Institute of Biotechnology

Sukurta: 31 July 2017

bti7 Saulėtekio, LT-10257 Vilnius
Tel. 223 4365, fax 223 4367
E-mail:
www http://www.bti.vu.lt/

Director – Prof. Habil. Dr. Kęstutis Sasnauskas

STAFF

92 research fellows (incl.58 holding research degrees), 53 doctoral students.

 

RESEARCH AREAS

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

DOCTORAL DISSERTATIONS MAINTAINED IN 2016

E. Kazlauskas. Thermodynamics of aryl-dihydroxyphenyl-thiadiazole binding to recombinant human HSP90.
S. Baranauskė. Structural-functional analysis of the plant small RNA methyltransferase HEN1.
G. Alzbutas. Salt resistance mechanism of halotolerant / halophilic prokaryotic DNases and halotolerance induction for bovine DNase I.
T. Karvelis. Type II CRISPR-Cas systems: from basic studies towards genome editing.

MAIN CONFERENCES ORGANIZED IN 2016

Prof. Daumantas Matulis, head of Department of Biothermodynamics and Drug Design, Chairman of the Lithuanian Biochemical Society headed the Organizational Committee of the 14th iternational conference of the Lithuanian Biochemical Society, June 27–30, 2016 held in Druskininkai, Lithuania.

MAIN SCIENTIFIC ACHIEVEMENTS IN 2016

Prof. Dr. Virginijus Šikšnys was awarded the Warren Alpert Foundation Prize as one of the CRISPR Pioneer scientists for elucidating bacterial defense system and recognizing its utility for gene editing.

Dr. Česlovas Venclovas, Dr. Justas Dapkūnas and Kliment Olechnovič showed the best performance in the Round 37 of CAPRI (Critical Assessment of PRedicted Interactions), a world-wide experiment on computational modeling of protein assemblies, held in collaboration with the 12th CASP (Critical Assessment of Structure Prediction) experiment.

DEPARTMENT OF PROTEIN - DNA INTERACTIONS

7 Saulėtekio, LT-10257 Vilnius
Tel. 223 4354, fax 223 4367
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, Dr. A. Gegeckas.
Junior research fellows: Dr. L. Jakutytė-Giraitienė, Dr. T. Karvelis, G. Kostiuk.
Other researchers: E. Stankė, I. Songailienė, M. Kazlauskienė, P. Toliušis, A. Merkys, A. Vaitkus.
Doctoral students: P. Toliušis, I. Songailienė, E. Stankė, A. Merkys, M. Kazlauskienė, A. Vaitkus, G. Drabavičius, A. Grybauskas.

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.

RESEARCH PROJECTS CARRIED OUT IN 2016

Projects Supported by University Budget

Structure-Function Relationship of Proteins and Protein Complexes. Prof. Dr. V. Šikšnys. 2016–2018.

Restriction and modification systems commonly act as the first line of intracellular defense against foreign DNA and function as sentries that guard bacterial cells against invasion by bacteriophage. R-M systems typically consist of two complementary enzymatic activities, namely restriction endonuclease (REase) and methyltransferase (MTase). In typical RM systems REase cuts foreign DNA but does not act on the host genome because target sites for REase are methylated by accompanying MTase. REases from 4000 bacteria species with nearly 330 differing specificities have been characterised. REases have now gained widespread application as indispensable tools for the in vitro manipulation and cloning of DNA. However, much less is known about how they achieve their function.
In the Laboratory of Protein-DNA Interactions we focus on the structural and molecular mechanisms of restriction enzymes. Among the questions being asked are: How do the restriction enzymes recognize the particular DNA sequence? What common structural principles exist among restriction enzymes that recognize related nucleotide sequences? How are the sequence recognition and catalysis coupled in the function of restriction enzymes? Answers to these questions are being sought using X-ray crystal structure determination of restriction enzyme-DNA complexes, site-directed mutageneses and biochemical studies to relate structure to function.

Main publications:

Kazlauskienė, M., Tamulaitis, G., Kostiuk, G., Venclovas, C., Šikšnys, V. 2016. Spatiotemporal Control of Type III-A CRISPR-Cas Immunity: Coupling DNA Degradation with the Target RNA Recognition. Molecular Cell, vol. 62(2), p. 295–306.

