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), 217 research fellows (incl. 145 holding research degree), 120 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/

Directors – Prof. Habil. Dr. Saulius Klimašauskas (until September 30th)
Dr. Vytautas Smirnovas (since October 1st)

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 2019

A. Osipenko. Development of new methods for small RNA labeling.
M. Zilnytė. Characterization of pore-forming toxin vaginolysin from Gardnerella vaginalis.
R. Žilionis. Defining cell populations and their conservation between human and mouse in airway epithelium and lung cancer by single cell RNA sequencing
D. Stravinskienė. Development of monoclonal and recombinant antibodies against carbonic anhydrases.

DEPARTMENT OF PROTEIN - DNA INTERACTIONS

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 223 4354
E-mail:

Head - Prof. Dr. Virginijus Šikšnys

STAFF

Chief research fellows: Prof. Dr. V. Šikšnys, Dr. S. Gražulis, Dr. G. Sasnauskas, Dr. M. Zaremba, Dr. G. Tamulaitis.
Senior research fellows: Dr. G. Tamulaitienė, Dr. E. Manakova, Dr. G. Gasiūnas, Dr. A. Šilanskas.
Research fellows: Dr. T. Šinkūnas, Dr. T. Karvelis, Dr. G. Kostiuk, Dr. P. Toliušis, Dr. A. Merkys, Dr. E. Zagorskaitė.
Junior research fellow: I. Songailienė.
Other researchers and technical staff: A. Tunevič, E. Raginis, K. Budrė, R. Žedaveinytė.
Doctoral students: A. Vaitkus, G. Drabavičius, A. Grybauskas, 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 defense systems Bacterial antivirus defense systems

Structural and molecular mechanisms of CRISPR-Cas machinery

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

SELECTED PUBLICATIONS 2019

Gordeeva, J., Morozova, N., Sierro, N., Isaev, A., Sinkunas, T., Tsvetkova, K., Matlashov, M., Truncaitė, L., Morgan, R. D., Ivanov, N. V., Siksnys, V., Zeng, L., Severinov, K. BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site. Nucleic Acids Res. 2019, 47: 253–265, https://doi.org/10.1093/nar/gky1125.

Mogila, I., Kazlauskiene, M., Valinskyte, S., Tamulaitiene, G., Tamulaitis, G., Siksnys, V. Genetic dissection of the type III-A CRISPR-Cas system Csm complex reveals roles of individual subunits. Cell Reports. 2019, 26: 2753–2765.e4, https://doi.org/10.1016/j.celrep.2019.02.029.

Slyvka, A., Zagorskaitė, E., Czapinska, H., Sasnauskas, G., Bochtler, M. Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping. Nucleic Acids Res. 2019, 47: 11943–11955, https://doi.org/10.1093/nar/gkz1017.

Tamulaitiene, G., Manakova, E., Jovaisaite, V., Tamulaitis, G., Grazulis, S., Bochtler, M., Siksnys, V. Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family. Nucleic Acids Res. 2019, 47: 997–1010, https://doi.org/10.1093/nar/gky1137.

Wilkinson, M., Drabavicius, G., Silanskas, A., Gasiunas, G., Siksnys, V., Wigley, D. B. Structure of the DNA-bound spacer capture complex of a type II CRISPR-Cas system. Molecular Cell. 2019, 75: 90–101.e5, https://doi.org/10.1016/j.molcel.2019.04.020.

PATENTS 2019

Granted:
Šikšnys, V., Gasiūnas, G., Karvelis, T., Lubys, A., Zaliauskienė, L., Glemžaitė, M., Smith, A. RNA-directed DNA Cleavage by the Cas9-crRNA Complex. EP2828386B1. Publication date: July 10, 2019.

Šikšnys, V., Kazlauskienė, M., Tamulaitis, G. Programmable RNA Shredding by the Type III-A CRISPR-Cas System of Streptococcus Thermophilus. US10385336B2. Publication date: August 20, 2019.

Šikšnys, V., Kazlauskienė, M., Tamulaitis, G. Programmable RNA Shredding by the Type III-A CRISPR-Cas System of Streptococcus Thermophilus. EP3189140B1. Publication date: October 23, 2019.

Applications:
Šikšnys, V., Gasiūnas, G., Karvelis, T. RNA-directed DNA cleavage by the Cas9-crRNA complex. JP2019030321A. Publication date: February 28, 2019.

Šikšnys, V., Gasiūnas, G., Karvelis, T. RNA-directed DNA cleavage by the Cas9-crRNA complex. US20190085329A1. Publication date: March 21, 2019.

Jurėnaitė-Urbanavičienė, S., Tamulaitis, G. Method for cloning and expression of PfoI restriction endonuclease. US20190300866A1. Publication date: November 28, 2019.

RESEARCH PROJECTS CARRIED OUT IN 2019

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 defense 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 behavior of individual protein molecules during interaction with NA. However, these methods are technically challenging and not always successful. Besides, due to labeling 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 labeling - 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 a NA fragment density and arrangement controllable way. It also allows direct monitoring of interaction of the labeled 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 defense 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.

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 is 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. Research on Prediction of Environmental Change in the Baltic Sea Based on Comprehensive (Meta)Genomic Analysis of Microbial Viruses (No. LJB-17-001). Dr. G. Gasiūnas. 2017–2019.

Cyanobacteria blooms have significant influence on the Baltic Sea ecosystem functioning and services, and thus, human well-being and competitiveness of the region. The effective management of cyanobacteria blooms largely depends on the understanding of factors that drive cyanobacteria population dynamics. Cyanophages (viruses that infect cyanobacteria) play a key role in controlling structure and proliferation of host population, in particular, in eutrophic aquatic ecosystems. However, the Baltic Sea viruses, and their role in controlling cyanobacteria blooms remain litlle understood. Therefore, in this project we will perform the metagenomic analysis and quantitative assessment of the Baltic Sea virus community to reveal their contribution to cyanobacteria bloom development. The aim of the project is to investigate the impact of viruses on the cyanobacteria population dynamics in the Baltic Sea.

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.

Research Council of Lithuania. Adaptation Mechanism in Class 2 CRISPR-Cas Systems (No. S-MIP-19-305). Dr. G. Sasnauskas. 2019–2022.

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. Habil. Dr. Saulius Klimašauskas

STAFF

Chief research fellows: Prof. Habil. Dr. S. Klimašauskas, Dr. G. Vilkaitis, Dr. V. Masevičius.
Senior research fellows: Dr. E. Kriukienė, Dr. R. Rakauskaitė.
Research fellows: Dr. M. Tomkuvienė, Dr. V. Stankevičius, Dr. A. Osipenko.
Junior research fellows: G. Urbanavičiūtė, Z. Staševskij, J. Ličytė, M. Mickutė, S. Gasiulė, P. Gibas, K. Kvederavičiūtė.
Other researchers and technical staff: A. Rukšėnaitė, D. Ikasalaitė, M. Malikėnas, M. Jazdauskaitė, B. Masiulionytė, K Skardžiūtė.
Doctoral student: M. Narmontė.

RESEARCH INTERESTS

Nucleic acids modification enzymes
Epigenome profiling
Biosynthesis of selenoproteins
Enzyme engineering

SELECTED PUBLICATIONS 2019

Daniūnaitė, K., Jarmalaitė, S., Kriukienė, E. Epigenomic technologies for deciphering circulating tumor DNA. Current Opinion in Biotechnology. 2019, 55: 23–29, https://doi.org/10.1016/j.copbio.2018.07.002.

Gasiulė, S., Dreize, N., Kaupinis, A., Ražanskas, R., Čiupas, L., Stankevičius, V., Kapustina, Ž., Laurinavičius, A., Valius, M., Vilkaitis, G. Molecular insights into miRNA-driven resistance to 5-fluorouracil and oxaliplatin chemotherapy: miR-23b modulates the epithelial–mesenchymal transition of colorectal cancer cells. Journal of Clinical Medicine. 2019a, 8: 2115, https://doi.org/10.3390/jcm8122115.

Gasiulė, S., Stankevičius, V., Patamsytė, V., Ražanskas, R., Žukovas, G., Kapustina, Ž., Žaliaduonytė, D., Benetis, R., Lesauskaitė, V., Vilkaitis, G. Tissue-specific miRNAs regulate the development of thoracic aortic aneurysm: the emerging role of KLF4 network. Journal of Clinical Medicine. 2019b, 8: 1609, https://doi.org/10.3390/jcm8101609.

Kweon, S.-M., Chen, Y., Moon, E., Kvederaviciutė, K., Klimasauskas, S., Feldman, D. E. 2019. An adversarial DNA N6-methyladenine-sensor network preserves polycomb silencing. Molecular Cell. 2019, 74: 1138–1147.e6, https://doi.org/10.1016/j.molcel.2019.03.018.

Tomkuvienė, M., Mickutė, M., Vilkaitis, G., Klimašauskas, S. Repurposing enzymatic transferase reactions for targeted labeling and analysis of DNA and RNA. Current Opinion in Biotechnology. 2019, 55: 114–123, https://doi.org/10.1016/j.copbio.2018.09.008.

RESEARCH PROJECTS CARRIED OUT IN 2019

National Research Projects

Research Council of Lithuania/European Social Fund. Single Molecule TOP-seq – an Innovative Technological Platorm 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 tumors 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 photosensitive 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 tumors 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 period 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 labeled 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.

International Research Projects

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

DNA methylation is a prevalent epigenetic modification in mammals, which is brought about by enzymatic transfer of methyl groups from the S-adenosylmethionine (SAM) cofactor by three known DNA methyltransferases (DNMTs). The most dramatic epigenomic reprogramming in mammalian development occurs after fertilization, whereby a global loss of DNA methylation is followed by massive reinstatement of new methylation patterns, different for each cell type. Although DNA methylation has been extensively investigated, key mechanistic aspects of these fascinating events remain obscure. The goal of this proposal is to bridge the gap in our understanding of how the genomic methylation patterns are established and how they govern cell plasticity and variability during differentiation and development. These questions could only be answered by precise determination of where and when methylation marks are deposited by the individual DNMTs, and how these methylation marks affect gene expression. To achieve this ambitious goal, we will metabolically engineer mouse cells to permit SAM analog-based chemical pulse-tagging of their methylation sites in vivo. We will then advance profiling of DNA modifications to the single cell level via innovative integration of microdroplet-based barcoding, precise genomic mapping and super-resolution imaging. Using this unique experimental system we will determine, with unprecedented detail and throughput, the dynamics and variability of DNA methylation and gene expression patterns during differentiation of mouse embryonic cells to neural and other lineages.

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

Centre for Addiction and Mental Health, Toronto (Canada)
Cambridge University, Cambridge (UK)
University of Paul Sabatier, Toulouse (France)
University of Stavanger, Stavanger (Norway)
International Institute of Molecular and Cell Biology, Warsaw (Poland)
University of Southern California, Los Angeles (USA)
RIKEN Yokohama (Japan)
INRA (France)
Tartu University (Estonia)
University of Stuttgart (Germany)
Stanford University (USA)
IMB Mainz (Germany)

OTHER RESEARCH ACTIVITIES

Prof. Habil. Dr. S. Klimašauskas –

• member/ chairman of the Biology division, 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 actions CM1303, CM1406;
• member of the advisory expert group, Strategic Council on Scientific Research, Technological Development and Innovations of Lithuania.

 

DEPARTMENT OF EUKARYOTE GENETIC ENGINEERING

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 223 4421
E-mail:

Head - Dr. Rasa Petraitytė-Burneikienė

STAFF

Chief research fellows: Dr. A. Gedvilaitė, Dr. R. Slibinskas.
Senior research fellows: Dr. R. Petraitytė-Burneikienė, Dr. A. Ražanskienė, Dr. G. Žvirblis, Dr. E. Čiplys, Dr. M. Juozapaitis.
Research fellows: Dr. V. Kazanavičiūtė, Dr. R. Ražanskas, Dr. D. Žiogienė, Dr. A. Bulavaitė, Dr. P. L. Tamošiūnas, Dr. M. Norkienė, Dr. M. Zaveckas, Dr. A. Abraitienė.
Junior research fellows: Dr. J. Lazutka, R. Zinkevičiūtė, E. Bakūnaitė, G. Mickienė, E. Žitkus.
Other researchers and technical staff: E. Rudokienė, O. Jančevskaja, D. Jaskytė, A. Šileikaitė, K. Juškaitė, N. Macijauskaitė, R. Drulytė.
Doctoral students: A. Špakova, J. Rainytė, A. Verbickaitė.
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 signaling regulation in Arabidopsis
Functions of PP2C phosphatases

SELECTED PUBLICATIONS 2019

Denkovskienė, E., Paškevičius, Š., Misiūnas, A., Stočkūnaitė, B., Starkevič, U., Vitkauskienė, A., Hahn-Löbmann, S., Schulz, S., Giritch, A., Gleba, Y., Ražanskienė, A. Broad and efficient control of Klebsiella pathogens by peptidoglycan-degrading and pore-forming bacteriocins klebicins. Sci Rep. 2019, 9: 1–11, https://doi.org/10.1038/s41598-019-51969-1.

