Institute of Biotechnology

Sukurta: 15 September 2013

bti8 V. A. Graičiūno, LT 02241 Vilnius
Tel. 260 2103
Fax 260 2116
E-mail:
www.ibt.lt

Director - Prof. Habil. Dr.  Kęstutis Sasnauskas

STAFF

104 research fellows (58 holding research degree), 50 doctoral students.

RESEARCH AREAS

Structural Biology and Bioinformatics

Genomics, Biomolecules and Biotechnologies: Fundamental and Applied Research

DOCTORAL DISSERTATIONS MAINTAINED IN 2015

T. Šinkūnas. In vitro reconstitution of DNA interference in a type I CRISPR-Cas system.

MAIN SCIENTIFIC ACHIEVEMENTS IN 2015

Dr. Linas Mažutis published a paper in the Cell journal as a shared first author (http://www.cell.com/cell/abstract/S0092-8674%2815%2900500-0).

Prof. Dr. V. Šikšnys and coleagues (T. Karvelis, G. Gasiūnas, A. Šilanskas, G. Bigelytė) developed a method that allows to expand the repertoire of Cas9 proteins available for genome editing (http://www.genomebiology.com/content/16/1/253).

The Royal Society of Chemistry (RSC) in the United Kingdom elected Prof. Habil. Dr. Saulius Klimašauskas as a Fellow of the Royal Society of Chemistry.

 

DEPARTMENT OF PROTEIN - DNA INTERACTIONS

8 V. A. Graičiūno, LT-02241 Vilnius
Tel. 260 2108, fax 260 2108
E-mail:

Head - Prof. Dr. Virginijus Šikšnys

STAFF

Chief research fellows: Prof. Dr. V. Šikšnys, Dr. S. Gražulis, Dr. G. Sasnauskas, Dr. M. Zaremba.
Senior research fellows: Dr. G. Tamulaitienė, Dr. E. Manakova, Dr. G. Tamulaitis, Dr. G. Gasiūnas.
Research fellows: Dr. A. Šilanskas, Dr. T. Šinkūnas.
Junior research fellows: Dr. D. Golovenko, Dr. L. Jakutytė-Giraitienė, G. Kostiuk.
Post doctoral student: Dr. L. Jakutytė-Giraitienė.
Other researchers: Dr. D. Golovenko.
Doctoral students: T. Karvelis, P. Toliušis, I. Songailienė, E. Zagorskaitė, A. Merkys, M. Kazlauskienė, A. Vaitkus.

RESEARCH INTERESTS

Structural and molecular mechanisms of restriction enzymes

Bacterial antivirus defence systems

RESEARCH PROJECTS CARRIED OUT IN 2015

National Research Projects

Research Council of Lithuania. Expansion of the Crystallography Open Database (COD) and Statistical Analysis of Crystal Structures (No. MIP-25/2013). Dr. S. Gražulis. 2013–2015.

The COD provides information about crystal lattices, atomic coordinates, temperature factors, as well as publication data that permit linking of structural data with described material properties. To date COD contains more than 210 thousand records.

The COD Web interface provides search capabilities to retrieve crystal data using crystallographic and physico-chemical data; it also permits researchers to upload their data automatically, and to deposit into COD published structures, pre-publication data, or submit crystal data as personal communications to COD.

With the implementation of the COD automated data deposition interface, more stringent requirements for data reliability seem to be appropriate.

Main publication:

Gražulis, S., Merkys, A., Vaitkus, A., Okulič-Kazarinas, M. 2015. Computing stoichiometric molecular composition from crystal structures. J. Appl. Cryst, vol. 48(1), p. 85–91.

Research Council of Lithuania. Investigation of RNA Interference in Bacteria (No.MIP‑40/2013). Dr. G. Tamulaitis. 2013–2015.

Immunity against viruses and plasmids in bacteria provided by CRISPR-Cas systems is mediated by a ribonucleoprotein effector complex. Type I (Cascade) and II (Cas9) effector complexes target foreign DNA. We discovered that the Csm complex (Type III-A) of Streptococcus thermophilus targets RNA and established a molecular mechanism for RNA degradation. We demonstrated that Csm complex offers a novel programmable tool for RNA degradation or modification.

Research Council of Lithuania. Structural and Functional Studies of Restriction Enzyme Family (No. MIP-41/2013). Dr. G. Tamulaitienė. 2013–2015.

This project aims at investigating structural and functional relationships of restriction endonucleases which share CCGG motif within their recognition sites. We determined crystal structure and DNA cleavage mechanism of restriction endonuclease AgeI, which is unique to Type IIP restriction enzymes. We also initiated crystallization and biochemical studies of restriction endonucleases Kpn2I and PfoI.

Main publication:

Tamulaitis, G., Rutkauskas, M., Zaremba, M., Grazulis, S., Tamulaitiene, G., Siksnys V. 2015. Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI. Nucleic Acids Res, vol. 43(16), p. 8100–8110.

Research Council of Lithuania. The Role of Cas1 ir Cas2 Proteins in Adaptation Mechanism of CRISPR-Cas systems (No. MIP 027/2014). Dr. G. Gasiūnas. 2014–2016.

Recently identified adaptive prokaryotic immune system CRISPR-Cas provides acquired immunity against viruses and plasmids. The mechanism of these systems is divided into 2 stages: adaptation and interference. Recent studies have uncovered molecular details underlying the interference step; however the mechanism of the adaptation stage remains to be established. In this project we are investigating the properties of Cas1 and Cas2 proteins and its role in the adaptation mechanism. 

Research Council of Lithuania. Single Molecule and Structural Studines of a New Type of Restriction Endonucleases (No. MIP 56/2015). Dr. M. Zaremba. 2015–2017.