Šikšnys, V., Gasiūnas, G. 2016. Rewiring Cas9 to Target New PAM Sequences. Molecular Cell, vol. 61(6), p. 793–794.

Labrie, V., Buske, O.J., Oh, E., Jeremian, R., Ptak, C., Gasiūnas, G., Maleckas, A., Petereit, R., Žvirblienė, A., Adamonis, K., Kriukienė, E., Koncevičius, K., Gordevičius, J., Nair, A., Zhang, A., Ebrahimi, A., Oh, G., Šikšnys, V., Kupčinskas, L., Brudno, M., Petronis, A. 2016. Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. Nature Structural & Molecular Biology, vol. 23, p. 566–573.

National Research Projects

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 Studies 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. CglI and NgoAVII are composed of two proteins: an R-protein, which is responsible for DNA target recognition and cleavage, and an N-protein, possessing an ATPase activity. It was demonstrated that in the case of the CglI system the R- and N-proteins assemble into a functional heterotetrameric protein complex with a R2N2 stoichiometry. Both catalytically active proteins and extensive ATP hydrolysis are required for specific DNA cleavage near the recognition sequence. Therefore, the restriction endonucleases CglI and NgoAVII employ a unique not yet elucidated catalytic mechanism for DNA cleavage. 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. Csm Effector Complex Labelling for Single Molecule FRET Experiments (No. APP-03/2016). Dr. G. Tamulaitis. 2016–2018.

Recently we have showed that the Type III-A CRISPR-Cas system Csm effector complex from Streptococcus thermophilus (StCsm) cleaves RNA at specific sequences. This specificity can be easily reprogrammed by changing the crRNA molecule in the complex, which is a desirable function for biotechnology. Recently, we have determined the capability of this complex to cleave single-stranded DNA as well. The goal of this project is to study relationship between RNA and DNA cleavage dynamics and to engineer a minimal StCsm complex in order to develop it as a molecular tool suitable for precise RNA manipulations in vitro and gene regulation in vivo. We will employ a combination of biochemical characterization methods, X-ray crystallography and single molecule FRET assay. Single molecule experiments of labelled StCsm complex will be performed in collaboration with the project partners from Leipzig University.

International Research Projects

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

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

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 SCIENTIFIC ACTIVITIES

Prof. Dr. V. Šikšnys –

  • member of the Lithuanian Academy of Sciences.

DEPARTMENT OF BIOLOGICAL DNA MODIFICATION

7 Saulėtekio av., LT-10257 Vilnius
Tel. 223 4350, fax 223 4367
E-mail:

Head - Prof. Habil. Dr. Saulius Klimašauskas FRSC

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.
Other researcher: A. Rukšėnaitė.
Doctoral students: S. Butkytė, P. Gibas, J. Ličytė, M. Mickutė.

RESEARCH INTERESTS

Nucleic acids modification enzymes
Epigenome profiling
Biosynthesis of selenoproteins
Enzyme engineering

RESEARCH PROJECTS CARRIED OUT IN 2016

Projects Supported by University Budget

Nucleic Acids Modification Enzymes: Structure, Mechanisms of Action and Directed Engineering. Prof. Habil. Dr. S. Klimašauskas. 2016–2018.

Main publications:

Labrie, V., Buske ,O. J., Oh, E., Jeremian, R., Ptak, C., Gasiūnas, G., Maleckas, A., Petereit, R., Žvirblienė, A., Adamonis, K., Kriukienė, E., Koncevičius, K., Gordevičius, J., Nair, A., Zhang, A., Ebrahimi, A., Oh, G., Šikšnys, V., Kupčinskas, L., Brudno, M., Petronis, A. 2016. Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. Nature Structural & Molecular Biology, vol. 23, p, 566–573.

Esyunina, D., Turtola, M., Pupov, D., Bass, I., Klimašauskas, S., Belogurov, G., Kulbachinskiy, A. 2016. Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases. Nucleic Acids Res., vol. 44(3), p. 1298–1308.

Butkytė, S., Čiupas, L., Jakubauskienė, E., Vilys, L., Mocevičius, P., Kanopka, A., Vilkaitis, G. 2016. Splicing-dependent expression of microRNAs of mirtron origin in human digestive and excretory system cancer cells. Clin. Epigenetics, vol. 8(33); doi:10.1186/s13148-016-0200-y.