Gasiulė, S., Dreize, N., Kaupinis, A., Ražanskas, R., Čiupas, L., Stankevičius, V., Kapustina, Ž., Laurinavičius, A., Valius, M., Vilkaitis, G. Molecular Insights into miRNA-Driven Resistance to 5-Fluorouracil and Oxaliplatin Chemotherapy: miR-23b Modulates the Epithelial–Mesenchymal Transition of Colorectal Cancer Cells. Journal of Clinical Medicine. 2019a, 8: 2115, https://doi.org/10.3390/jcm8122115.

Gasiulė, S., Stankevičius, V., Patamsytė, V., Ražanskas, R., Žukovas, G., Kapustina, Ž., Žaliaduonytė, D., Benetis, R., Lesauskaitė, V., Vilkaitis, G. Tissue-specific miRNAs regulate the development of thoracic aortic aneurysm: the emerging role of KLF4 network. Journal of Clinical Medicine. 2019b, 8: 1609, https://doi.org/10.3390/jcm8101609.

Rasche, A., Lehmann, F., König, A., Goldmann, N., Corman, V. M., Moreira-Soto, A., Geipel, A., Riel, D. van, Vakulenko, Y. A., Sander, A.-L., Niekamp, H., Kepper, R., Schlegel, M., Akoua-Koffi, C., Souza, B. F. C. D., Sahr, F., Olayemi, A., Schulze, V., Petraityte-Burneikiene, R., Kazaks, A., Lowjaga, K. A. A. T., Geyer, J., Kuiken, T., Drosten, C., Lukashev, A. N., Fichet-Calvet, E., Ulrich, R. G., Glebe, D., Drexler, J. F. Highly diversified shrew hepatitis B viruses corroborate ancient origins and divergent infection patterns of mammalian hepadnaviruses. PNAS. 2019, 116: 17007–17012, https://doi.org/10.1073/pnas.1908072116/

Špakova, A., Šimoliūnas, E., Batiuškaitė, R., Pajeda, S., Meškys, R., Petraitytė-Burneikienė, R. Self-assembly of tail tube protein of bacteriophage vB_EcoS_NBD2 into extremely long polytubes in E. coli and S. cerevisiae. Viruses. 2019, 11: 208, https://doi.org/10.3390/v11030208.

RESEARCH PROJECTS CARRIED OUT IN 2019

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 an 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.

International Research Projects

Research Council of Lithuania. Studying of Human Parvovirus B19, Bocavirus And Parvovirus 4 Involvement In Inflammatory Neurological Diseases Using Interdisciplinary Approach (No. TAP LLT-3/2017). Dr. R. Petraitytė-Burneikienė. 2017–2019.

Meningitis, encephalopathy and encephalitis are serious diseases of the central nervous system that often are caused by a viral infection, but in most cases their etiology remains unknown. Parvovirus human parvovirus B19, human bocavirus and human parvovirus 4 are members of Parvoviridae family. There are hypothesis of B19 as a cause of extremely wide range of clinical manifestations including neurological diseases. The aim of this project is to study the involvement of human parvoviruses on etiopathogenesis of meningitis and encephalitis/meningoencephalitis with unknown etiology and unspecified encephalopathy in adult population as well as to develop rapid serodiagnostic and molecular diagnosis detection tools for parvovirus infection using interdisciplinary approach.

Contractual Research

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

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

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

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

OTHER RESEARCH ACTIVITIES

Prof. Habil. Dr. 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

STAFF

Chief research fellow: Dr. L. Mažutis.
Junior research fellows: J. Nainys, V. Milkus, Dr. R. Žilionis.
Other researchers and technical staff: L. Karpus, J. Ritmejeris, R. Kisielius, I. Maželis, E. Gegevičius, J. Žvirblytė, A. Želvytė.
Doctoral students: G. Stonytė, K. Goda, L. Camissi.

RESEARCH INTERESTS

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

SELECTED PUBLICATIONS 2019

Jones, K. B., Furukawa, S., Marangoni, P., Ma, H., Pinkard, H., D’Urso, R., Zilionis, R., Klein, A. M., Klein, O. D. Quantitative clonal analysis and single-cell transcriptomics reveal division kinetics, hierarchy, and fate of oral epithelial progenitor cells. Cell Stem Cell. 2019, 24: 183–192.e8, https://doi.org/10.1016/j.stem.2018.10.015.

Leonavicius, K., Nainys, J., Kuciauskas, D., Mazutis, L. Multi-omics at single-cell resolution: comparison of experimental and data fusion approaches. Current Opinion in Biotechnology. 2019, 55: 159–166, https://doi.org/10.1016/j.copbio.2018.09.012.

Sharir, A., Marangoni, P., Zilionis, R., Wan, M., Wald, T., Hu, J.K., Kawaguchi, K., Castillo-Azofeifa, D., Epstein, L., Harrington, K., Pagella, P., Mitsiadis, T., Siebel, C. W., Klein, A. M., Klein, O. D. A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage. Nat Cell Biol. 2019, 21: 1102–1112, https://doi.org/10.1038/s41556-019-0378-2.

Šimoliūnas, E., Truncaitė, L., Rutkienė, R., Povilonienė, S., Goda, K., Kaupinis, A., Valius, M., Meškys, R. The robust self-assembling tubular nanostructures formed by gp053 from phage vB_EcoM_FV3. Viruses. 2019, 11: 50, https://doi.org/10.3390/v11010050.

Zilionis, R., Engblom, C., Pfirschke, C., Savova, V., Zemmour, D., Saatcioglu, H. D., Krishnan, I., Maroni, G., Meyerovitz, C. V., Kerwin, C. M., Choi, S., Richards, W. G., De Rienzo, A., Tenen, D. G., Bueno, R., Levantini, E., Pittet, M. J., Klein, A. M. Single-cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species. Immunity. 2019, 50: 1317–1334.e10, https://doi.org/10.1016/j.immuni.2019.03.009.

PATENTS 2019

Granted:
Italiano J., Mažutis L., Thon J. N., Weitz D. A. System and method for a biomimetic fluid processing. US10343163B2. Publication date: July 09, 2019.

Applications:
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. US20190002943A1. Publication date: January 03, 2019.

Weitz D. A., Klein A. M., Akartuna I., Mažutis L., Kirschner W. M. Systems and methods for barcoding nucleic acids. EP3456846A1. Publication date: March 20, 2019.

Italiano J., Mažutis L., Thon J.N., Weitz D.A. System and method for a biomimetic fluid processing. US20190283027A1. Publication date: September 19, 2019.

RESEARCH PROJECTS CARRIED OUT IN 2019

National Research Projects

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

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

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.

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

Harvard Medical School (USA)
Harvard University, School of Engineering and Applied Sciences (USA)
Columbia University (USA)
CALTECH (USA)
ETH Zurich (Switzerland)

OTHER RESEARCH ACTIVITIES

Dr. L. Mažutis –

• participant of Human Cell Atlas and Human Tumor Atlas international projects;
• Start-up “Droplet Genomics”, Vilnius, LT;
• Start-up “Platelet Biogenesis” Inc. Boston, MA, USA.

 

DEPARTMENT OF IMMUNOLOGY AND CELL BIOLOGY

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 223 4360
E-mail:

Head - Dr. Aurelija Žvirblienė

STAFF

Chief research fellows: Dr. A. Žvirblienė, Dr. M. Plečkaitytė.
Senior research fellows: Dr. I. Kučinskaitė-Kodzė, Dr. A. Kanopka.
Research fellows: Dr. P. Stakėnas, Dr. E. Jakubauskienė, Dr. D. Stravinskienė.
Junior research fellows: I. Dalgėdienė, I. Pečiulienė, L. Vilys.
Other researchers and technical staff: D. Bakonytė, D. Pamedytytė, L. Diglienė, D. Gedgaudienė.
Doctoral students: A. Lučiūnaitė, M. Simanavičius, A. Imbrasaitė.

RESEARCH INTERESTS

Monoclonal and recombinant antibodies
Molecular epidemiology of Mycobacterium tuberculosis
Alternative splicing

SELECTED PUBLICATIONS 2019

Lučiūnaitė, A., McManus, R. M., Jankunec, M., Rácz, I., Dansokho, C., Dalgėdienė, I., Schwartz, S., Brosseron, F., Heneka, M. T. Soluble Aβ oligomers and protofibrils induce NLRP3 inflammasome activation in microglia. Journal of Neurochemistry. 2019, e14945. https://doi.org/10.1111/jnc.14945.

Peciuliene, I., Vilys, L., Jakubauskiene, E., Zaliauskiene, L., Kanopka, A. Hypoxia alters splicing of the cancer associated Fas gene. Experimental Cell Research. 2019, 380: 29–35, https://doi.org/10.1016/j.yexcr.2019.04.015.

Ragaliauskas, T., Plečkaitytė, M., Jankunec, M., Labanauskas, L., Baranauskiene, L., Valincius, G. Inerolysin and vaginolysin, the cytolysins implicated in vaginal dysbiosis, differently impair molecular integrity of phospholipid membranes. Sci Rep 9. 2019, 1–11, https://doi.org/10.1038/s41598-019-47043-5.

Stravinskiene, D., Imbrasaite, A., Petrikaite, V., Matulis, D., Matuliene, J., Zvirbliene, A. New Monoclonal Antibodies for a Selective Detection of Membrane-Associated and Soluble Forms of Carbonic Anhydrase IX in Human Cell Lines and Biological Samples. Biomolecules. 2019, 9: 304, https://doi.org/10.3390/biom9080304.

Takkinen, K., Žvirblienė, A. Recent advances in homogenous immunoassays based on resonance energy transfer. Current Opinion in Biotechnology. 2019, 55: 16–22, https://doi.org/10.1016/j.copbio.2018.07.003.

RESEARCH PROJECTS CARRIED OUT IN 2019

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.

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: (i) a detailed description of strain genotypes, with their comparison to each other and to those circulating in Europe and worldwide; (ii) assessment of TB transmission both within and between the two countries; (iii) 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. 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 Nr. 52-1705/TPS-600000-974 with UAB Imunodiagnostika, Vilnius. Characterization of Protein Allergens and Development of Allergen-Specific Antibodies. Dr. A. Žvirblienė. 2017–2019.

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.

Contract Nr. 51-1705/TPS-600000-966 with UAB Imunodiagnostika, Vilnius. Development of Antibodies against Chemical Allergens. Dr. A. Žvirblienė. 2017–2019.

The aim of this project is to develop tools for diagnostics of drug allergy. Polyclonal and/or monoclonal antibodies against chemical compounds (haptens) that are implicated in causing drug allergy are generated. To evaluate the immunogenity of haptens, they are coupled to diferent protein carriers capable of inducing T cell-dependent B cell response in mice.

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)

 

DEPARTMENT OF BIOTHERMODYNAMICS AND DRUG DESIGN

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 223 4364
E-mail:

Head - Dr. Daumantas Matulis

STAFF

Chief research fellows: Dr. D. Matulis, Dr. V. Smirnovas.
Senior research fellows: Dr. A Zubrienė, Dr. V. Petrikaitė, Dr. V. Petrauskas, Dr. J. Matulienė, Dr. V. Dudutienė, Dr. L. Baranauskienė, Dr. E. Čapkauskaitė.
Research fellows: Dr. E. Kazlauskas, Dr. V. Juozapaitienė, Dr. Š. Grincevičienė, Dr. A. Smirnov.
Junior research fellows: V. Michailovienė, J. Jachno, A. Zakšauskas, Dr. J. Kazokaitė.
Other researchers and technical staff: A. Mickevičiūtė, D. Lingė, L. Davidian, T. Šneideris.
Doctoral students: A. Janonienė, J. Smirnovienė, G. Skvarnavičius, M. Žiaunys, S. Daunys, A. Sakalauskas, A. Petrošiūtė, V. Paketurytė, M. Gedgaudas.

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 sytnhetic sulfonamide-bearing ligands is being studied both energetically and structurally. Nearly 100 protein-ligand crystal structures were solved and deposited to the PDB. Over 5000 reactions were measured yielding the Gibbs energy, enthalpy, entropy, and volume correlations with the chemical and crystallographical structural features of the ligand and protein. Most promising compounds that bound CA IX, an anticancer target, with subnanomolar affinity and significant selectivity over other human isoforms, are being tested in cancer cell lines, and in animals for biological development as anticancer drugs.

SELECTED PUBLICATIONS 2019

Baranauskiene, L., Kuo, T.-C., Chen, W.-Y., Matulis, D. Isothermal titration calorimetry for characterization of recombinant proteins. Current Opinion in Biotechnology. 2019, 55: 9–15, https://doi.org/10.1016/j.copbio.2018.06.003.

Kairys, V., Baranauskiene, L., Kazlauskiene, M., Matulis, D., Kazlauskas, E. Binding affinity in drug design: experimental and computational techniques. Expert Opinion on Drug Discovery. 2019, 14: 755–768, https://doi.org/10.1080/17460441.2019.1623202.