The objects of research of this project CglI and NgoAVII belong to a new type of restriction endonucleases that according to their genetic organization, composition of protein complex and mode of action differ from other types of restriction endonucleases. Elucidation of the structural mechanism of the new type ATP-dependent restriction endonucleases is the major focus of this research project. The following questions will be addressed: what conformational changes occur in the proteins upon specific DNA target recognition; how is an ATPase activated; whether and how do proteins translocate on DNA; how is a double-stranded DNA break introduced; what is the structure of the functional RN-complex.

Research Council of Lithuania. Structure‐Function Relationship of the B3 DNA Binding Domains (No. MIP 106/2015). Dr. G. Sasnauskas. 2015–2018.

Approximately 10% of all transcription factors in the flowering plants contain one or several small (~110 amino acids) B3 DNA binding domains. The biochemical and structural data on B3 domains is very limited: DNA binding in vitro was demonstrated only for a few members of this family, and only one structure of the DNA-bound protein was solved. Our aim is to determine the relationship between the amino acid sequences (and the underlying structures) of the B3 domains and their function. To this end we will employ a combination of computational and biochemical characterization methods, site-specific mutagenesis, and X-ray crystallography.

Research Council of Lithuania. Projects of the European Social Fund under Global Grant Measure. Structure and Molecular Mechanisms of Bacterial Antivirus Defence Systems. (No. VP1-3.1.-ŠMM-07-K-01-100). Prof. Dr. V. Šikšnys. 2011–2015.

Adaptive microbial immune system, named CRISPR (clustered regularly interspaced short palindromic repeats), provides acquired immunity against viruses and plasmids. Recently CRISPR systems came to prominence as genome editing tools that allow to accurately target any DNA sequence in the human genome. An international team of scientists including prof. Siksnys group at the Institute of Biotechnology of Vilnius University used single-molecule DNA supercoiling to analyse the dynamics of R-loop formation and dissociation for both Cascade- and Cas9-based CRISPR-Cas systems.

Main publications:

Rutkauskas, M., Sinkunas, T., Songailiene, I., Tikhomirova, M.S., Siksnys, V., Seidel, R. 2015. Directional R-loop formation by the CRISPR-Cas surveillance complex cascade provides efficient off-target site rejection. Cell Reports, vol. 10(9), p. 1534–1543.

Glemzaite, M., Balciunaite, E., Karvelis, T., Gasiunas, G., Grusyte, M.M., Alzbutas, G., Jurcyte, A,. Anderson, E.M., Maksimova, E., Smith, A.J., Lubys, A., Zaliauskiene, L., Siksnys, V. 2015. Targeted gene editing by transfection of in vitro reconstituted Streptococcus thermophilus Cas9 nuclease complex. RNA Biol, vol. 12(1), p. 1–4.

Sinkunas, T., Gasiunas, G., Siksnys, V. 2015. Cas3 nuclease-helicase activity assays. In: M. Lundgren, E. Charpentier, P.C. Fineran (Eds.). CRISPR: Methods and Protocols. Series: Methods in Molecular Biology, vol. 1311, p. 277–291.

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

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

OTHER SCIENTIFIC ACTIVITIES

Prof. Dr. V. Šikšnys –

  • member of the Lithuanian Academy of Sciences.

 

DEPARTMENT OF BIOLOGICAL DNA MODIFICATION

8 V. A. Graičiūno, LT-02241 Vilnius
Tel. 260 2114, fax 260 2116
E-mail:

Head - Prof. Habil. Dr. Saulius Klimašauskas

STAFF

Chief research fellow: Prof. Habil. Dr. S. Klimašauskas.
Senior research fellows: Dr. E. Kriukienė, Dr. Z. Liutkevičiūtė, Dr. R. Rakauskaitė, Dr. G. Vilkaitis.
Research fellows: Dr. D.Daujotytė, Dr. J. Gordevičius, Dr. G. Lukinavičius.
Junior research fellows: Dr. M. Tomkuvienė, Dr. R. Gerasimaitė, S. Baranauskė, G. Urbanavičiūtė, A. Osipenko, Z. Staševskij.
Doctoral students: S. Butkytė, P. Gibas, J. Ličytė, M. Mickutė.

RESEARCH INTERESTS

Nucleic acids modification enzymes
Epigenome profiling
Biosynthesis of selenoproteins

RESEARCH PROJECTS CARRIED OUT IN 2015

Projects Supported by University Budget

Nucleic Acids Modification Enzymes: Structure, Mechanisms of Action and Directed Engineering. Prof. Habil. Dr. S. Klimašauskas. 2011–2015.

Enzymatic methylation of DNA and RNA proceeds via multiple steps including substrate binding, target base flipping, vast conformational rearrangements in the enzyme, covalent activation of the target cytosine and catalytic transfer. We employ biochemical, biophysical and kinetic analyses combined with x-ray crystallography and protein engineering to delineate the elementary steps and use this knowledge to improve catalytic properties of the natural enzymes.

National Research Projects

Research Council of Lithuania. Genomic Mapping of Covalently Tagged CpG Sites. (No. MIP-45/2013). Dr. E. Kriukienė. 2013–2015.

The project is focused on developing new epigenetic tools for large-scale DNA modification profiling at single base resolution of all individual CpGs across the entire genome. The new approaches combine covalent derivatization of unmethylated or hydroxymethylated CG sites with suitable compounds by treatment with DNA cytosine-5 methyltransferases and subsequent mapping of such sites by next generation sequencing technologies.

Research Council of Lithuania. Identification and Analysis of Small Non-Coding RNAs of Gram-Positive Lactic Acids Bacteria Involved in Resistance to Antibacterial Agents (No. MIP 59/2015). Dr. G. Vilkaitis. 2015–2018.

The aim is to identify and characterize Lactococcus lactis and Lactobacillus casei small non-coding RNAs responsible for their resistance to lysozyme, beta-lactam and glycopeptide antibiotics applying functional-genetic and next-generation sequencing based analysis. In order to overcome the most common sequencing biases we will try to create and implement the new bacterial sRNA specific bias-reducing method for RNA sequencing library preparation.

