence of Respiratory Diseases and Allergies in Primary School Students (S-MIP-20-52). 2020–2022. Dr V.Valskys – research group member.

International Research Projects

EU Life programme. Algae – Economy Based Ecological Service of Aquatic Ecosystem (life17 env/lt/000407). Dr V.Valskys. 2018–2023.

The project AlgaeService for LIFE seeks to promote best practices in ecological service and the circular economics approach by implementing innovative complex system which has both demonstration and innovation character.

International Research Networks

COST Action: CA15114. STSM Evaluation of antifungal activity of silver nanocomposites against various clinically relevant yeast and fungi (Request reference number: ECOST-STSM-Request-CA15114-45747). Dr V. Kalcienė.

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

Nature Research Centre (Lithuania)
Vilnius Gediminas Technical University (Lithuania)
University of Latvia (Latvia)
Lithuanian Geological Survey (Lithuania)
Boston University (USA)
National Institute of Chemical Physics and Biophysics (NICPB) (Estonia)
Natural Resources Institute (Finland)

OTHER RESEARCH ACTIVITIES

Dr. A. Ulevičius –

• honorary member of Gesellschaft für Wildtier- und Jagdforschung (GWJF), Halle, Germany;
• reviewer of journals Zoology and Ecology, American Middland Naturalist, European Journal for Wildlife Research, Aquatic Ecology.

Dr V. Kalcienė –

• associate member of Royal Society of Chemistry;
• member of Society of Environmental Toxicology and Chemistry;
• member of Lithuanian Biochemical Society.

Dr I. Nedveckytė –

• associate member of Baltic-American Biotaxonomy Institute.

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. A. Ulevičius – expert of study program group in the field of Environmental science; member of expert group of wolf population management in Lithuania by the Ministry of Environment; member of expert group of Game and Trophies by the Lithuanian Council of Hunters and Fishermen.
• Assist. Dr V. Kalcienė, Assist. Dr I. Nedveckytė – experts of study program group in the field of Ecology.

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES

• Dr A. Ulevičius – consultations on the non-arable agricultural technologies to preserve and sustainably use the top soil. Seminar was organized by land owners in Ukmergė district (Krikštėnai) on October 2020. Expert conclusion for the Ministry of Environment on the wolf hunting bag quota for the season 2020/2021.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Assist. Dr A. Samas – Academic committee member in activities of one ARQUS project named “Climate Risks”.