Simon, R. P., Rumpf, T., Linkuviene, V., Matulis, D., Akhtar, A., Jung, M. Cofactor Analogues as Active Site Probes in Lysine Acetyltransferases. J. Med. Chem. 2019, 62: 2582–2597, https://doi.org/10.1021/acs.jmedchem.8b01887.

Sneideris, T., Sakalauskas, A., Sternke-Hoffmann, R., Peduzzo, A., Ziaunys, M., Buell, A. K., Smirnovas, V. The environment is a key factor in determining the anti-amyloid efficacy of EGCG. Biomolecules. 2019, 9: 855, https://doi.org/10.3390/biom9120855.

PATENTS 2019

Granted:
Matulis D., Dudutienė V., Zubrienė A. Fluorinated benzenesulfonamides as inhibitors of carbonic anhydrase. EP2914583B1. Publication date: February 27, 2019.

RESEARCH PROJECTS CARRIED OUT IN 2019

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 that 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 isoformselective 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 stoppedflow assay, and surface plasmon resonance. The thermodynamic and kinetic parameters will be partitioned to the different structural interactions between the ligand and CA (Zn-sulfonamide 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 CAinhibitor interactions, but could be extended to other drug design projects where there are no highaffinity ligands available yet.

International Research Projects

Research Council of Lithuania. Understanding Prion Peptide Fibril-Induced Aggregation of Prion Protein (No. TAP LLT-1/2017). Dr. V. Smirnovas. 2017–2019.

Prion-like spreading may be employed in a number of fatal neurodegenerative disorders, including such as Alzheimer’s and Parkinson’s diseases. Understanding all possible mechanisms of such spreading would be a big step towards curing these diseases.
Recent work showed that prion protein aggregation can be induced by short peptides. It seems that either structure of peptide-induced prion protein aggregates (piPrP) or the mechanism of its formation is different from the current knowledge in the field.
We propose a comprehensive study of piPrP structure, starting from low-resolution methods as Fourier transform infrared (FTIR) spectrometry and proteinase K (PK) resistance studies, but focusing on medium and high-resolution methods in hydrogen exchange mass spectrometry (HXMS), electron spin resonance spectrometry (ESR), and solid-state nuclear magnetic resonance spectroscopy (ssNMR). High-resolution structure will lead to the ultimate goal of our research – getting deeper into mechanisms of prion-like self-replication of amyloid fibrils.

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 the 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

Senior research fellow: Dr. I. Matijošytė.
Junior research fellow: R. Šiekštelė.
Other researcher: A. Veteikytė.
Affiliated: Prof. emeritus G. Dienys.

RESEARCH INTERESTS

Biocatalysts and their application

RESEARCH PROJECTS CARRIED OUT IN 2019

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 2019, 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.

Contractual Research

Investigation of the Iomaterial Treatment by Chemical and Biotechnological Methods. JSC Nagenus, Lithuania, Dr. I. Matijošytė.
The aim is to evaluate and define the best treatment method and opimal conditions of three different kind of biomass.

Search and Investigation of New Microorganisms Possessing Biogeocenosis Features.
JSC Bioenergy LT, Lithuania, Dr. I. Matijošytė.

Purification of Casein Glycomacropeptide.
Pienas LT, Lithuania, Dr. I. Matijošytė.

Collaboration Contracts

Cooperation on Biotransformations of Various Lignocellulosic Based Biomass into Added Value Products. Latvian State Institute of Wood Chemistry, Cooperation Agreement N° BS-15600-1341 (2018-07-30, I. Matijošytė (open-ended).

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

Latvian State Institute of Wood Chemistry (Latvia)
University of Applied Sciences Northwestern (Switzerland)
University of Ljubljana (Slovenia)
National Institute of Biology (Slovenia)
Leiden University (the Netherlands)
University of Milan (Italy)

OTHER RESEARCH ACTIVITIES

Dr. I. Matijošytė –

• national representative in State Representative Group (SRG) at Bio-Based Industry Joint Undertaking;
• president of Lithuanian Biotechnology Association;
• scientific member of European Section of Applied Biocatalysis (ESAB, EFB).

 

DEPARTMENT OF BIOINFORMATICS

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 223 4368
E-mail:
Website: http://bioinformatics.lt

Head - Dr. Česlovas Venclovas

STAFF

Chief research fellow: Dr. Č. Venclovas.
Senior research fellows: Dr. V. Kairys, Dr. M. Margelevičius.
Research fellows: Dr. J. Dapkūnas, Dr. A. Timinskas, Dr. D. Kazlauskas, Dr. K. Olechnovič.
Other researcher: K. Timinskas.
System administrator: R. Dičiūnas.
Doctoral student: A. Nausėdas.

RESEARCH INTERESTS

Protein three-dimensional (3D) structure modeling
Analysis of 3D structure of proteins and nucleic acids
Analysis of genomes and proteomes
Distant homology detection between protein families
Protein-protein and protein-nucleic acids interactions
Molecular mechanisms of DNA replication, recombination and repair in the context of 3D structures

SELECTED PUBLICATIONS 2019

Kazlauskas, D., Varsani, A., Koonin, E.V., Krupovic, M. Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids. Nat Commun . 2019, 10: 1–12, https://doi.org/10.1038/s41467-019-11433-0.

Olechnovič, K., Monastyrskyy, B., Kryshtafovych, A., Venclovas, Č. Comparative analysis of methods for evaluation of protein models against native structures. Bioinformatics. 2019, 35: 937–944, https://doi.org/10.1093/bioinformatics/bty760.

Olechnovič, K., Venclovas, Č. VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes. Nucleic Acids Res. 2019, 47: W437–W442, https://doi.org/10.1093/nar/gkz367.

Timinskas, K., Venclovas, Č. New insights into the structures and interactions of bacterial Y-family DNA polymerases. Nucleic Acids Res. 2019, 47: 4393–4405, https://doi.org/10.1093/nar/gkz198.

Wolf, Y. I., Kazlauskas, D., Iranzo, J., Lucía-Sanz, A., Kuhn, J. H., Krupovic, M., Dolja, V. V., Koonin, E. V. Reply to Holmes and Duchêne, “Can sequence phylogenies safely infer the origin of the global virome?”: deep phylogenetic analysis of RNA viruses is highly challenging but not meaningless. mBio. 2019, 10, https://doi.org/10.1128/mBio.00542-19.

RESEARCH PROJECTS CARRIED OUT IN 2019

Projects Supported by University Budget

Computational Studies of Protein Structure, Function and Evolution. Dr. Č. Venclovas. 2017–2019.

In 2019, our focus in methods development continued to be the estimation of protein structure accuracy and the analysis of protein-protein interactions. Along with methods development, our major efforts were directed at application of computational methods to studies of prokaryotic CRISPR-Cas defence systems (jointly with Prof. Virgis Siksnys) and archaeo-eukaryotic primases in bacterial genomes (jointly with Dr. Mart Krupovic at Institut Pasteur, Paris).

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 analyzing 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 Modeling (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 affect the entire field of biomedicine. The most reliable approach for predicting protein structure today is modeling 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 modeling 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 modeling. 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)
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 OF MEDICAL EPIGENOMICS

7 Saulėtekio ave., LT-10257 Vilnius
E-mail:

Head - Dr. Artūras Petronis

STAFF

Chief research fellow: Dr. A. Petronis.
Junior research fellows: A. Kriščiūnas, K. Koncevičius.
Other researcher: T. Bareikis.

RESEARCH PROJECTS CARRIED OUT IN 2019

National Research Projects

Research Council of Lithuania. The Role of Epigenetic Oscillations in Predicting Biological Age (No. S- MIP-19-192). Dr. A. Petronis. 2019–2022.

SELECTED PUBLICATIONS 2019

Li, P., Marshall, L., Oh, G., Jakubowski, J. L., Groot, D., He, Y., Wang, T., Petronis, A., Labrie, V. Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer’s disease pathology and cognitive symptoms. Nat Commun. 2019, 10: 1–14, https://doi.org/10.1038/s41467-019-10101-7.

Oh, G., Koncevičius, K., Ebrahimi, S., Carlucci, M., Groot, D. E., Nair, A., Zhang, A., Kriščiūnas, A., Oh, E. S., Labrie, V., Wong, A. H. C., Gordevičius, J., Jia, P., Susic, M., Petronis, A. Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease. Genome Biology. 2019, 20: 2, https://doi.org/10.1186/s13059-018-1608-9.

Pai, S., Li, P., Killinger, B., Marshall, L., Jia, P., Liao, J., Petronis, A., Szabó, P. E., Labrie, V. Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis. Nat Commun. 2019, 10: 1–12, https://doi.org/10.1038/s41467-019-09786-7.

Petronis, A., Labrie, V. The crossroads of psychiatric epigenomics. World Psychiatry. 2019, 18: 353–354, https://doi.org/10.1002/wps.20675.

 

 

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 2019

M. Gasiūnienė. Regulation of the functioning and epigenetic mechanisms of amniotic fluid-derived stem cells.
J. Jakubovska. Modified pyrimidine nucleotides for the synthesis of oligonucleotides.
D. Ratautas. Nanostructured bioelectrocatalytic systems based on oxidoreductases.
V. Petkevičius. The investigation of pyridine ring attacking oxygenases.

DEPARTMENT OF BIOANALYSIS

7 Saulėtekio ave., LT-10257
Tel. 223 4389
E-mail:

Head – Dr. Marius Dagys

STAFF

Chief research associate: Dr. J. Razumienė.
Senior research associates: Dr. R. Šimkus, Dr. R. Vidžiūnaitė.
Research associates: Dr. L. Tetianec, Dr. M. Dagys, Dr. I. Šakinytė.
Junior research associates: I. Bratkovskaja, A. Laurynėnas, Dr. D. Ratautas.
Senior specialist: V. Gurevičienė.
Doctoral students: J. Gružauskaitė, I. Radveikienė, M. Butkevičius, E. Ramonas.

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 2019

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 publication:

Voitechovič, E., Jančienė, R., Mikulskienė, G., Vektarienė, A., Vektaris, V., Razumienė, J. Synthesis and DFT characterisation of 2-arylamino-1,4-benzoquinone derivatives as potential electron transfer mediators. Chemija. 2019, 115–126.

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. J. 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. M. 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.

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

Heads – Habil. Dr. Narimantas Čėnas

STAFF

Chief research fellow: Habil. Dr. N. Čėnas.
Senior research fellows: Dr. Ž. Anusevičius, Dr. K. Krikštopaitis, Dr. J. Šarlauskas.
Research fellows: Dr. L. Kosychova, Dr. A. Marozienė, Dr. L. Misevičienė.
Junior research fellows: E. Polmickaitė-Smirnova, B. Valiauga.
Doctoral student: M. Lesanavičius.

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2019

Project Supported by University Budget

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

Our previous studies of S. aureus flavohemoglobin (FHb) (Moussaoui, M. et al., Free Radical Biology and Medicine, 2018; 123: 105-115) demonstrated that econazole, ketoconazole and miconazole binding at heme domain, stimulated the reduction of quinones proceeding through FAD cofactor. We have shown that these compounds increased the bacteriostatic activity of quinones and nitrofurans towards S. aureus, thus demonstrating the involvement of FHb in their action. A series of aromatic N-oxides (ArN→O) has been synthesized for monitoring the bacterial N-oxidation of pyridine derivatives. The formation of different porphyrins under various conditions of incubation of Salmonella enterica with 5-aminolevulinic acid was characterized, which is instrumental in the understanding of mechanisms of bactericidal photodynamic therapy. We demonstrated that there exists a certain parallelism between the efficiency of inhibition of trypanothione reductase by vinylquinoline-substituted nitrofurans and their activity against Trypanosoma brucei. We further detalized the catalysis mechanism of Plasmodium falciparum ferredoxin:NADP+ reductase (PfFNR), showing that its different redox states are responsible for transhydrogenase and acceptorreductase activities. The experiments with varied ionic strength have shown that charged electron acceptors are reduced through nicotinamide-binding domain of NADP(H). The kinetic studies of E. coli nitroreductase-A S41Y/E99G/L103M/R225P/F227S mutant revealed the effect of mutations on the binding of NADP(H).

Main publications:

Petkevičius, V., Vaitekūnas, J., Tauraitė, D., Stankevičiūtė, J., Šarlauskas, J., Čėnas, N., Meškys, R. A biocatalytic synthesis of heteroaromatic N-oxides by whole cells of Escherichia coli expressing the multicomponent, soluble di-iron monooxygenase (SDIMO) PmIABCDEF. Advanced synthesis and catalysis. 2019, 361: 2456–2465.

Polmickaitė-Smirnova, E., Bagdonas, S., Anusevičius, Ž. Sensitization of Salmonella enterica with 5-aminolevulinic acid-induced porphyrins: a spectroscopic study. Photochemical and photobiological sciences. 2019, 18: 2730–2739.