National Research Projects

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.

During this project we will try to identify and characterize Lactococcus lactis and Lactobacillus casei small non-coding RNAs responsible for their resistance to lysozyme, beta-lactam and glycopeptide antibiotics. For this we will apply 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.

Research Council of Lithuania. Age-Related Remodelling of Aorta and Dilatative Pathology of Ascending Aorta: Search for Epigenetic Biomarkers (No. SEN-05/2016). Dr. G. Vilkaitis. 2016–2018.

Ageing is a non-modifiable risk factor for development of cardiovascular diseases but the underlying molecular remodelling mechanisms of ageing vessels has not been investigated sufficiently yet. In recent years a breakthrough in epigenetic studies of mechanisms involved in medial smooth muscle cells phenotypic changes, especially in the field of non-coding RNAs was demonstrated. The aim of this project is to profile selected non-coding RNAs involved in morphogenesis of ascending aorta aneurysm and in age-related aortic remodelling. Clinical, histomorphometric, and epigenetic studies will be performed to evaluate the clinical feasibility of these ncRNAs as biomarkers for ascending aorta aneurysm diagnostics and prognosis.

International Research Projects

National Institutes of Health, USA (NIH/NHGRI). Direct Single Nucleotide Mapping of Genomic Cpg Marks. (R21HG007200) Prof. S. Klimašauskas. 2013–2016.

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 DNA methylation. In the mammalian genome, cytosines (C) were long known to exist in two functional states: unmethylated or methylated at the 5-position of the pyrimidine ring (5mC). Recent studies of genomic DNA from the human and mouse brain, neurons and from mouse embryonic stem cells found that a substantial fraction of 5mC in CpG dinucleotides is converted to 5-hydroxymethylcytosine (hmC) by the action of oxygenases. These findings provided important clues in a long elusive mechanism of active DNA demethylation and bolstered a fresh wave of studies in the area of epigenetic regulation in mammals. However, such studies are hindered by the shortcomings of available experimental techniques for genome-wide epigenome analysis. 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, Toronto (Canada)
University of Paul Sabatier, Toulouse (France)
Institute of Molecular Genetics, Moscow (Russia)
Hokkaido Universitym Sapporo (Japan)
University of Stavanger, Stavanger (Norway)

OTHER SCIENTIFIC ACTIVITIES

Prof. Habil. Dr. S. Klimašauskas –

  • editorial advisory board member of the journal Open Life Sciences, https://www.degruyter.com/view/j/biol;
  • editorial board member of the journal Proceedings of the Estonian Academy of Sciences, http://www.kirj.ee/13226/;
  • management committee member, COST actions CM1303, CM1406;
  • member of the Lithuanian Academy of Sciences;
  • fellow of the Royal Society of Chemistry.

DEPARTMENT OF EUKARYOTE GENETIC ENGINEERING

7 Saulėtekio av., LT-10257 Vilnius
Tel. 223 4358, fax 223 4367
E-mail:

Head - Dr. Gintautas Žvirblis

STAFF

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

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2016

National Research Projects

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

Plant survival depends on adaptation to environment. Cell signaling via mitogen-activated protein kinases (MAPKs) and protein phosphatases is important to ensure responses enabling plant adaptation to stress. 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. Investigation of Synthesis Regulation of Proteins Associated with Alzheimer Disease Development (No. SEN-05/2015). Prof. Habil. Dr. K. Sasnauskas. 2015–2018.

It has been shown recently that the majority of eukaryotic gene has a surprisingly large variety of protein translation start point in noncoding 5’-end of mRNA. About 50% of annotated in gene bank human mRNA have at least several additional open reading frames (ORF) in non-coding 5’-end of mRNA. The project goal 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.

Main publication:

Baranauskas, A., Dapkūnas, Ž., Nekrašė, G., Pesliakas, H.J., Mištinienė, E., Mickienė, G., Žvirblis, G. National patent No. LT2016-100, Dimeric fragment of antibody neutralizing cytolytic activity of vaginolyzin. Priority date October 03 2016.

International Research Projects

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

Signaling 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 to extend the knowledge on plant cell signaling pathways in responses to pathogens. Thus, specific functions of protein phosphatases acting in signaling 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.