Projects of the European Social Fund under Global Grant Measure. Molecular Tools for Epigenomics and Rnomics. (No. VP1-3.1.-ŠMM-07-K-01-105). Prof. Habil. Dr. S. Klimašauskas. 2011–2015.

Functional analysis of biological systems requires visualization of biomolecules in cells and organisms. This project is dedicated to the development of new techniques that permit detection and mapping of modified cytosine nucleotides in mammalian genomes. Our key strategy is based on utilization of newly discovered enzymatic transformations of DNA. Substantial efforts are also devoted to analysis of small non-coding RNAs and for programmable sequence-specific labelling of other cellular RNAs.

International Research Projects

National Institutes of Health (NIH), USA. Direct Single Nucleotide Mapping of Genomic CpG Marks. Prof. S. Klimašauskas. 2013–2015.

Over the past decade, epigenetic phenomena claimed a central role in cell regulatory processes and proved important factors for understanding complex human diseases. One of the best understood epigenetic mechanisms is modification of cytosine residues in DNA. This project is dedicated to developing a break-through technique for genome-wide analysis of the modification status of CpG dinucleotides that combines single-base resolution with targeted and economic sequencing of the genome. 

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

Centre for Addiction and Mental Health, University of Toronto (Canada)
Institute for Organic Chemistry (Germany)
University of Paul Sabatier (France)
Institute of Molecular Genetics (Russia)
LEBS, Gif-sur-Yvette (France) 

OTHER SCIENTIFIC ACTIVITIES

Prof. Habil. Dr. S. Klimašauskas –

  • editorial advisory board member of the Central European Journal of Biology, http://www.versita.com/cejb/editors/;
  • editorial board member of the Proceedings of the Estonian Academy of Sciences, http://www.kirj.ee/13226/;
  • management committee member, COST action CM1303;
  • member of the Lithuanian Academy of Sciences;
  • fellow of the Royal Society of Chemistry.

 

DEPARTMENT OF EUKARYOTE GENETIC ENGINEERING

8 V. A. Graičiūno, LT-02241 Vilnius
Tel. 260 2104, fax 260 2116
E-mail:

Head - Assoc. Prof. Dr. Gintautas Žvirblis

STAFF

Chief research fellows: Habil. Dr. I. Meškienė, Prof. Habil. Dr. K. Sasnauskas, Dr. A. Gedvilaitė, Dr. A. Schweighofer.
Senior research fellows: Assoc. Prof. Dr. G. Žvirblis, Dr. R. Petraitytė-Burneikienė, Dr. A. Ražanskienė, Dr. R. Slibinskas, Dr. A. Schweighofer, Dr. G.F. Kaubrys.
Research fellows: Dr. R. Abraitis, Dr. E. Čiplys, Dr. M. Ger, Dr. V. Kazanavičiūtė.
Junior research fellows: Dr. A. Abraitienė, Dr. A. Bulavaitė, Dr. M. Zaveckas, R. Vorobjovienė, J. Lazutka, R. Ražanskas, P.L. Tamošiūnas, K. Kvederavičiūtė, D. Žiogienė, A. Vaitkevičius, P Starkevič.
Doctoral students: E. Bakūnaitė, N. Macijauskaitė, G. Mickienė, M. Norkienė, U. Starkevič, I. Širkė, R. Vorobjovienė, R. Zinkevičiūtė, J. Lazutka, Š. Paškevičius, Ž. Dapkūnas, K. Kvederavičiūtė, J. Nainys, E. Žitkus. 

RESEARCH INTERESTS

Synthesis of recombinant proteins
Molecular tools for diagnostics
Cell signalling regulation in Arabidopsis
Functions of PP2C phosphatases 

RESEARCH PROJECTS CARRIED OUT IN 2015

National Research Projects

Research Council of Lithuania. Signalling Components in Stem Cells (No. MIP-003/2014). Dr. A. Schweighofer. 2014–2016.

Our study of Arabidopsis thaliana MAPK and phosphatase gene expression during stomata cell development and in response to stress enabled identification of specific MAPKs and PP2C phosphatase gene expression, suggesting their role in development of stomata, which are cells essential in water/gas exchange between plant and environment and thus supporting our ecosystem.

Research Council of Lithuania. Synthesis of Schmallenberg Virus Proteins and their Application for Diagnostic Means (No. MIP-44/2013). Prof. Habil. Dr. K. Sasnauskas. 2013–2015.

To develop improved reagents for Schmallenberg virus serology a high-level yeast expression system was employed to produce recombinant SBV nucleocapsid (N) protein. Our study demonstrates that yeast expression system is suitable for high-level production of recombinant nucleocapsid protein and provides the first evidence on the presence of SBV‑positive antibodies in cow serum specimens collected in Lithuania.

Main publication:

Lazutka, J., Spakova, A., Sereika, V., Lelesius, R., Sasnauskas, K., Petraityte – Burneikiene, R. 2015. Saliva as an alternative specimen for detection of Schmallenberg virus-specific antibodies in bovines. BMC Veterinary Research, vol. 11(1), p. 237.

Research Council of Lithuania. Expression Analysis of Anthocyanin Biosynthesis Genes in Horticultural Plants (No. SVE-06/2012). Dr. V. Kazanavičiūtė. 2012–2015.

The aim of the project is to explore anthocyanin biosynthesis pathways and their regulation in Fragaria, Prunus and Ribes plants. Functional positive regulators of anthocyanin biosynthesis pathway were identified in sweet cherry. It was shown that expression profile of Prunus and Ribes genes involved in anthocyanin biosynthesis pathway is species and variety-specific and strongly depends on the berry ripening stage

Main publication:

Starkevic, P., Paukstyte, J., Kazanaviciute, V., Denkovskiene, E., Stanys, V., Bendokas, V., Siksnianas, T., Razanskiene, A., Razanskas, R. 2015. Expression and Anthocyanin Biosynthesis-Modulating Potential of Sweet Cherry (Prunus avium L.) MYB10 and bHLH Genes. PLoS One, vol. 10(5), e0126991. doi:10.1371/journal.pone.0126991.