National Research Projects

Research Council of Lithuania: Redox Chemistry, Biochemistry and Cytotoxicity of Aromatic Nitrocompounds and N-Oxides: New Insighths (No. DOTSUT-34/09.33-LMT-K712-01-0058). Habil. Dr. 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) we found that the reduction of nitroaromatic compounds presumably by PfFNR and their inhibition of Plasmodium falciparum glutathione reductase are two main factors determining their antiplasmodial in vitro activity; ii) studying single-electron reduction of nitroaromatic compounds by NADPH:cytochrome P-450 reductase (P-450R), adrenodoxin reductase/adrenodoxin (ADR/ADX) and PfFNR, we further characterized the previously unknown single-electron reduction potentials (E¹₇) of a number of nitroaromatic compounds; iii) the parallel studies of reactions of quinones and aromatic N-oxides with P-450R and ADR/ADX revealed that in spite of their similar reactivity vs. E¹₇ relationships, the oxic cytotoxicity of ArN→O is by one order of magnitude higher than that of quinones. It was explained mainly by the additional action of cytochromes P-450 and NAD(P)H:quinone oxidoreductase (NQO1), and iv) the synthesis of novel nitroaromatic compounds in particular nitrothiophenes, and novel ArN→O derivatives are continued for further enzymatic and cytotoxicity studies.

Main publications:

Nemeikaitė-Čėnienė, A., Šarlauskas, J., Jonušienė, A., Marozienė, A., Misevičienė, L., Yantsevich, A. V., Čėnas, N. Kinetics of flavoenzyme-catalyzed reduction of tirapazamine derivatives: implications for their prooxidant cytotoxicity. International Journal of Molecular Sciences. 2019, 20: 4602.

Šarlauskas, J., Polmickaitė-Smirnova, E., Čėnas, N., Krikštopaitis, K., Anusevičius, Ž. The QSAR study for antibacterial activity of structurally diverse nitroaromatics. Chemija. 2019, 30: 41–48.

Marozienė, A., Lesanavičius, M., Davioud-Charvet, E., Aliverti, A., Grellier, P., Šarlauskas, J., Čėnas, N. Antiplasmodial activity of nitroaromatic compounds: correlation with their reduction potential and inhibitory action on Plasmodium falciparum glutathione reductase. Molecules. 2019, 24: 4509.

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). Habil. Dr. N. Čėnas. 2019–2020.

Kinetic properties of 6 derivatives of plasmodione in reactions with P-450R, ADR/ADX, PfFNR, NO-synthase, and ascorbate were determined. They correlate with those of model quinones with E¹₇ values of -0.16 - -0.26 V.

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)

 

DEPARTMENT OF BIOELECTROCHEMISTRY AND BIOSPECTROSCOPY

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 223 4394
E-mail:

Head – Dr. Gintaras Valinčius

STAFF

Chief research fellows: Dr. G. Valinčius, Habil.Dr. G. Niaura (part time).
Senior research fellow: Dr. G. Preta.
Research fellows: Dr. R. Budvytytė, Dr. M. Jankunec, Dr. T. Ragaliauskas.
Junior research fellows: Dr. B. Pavliukevičienė, J. Borzova.
Senior specialists: M. Talaikis, Dr. A. Bulovas, T. Penkauskas.
Doctoral students: I. Aleknavičienė, K. Majauskaite, 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 experimenta data analysis

RESEARCH PROJECTS CARRIED OUT IN 2019

Project Supported by University Budget

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

The pore-forming toxins, inerolysin (INY) and vaginolysin (VLY) produced by vaginal bacteria Lactobacillus iners and Gardnerella vaginalis were studied using the artificial cholesterol-rich tethered bilayer membranes (tBLMs). The electrochemical impedance spectroscopy (EIS) of tBLMs attested for the toxin-induced impairment of the integrity of phospholipid membranes. This observation was in line with the atomic force microscopy data demonstrating formation of oligomeric protein assemblies in tBLMs. These assemblies exhibited different morphologies: VLY mostly formed complete rings, whereas INY produced arciform structures. We found that both EIS (membrane damage) and the surface plasmon resonance (protein binding) data obtained on tBLMs are in-line with the data obtained in human cell lysis experiments. EIS, however, is capable of capturing effects inaccessible for biological activity assays. Specifically, we found that the INY-induced damage of tBLMs is nearly a linear function of membrane cholesterol content, whereas VLY triggered significant damage only at high (50 mol%) cholesterol concentrations. The observed differences of INY and VLY activities on phospholipid membranes might have clinical importance: both toxin-producing bacteria have been found in healthy vagina and dysbiosis, suggesting the need for adaptation at different vaginal conditions.

Main publications:

Ragaliauskas, T., Plečkaitytė, M., Jankunec, M., Labanauskas, L., Baranauskiene, L., Valinčius, G. Inerolysin and vaginolysin, the cytolysins implicated in vaginal dysbiosis, differently impair molecular integrity of phospholipid membranes. Scientific Reports. 2019, 9: 10606.

Pampuščenko, K., Morkunienė, R., Šneideris, T., Smirnovas, V., Budvytytė R., Valinčius, G., Brown, G. C., Borutaite, V. Extracellular tau induces microglial phagocytosis of living neurons in cell cultures. Journal of Neurochemistry. 2019, art. no: UNSP e14940, doi: 10.1111/jnc.14940.

In collaboration with the Faculty of Mathematics and Informatics at Vilnius University, we continued developing mathematical analysis tools for the electrochemical impedance response from tBLMs. Specifically, impact of heterogeneity on EIS response was analysed. Finite element analysis (FEA) reveals that random distribution of defects in tethered bilayers results in qualitatively similar electrochemical impedance spectroscopy (EIS) response as bilayers with regularly arrayed defects. Such similarity leads to a broader conclusion that the microheterogeneity of tBLMs, which is possibly always the case in real systems, may be of lesser importance as far as qualitative aspects of the system are interrogated by the EIS. In addition, we proposed a simple algorithm that allows calculation of defect density as well as evaluation of the physical size of defects in membrane, in case of heterogeneous distribution of defects in tBLMs.

Main publication:

Raila, T., Penkauskas, T., Jankunec, M., Dreižas, G., Meškauskas, T., Valinčius, G. Electrochemical impedance of randomly distributed defects in tethered phospholipid bilayers: Finite element analysis. Electrochimica Acta. 2019, 299: 863–874.

We have employed a lipid system that forms highly swollen sponge phases to entrap aspartic protease (34 kDa), an enzyme used for food processing, e.g., to control the cheese-ripening process. Using the Raman spectroscopy data, we showed that minor conformational changes assigned to the lipid molecules confirm the lipid-protein interactions. However, the peaks assigned to the protein showed that the structure was not significantly affected. This was consistent with the higher activity presented by the encapsulated aspartic protease compared to the free enzyme stored at the same temperature. Together with colleagues from Lund University, based on the results, we discuss the large potential of lipid sponge phases as carriers for proteins.

Main publications:

Valldeperas, M., Talaikis, M., Dhayal, S. K., Velička, M., Barauskas, J., Niaura, G., Nylander, T. Encapsulation of aspartic protease in nonlamellar lipid liquid crystalline phases. Biophysical Journal. 2019, 17(5): 829–843, doi: 10.1016/j.bpj.2019.07.031.

Penkauskas, T., Preta, G. Biological applications of tethered bilayer lipid membranes. Biochemie. 2019, 157:131–141.

Talaikis, M., Valldeperas, M., Matulaitienė I., Borzova, J. L., Barauskas, J., Niaura, G., Nylander, T. On the molecular interactions in lipid bilayer-water assemblies of different curvatures. J. Phys.Chem. B. 2019, 123(12): 2662–2672.

National Research Council Projects

Research Council of Lithuania. Project QAPHOMEDA (No. P-MIP-19-394). Dr. G. Valinčius. 2019–2022.

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 Lifescience, Swansea University (United Kingdom)

OTHER RESEARCH ACTIVITIES

Dr. G. Valinčius –

• editorial board member of the journal Chemija;
• member of the Lithuanina 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.

Habil. Dr. G. Niaura –

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

Dr. R. Budvytytė –

• member of the American Biophysical Society.

 

DEPARTMENT OF BIOLOGICAL MODELS

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 223 4408
E-mail:

Head – Dr. Virginija Bukelskienė

STAFF

Senior research fellows: Dr. V. Bukelskienė, Dr. D. Baltriukienė, Dr. A. Burokas.
Junior research fellow: M. Alksnė.
Doctoral students: E. Šimoliūnas, I. Rinkūnaitė, P. Barasa, A. K. Vijaya, V. Baranauskas, M. Grubliauskaitė, E. M. Meškytė, J. Mingaila.
Veterinary doctor: A. Ščerbavičienė.
Assistants: J. Kernagytė, V. Untanienė, L. Vaškevičienė.

RESEARCH INTERESTS

Laboratory animals, cell culture, stem cells, tissues engineering, microbiota

RESEARCH PROJECTS CARRIED OUT IN 2019

Project Supported by University Budget

Development of the Cell Technologies for Regenerative Medicine and their Evaluation on Biological Models. Dr. V. Bukelskienė. 2014–2018.

Mechanical effects of extracellular matrix on cell fate. To find out how tissue cells respond to changes in the mechanical environment, collagen-coated polyacrylamide hydrogels were cross-linked to various degrees to modify the mechanical microenvironment to elucidate how healthy human gingiva-derived mesenchymal stem cells and cancerous human breast cancer cell line MCF–7 cells respond to the matrix stiffness in terms of morphology, cell cycle regulation, adhesion, proliferation, MAPK expression and response to oxidative stress.

Main publications:

Alksne, M., Simoliunas, E., Kalvaityte, M., Skliutas, E., Rinkunaite, I., Gendviliene, I., Baltriukiene, D., Rutkunas, V., Bukelskiene, V. The effect of larger than cell diameter polylactic acid surface patterns on osteogenic differentiation of rat dental pulp stem cells. Journal of Biomedical Materials Research: Part A. 2019, 107A: 174–186.

Balčiūnas, E., Baldock, S., Dreižė, N., Grubliauskaitė, M., Coultas, S., Rochester, D. L., Valius, M., Hardy, J. G., Baltriukienė, D. 3D printing hybrid organometallic polymer-based biomaterials via laser two-photon polymerization. Polymer International. 2019, 68(11): 1928–1940.

Balčiūnas, E., Dreižė, N., Grubliauskaitė, M., Urnikytė, S., Šimoliūnas, E., Bukelskienė, V., Valius, M., Baldock, S., Hardy, J. G., Baltriukienė, D. Biocompatibility investigation of hybrid organometallic polymers for sub-micron 3D printing via laser two-photon polymerisation. Materials. 12: 3932.

Project co-financed by European Union Structural Funds (SMART)

Targeting the Microbiota-Gut-Brain Axis in Alzheimer’s Disease: The Role of the Endocannabinoid System. Dr. A. Burokas. 2019–2023.

With the growing number of facts about the effects of the microbiota on various physiological processes in the body, its exploration has been chosen not only to better understand the mechanism of AD progression, but also to use it as a biomarker in order to create a method for early diagnosis of the disease, which would enable doctors to start treatment much earlier. Therefore, this multidisciplinary project has brought together a team of neurobiologists, biochemists and microbiologists who, in finding out the mechanism of diabetes-induced AD development, would open up new opportunities for both AD biomedical diagnosis and personalized medicine.

International Research Projects

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

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

The activity is aimed at the study of tissue regeneration of the eye using experimental rabbits.

Contractual Research

To Assess Feed Additives Toxicity by Using Laboratory Mice. Centrinis parkas, UAB. Dr. V. Bukelskienė.

Evaluation of the Biological Activity of the Products. Valentis, UAB. Dr. V. Bukelskienė.

Main publication:

Šimoliūnas, E., Rinkūnaitė, I., Bukelskienė, Ž., Bukelskienė, V. Bioavailability of Different Vitamin D Oral Supplements in Laboratory Animal Model. Medicina-Lithuania. 2019, 55.

Cell-based study (research service for the project of Smart Prosthetic Dentistry); Baltic Orthoservice UAB, Dr. V. Bukelskienė.

Study of the biocompatibility and differentiation potential of anisotropic composite and anisotropic bioactive composite scaffolds in vitro (using human / animal primary cell cultures) and in vivo (using laboratory rabbits); 3D Creative, UAB; Dr. V. Bukelskienė.

In vitro and in vivo study of the biocompatibility of new materials; Prodentum, UAB, Dr. V. Bukelskienė.

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

Vilnius University, Faculty of Physics, Laser Research Centre (Lithuania)
Vilnius University, Faculty of Medicine (Lithuania)
Vilnius University, Hospital Santaros klinikos, Centre of Heart and Chest Surgery (Lithuania)
Vilnius University, Hospital Santaros klinikos, Abdominal Suregry Centre (Lithuania)
Vilnius University, Faculty of Medicine, Institute of Odontology (Lithuania)
UAB Thermo Fisher Scientific Baltics (Lithuania)
UAB Prodentum (Lithuania)
UAB Centrinis parkas (Lithuania)
UAB Experimentica (Lithuania)
UAB Baltic Orthoservice (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.