SECTOR OF MICROTECHNOLOGIES

7 Saulėtekio av., LT-10257 Vilnius
Tel. 223 4356, fax 223 4367
E-mail:

Head - Dr. Linas Mažutis

STAFF

Chief research fellow: Prof. A. Janulaitis.
Junior research fellow: K. Leonavičius.
Other researchers: D. Kučiauskas, J. Skerniškytė, R. Galinis, K. Simutis, V. Milkus, G. Stonytė, G. Zubaitė, J. Nainys.
Doctoral students: R. Galinis, J. Rutkauskaitė, V. Kiseliovas, V. Milkus, R. Žilionis, J. Nainys.

RESEARCH INTERESTS

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

RESEARCH PROJECTS CARRIED OUT IN 2016

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.

All evolutionary systems, whether in nature or in the laboratory, share a common principle: they require a link between genotype (a nucleic acid that can be replicated) and phenotype (a functional trait such as binding or catalytic activity). In nature, such a link is achieved via compartmentalization of genes within living cells. In the laboratory, various biochemical means can be exploited but most of the assays have limited throughput and is challenging to maintain a link between a gene and the diffusive reaction products of enzymatic activity. Furthermore, since selections must be performed for each target individually, large numbers of targets impose serious technical limitations. In this project we are 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.

Main publications:

Galinis, R., Stonytė, G., Kiseliovas, V., Žilionis, R., Studer, S., Hilvert, D., Janulaitis, A., Mažutis, L. 2016. DNA nanoparticles for improved protein synthesis in vitro. Angew Chem. Int. Ed. Engl., vol. 55(9), p. 3120–3.

Einav, T., Mažutis, L., Phillips, R. 2016. Statistical Mechanics of Allosteric Enzymes. J. Phys. Chem. B, vol. 120(26), p. 6021–37.

H2020 FRAMEWORK PROGRAMME: High Throughput Screening of Single-Cells Using Droplet Microfluidics — Cells-In-Drops (No. 705791). Dr. L. Mažutis. 2016–2018.

Analysis of single-cells is becoming increasingly important in different branches of biology and biomedicine. Many useful techniques have been developed to profile and even selectively purify single-cells, however, the demand for methods with better analytical performance and improved high-throughput capabilities, remains very high. Droplet microfluidics can fulfill this demand by bringing higher throughput, scalability and single molecule resolution. In this project, a droplet microfluidics platform we aim to develop a system for high-throughput single-cell screening and sequencing of immune cells, including primary B-cells that produce therapeutic antibodies or biomolecules of biomedical interest. We are using cell compartmentalization into microfluidic droplets together with capture beads and barcoded DNA primers that enable a direct establishment of the linkage between the genotype (genes or mRNA) and phenotype (binding, regulatory or activity of secreted proteins). Like no other system available to-date this technological approach should provide a unique way to identify the primary sequence of heavy and light IgG genes encoding functional monoclonal antibodies directly from single-cells, without a need to perform gene cloning or cell immortalization. The results of this work are likely to bring a significant impact not only in applied biological sciences but also in biotechnology and biomedicine.

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 (Switzerland)

OTHER SCIENTIFIC ACTIVITIES

Dr. L. Mažutis –

  • 2016 Marie Curie Individual Fellowship (EU)

DEPARTMENT OF IMMUNOLOGY AND CELL BIOLOGY

7 Saulėtekio av., LT-10257 Vilnius
Tel. 223 4360, fax 223 4367
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 fellow: Dr. P. Stakėnas.
Junior research fellows: I. Dalgėdienė, R. Lasickienė, E. Jakubauskienė, I. Pečiulienė, V. Simanavičienė, A. Vaitiekaitė, M. Jasulionis.
Other researchers: D. Stravinskienė, D. Bakonytė, L. Vilys, M. Simanavičius.
Doctoral students: I. Dalgėdienė, D. Stravinskienė, V. Simanavičienė, L. Vilys, M. Janulaitienė, M. Zilnytė, V. Rubinaitė, A. Lučiūnaitė, M. Simanavičius.