Research Council of Lithuania. Investigation of Synthesis Regulation of Proteins Associated with Alzheimer Disease Development (No. SEN-05/2015). Prof. Habil. Dr. K. Sasnauskas. 2015–2018.

The aim of the project is to create immunochemical, antibody-based methods that allow to test small ORF encoded polypeptides. Such methods will help identify small polypeptides and determine role of these peptides in the regulation of biosynthesis of AD related proteins and provide new opportunities for disease prevention and early diagnosis.

Research Council of Lithuania. Construction of Antibody Fragments with Activity Prolongation and Development of Sample (model) for Medical Device (No. TEC-01/2015). Dr. G. Žvirblis. 2015–2016.

The project is aimed at constructing oligomeric recombinant single-chain antibodies (scFv) with activity prolongation and to test their stability and biological activity in vitro and in vivo. Specific single‐chain antibody (scFv), neutralizing the toxin of Gardnerella vaginalis bacteria vaginolysin, pathogenic factor of bacterial vaginosis (BV) ‐ has been selected. According to the technology developed by the applicants monomeric scFv antibody will be joined into bigger oligomeric molecules via specific linker sequences maintaining the scFv activity and higher stability. The objects of this investigation are unique neutralizing single‐chain antibodies that are directed against toxin of G. vaginalis and model ovules with anti‐BV effect.

Research Council of Lithuania. Projects of the European Social Fund under Global Grant Measure. The Use of Genome-Wide Analysis for Engineering of New Yeast Strains with Improved Heterologous Expression. (No. VP1-3.1.-ŠMM-07-K-02-038). Dr. R. Slibinskas. 2012–2015.

The project is aimed at generating new yeast Saccharomyces cerevisiae strains capable of efficient expression of heterologous proteins, by using genome-scale analysis. First, we identified genes implicated in successful protein production experiments by analysis of whole genome or proteome. Then the expression of these genes was increased or suppressed by using genetic engineering methods with subsequent selection of strains with improved measles hemagglutinin translocation and invertase secretion.

Main publication:

Zinkeviciute, R., Bakunaite, E., Ciplys, E., Razanskas, R., Raskeviciute, J., Slibinskas, R. 2015. Heat shock at higher cell densities improves measles hemagglutinin translocation and human GRP78/BiP secretion in Saccharomyces cerevisiae. New Biotechnology, vol. 32(6), p. 690–700.

National Integrated Programme

Biotechnology and Biopharmacy: Fundamental and Applied Research (No. VP1-3.1-ŠMM-08-K-01-005). Prof. Habil Dr. K. Sasnauskas. 2012–2015.

The project consists of four different topics. The results obtained for each of these topics are as follows: 1) synthesis of prokaryotic and eukaryotic DNA methylases M.HpaII, M.SssI, M.MpeI, DNMT3A, DNMT3B was investigated in yeast;  2) monoclonal antibodies against surface proteins VP1 of human polyomaviruses KIPyV, WUPyV, PyV6 and PyV7 were generated; 3) a comparison was made of death pathways in the primary and cancer cells after mTHPC induced photodynamic effect; 4) optimization of synthesis of recombinant glycerophosphate oxidase expression in Escherichia coli has been carried out.

Main publication:

Norkiene, M., Stonyte, J., Ziogiene, D., Mazeike, E., Sasnauskas, K., Gedvilaite, A. 2015. Production of recombinant VP1-derived virus-like particles from novel human polyomaviruses in yeast. BMC Biotechnology, vol. 15, p.68. 

Joint Research Programme

Development of New Generation Means for Virus Diagnostics and Prophylaxis and Application in Veterinary Medicine (No. VP1-3.1-ŠMM-10-V-02-017). Dr. A. Gedvilaitė. 2013–2015.

The aim of the project is to develop new generation tools for PCV2 diagnostics and prophylaxis. The genomes of PCV2b type virus spread in Lithuania were determined and virus capside protein formed particles (Cap VLPs) produced in yeast were used for the generation of PCV2-specific MAbs, vaccination of pigs and development of new sensitive and specific diagnostic test - indirect IgG PCV2 Cap VLP-based ELISA.

Main publication:

Zaveckas, M., Snipaitis, S., Pesliakas, H., Nainys, J., Gedvilaite, A. 2015. Purification of recombinant virus-like particles of porcine circovirus type 2 capsid protein using ion-exchange monolith chromatography. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci, vol. 991, p. 21–28. 

International Research Projects

SWISS-LT. Signaling Control of Pathogen Induced Plant Immunity (CH-3-SMM-01/10). Dr. I. Meškienė. 2013–2016.

Signalling control of pathogen induced plant immunity, which is funded by Lithuanian-Swiss cooperation programme to reduce economic and social disparities within the enlarged European Union, under project agreement No CH-3-ŠMM-01/10, implemented by Vilnius University and Fribourg University aims at extending the knowledge on plant cell signalling pathways in responses to pathogens. Towards this aim the specific functions of protein phosphatases acting in signalling pathways induced by plant pathogens have been studied by application of molecular biology, biochemistry and cell biology.

Contractual Research

Recombinant Viral Proteins. Abcam Ltd, London, UK. Dr. G. Žvirblis.

Recombinant Viral Proteins. Euroimmun AG, Germany. Dr. A. Ražanskienė.

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)

Institute of Virology, Slovak Academy of Sciences (Slovakia)

OTHER SCIENTIFIC ACTIVITIES

Habil. Dr. I. Meškienė –

  • editorial board member of the Frontiers;
  • editorial board member of the Frontiers in Technical Advances in Plant Science;
  • reviewer of the BioMed Central; The Plant Journal; The Plant Cell; PLoS One.