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/;
• scientific supervisor of the Extramural School of Young Biochemists at Lithuanian Centre of Non-formal Youth Education, (http://www.lmnsc.lt/lt/jaunuju_biochemiku_mokykla);
• member of the Lithuanian Biochemical Society.

 
DEPARTMENT OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 223 4386
E-mail:

Head – Dr. Rolandas Meškys

STAFF

Chief research fellow: Dr. R. Meškys.
Senior research fellows: Dr. V. Časaitė, Dr. D. Tauraitė, Dr. L. Truncaitė, Dr. L. Kalinienė, Dr. J. Urbonavičius (part-time).
Research fellows: Dr. R. Gasparavičiūtė, Dr. R. Rutkienė, Dr. S. Povilonienė, Dr. J. Stankevičiūtė, Dr. A. Zajančkauskaitė, Dr. E. Šimoliūnas, Dr. A. Aučynaitė.
Junior research fellows: R. Meškienė, Dr. R. Stanislauskienė, Dr. V. Petkevičius, J. Vaitekūnas, N. Urbelienė, M. Sadauskas.
Doctoral students: A. Krikštaponis, A. Noreika, M. Šimoliūnienė.

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2019

Project Supported by University Budget

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

Self-assembling structures open up exciting opportunities for the development of various tools, including biosensors, energy storage devices, drug delivery systems and nanobiopolymeric scaffolds. Therefore, it is not surprising that viruses, including bacteriophages, have been used for the preparation of nanoscaled materials. The recombinant phage tail sheath protein, gp053, from Escherichia coli infecting myovirus vB_EcoM_FV3 was able to self-assemble into long, ordered and extremely stable tubular structures (polysheaths) in the absence of other viral proteins. In addition, we showed that the tail tube protein of bacteriophage vB_EcoS_NBD2 formed extremely long polytubes in E. coli and S. cerevisiae. Novel NBD2 polytubes could be used as flexible, extremely long platforms for foreign epitope display via genetic fusion or chemical modifications and may be also useful for the fabrication of various nanowires.

Main publications:

Šimoliūnas, E., Truncaitė, L., Rutkienė, R., Povilonienė, S., Goda, K., Kaupinis, A.,Valius, M., Meškys, R. The robust self-assembling tubular nanostructures formed by gp053 from phage vB_EcoM_FV3. Viruses. 2019, 11: 50.

Špakova, A., Šimoliūnas, E., Batiuškaitė, R., Pajeda, S., Meškys, R., Petraitytė-Burneikienė, R. Self-assembly of tail tube protein of bacteriophage vB_EcoS_NBD2 into extremely long polytubes in E. coli and S. cerevisiae. Viruses. 2019, 11: 208.

National Research Projects

Research Council of Lithuania. Bacteriophage Control of Nitrogen Cycling in Cyanobacteria: from Cells to Community (No. P-MIP-17-6), Dr. S. Šulčius (Nature Research Center), work package leader Dr. E. Šimoliūnas. 2017–2019.

Filamentous cyanobacteria have an important role in nitrogen cycling in the Baltic Sea, and it could be expected that viruses infecting these cyanobacteria would affect these processes as well. The results of the project will provide insights into how virus-mediated changes at cell (e.g. regulation of gene expression levels) and population (e.g. growth restriction and lysis) level shape the ecologically relevant traits (e.g. N2-fixation, N-release and production of non-ribosomal peptides) of filamentous cyanobacteria in the Baltic Sea, and therefore ecosystem functioning and productivity.

Main reference:

Šimoliūnas, E., Tominaga, K., Alzbutas, G., Morimoto, D., Nilsson, E., Šimoliūnienė, M., Holmfeldt, K., Yoshida, T., Šulčius, S. Diversity of cyanophages infecting diazotrophic toxin producing cyanobacterium Nodularia spumigena from the Baltic Sea. 11^th International Conference on Toxic Cyanobacteria (ICTC), May 5–10 2019, Kraków, Poland (Poster).

Research Council of Lithuania. Research on Prediction of Environmental Change in the Baltic Sea Based on Comprehensive (Meta)Genomic Analysis of Microbial Viruses (No. S-LJB-17-1), Dr. S. Šulčius (Nature Research Center), work package leader Dr. E. Šimoliūnas. 2017–2019.

The aim of the project is to investigate the impact of viruses on the cyanobacteria population dynamics in the Baltic Sea. The results of this project will provide not only insights into the role of cyanophages in population dynamics and antagonistic coevolution between cyanobacteria and their viruses but also the culture collection of the Baltic Sea cyanophages will be established and reference genome database of Baltic cyanobacteria viruses will be created and made available for scientific community for further investigations of Baltic Sea cyanophage biology, ecology and evolution.

Main publication:

Šulčius, S., Šimoliūnas, E., Alzbutas, G., Gasiūnas, G., Jauniškis, V., Kuznecova, J., Sini S., Nilsson, E., Meskys, R., Roine, E., Paškauskas, R., Holmfeldt, K. Genomic characterisation of cyanophage vB_AphaS-CL131 infecting filamentous diazotrophic cyanobacteria Aphanizomenon flos-aquae reveals novel insights into virus-bacterium interactions. Appl. Environ. Microbiol. 2019, 85: e01311–18.

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.

Samples were collected from the two spots of Curonian lagoon every month for the half of year (from April to October). DNA and RNA were extracted from all samples. Later, they will be used for amplification and quantification of nifH genes and its transcripts.

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).

International Research Projects

EU Horizon2020 Program. H2020-BG-2014-2. Industrial Applications of Marine Enzymes: Innovative Screening and Expression Platforms to Discover and Use the Functional Protein Diversity from the Sea (Inmare). Dr. R. Meškys. 2015–2019.

The main focus is the development of the innovative enzyme-screening techniques, involving the construction of tailored microorganisms and the synthesis of smart substrates. Screening systems for hydrolases based on modified uracils or uridines were established by using E. coli strains harboring pyrFEC mutations. Various oxidoreductases and hydrolases have been screened using the metagenomics libraries.

Main publications:

Urbelienė, N., Kutanovas, S., Meškienė, R., Gasparavičiūtė, R., Tauraitė, D., Koplūnaitė, M., Meškys, R. Application of the uridine auxotrophic host and synthetic nucleosides for a rapid selection of hydrolases from metagenomic libraries. Microb. Biotechnol. 2019, 12: 148–160.

Ferrer, M., Méndez-García, C., Bargiela, R., Chow, J., Alonso, S., García-Moyano, A., Bjerga, G. E. K., Steen, I. H., Schwabe, T., Blom, C., Vester, J., Weckbecker, A., Shahgaldian, P., de Carvalho, C. C. C. R., Meskys, R., Zanaroli, G., Glöckner, F. O., Fernández-Guerra, A., Thambisetty, S., de la Calle, F., Golyshina, O. V., Yakimov, M. M., Jaeger, K. E., Yakunin, A. F., Streit,W. R., McMeel, O., Calewaer,J. B., Tonné, N., Golyshin, P. N. The INMARE Consortium. Decoding the ocean’s microbiological secrets for marine enzyme biodiscovery. FEMS Microbiol. Lett. 2019, 366: 1.

Petkevičius, V., Vaitekūnas, J., Tauraitė, D., Stankevičiūtė, J., Šarlauskas, J., Čėnas, N., Meškys, R. A biocatalytic synthesis of heteroaromatic N-oxides by whole cells of Escherichia coli expressing the multicomponent, soluble di-iron monooxygenase (SDIMO) PmlABCDEF. Adv. Synth. Catal. 2019, 361: 2456–2465.

Contractual Research

Development of Methods for Elimination of Gliadin-Based Peptides from Protein Mixtures. AB Roquette Amilina, 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

Chief research associate: Prof. Dr. R. Navakauskienė.
Senior research fellows: Dr. V. V. Borutinskaitė, Dr. A. Kalvelytė.
Research fellows: Dr. A. Imbrasaitė, Dr. N. Krestnikova, Dr. G. Treigytė, Dr. G. Valiulienė.
Junior research fellows: A. Stulpinas, A. Vaitkevičienė.
Doctoral students: R. Baušytė, A. Stulpinas, B. Vaigauskaitė, A. Zentelytė, D. Žukauskaitė.

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2019

Project Supported by University Budget

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

Assessement of gene expression changes in stem and cancer cells. Human cancer cells (acute myeloid leukemia 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., Zentelytė, A., Wojtas, B., Baronaitė, S., Krasovskaja, N., Savickienė, J., Gielniewski, B., Kaminska, B., Utkus, A., Navakauskienė, R. DNMT inhibitors effectively induce gene expression changes suggestive of cardiomyogenic differentiation of human amniotic fluid-derived mesenchymal stem cells via chromatin remodeling. Journal Tissue Engeneering and Regenerative Medicine. 2019, 13: 469–481, doi: 10.1002/term.2800.

Vitkevičienė, A., Skiauterytė, G., Žučenka, A., Stoškus, M., Gineikienė, E., Borutinskaitė, V., Griškevičius, L., Navakauskienė, R. HDAC and HMT inhibitors in combination with conventional therapy: a novel treatment option for acute promyelocytic leukemia. Journal of Oncology. 2019 Jul 18, 2019: 6179573, doi: 10.1155/2019/6179573.

Vitkevičienė, A., Janulis, V., Žučenka, A., Borutinskaitė, V., Kaupinis, A., Valius, M., Griškevičius, L., Navakauskienė, R. Oxidative phosphorylation inhibition induces anticancerous changes in therapy-resistant-acute myeloid leukemia patient cells. Molecular Carcinogenesis. 2019 Aug 6. doi: 10.1002/mc.23092.

National Research Projects

Agency for Science, Innovation and Technology. Technical Feasibility Study of Stem Cell Application in Infertility Treatment. Prof. R. Navakauskienė. 2019.

Research Council of Lithuania. 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 SMART project in 2019, the efficacy of conventional and targeted drugs, from different stages of clinical trials and FDA approval, selected to inhibit the intracellular signalling molecules of mitogen-activated protein kinases (MAPKs) and PI3K/AKT pathways, individually or in combinations, were examined regarding target activity by using a panel of phenotypically and genotypically different patient-derived lung cancer primary cell lines. The mechanisms of identified compensatory feedback loops between ERK1 /2 and AKT were examined. Results have been presented at Cancer Research and Oncology Conference (Barcelona, 2019).
Within the frame of the project, we have reviewed the topic of cellular death (Stulpinas and Kalvelytė, 2019) and 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. Recent approaches encompassing the phenotypic cell heterogeneity for anticancer drug efficacy evaluation IntechOpen. 2019, doi: 10.5772/intechopen.89395.

International Research Projects

COST action CA15138 European Network of Multidisciplinary Research and Translation of Autophagy Knowledge (TRANSAUTOPHAGY). Dr. V. Borutinskaitė. 2015–2019.

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

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

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

OTHER RESEARCH ACTIVITIES

Prof. R. Navakauskienė –

• member of American Society for Cell Biology;
• 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 Mokslininkų str., LT-08412 Vilnius
Tel. 272 9058
E-mail:

Head – Dr. Regina Jančienė

STAFF

Senior research fellow: Dr. R. Jančienė.
Research fellow: 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 2019

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 synthesis of a model compound, dimesyltetraethylene glycol, and its interaction with various azides was investigated. Dimesyltetraethylene glycol was synthesized by reaction of tetraethylene glycol with methansulphochloride. For substitution of mesyl groups by azido groups, several organic and inorganic azides were tested. The best results were obtained with sodium azide and α,ω-diazidotetraethylenglycol of high yield and purity was synthesized. For the synthesis of mono-amino-substituted product, several reduction agents were tested. Optimal reaction conditions for the synthesis of diazido and mono-amino derivatives were established in various volumes. The results of these studies are used to the synthesis of ethylene glycol derivatives of various polymerization degree (n=4÷18).

The synthesis of 3,6‐dichloro‐1,2,4,5‐tetrazine was investigated and multistep synthesis scheme was created. The synthesis of 3,6‐dichloro‐1,2,4,5‐tetrazine was performed in 5 steps. After optimization of each step, the total yield of 3,6‐dichloro‐1,2,4,5‐tetrazine was 45 %.
Cyclization of p-cyano-o-nitrobenzyl-p-cyanophenylketone was further investigated. The reaction in the solution of acetic acid gave 2-(4-cyanophenyl)-1H-indolo-6-carbonitrile with moderate yield only in the case of reaction from small amounts of corresponding nitroderivative. Moreover, in this reaction, considerable amount of N-hydroxyindole derivative was formed and fractional crystallization for its separation was required. It was established that these disadvantages of reductive cyclization reaction may be avoided using polar solvents and equivalent amount of acetic acid. Optimal reaction solvent was determined after a series of experiments and allowed to enlarge the input of the reaction. The shortened time of indole synthesis made DAPI synthesis more economical.

Main publications:

Janciene, R., Mikulskiene, G. The complete 1H and 13C NMR spectra assignments of N-(2-nitrobenzoyl)-1,5-benzodiazepin-2-one and dihydroquinazolino[3,2-α]benzodiazepine derivatives. Magnetic Resonance in Chemistry. 2019, 57(11): 968–974.