RESEARCH INTERESTS

Monoclonal and recombinant antibodies
Molecular epidemiology of Mycobacterium tuberculosis
Alternative splicing

RESEARCH PROJECTS CARRIED OUT IN 2016

Projects Supported by University Budget

Development of Novel Antibodies and Testing of Their Properties. Dr. A. Žvirblienė. 2016–2020.

Main publication:

Butkytė, S., Čiupas, L., Jakubauskienė, E., Vilys, L., Mocevičius, P., Kanopka, A., Vilkaitis, G. 2016. Splicing-dependent expression of microRNAs of mirtron origin in human digestive and excretory system cancer cells. Clin. Epigenetics, vol. 8(33), doi: 10.1186/s13148-016-0200-y.

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. In order to develop serologic assays for HEV infection, full length HEV-3 and rat HEV capsid proteins were produced in yeast, purified and examined by electron microscopy. A collection of HEV-specific monoclonal antibodies was generated. The recombinant antigens and monoclonal antibodies were used to develop IgM/IgG capture and competitive ELISAs for detection of virus-specific antibodies in blood serum. This study is performed in collaboration with Friedrich-Loeffler Institute (Germany).

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. The profiles of circulating miRNAs (-146b, -221, -222, -181, -21) in patients with PTC, benign nodules and healthy controls were investigated. The levels of all three miRNAs were significantly increased in PTC when compared to healthy thyroid tissue.

Contractual Research

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

7 Saulėtekio av., LT-10257 Vilnius
Tel. 223 4364, fax 223 4367
E-mail:

Head - Dr. Daumantas Matulis

STAFF

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

RESEARCH INTERESTS

Thermodynamics and kinetics of protein
Fundamental understanding of the protein
Ligand molecular recognition process

RESEARCH PROJECTS CARRIED OUT IN 2016

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.

Main publication:

Toleikis, Z., Sirotkin, V. A., Skvarnavičius, G., Smirnovienė, J., Roumestand, C., Matulis, D., Petrauskas, V. 2016. Volume of Hsp90 protein–ligand binding determined by fluorescent pressure shift assay, densitometry, and NMR. The Journal of Physical Chemistry B, vol. 20, p. 9903–9912.

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

Oncological diseases are one of the main causes of life quality deterioration and mortality for older people. Therefore it is very important to develop novel, efficient and noninvasive diagnostic methods of oncological diseases (including cervical cancer) and investigate markers of cancerous processes that may be helpful in diagnosis. One of such markers could be human carbonic anhydrase IX (CA IX). There are 12 catalytically active carbonic anhydrase isoforms in the human body that catalyze the reversible reaction of carbon dioxide hydration. Most of the isoforms perform vital functions in all human tissues. However, CA IX is exceptional because it nearly does not express in healthy tissues, but highly overexpressed in hypoxic cancerous tumors. The goal of this project is to develop the 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 analyze the potency of CA IX as a general serological marker of hypoxic tumors. Fluorescent and positron-emitting probes will be attached to CA IX antibodies and CA IX-selective inhibitors synthesized in our laboratory to analyze their potency for the visualization of cancerous tissues. This project should help solve the issues of more accurate, less invasive and earlier diagnosis of cancer and help to improve the future of older people.

Main publication:

Juozapaitienė, V., Bartkutė, B., Michailovienė, V., Zakšauskas, A., Baranauskienė, L., Satkūnė, S., Matulis, D. 2016. Purification, enzymatic activity and inhibitor discovery for recombinant human carbonic anhydrase XIV. Journal of Biotechnology, doi: 10.1016/j.jbiotec.2016.10.018.

International Research Projects

Research Council of Lithuania. Design of Anticancer Pharmaceutical Compounds Using Structure and Energetics of Lead – Target Interaction (No. TAP LLT-1/2016). Dr. D. Matulis. 2016–2018.

The three research teams of this proposal, Taiwanese, Latvian, and Lithuanian, have combined their efforts to improve the knowledge of protein – drug recognition and to make compounds that would be proposed to develop as drugs primarily against cancer. We have significant experience and continue to use the target-based drug discovery approach. Protein targets will be part of the epigenetic proteins, mostly metalloenzymes containing zinc in their active site. Metalloenzymes are widely distributed in human body and their mis-activity or mis-regulation causes numerous diseases.