 

MICRO TECHNOLOGIES SECTOR

8 V. A. Graičiūno, LT-02241 Vilnius
Tel. 260 2888, fax 260 2116
E-mail: 

Head - Dr. Linas Mažutis

STAFF

Chief research fellow: Prof. A. Janulaitis.
Doctoral students: R. Žilionis, J. Nainys, J. Rutkauskaitė, V. Kiseliovas, R. Galinis, V. Milkus.

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2015

International Research Projects

SWISS-LT. Directed Evolution of Computer Designed Enzymes Using Droplet-Based Microfluidics (No. CH-3-SMM-01/03). Dr. L. Mažutis. 2012–2016.

This project is aimed at developing a microfluidic system for completely in vitro directed evolution of proteins. By compartmentalizing genes and all components necessary for their in vitro expression we are creating a population of artificial cells that can be selected at conditions incompatible with living systems.

FP7. Integrated Microfluidic System for Long Term Cell Cultivation, Monitoring and Analysis. BioCellChip. Dr. L. Mažutis. 2012–2015.

The aim of the project is to develop a microfluidic human platelet bioreactor that recapitulates bone marrow stiffness, extracellular matrix composition, micro-channel size, hemodynamic vascular shear stress, and endothelial cell contacts, and it supports high-resolution live-cell microscopy and quantification of platelet production. Physiological shear stresses triggered proplatelet initiation, reproduced ex vivo bone marrow proplatelet production, and generated functional platelets. Modelling human bone marrow composition and hemodynamics in vitro obviates risks associated with platelet procurement and storage to help meet growing transfusion needs.

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

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

 

DEPARTMENT OF IMMUNOLOGY AND CELL BIOLOGY

8 V. A. Graičiūno, LT-02241 Vilnius
Tel. 260 2117, fax 260 2116
E-mail:

Head - Dr. Aurelija Žvirblienė

STAFF

Chief research fellow: Dr. A. Žvirblienė.
Senior research fellows: Dr. I. Kučinskaitė-Kodzė, Dr. M. Plečkaitytė, Dr. J. Matulienė, Dr. A. Kanopka.
Research fellows: Dr. I. Kučinskaitė-Kodzė, Dr. P. Stakėnas.
Junior research fellows: I. Dalgėdienė, D. Dekaminavičiūtė, E. Jakubauskienė, I.Pečiulienė, R. Lasickienė, V. Simanavičienė, M. Jasulionis.
Doctoral students: I. Dalgėdienė, D. Dekaminavičiūtė, M. Janulaitienė, V. Rubinaitė, V. Simanavičienė, L. Vilys, M. Zilnytė. 

RESEARCH INTERESTS

Monoclonal and recombinant antibodies
Molecular epidemiology of Mycobacterium tuberculosis
Alternative splicing 

RESEARCH PROJECTS CARRIED OUT IN 2015

Projects Supported by University Budget

Development of Monoclonal and Recombinant Antibodies. Dr. A. Žvirblienė. 2011–2015.

The project aims at developing novel antibodies with diagnostic potential. A panel of new monoclonal antibodies against yeast-expressed capsid proteins of human bocaviruses has been developed. Fine epitope mapping of the antibodies has been performed. In collaboration with company ArcDia (Finland), the reactivities of the antibodies with native bocaviruses have been investigated to evaluate their potential for a direct detection of bocaviruses in clinical samples.

Research on Molecular Epidemiology of Mycobacterium tuberculosis. Dr. P. Stakėnas. 2011–2015.

Incidence of multidrug-resistant tuberculosis in Lithuania is one of the highest in the world. The aims of the project were to characterize population of M. tuberculosis complex bacteria by the means of molecular epidemiology and to clarify the genetic determinants of drug resistance. In 2015 we continued to search the strains of M. tuberculosis from Lithuania by MIRU-VNTR genotyping.

Main publication:

Merker, M., Blin, C., Mona, S., Duforet-Frebourg, N., Lecher, S., Stakenas, P., et al. 2015. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage.Nat Genet., March, vol. 47(3), p. 242–9.
doi: 10.1038/ng.3195. Epub 2015 Jan 19.

National Research Projects

Research Council of Lithuania. Development of new diagnostic tools for hepatitis E virus (HEV) infection and studies on HEV prevalence in Lithuania. (No. MIP-039/2015). Dr. I. Kučinskaitė-Kodzė. 2015–2018.

The project aims at developing novel diagnostic tests for HEV GT3 and rat HEV suitable for serologic detection of HEV infection and seroepidemiological studies, as well as a direct detection of HEV in infected tissues. The project should provide new data on the prevalence and phylogenesis of HEV GT3 and rat HEV in Lithuania. The work will be performed in collaboration with the research group of Friedrich-Loeffler Institute (Germany) that have discovered rat HEV.

Research Council of Lithuania. National program „Healthy ageing“. Investigation of Genetic and Epigenetic Prognostic Markers for Prediction of Clinical Course of Papillary Thyroid Cancer (PTC) in Different Age Groups. (No. SEN-14/2015). Dr. A. Žvirblienė. 2015–2018.

The project is carried out in collaboration with the Lithuanian University of Health Sciences. The aim of the project is to identify specific miRNA as biomarkers for early diagnosis of PTC and to determine their diagnostic utility for predicting disease aggressiveness and clinical outcome. Investigation of circulating miRNAs (-146b, -221, -222, -181, -21) profiles in patients with PTC, benign nodules and healthy controls may help to differentiate benign nodules from malignancies and develop guidelines for early diagnosis of PTC. 

Research Council of Lithuania. Projects of the European Social Fund under Global Grant Measure. Novel Chimeric Proteins with Antiviral Activity. (No. VP1-3.1-ŠMM-07-K-02-039). Dr. A. Žvirblienė. 2012–2015.