Butkus, S., Rickus, M., Sirutkaitis, R., Paipulas, D., Sirutkaitis, V. Fabrication of high aspect ratio channels in fused silica using femtosecond pulses and chemical etching at different conditions. Journal of Laser Micro Nanoengineering. 2019, 14(1): 19–24, doi: 10.2961/jlmn.2019.01.0004.

Macernyte, L., Skruibis, J., Vaicaitis, V., Sirutkaitis, R., Balachninaite, O. Femtosecond laser Mmcromachining of soda-lime glass in ambient air and under various aqueous solutions. Micromachines. 2019l, 10(6): 354, doi: 10.3390/mi10060354.

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 Polyethylene Glycol Diazides by Reacting Polyethyleneglycol-Dimesylates with Sodium Azide. 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 and Optimization of the Synthesis of 3,6-Dichloro-S-Tetrazine. Contract with UAB Certumtech. 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.

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 Certumtech (Lithuania)

 

PROTEOMICS CENTRE

7 Saulėtekio ave., LT-10257, Vilnius
Tel. 223 4410
E-mail:

Head – Dr. Mindaugas Valius

STAFF

Senior research fellows: Dr. M. Valius, Dr. J. Cicėnas.
Research fellows: Dr. A. Kaupinis, Dr. M. Ger.
Junior research fellow: N. Dreižė.
Doctoral students: S. Urnikytė, E. Žalytė, G. Karzaitė, I. Meškinytė.

RESEARCH AREAS

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

RESEARCH PROJECTS CARRIED OUT IN 2019

Project Supported by University Budget

New Technologies for Tumor Diagnosis and Treatment Based on Nano-Materials and Proteomics. Dr. M. Valius. 2014–2019.

Main publications:

Peterman, E., Gibieža, P., Schafer, J., Skeberdis, V. A., Kaupinis, A., Valius, M., Heiligenstein, X., Hurbain, I., Raposo, G., Prekeris, R. The post-abscission midbody is an intracellular signaling organelle that regulates cell proliferation. Nat Commun. 2019, 18, 10(1): 3181, doi: 10.1038/s41467-019-10871-0.

Kuciauskas, D., Dreize, N., Ger, M., Kaupinis, A., Zemaitis, K., Stankevicius, V., Suziedelis, K., Cicenas, J., Graves, L. M., Valius, M. Proteomic analysis of breast cancer resistance to the anticancer drug RH1 reveals the importance of cancer stem cells. Cancers (Basel). 2019, 11, 11(7). pii: E972. doi: 10.3390/cancers11070972.

Gasiulė, S., Dreize, N., Kaupinis, A., Ražanskas, R., Čiupas, L., Stankevičius, V., Kapustina, Ž., Laurinavičius, A., Valius, M., Vilkaitis, G. miR-23b modulates the epithelial-mesenchymal transition of colorectal cancer cells. J Clin Med. 2019, 2, 8(12). pii: E2115. doi: 10.3390/jcm8122115.

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 Farmacology, Chapel Hill (USA)
Lithuania National Cancer Center, Vilnius (Lithuania)
Vilnius University Hospital Santariskiu Klinikos, Vilnius (Lithuania)
Nation Center of Patology, Vilnius (Lithuania)
Lithuanian University of Health Science, Institute of Cardiology, Kaunas (Lithuania)

OTHER RESEARCH ACTIVITIES

Dr. M. Valius –

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

Dr. J. Cicėnas –

• collection editor (Kinases and cancer) of the Cancers.

 

INSTITUTE OF BIOSCIENCES

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 239 8200
E-mail:
www http://www.gf.vu.lt

Director – Prof. Habil. Dr. Juozas Lazutka

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 2019

A. Voicik. Investigation of the dependence of brain auditory steady – state responses on stimulation type.
A. Kalnaitytė. The photostability and phototoxicity studies of biocompatible nanoparticles in model biosystems.
S. Činčiūtė. Effects of sex and handedness on the hemodynamic response obtained in the human prefrontal cortex.
A. Gricajeva. Search and analysis of novel bacterial lipolytic enzymes.
J. Skerniškytė. Molecular mechanisms of Acinetobacter baumannii pathogenesis.
E. Kukcinavičiūtė. The response of chemoresistant human colorectal cancer cells HCT116 to cytotoxic treatment.
A. Mikalkėnas. Modified nucleotides in nucleic acid biosynthesis: application aspects.

MAIN CONFERENCES ORGANIZED IN 2019

11th conference of the Lithuanian Neuroscience Association (LNA), November 29, 2019

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

• Dr. Urtė Neniškytė: L’Oréal-UNESCO for Women in Science International Rising Talents;
  Presidential award of the Knight’s Cross of the Lithuanian Grand Duke Gediminas.

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

• Urtė Neniškytė. Committee member at Young Division of International Brain Research Organization.
• Aidas Alaburda. National expert for European Research Council (ERC) (Future and Emerging Technologies (FET) and Marie Skłodowska-Curie Actions (MSCA).
• Jurga Turčinavičienė. Member of the GMO experts committee, http://gmo.am.lt/page?page=itemList&entity=biosafetyExpert
• Andrius Petrašiūnas. Member of the Lithuanian Red Data Book Committee.

CONSULTATIONS PROVIDED BY THE UNIT TO THE PUBLIC OR ECONOMIC ENTITIES

Consultations on the identification and use of animals, protists, plants, fungi and lichens. Nature protection, forestry and agriculture specialists, naturalists and other individuals have been consulted by scientists of Botany and Mycology Group and Zoology Department.

 

DEPARTMENT OF BIOCHEMISTRY AND MOLECULAR BIOLOGY

STAFF

Professors: Dr. E. Sužiedėlienė, Dr. S. Serva, Prof. V. Starkuvienė (part-time). K. Sužiedėlis (part-time).
Associate professors: Dr. D. Dabkevičienė, Dr. A. Markuckas, Dr. A. Sasnauskienė, Dr. A. Zimkus, Dr. V. Jonušienė, Dr. D. Labeikytė.
Lecturer: Z. Žitkus.
Senior research fellows: Dr. J. Armalytė, Dr. A. Zimkus.
Research fellows: Dr. V. Jonušienė, Dr. A. Sasnauskienė, Dr. D. Labeikytė.
Junior research fellows: A. Konovalovas, J. Skerniškytė, A. Mikalkėnas, E. Kukcinavičiūtė.
Doctoral students: L. Kunigėnas, L. Aitmanaitė, R. Krasauskas, V. Žitkutė, E. Celitan, R. Prokarenkaitė.

RESEARCH INTERESTS

Molecular determinants of virus cycle. Antivirals
Biochemical mechanisms of cellular response to photooxidation and cytotoxic treatment
Bacterial stress responses, pathogenesis, antibiotic resistance

RESEARCH PROJECTS CARRIED OUT IN 2017

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 changes in growth factors and cytokine expression; 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:

Armalytė, J., Skerniškytė, J., Bakienė, E., Krasauskas, R., Šiugždinienė, R., Kareivienė, V., Kerzienė, S., Klimienė, I., Sužiedėlienė, E., Ružauskas, M. Microbial diversity and antimicrobial resistance profile in microbiota from soils of conventional and organic farming systems. Front Microbiol. 2019, doi: 10.3389/fmicb.2019.00892.

Skerniškytė, J., Krasauskas, R., Péchoux, C., Kulakauskas, S., Armalytė, J., Sužiedėlienė, E. Surface-related features and virulence among Acinetobacter baumannii clinical isolates belonging to international clones I and II. Front Microbiol. 2019, doi: 10.3389/fmicb.2018.03116.

Grigaitis, P., Jonusiene, V., Zitkute, V., Dapkunas, J., Dabkeviciene, D., Sasnauskiene, A.
Exogenous interleukin-1α signalling negatively impacts acquired chemoresistance and alters cell adhesion molecule expression pattern in colorectal carcinoma cells HCT116. Cytokine. 2019, doi: 10.1016/j.cyto.2018.11.031.

Vilnius University funded project

Investigation of Biogenesis of Totiviridae Family Virus ScV-LA in Native Environment (Nr. MSF-JM-7). Project leader A. Konovalovas, 2019.

National Research Projects

Research Council of Lithuania. Redox Chemistry, Biochemistry and Cytotoxicity of Aromatic Nitrocompounds and n-oxides: a New Look (Nr 09.3.3-LMT-K-712-01-0058). Participant V. Jonušienė. Project leader Dr. N. Čėnas. 2015–2018.

International grants:
Baltic-German University Liaison Office (funded by DAAD) project Life Cycle of Yeast dsRNA Viruses Uncovered by Advanced Fluorescent Microscopy. Project leader S. Serva, 2019.

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

Lithuanian University of Health Sciences (Lithuania)
Nature Research Centre (Lithuania)
Heidelberg University (Germany)
University of Ostrava (Czech Republic)
Universite Libre de Brussels (Belgium)
University of Haifa (Israel)
Université Paris-Saclay (France)

OTHER RESEARCH ACTIVITIES

Prof. E. Sužiedėlienė –

• member of the Research Council of Lithuania.

Prof. S. Serva –

• secretary of the Lithuanian Biochemical Society;
• member of Biomedical and Agricultural Expert Board at Lithuanian Agency for Science, Innovation and Technology.

 

DEPARTMENT OF BOTANY AND GENETICS

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 239 8257
E-mail:

Head – Prof. Habil. Dr. Juozas Lazutka

STAFF

Professors: Dr. S. Jarmalaitė, Dr. E. Kutorga, Habil. Dr. I. Pašakinskienė (part-time), Habil. Dr. V. Rančelis (emeritus), Dr. G. Slapšytė, 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).
Assistants: Dr. I. Prigodina Lukošienė.
Junior assistants: P. Venckus, A. Stapulionytė, K. Stuopelytė.
Lecturers: S. Juzėnas, A. Meldžiukienė.
Senior research fellow: Dr. V. Kleizaitė.
Research fellows: 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.
Junior research fellows: M. Rasimavičius.
Senior biologist: Dr. J. Rukšėnienė.
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.

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
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

RESEARCH PROJECTS CARRIED OUT IN 2019

Projects Supported by University Budget

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

Genotoxicity of B. officinalis, G. officinalis, V. luteum and V. hirundinaria extracts, which demonstrated strong antioxidant capacity, was tested using chromosome aberration, sister chromatid exchange (SCE), cytokinesis-block micronucleus and alkaline single-cell gel electrophoresis (comet) assays in human lymphocytes in vitro and Ames Salmonella/microsome test. All tested extracts were not mutagenic in S. typhimurium strains TA98 and TA100 with and without metabolic activation and did not induce chromosome aberrations in human lymphocytes in vitro. Extract from G. officinalis was the only one, which induced significant increase in micronuclei, indicating possible aneugenic effect. All investigated plant extracts induced DNA damage evaluated by the comet assay, while B. officinalis and V. luteum extracts induced slight increase in SCE values. The determined variation in response might be due to the plant extract tested and donor susceptibility.

In collaboration with industrial partners, the possible harmful impact of the brand-new 206 nm femtosecond laser Pharos on bone marrow, skin and corneal cells was studied. It was demonstrated that the DNA-damaging effect of laser irradiation was mostly dependent on the wavelength, but the influence of such a parameter as beam delivery to the target was also revealed.

DNA methylation and gene expression changes were analysed in renal and lung tumours, and liquid biopsies from cancer patients.

Main publications:

Slapšytė, G., Dedonytė, V., Adomėnienė, A., Lazutka, J. R., Kazlauskaitė, J., Ragažinskienė, O., Venskutonis, P. R. Genotoxic properties of Betonica officinalis, Gratiola officinalis, Vincetoxicum luteum and Vincetoxicum hirundinaria extracts. Food Chem. Toxicol. 2019, 134: 110815.

Morkunas, V., Urbonaite, G., Gabryte-Butkiene, E., Sobutas, S., Vengris, M., Danielius, R., Ruksenas, O. DNA-damaging effect of different wavelength (206 and 257 nm) femtosecond laser pulses. Photobiomodulation, Photomedicine, and Laser Surgery. 2019, 37: 254–261.

Bakavicius, A., Daniunaite, K., Zukauskaite, K., Barisiene, M., Jarmalaite, S., Jankevicius, F. Urinary DNA methylation biomarkers for prediction of prostate cancer upgrading and upstaging. Clin Epigenetics. 2019, 11(1): 115.

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

Genetic polymorphism is very important 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. Genetic structure of Medicago sativa populations and cultivars was studied using ISSR markers. Polluted-soil-induced oxidative stress was evaluated using Tradescantia clone 4430, which is widely used for genotoxicity evaluations, employing biochemical and molecular markers after long-term exposure.

Further investigation into the application of numerous barley lines, resulting from the segregation of dihybrids of different developmental barley mutants, was carried out. In total, 231 lines were analysed in distinct generations (corresponding to F9–15) for decorative quality and quantitative characters. Wider spectra of attractive lines were selected among the offspring of tweaky spike2 (tw2) × Lemma hooded and tw2× Brittle rachis cross-combinations. Several lines are also valuable for high protein content.