Main publication:

Linkuvienė, V., Krainer, G., Chen, W.-Y., Matulis, D. 2016. Isothermal titration calorimetry for drug design: Precision of the enthalpy and binding constant measurements and comparison of the instruments. Anal. Biochemistry, vol. 515, p. 61–64.

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)

OTHER SCIENTIFIC ACTIVITIES

Dr. D. Matulis –

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

SECTOR OF APPLIED BIOCATALYSIS

7 Saulėtekio av., LT-10257 Vilnius
Tel. 223 4371, fax 223 4367
E-mail:

Head - Dr. Inga Matijošytė

STAFF

Research fellow: Dr. I. Matijošytė.
Junior research fellows: M. Šulcienė, R. Šiekštelė.
Other researchers: A. Veteikytė, A. Sirvydaitė.
Doctoral students: V. Matikevičienė, M. Šulcienė.

RESEARCH INTERESTS
 
Biocatalysts and their application

RESEARCH PROJECTS CARRIED OUT IN 2016

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 2016 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 Biogeocenosis of Microorganismas. JSC BioenergyLT, N° MTS-560000-895, Lithuania, Dr. I. Matijošytė.

The aim was to investigate the company’s biological products, microorganisms, for their biogeocenosis properties.

Investigation of Milk Fractionation and its Structural Features. JSC BioenergyLT, N° MTS-560000-1624, Lithuania, Dr. I. Matijošytė.

The aim was to investigate and to define optimal parameters for milk fractionation and to explore the structural properties of the obtained fractions.

Collaboration contracts

Enzymes and their application in detergents. SC Naujoji Ringuva, N° B1-560000-153, I. Matijošytė, (open-ended).

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

University of Applied Sciences (Switzerland)
TU Delft (the Netherlands)
Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB (Germany)
Pöyry Management Consulting Oy (Finland)
Proviron Industries NV (Belgium)
Leiden University (the Netherlands)
University of Seville (Spain)
University of Turin (Italy)
Max Plank Institute for Developmental Biology (Germany)

OTHER SCIENTIFIC ACTIVITIES

Dr. I. Matijošytė –

  • MC substitute member of COST Action 1303.
  • national representative in State Representative Group (SRG) at Bio-Based Industry Joint Undertaking.

A. Veteikytė –

  • laboratory experiments for schoolchildren during European Biotech Week 2016.

DEPARTMENT OF BIOINFORMATICS

7 Saulėtekio, LT-10257 Vilnius
Tel. 223 4368, fax 223 4367
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.
Junior research fellow: Dr. D. Kazlauskas.
Doctoral students: K. Olechnovič, K. Timinskas, V. Raškevičius.
System administrator: R. Dičiūnas.

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

RESEARCH PROJECTS CARRIED OUT IN 2016

Projects Supported by University Budget

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

In 2016 we have been actively involved in both the development and application of bioinformatics methods. During summer we participated in world-wide CAPRI (Critical Assessment of PRediction of Interactions) and CASP (Critical Assessment of Protein Structure Prediction) competitions. We achieved top results in CAPRI and showed strong performance in CASP demonstrating the effectiveness of our computational tools. In the area of application of bioinformatics methods we performed a global analysis of viral DNA replication systems and discovered previously unnoticed logic in their composition. Application of bioinformatics methods also contributed significantly to the novel findings in joint computational and experimental (Prof. Šikšnys) studies of prokaryotic CRISPR-Cas immunity systems.

Main publications:

Venclovas, Č. 2016. Structure of Csm2 elucidates the relationship between small subunits of CRISPR-Cas effector complexes. FEBS Lett, vol. 590, p. 1521–1529.

Kazlauskienė, M., Tamulaitis, G., Kostiuk, G., Venclovas, Č., Šikšnys, V. 2016. Spatiotemporal Control of Type III-A CRISPR-Cas Immunity: Coupling DNA Degradation with the Target RNA Recognition. Molecular Cell, vol. 62, p. 295–306.

Kazlauskas, D., Krupovic, M., Venclovas, Č. 2016. The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes. Nucleic Acids Res, vol. 44, p. 4551–4564.

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

Most departments at 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)
Institut Pasteur, Département de Microbiologie, Paris (France)

OTHER SCIENTIFIC ACTIVITIES

Dr. Č. Venclovas –

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