The project aims at developing novel recombinant proteins with virus-neutralizing activity and capability to induce virus-specific cellular immune response. Monoclonal and recombinant antibodies against hepatitis B virus (HBV) surface antigen have been developed. In collaboration with Justus-Liebig University Giessen, the HBV-neutralizing capability of the antibodies has been demonstrated. Chimeric virus-like particles (VLPs) with inserted HBV T cell-specific epitopes as well as pseudo type VLPs harbouring the Fc-engineered anti-HBV molecules have been generated.

Main publications:

Gedvilaite, A., Kucinskaite-Kodze, I., Lasickiene, R., Timinskas, A., Vaitiekaite, A., Ziogiene, S., Zvirbliene, A. 2015. Evaluation of Trichodysplasia Spinulosa-associated polyomavirus capsid protein as a new carrier for construction of chimeric virus-like particles harbouring foreign epitopes. Viruses, vol. 7, p. 4204–4229.

Pleckaityte, M., Bremer, C.M., Gedvilaite, A., Kucinskaite-Kodze, I., Glebe, D., Zvirbliene, A. 2015. Construction of polyomavirus-derived pseudotype virus-like particles displaying a functionally active neutralizing antibody against hepatitis B virus surface antigen. BMC Biotechnology, vol. 15, p. 85.

Kucinskaite-Kodze, I., Pleckaityte, M., Bremer, C.M., Seiz, P.L., Zilnyte, M., Bulavaite, A., Mickiene, G., Zvirblis, G., Sasnauskas, K., Glebe, D., Zvirbliene, A. 2015. New broadly reactive neutralizing antibodies against hepatitis B virus surface antigen. Virus Res., Nov 2, pii: S0168-1702(15)30103-9. doi: 10.1016/j.virusres.2015.10.024.

Miniaturised Phospholipid Biosensors - MiniFOB. (No. VP1-3.1-ŠMM-10-V-02-024). Dr. A. Žvirblienė. 2013–2015.

The project was carried out in collaboration with the Institute of Biochemistry. Recombinant Cholesterol-Dependent Bacterial Cytolysins have been Generated and Investigated for their Ability to Interact with Artificial Tethered Bilayer Membranes (tBLMs). The applicability of tBLMs as a potential bioanalytical platform for the detection of pore-forming cytolysins has been demonstrated.

Main publication:

Zilnyte, M., Venclovas, C.,Zvirbliene, A., Pleckaityte, M. 2015. The cytolytic activity of vaginolysin strictly depends on cholesterol and is potentiated by human CD59. Toxins (Basel), Jan 13, vol. 7(1), p. 110–28. doi: 10.3390/toxins7010110.

International Research Projects 

Contractual Research

Generation of Monoclonal Antibodies. Abcam Ltd, UK. Dr. A. Žvirblienė.

Generation of Monoclonal Antibodies. Santa Cruz Biotechnology Inc., US. Dr. A. Žvirblienė.

Cloning and Stability Testing of Hybridomas Producing Antibodies Against DNA Polymerases. Contract APS-56000-918 with Thermo Fisher Scientific/Fermentas. Dr. A. Žvirblienė.

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

8 V. A. Graičiūno, LT-02241 Vilnius
Tel. 269 1884, fax 260 2116
E-mail:

Head - Dr. Daumantas Matulis

STAFF

Chief research fellow: Dr. D. Matulis.
Senior research fellows: Dr. P. Cimmperman, Dr. J. Matulienė, Dr. V. Petrauskas, Dr. V. Smirnovas, Dr. A Zubrienė.
Research fellows: Dr. L. Baranauskienė, Dr. E. Čapkauskaitė, Dr. V. Dudutienė, Dr. V. Petrikaitė, Dr. Z. Toleikis.
Junior research fellows: Dr. V. Juozapaitienė, D. Dekaminavičiūtė, Š. Grincevičienė, J. Jachno, E. Kazlauskas, J. Kazokaitė, V. Linkuvienė, V. Michailovienė, A. Zakšauskas.
Other researchers: Affiliated Prof. G. Dienys.
Doctoral students: J. Kazokaitė, V. Linkuvienė, R. Mališauskas, A. Smirnov, T. Šneideris, D.D. Timm, A. Vegytė. 

RESEARCH INTERESTS

Function and inhibition of carbonic anhydrases 

RESEARCH PROJECTS CARRIED OUT IN 2015

National Research Projects

Research Council of Lithuania. Protein Ligand Binding Volume and its Application in Drug Design. (No. MIP 004/2014). Dr. V. Petrauskas. 2014–2016.

This project is devoted to analyse the thermodynamics of protein volume changes, which are associated with the protein-ligand and protein-protein interactions. The change in the protein volume during the event of ligand binding exhibits a connection with the protein-ligand affinity. The detailed understanding of these thermodynamic variables would stimulate the progress in the rational drug design. The research is conducted with a special attention to the proteins involved in cancer progression and therapy.

Research Council of Lithuania. Investigation of Human Carbonic Anhydrase IX as Cancer Biomarker for Application in Cancer Diagnostics, Visualization and Prognosis (No. SEN-04/2015). Dr. J. Matulienė. 2015–2018.

The goal of this project is to develop methods of diagnostics and visualization of oncological diseases with the help of the technologies enabling the detection of CA IX in human tissues. To reach this goal we will use monoclonal CA IX antibodies for the immunochemical systems to determine the levels of CA IX in the patient blood and cervical cancer tissues. The potential of CA IX as a diagnostic and prognostic marker for the cervical cancer and pre-cancer stages will be evaluated. We will also analyse the potency of CA IX as a general serological marker of hypoxic tumours. Fluorescent and positron-emitting probes will be attached to CA IX antibodies and CA IX-selective inhibitors synthesized in our laboratory to analyse their potency for the visualization of cancerous tissues.

Research Council of Lithuania. Projects of the European Social Fund under Global Grant Measure. Design of Selective Carbonic Anhydrase, Hsp90, and Hsp70 Inhibitors and Investigation of their Anticancer Properties. (No. VP1-3.1-ŠMM-07-K-02-009). Dr. D. Matulis. 2012–2015.