Main publications:

Šiukšta, R., Bondzinskaitė, S., Kleizaitė, V., Žvingila, D., Taraškevičius, R., Mockeliūnas, L., Stapulionytė, A., Mak, K., Čėsnienė, T. Response of Tradescantia plants to oxidative stress induced by heavy metal pollution of soils from industrial areas. Environmental Science and Pollution Research. 2019, 26: 44–61.

Vaitkūnienė, V., Šiukšta, R., Leistrumaitė, A., Rančelis, V. Prospective use of barley spike/flower homeotic single and double mutants for ornamental purposes. Euphytica. 2019, 215: 127.

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

Studies in the wood-inhabiting fungal communities on dead wood of Scots pine (Pinus sylvestris) under varying duration and intensity of cormorant nesting have been undertaken. Analyses based on records of fruiting structures of fungi showed that fungal communities in the cormorant colony differed from communities in unaffected forest. The rate of ornithogenic change was rapid: a shift in fungal assemblages was evident by the third year of expansion of the bird colony into unaffected forest. Investigations on a sexual and asexual reproduction, and the hybridization of taxa within the genus Diphasiastrum (Lycopodiophyta) were summarized. Studies on Cyanobacteria preserved at Vilnius University Herbarium were performed.

Main publications:

Iršėnaitė, R., Arslanova, T., Kasparavičius, J., Kutorga, E., Markovskaja, S., Matulevičiūtė, D., Taraškevičius, R., Motiejūnaitė, J. Effects of a great cormorant colony on wood-inhabiting fungal communities in a coastal Scots pine forest. Fungal Ecology. 2019, 41: 82–91. https://doi.org/10.1016/j.funeco.2019.03.010.

Schnittler, M., Horn, K., Kaufmann, R., Rimgailė-Voicik, R., Klahr, A., Bog, M., Fuchs, J., Bennert, H. W. Genetic diversity and hybrid formation in Central European club-mosses (Diphasiastrum, Lycopodiaceae) – New insights from cp microsatellites, two nuclear markers and AFLP. Molecular Phylogenetics and Evolution. 2019, 131: 181–192.

Briškaitė, R., Rasimavičius, M. Collection of Cyanobacteria in Vilnius University Herbarium. Cyanoprokaryota/Cyanobacteria: Systematic, Ecology, Distribution. Proceedings of the 2nd international conference, September 16–21, 2019, Syktyvkar, Russia. Syktyvkar: Institute of Biology, Komi Scientific Centre, UB RAS. 2019, 304 p. doi: 10.31140/book-2019-03. ISBN 978-5-6042182-7-3.

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. 2019.

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 by black and white line drawings, and colour photographs of fungi.

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 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 publication:

Maleckaite, R., Zalimas, A., Bakavicius, A., Jankevicius, F., Jarmalaite, S., Daniunaite, K. DNA methylation of metallothionein genes is associated with the clinical features of renal cell carcinoma. Oncol Rep. 2019 June, 41(6): 3535–3544.

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

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

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 (Finland)
HUSLAB, Helsinki University Hospital (Finland)

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 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.

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 (expert in Botany).

Prof. J. R. Naujalis –

• editorial board member of the journal Biologija;
• editorial board member of the journal Scripta Horti Botanici Universitatis Vytauti Magni;
• member of the Lithuanian Academy of Sciences.

Prof. J. R. Lazutka –

• editor-in-Chief of the journal Open Life Sciences.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Meldžiukienė A. Winter and summer camps for children Nature Cognitive at VU LSC.
  National Science festival Spaceship Earth, Lead seminars, activities and excursions.
  A number botanical sightseeing excursions at VU LSC for schoolchildren and
  kindergarteners.
• Rasimavičius M. Public exhibition of herbaria at Plungė municipal library From the past to the present, from the present to the future.
  Interviews at the Lithuanian TV programme Good morning, Lithuania, on Herbarium of Vilnius University. https://www.lrt.lt/mediateka/irasas/1013714863/labas-rytas-lietuva-i-dalis?fbclid=IwAR3bM4nEgzAZrJTsbEStePiJLEyLFELmDKK2ZUAoJmf-LG1t3pIEyZaEhQ4,
  TV programme Consumer control, https://www.lrt.lt/mediateka/irasas/2000065453/vartotoju-kontrole.
• Tupčiauskaitė J. Public botanical excursion What blooms here? in Vilnius University Botanical Garden, 18 May, 2019.

 

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: A. Gegeckas, R. Gudiukaitė, R. Kananavičiūtė.
Lecturers: J. Raugalas, R. Petkauskaitė, A. Gricajeva, I. Burneikienė. J. Lebedeva, J. Jurgelevičiūtė, R.Ražanskas (part-time), Ž. Dapkunas (part-time)
Researcher: A. Kaunietis.
Specialists: J. Lekavičiūtė, R.J urkevičienė.
Doctoral students: A. Gricajeva, R. Bikmurzinas, T. Kirtiklienė, J. Jurgelevičiūtė, K. Čekuolytė, V. Malūnavičius.

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 the 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 2019

Projects Supported by University Budget

Selection of Microorganisms and Researches for Innovative Biotechnology Creation. Prof. Dr. L. Kalėdienė. 2019.

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. For the industrial implementations, especially in the area of the organic synthesis, immobilized enzymes are preferred. Therefore, it is important to examine new types of immobilization sorbents.

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. 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:

Kaunietis, A., Buivydas, A., Citavicius, D., Kuipers, O. Heterologous biosynthesis and characterization of a glycocin from a thermophilic bacterium. Nature Communications. 2019, 10, art. no. 1115.

Vaičikauskaitė, M., Ger, M., Valius, M., Maneikis, A., Lastauskienė, E., Kalėdienė, L., Kaunietis, A. Geobacillin 26 - high molecular weight bacteriocin from a thermophilic bacterium. International Journal of Biological Macromolecules. 2019, 141: 333–344.

Gricajeva, A., Bikute, I., Kalediene, L. Atypical organic-solvent tolerant bacterial hormone sensitive lipase-like homologue EstAG1 from Staphylococcus saprophyticus AG1: synthesis and characterization. International Journal of Biological Macromolecules. 2019, 130: 253–265.

Molecular Microbiology of Prokaryotes for Modern Biotechnology and Biopharmacy. Prof. Dr. N. Kuisienė. 2018.

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 publications:

Bukelskis, D., Dabkeviciene, D., Lukoseviciute, L., Bucelis, A., Kriaučiūnas, I., Lebedeva, J., Kuisiene, N. Screening and transcriptional analysis of polyketide synthases and non-ribosomal peptide synthetases in bacterial strains from Krubera–Voronja Cave. Front. Microbiol. 2019, 10: 2149.

Tratulyte, S., Miciuleviciene, J., Kuisiene, N. First genotypic characterization of toxigenic Clostridioides difficile in Lithuanian hospitals reveals the prevalence of the hypervirulent ribotype 027/ST1. Eur. J. Clin. Microbiol. Infect. Dis. 2019, 38(10): 1953–1959.

Determination of the Microorganisms Synthesized Antimicrobial Compounds, Protein Engineering and Application in Biotechnology. Assoc. prof. E. Lastauskienė. 2019.

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 analysed 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 publications:

Novickij, V., Staigvila, G., Gudiukaitė, R., Zinkevičienė, A., Girkontaitė, I., Paškevičius, A., Švedienė, J., Markovskaja, S., Novickij, J., Lastauskienė, E. Nanosecond duration pulsed electric field together with formic acid triggers caspase-dependent apoptosis in pathogenic yeasts. Bioelectrochemistry. 2019, 128: 148–154.

Druteika, G., Sadauskas, M., Malunavicius, V., Lastauskiene, 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. 2019, https://doi.org/10.1016/j.ijbiomac.2019.10.163.

Novickij, V., Staigvila, G., Gudiukaitė, R., Zinkevičienė, A., Girkontaitė, I., Paškevičius, A., Švedienė, J., Markovskaja, S., Novickij, J., Lastauskienė, E. Nanosecond duration pulsed electric field together with formic acid triggers caspase-dependent apoptosis in pathogenic yeasts. Bioelectrochemistry. 2019, 128: 148–154.

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: PhD Nomeda Kuisienė. 2017–2020.

Main publication:

Bukelskis, D., Dabkeviciene, D., Lukoseviciute, L., Bucelis, A., Kriaučiūnas, I., Lebedeva, J., Kuisiene, N. Screening and transcriptional analysis of polyketide synthases and non-ribosomal peptide synthetases in bacterial strains from Krubera–Voronja Cave. Front. Microbiol. 2019, 10: 2149.

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)
Centre for Physical Sciences and Technology (Lithuania)
The 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)

OTHER RESEARCH ACTIVITIES

Prof. L. Kalėdienė –

• President of Lithuanian Microbiological Society;
• member of Lithuania’s Genetically Modified Organisms Experts Committee.

Prof. N. Kuisienė –

• vice president of Lithuanian Microbiological Society.

Assoc. Prof. E. Lastauskienė -

• financier of Lithuanian Microbiological Society.

Asisst. A. Gegeckas -

• member of the board of Lithuanian Microbiological Society.

MOST IMPORTANT RESEARCH DISSMENATION ACTIVITIES

• National Science festival Spaceship Earth - International Microorganisms Day, whole day event for education in microbiology.
• Eglė Lastauskienė. Participation in the project Scientists for Schools of the Ministry of Education, Science and Sports of the Republic of Lithuania.
  Lecture in the Health Day of Vilnius University Stress: do microbes play with our nerves?
  Lecture Invisible friends of the brain in the Brain Research Week.

 

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.
Associate professors: Dr. R. Grikšienė, Dr. V. Kisnierienė, Dr. G. Svirskis (part-time), Dr. M. Korostenskaja (part-time).
Lecturers: Dr. R. Buišas, A. Daktariūnas, V. Gėgžna, I. Lapeikaitė, E. Pipinis, V. Survilienė, V. Pupkis
Senior research fellow: Dr. M. Mitkus
Research fellows: Dr. V. Kisnierienė, Dr. U. Neniškytė.
Junior research fellows: A. Daktariūnas, A. Voicikas.
Doctoral students: D. Dankin, A. Šlėktaitė, E. Janėnaitė, D. Leščiūtė-Krilavičienė, I. Lapeikaitė, A. Kalnaitytė, A. Voicikas, S. Mėlynytė, R. Mončiunskaitė, T. Paulauskas, E. Pipinis, V. Parčiauskaitė, R. Dulinskas, S. Venclovė, 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, V. Pupkis, E. Voronovič, I. Zelionkaitė, D. Pamedytytė.

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2019

Projects Supported by University Budget

Theoretical, Electrophysiological and Psychophysical Investigation of Information Coding and Processing. Prof. O. Rukšėnas. 2016–2020.

In comparison to controls, patients showed 1) intact but slower low gamma responses that correlated to the prevalence of hallucinations, and 2) reduced high gamma responses that negatively correlated to the total PANSS scores.
A significant difference in phase-locking was found between minimally conscious and vegetative state patients. Phase-locking within a low-gamma window positively correlated with the CRS-R total score and with the scores of the Auditory and Visual subscales. No between-group differences or any significant correlations with CRS-R scores in the high-gamma window were observed.
Salinity stress is critical for plants and impacts on excitability. Effect of NaCl on electrical signalling of single Nitellopsis obtusa (Characeaen) cells was investigated using glass-microelectrode technique in current-clamp mode. The Action Potentials (AP) of brackish Characeae Nitellopsis obtusa, obtained in artificial pond water (APW) and under osmotic stress of 90 or 180mM sorbitol or saline stress of 50 or 100mM NaCl, were investigated. The 15min exposure to sorbitol slightly increased the AP duration, without greatly affecting the AP shape or the pre-excitation resting potential (PD). The exposure to 180mM Sorbitol caused a greater widening. Immediate exposure to 50mM NaCl had a slight effect on AP. After 30min saline exposure, the AP became wider and pre-excitation resting PD depolarized slightly. After 60min, the AP shape changed drastically. AP form is affected gradually with the 60min exposure showing a transition from slightly extended “normal” AP to a typical rectangular saline AP. Spontaneous repetitive APs due to sudden resting PD decline upon exposure of the cell to 100mM NaCl was observed. 100m NaCl APW had strong effect on the AP, extending the duration nearly to 20 s in 90min of saline exposure. AP peak potential remained relatively constant, despite the increase of Cl− concentration in the medium from 1.3mM in APW to 50 and 100mM in the saline media.
The detailed knowledge of salinity effect on the AP mechanism is likely to be applicable to cells in plant roots, which are exposed to changing levels of salt.
Long-term synaptic potentiation can be described as a chain of biochemical reactions with a positive feedback. When linear terms are used to describe the rate of reactions, the system does not exhibit any effect on memory. Introduction of Michaelis- Menten kinetics leads to a significant memory effect (order of minutes), however the system do no exhibit a true bistability.

National Research Projects

Importance of the Relation between Microbiota-Intestines-Brain for the Development of Alzheimer’s Disease: Influence of Endocannabinoid System, Nr. 01.2.2-LMT-K-718-02-0014, Project leader - Dr. Aurelijus Burokas. 2019–2023.

Development of Scientific Competences of Scientists, Other Researchers, Students via Practical research Activities, Nr. 09.3.3-LMT-K-712. Project leaders - Dr. A. Alaburda, Dr. V. Kisnierienė.

International Research Projects

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

Adaptation of the System of Transfer of Electrical Signals Long Distances to Plants Moving from Water to Land. Leader Dr. Vilma Kisnierienė (repr. Of Lithuania). 2018–2021.

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

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 Centre 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)
University of Saltsburg (Austria)
Tubingen University (Germany)
School of Physics, University of Wollongong, Wollongong (Australia)
Department of Biophysics, Institute of Biology and Biochemistry, Maria Curie-Skłodowska University, Lublin (Poland)
Kobe University (Japan)
Lund University (Sweden)
Centre for Information and Neural Networks (Japan)

OTHER RESEARCH ACTIVITIES

Prof. A. Alaburda -

• board member of the Lithuanian Society for Neurosciences;
• board member of Lithuanian Biophysical Society;
• European Commission expert.

Dr. R. Buišas -

• member of the Lithuanian Society for Neurosciences.

Assoc. Prof. I. Griškova-Bulanova -

• board member of the Lithuanian Society for Neurosciences;
• 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;
• ember of the International Society for Brain Electromagnetic Topography;
• scientific committee member of 27^th European Congress of Psychiatry, Warsaw, Poland.

Assoc. Prof. R. Grikšienė:

• treasurer and board member of the Lithuanian Society for Neurosciences.

Assoc. Prof. V. Kisnierienė -

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

I. Lapeikaitė -

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

V. Pupkis –

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

Dr. M. Mitkus -

• member of the Lithuanian Society for Neurosciences;
• member of European Ornithologists’ Union;
• member of International Society for Neuroethology.

Prof. O. Rukšėnas -

• President of the Lithuanian Society for Neurosciences;
• 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;
• European Commission expert;
• member of Federation of European Neuroscience Societies (FENS) governing board;
• member of the DANA Alliance for Brain Initiatives;
• member of European Dana Alliance for the Brain.

Dr. A. Šoliūnas -

• member of the Lithuanian Society for Neurosciences.

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 Society for Neurosciences;
• member of the Biochemical Society;
• member of Lithuanian Biochemical Society;
• board member of the Research Council of Lithuania.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Neniškytė U. Meeting with the high school students in Vilnius, Zarasai, Dusetos and elsewhere. Presentations on autism at the Seimas, conferences etc. Participation at panel discussions, interview, appearance at TV and radio programmes. Panel discussion The Journey to Success at the International Conference of Life Sciences, The COINS 2019, Vilnius, Lithuania, February 26, 2019. Meeting with the participants of the international programme Bring Together Lithuania at the Lithuanian National Commission for UNESCO, June 19, 2019.
• Rukšėnas O. Public lectures (What’s new in brain research?, Current concepts and problems in neurobiology), Panel discussions and discussions (Brain gender - to talk or not to talk? etc.).
• Grikšienė R. Presentation Does hormonal contraception affect our cognitive functions and emotions? Conference Neuropsychology: What Our Brain Can, Vytautas Magnus University, Kaunas, 2019.
• Kisnierienė V. Lecture Can we understand what plants are talking about? at the event Spaceship Earth 2019. Night of investigators 2019 Open laboratory: what plants are sensing?

 

 

DEPARTMENT OF ZOOLOGY

7 Saulėtekio ave., LT-10257 Vilnius
Tel. + 370 5 239 8264
E-mail: .

Head – Prof. Habil. Dr. Rimantas Rakauskas

STAFF

Professors: Dr. S. Podėnas, Habil. Dr. R. Rakauskas, Dr. K. Arbačiauskas (part-time).
Associate professors: Dr. E. Bukelskis, Dr. J. Turčinavičienė, Dr. V. Podėnienė, Dr. R. Bernotienė (part-time), Dr. A. Kaupinis (part-time), Dr. A. Petrašiūnas, Dr. A. Križanauskienė (part time).
Assistant: Dr. G. Skujienė.
Lecturers: Dr. M. Biteniekytė, Dr. R. Aukštikalnienė, S. Skuja.
Senior researcher: Dr. J. Havelka.
Doctoral students: J. Danilov, M. Adomaitis, A. Kamarauskaitė, I. Gorban.

RESEARCH INTERESTS

Ecosystems and global change
Mapping and catalogization of fauna
Rare and endangered species both in terrestrial and limnic systems
Biosystematic studies in insects (Hemiptera, Sternorrhycha: Aphididae and Diptera: Tipulomorpha), spiders (Araneae), snails and slugs (Mollusca: Gastropoda)

RESEARCH PROJECTS CARRIED OUT IN 2019

Projects Supported by University Budget

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

Distribution, host specificity and molecular (mitochondrial COI and nuclear EF-1α) diversity of adelgid aphid species (Hemiptera: Adelgidae) in Lithuania was accomplished. Key to the aquatic crane flies larvae of North America is published. Survey on egg-larvae of Family Tipulidae is continued. A preliminary review of winter gnat (Diptera, Trichoceridae) fauna of Romania and Norway was performed, short insect collecting trip to Spitsbergen carried out. Taxonomic studies of the Korean Dicranomyia crane flies (Diptera: Limoniidae) performed. Analysis of the biodiversity of spiders and dipterous insects of Lithuania continued. The invasive slugs’ (species Arion lusitanicus) control studies performed. Distribution analysis of Vertigo geyeri (a snail of EU interest) in North Lithuania performed. Monitoring of fish communities in Lithuanian lakes was continued. Monitoring of black storks, birds of prey and owls in forests of eastern and southern Lithuania continued.

Main publications:

Gelhaus, J. K., Podeniene, V. Tipuloidea. In: An Introduction to the Aaquatic Iinsects of North America. Kendell Hunt publishing company. 2019, 1023–1071.

Kamarauskaitė, A., Skuja, S., Treinys, R. Nesting habitat overlap between the Common Buzzard Buteo buteo and the lesser spotted eagle Clanga pomarina for conservation planning in Natura 2000 sites. Bird Study. 2019, 66(2): 224–233. doi: 10.1080/00063657.2019.1654976.

Podeniene, V., Naseviciene, N., Podenas, S. Notes on the first instar larvae of the genus Tipula. Zootaxa. 2019, 90–110. doi: 10.11646/zootaxa.4567.1.5.

National Research Projects

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

Project supported by Ministry of Agriculture. Role of Blood Sucking and Other Insects in Mechanical Transmission of African Swine Fever Virus to Pig Farms and Wild Boar Populations (No MT-19-3). Assoc. Prof. J. Turčinavičienė. 2019.

Research Council of Lithuania. International Cooperation Enhancement and Qualification Internship at the University of Drexel Natural Sciences Academy (USA) (No. 09.3.3-LMT-K-712). Prof. S Podėnas. 2019.

International Research Projects

National Institute of Biological Resources (South Korea). Korean Indigenous Species Project (No NIBR201920108). Prof. S. Podėnas, Assoc. Prof. V. Podėnienė.

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)

OTHER RESEARCH ACTIVITIES

Assoc. Prof. E. Bukelskis –

• Chairman the Fisheries Council 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);
• Head of the Laboratory of Entomology, Institute of Ecology, Nature Research Centre (Lithuania).

Prof. R. Rakauskas –

• expert of the National Centre for Quality Assessment in Higher Education;
• expert of the Research Council of Lithuania.
• member of the Lithuanian Entomological Society.

Assoc. Prof. J. Turčinavičienė –

• 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).

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 Commission of the Lithuanian Language;
• member of the Council of the Invasive Species Control of Lithuania;
• member of Bioethics Society.
• external expert of The State Commission of the Lithuanian Language (zoologist) ;
• member of the Working Group on Wildlife Welfare.

Assoc. Prof. A. Petrašiūnas –

• 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.

MOST IMPORTANT RESEARCH DISSEMINATION ACTIVITIES

• Petrašiūnas A. Project Children’s University – If insects disappeared, would we disappear as well?
• Biteniekytė M. Project Children’s University - Spiders in Lithuania and the whole world.
• Dubonikas G. (S. Skuja, G. Skujienė) Biodiversity studies of Vilnius University Life Sciences Centre (VU GMC) contribute intensively to the preservation of Lithuanian nature. In Aukštadvaris Regional Park, students of the LSC found a snail species newly recorded in the Lithuanian Red Book in VU https://naujienos.vu.lt/tag/slapioji-siurpene/
• Guided tours and educational tours in the Vilnius University Museum of Zoology, during 4 years 20312 visitors.
• Lectures, presentations by the Department staff.

 

CENTRE FOR ECOLOGY AND ENVIROMENTAL RESEARCH

7 Saulėtekio ave., LT-10257 Vilnius
Tel. 239 8299
E-mail:

Head – Prof. Dr. Alius Ulevičius

STAFF

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

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2019

Projects Supported by University Budget

Vehicle-Animal Collisions and Their Natural and Anthropogenic Factors. Dr. G.Ignatavičius, Dr. A. Ulevičius, Dr. V.Valskys, 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 modeling. Roe deer (Capreolus capreolus) behaviour can change hourly, daily, weekly, annually and throughout an individual’s life. Therefore, understanding the temporal behavioural 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.

Ecotoxicity Estimation of Surface Water Sewage with Standard Bioassay Test-Aliivibrio fischeri and Luminescent Escherichia coli. Dr. V. Kalcienė.
An 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 origin and migration of different pollutants through various environments may enable proper preventive means.

Chemoreception of Phytophagous Insects and Plant Allelopathy and Materials Cycling. Dr. I. Nedveckytė, 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 were investigated.

The elemental composition of organisms belongs to a suite of functional traits that may adaptively respond to fluctuating selection pressures. Predation risk and resource limitations impose selection pressures on organisms’ developmental time and are further associated with variability in energetic and behavioural traits. We compared elemental body composition, latency to resume activity and resting metabolic rate of western stutter-trilling crickets (Gryllus integer) in three selection lines that differ in developmental speed. We found that slowly developing crickets had significantly higher body carbon, lower body nitrogen and higher carbon-to-nitrogen ratio than rapidly developing crickets. Slowly developing crickets resumed activity faster in an unfamiliar relative to a familiar environment. The rapidly developing crickets did the opposite. The results highlight the tight association between life history, physiology and behaviour.

Main publication:

Trakimas, G., Krams, R., Krama, T., Kortet, R., Haque, S., Luoto S., Eichler Inwood, S., Butler, D. M., Jõers, P., Hawlena, D., Rantala, M. J., Elferts, D., Jorge Contreras-Garduño, J., Krams, I. ecological stoichiometry: a link between developmental speed and physiological stress in an omnivorous insect. Frontiers in Behavioural Neuroscience. 2019, 13: 42.

National Research Projects

Research Council of Lithuania. Assessment of Cumulative Toxicity Impact in the Aquatic Organisms Induced by Different Types of Stressors, ACTIS. Dr. Virginija Kalcienė. 2017–2020.

Acetylcholine esterase activity changes in haemolymph of Molluscs under the heavy metals mixture expose were revealed. Environmental effects associated with the release of various metals even at maximum permissible concentrations (MPC) to the aquatic ecosystems are evident. In the present work, time-dependent increase in accumulated metals amount in gills of Anodonta cygnea after exposure to complex metal mixture at various time points was investigated. Significant increase of Cu and Cd was determined after 7-day exposure; moreover, significantly elevated concentration of Cu was measured and after 14-day treatment. Concentrations of Cu, Ni, Cr, Pb, and Cd were statistically increased in gills tissue after 28-day treatment. After short-term (4 days) exposure, statistically significant inhibition of AChE activity in haemolymph of metal mixture-exposed mussels, in comparison to control and pre-exposure group, was found. Comparison of investigated responses in different tissue of A. cygnea discloses new information about metal mixture (at MPC) influences at different treatment time. According to the obtained geno- and cytotoxicity data, it is suggested that gills are the tissue that is more sensitive.

Main publication:

Butrimavičienė, L., Stankevičiūtė, M., Kalcienė, V., Jokšas, K., Baršienė, J. Genotoxic, cytotoxic and neurotoxic responses in Anodonta cygnea after complex metal mixture treatment. Environmental Science and Pollution Research. 2019, 26(8): 7627–7639. Experimentalis et Applicata, 165(2–3): 129–137.

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

The pollution of sediments of water bodies in the fish farm ponds as well as the contents of heavy metals in the bottom sediments were assessed by geological core techniques and a consequent chemical analysis.
Assessment of bottom sediment ecotoxicity by analysing the inhibitory effect of bottom sediment aqueous extracts on the luminescence of the Aliivibrio fischeri bio-standard test standard.

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)

OTHER RESEARCH ACTIVITIES

Dr. V. Kalcienė –

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