The synthesized inhibitor binding energetics are measured by biophysical methods, primarily fluorescent thermal shift assay (FTSA), pressure shift assay (PSA) and isothermal titration Calorimetry (ITC). Target proteins have been produced in large scale by molecular cloning and chromatographic purification. Compound effects on cultured human cancer cell lines are being tested.

Main publications:

Morkunaite, V., Gylyte, J., Zubriene, A., Baranauskiene, L., Kisonaite, M., Michailoviene, V., Juozapaitiene, V., Todd, M.J., Matulis, D. 2015. Intrinsic thermodynamics of sulfonamide inhibitor binding to human carbonic anhydrases I and II. J. Enzyme Inhib. Med. Chem, vol. 30(2), p. 204–211.

Kazokaite, J, Milinaviciute, G., Smirnoviene, J., Matuliene, J., Matulis, D. 2015. Intrinsic binding of 4-substituted-2,3,5,6-tetrafluorobenezenesulfonamides to native and recombinant human carbonic anhydrase VI. FEBS J., vol. 282(5), p. 972–983.

Dudutiene V., Zubriene A., Smirnov A., Timm D. D., Smirnoviene J., Kazokaite J., Michailoviene V., Zaksauskas A., Manakova E., Grazulis S. and Matulis D. 2015. Functionalization of fluorinated benzenesulfonamides and their inhibitory properties toward carbonic anhydrases. ChemMedChem, vol. 10, p. 662–687, doi: 10.1002/cmdc.201402490.

Research Council of Lithuania. Projects of the European Social Fund under Global Grant Measure. Exploring Flavones as Universal Inhibitors of Amyloid-Like Fibril Formation. (No. VP1-3.1-ŠMM-07-K-02-020). Dr. V. Smirnovas. 2012–2015.

This project is dedicated to studies of flavone derivatives as potential inhibitors of amyloid-like fibrillation. We tested 265 different flavones impact on insulin fibrillation kinetics. We demonstrated that usual ThT fluorescence intensity assay may detect a number of false positives and false negatives, which could be excluded using kinetic curves. We identified 5 very good inhibitors of insulin aggregation, these are going to be tested with other amyloid-forming proteins to find out if universal inhibitor could be identified.

Main publications:

Sneideris, T., Baranauskiene, L., Cannon, J.G., Rutkiene, R., Meskys, R., Smirnovas, V. 2015. Looking for a generic inhibitor of amyloid-like fibril formation among flavone derivatives. Peer J, vol. 3, p. e1271; doi: 10.7717/peerj.1271.

Sneideris, T., Darguzis, D., Botyriute, A., Grigaliunas, M., Winter, R., Smirnovas, V. 2015. pH-driven polymorphism of insulin amyloid-like fibrils. PLoS One, Aug 27, vol. 10(8):e0136602; doi:10.1371/journal.pone.0136602.

Malisauskas, R., Botyriute, A., Cannon, J.G., Smirnovas, V. 2015. Flavone derivatives as inhibitors of insulin amyloid-like fibril formation. PLoS One, Mar 23, vol. 10(3):e0121231; doi:10.1371/journal.pone.0121231.

International Research Projects

FP7. Towards Construction of a Comprehensive Map of Amyloid-Ligand Interactions:(-)-Epigallocatechin 3-Gallate and Insulin Amyloid. (EGCG+INSULIN=). Dr. V. Smirrnovas. 2011–2015.

The project is dedicated to the studies of insulin amyloid-like fibril formation and its interaction with epigallocatechin gallate (EGCG). EGCG was reported as an inhibitor of amyloid-like fibril formation in case of many proteins. We found out that stable EGCG does not really affect insulin fibrillation, however, upon oxidation it becomes a very good inhibitor. It also affects fibril elongation, but the effect is much weaker. 

Contractual Research

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

Institute of Medical Technology, University of Tampere (Finland)
International Institute of Molecular and Cell Biology (Poland)
Lead Generation Biology at Johnson & Johnson Pharmaceutical Research and Development (USA)
Cancer Research Centre, University of Edinburgh (UK)
University of Tubingen (Germany) 

OTHER SCIENTIFIC ACTIVITIES

Dr. D. Matulis –

  • editorial board member of the international journal BMC Biophysics;
  • President-elect of the Lithuanian Biochemical Society.

 

APPLIED BIOCATALYSIS SECTOR

8 V. A. Graičiūno , LT-02241 Vilnius
Tel. (+370 5) 240 4679, fax (+370 5) 260 2116
E-mail:

Head - Dr. Inga Matijošytė

STAFF

Research fellow: Dr. I. Matijošytė.
Junior research fellows: Dr. R. Gruškienė, M. Šulcienė, R. Šiekštelė.
Principal investigators: A. Veteikytė, A. Sirvydaitė, G. Čiuta.
Doctoral students: V. Matikevičienė, M. Šulcienė. 

RESEARCH INTERESTS

Biocatalysts and their application

RESEARCH PROJECTS CARRIED OUT IN 2015

Projects Supported by University Budget

Development and Investigation of Novel Biocatalysts and their Respective Processes. Dr.  I. Matijošytė. 2015–2017.

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 2015 the research was focused on analysis of gene cluster isolated from constructed metagenomic library; development of screening systems for targeted enzyme activities; development of protein expression systems for biocatalyst production; investigation of LOX enzymes for biopolyol synthesis; exploring carrier-free immobilization methods. 

Main publications:

Gruskienė, R., Kairys, V. Matijošytė, I. 2015. CLEA-based immobilization of methylotropic yeast alcohol oxidase: influence on storage stability and reaction efficiency. Org. Process Res. Dev., doi: 10.1021/acs.oprd.5b00291.

Siekstele, R., Veteikyte, A., Tvaska, B., Matijošytė, I. 2015. Yeast Kluyveromyces lactis as host for expression of the bacterial lipase: cloning and adaptation of the new lipase gene from Serratia sp. J. Ind. Microbiol. Biotechnol., vol. 42, p. 1309–1317. 

Contractual Research

Identification of Biosamples by 16S RNA Coding DNA Sequences. JSC BioenergyLT, No MTS-560000-1086, Lithuania, Dr. I. Matijošytė.

The aim was to investigate the company’s biological products by performing 16S RNA coding sequences.

Microbiogical Analysis of Biosamples. JSC BioenergyLT, No MTS-560000-828, Lithuania, Dr. I. Matijošytė.

The aim was to carry out microbiological analysis of company’s biological products. The objective of investigation was to identify the cultivation conditions with respect to viability of the cultured cells in biological products.

Microbiogical Analysis of Biosamples. JSC BioenergyLT, No MTS-560000-1136, Lithuania, Dr. I. Matijošytė.

The aim was to carry out microbiological analysis of biological samples. The objective of investigation was to identify the cultivation conditions with respect to viability of the cultured cells in biological products.

Feasibility study on Development of Environmentally Friendly Household Chemical Products. JSC Akses, No MTS-560000-3061, Dr. I. Matijošytė.

The feasibility study was carried out to analyse the use of enzymes in the household chemical industry (detergents and cleaning agents).

Feasibility Study on Bioplastics for Food and Consumer Products Packaging. JSC Noventus, No MTS-560000-3062, Dr. I. Matijošytė.

The feasibility study was carried out to overview and analyse currently used bioplastics in plastic production technology, their biodegradability, technological aspects of production of bioplastics, etc.

Investigation and Development of Various Compositions of Biological Products. JSC BioenergyLT, No MTS-560000-2521, Dr. I. Matijošytė.

The aim was to create a different composition of biological products and to evaluate their effectiveness. The objectives of investigation were to establish new components-additives, to identify physico-chemical properties and their variation depending on composition and to determine the influence of new biological compositions on viability of cell cultures.

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

University of Applied Sciences (Switzerland)
TU Delft (Netherlands)
Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB (Germany)
Pöyry Management Consulting Oy (Finland)
Proviron Industries NV (Belgium)

OTHER SCIENTIFIC ACTIVITIES

Dr. I. Matijošytė -

  • MC substitute member of COST Action 1303.

 

DEPARTMENT OF BIOINFORMATICS

8 V. A. Graičiūno, LT-02241 Vilnius
Tel. 269 1881, fax 260 2116
E-mail:

Head - Dr. Česlovas Venclovas

STAFF

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

RESEARCH INTERESTS

Protein three-dimensional (3D) structure modelling

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

RESEARCH PROJECTS CARRIED OUT IN 2015

Projects Supported by University Budget

Computational Studies of Protein Structure, Function and Evolution. Dr. Č. Venclovas. 2014–2016.

In 2015 we have been mostly involved in collaborative studies with experimentalists. In one of the studies together with researchers from Hungary and US we explored the mechanism of action of human protein HLTF in postreplication DNA repair. We found that the repair function of HLTF depends on its HIRAN domain, responsible for recruitment of HLTF to the stalled replication forks. In another collaborative study we helped experimentalists from the Institute of Biotechnology to characterize proteins and genomes of polyomaviruses.

Main publications:

Achar, Y.J., Balogh, D., Neculai, D., Juhasz, S., Morocz, M., Gali, H., Dhe-Paganon, S.,Venclovas, Č., and Haracska, L. 2015. Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling. Nucleic Acids Res, vol. 43, p.10277–10291.

Gedvilaite, A., Kucinskaite-Kodze, I., Lasickiene, R., Timinskas, A., Vaitiekaite, A., Ziogiene, D., Zvirbliene, A. 2015. Evaluation of Trichodysplasia Spinulosa-associated polyomavirus capsid protein as a new carrier for construction of chimeric virus-like particles harboring foreign epitopes. Viruses, vol. 7, p. 4204–4229.

Nainys, J., Timinskas, A., Schneider, J., Ulrich, R.G., Gedvilaite, A. 2015. Identification of two novel members of the tentative genus Wukipolyomavirus in wild rodents. PLoS One, vol. 10:e0140916.

National Research Projects

Research Council of Lithuania. Bayesian Nonparametrics for Detection of Distant Protein Homology. (No. MIP-49/2013). Dr. M. Margelevičius. 2013–2015.

The project aims at increasing the sensitivity to remotely homologous proteins and the accuracy of alignments between multiple sequence alignments, or profiles. Modelling profile contexts, fixed-length profile fragments is engaged to achieve this goal. We show that a hierarchical Dirichlet process mixture model developed to describe the distribution of profile contexts and integrated into a new profile comparison method leads to a significant increase in both sensitivity and alignment quality.

Research Council of Lithuania. Projects of the European Social Fund under Global Grant Measure. Making Use of Large-Scale Biological Data for the Development of a New Method to Assess Protein Models and for Studying DNA Replication and Repair Systems in Bacteria and Viruses. (No. VP1-3.1.-ŠMM-07-K-03-004). Dr. Č. Venclovas. 2013–2015.

Using large-scale analysis of protein structural data we have developed a new method for the estimation of protein model quality. We also used computational analysis of the available genomes and proteomes to achieve a deeper understanding of DNA replication and repair systems in bacteria and viruses. In particular we established the diversity and distribution of DNA polymerases in bacteria and identified universal patterns within DNA replication systems of double-stranded DNA viruses.

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

Vilnius University Institute of Biotechnology (Lithuania)

Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas (Lithuania)

Institute of Molecular and Cell Biology, University of Tartu (Estonia)

Institute of Genetics, Biological Research Centre, Szeged (Hungary)

Institut Pasteur, Département de Microbiologie, Paris (France)

OTHER SCIENTIFIC ACTIVITIES

Dr. Č. Venclovas -