The institute of Biotechnology has become a recognized leader in life sciences. The Institute strives to maintain the highest standards of scientific endeavour and technological advance in a broadly defined field of molecular biotechnology, including nucleic acid and protein technologies, bioinformatics, molecular and immune diagnostics, drug design, microfluidic, next generation genome editing and epigenomics.
Department of Protein - DNA Interactions
The overall research theme in our lab is the structural and functional characterization of enzymes and enzyme assemblies that contribute to the bacteria defense systems which target invading nucleic acids. In particularly, we are involved in the deciphering structural and molecular mechanisms of restriction enzymes, and the molecular machinery involved in the CRISPR function. We are using X-ray crystallography, mutagenesis, and functional biochemical and biophysical assays to gain information on these systems.
Department of Biological DNA Modification
Department of Eukaryote Gene Engineering
Department of Eukaryote Gene Engineering is focused on the research directions of recombinant viral and human protein analysis, expression and assembly of proteins into virus-like particles (VLPs) as well as mechanisms of plant signaling and biosynthesis. We are using methods of gene cloning and expression in different host systems, electron microscopy, immunological and functional biochemical assays of proteins, biosynthesis and purification of essential amounts of target recombinant proteins with application area including diagnostics and therapeutics.
Department of Immunology and Cell Biology
Monoclonal and recombinant antibodies are widely used in biotechnology, medicine and biomedical science. Monoclonal antibodies produced using traditional hybridoma-based technologies are valuable research tools and clinical diagnostic reagents. Recombinant antibodies generated by gene engineering approaches are increasingly being used as therapeutic agents for treatment of cancer, autoimmune and infectious diseases. So, there is strong need for novel well-characterized antibodies with desired specificities and other characteristics.
Our team has a strong expertise in development and characterization of monoclonal and recombinant antibodies. We have generated more than 500 monoclonal antibodies against different targets: viral antigens, bacterial virulence factors, cellular proteins, cytokines, hormones. The largest antibody collection is generated against viral antigens, including measles, mumps, human parainfluenza viruses, henipaviruses, hantaviruses, parvoviruses, human bocaviruses, hepatitis B virus, hepatitis E virus (1) and others. These antibodies are valuable tools for investigating antigenic structure of viruses (2), development of diagnostic assays and prevalence studies of viral infections. Virus research is carried out in collaboration with Prof. Dr. R.Ulrich (Friedrich-Loeffler-Institute, Greifswald, Insel-Riems, Germany), Prof. Dr. D. Glebe (Giessen University, Germany), J.O.Koskinen (ArcDia International Oy Ltd, Turku, Finland) and other partners. We have also generated a collection of antibodies against bacterial cytolysins and exploited them both for structural studies and quantitation of cytolysins (3). In collaboration with our colleagues from the Department of Eukaryote gene engineering, we have developed a new technology for the use of virus-like particles as a carrier for target epitopes to increase their immunogenicity. This approach provides possibilities to generate antibodies against short and non-immunogenic protein sequences. For construction of recombinant antibodies, gene sequences encoding the variable parts of immunoglobulin heavy and light chains are cloned from hybridoma cells producing well-characterized monoclonal antibodies against the target of interest. Recombinant antibodies are developed in different formats - as single chain antibodies (scFv) and Fc-engineered antibodies where the scFv derived from hybridoma cells are joined to human IgG Fc fragment. Also, we have exploited recombinant virus-like particles as a carrier for antibody molecules, both scFv and Fc-engineered scFv. This innovative approach allows generation of recombinant multimeric antibodies displayed on virus-like particles as demonstrated for vaginolysin- specific antibodies and neutralizing antibodies against hepatitis B virus (4).
Takkinen K, Žvirblienė A. Recent advances in homogenous immunoassays based on resonance energy transfer. Curr Opin Biotechnol. 2018; 55: 16-22
Simanavicius M, Tamosiunas PL, Petraityte-Burneikiene R, Johne R, Ulrich RG, Zvirbliene A, Kucinskaite-Kodze I. Generation in yeast and antigenic characterization of hepatitis E virus capsid protein virus-like particles. Appl Microbiol Biotechnol. 2018, 102(1): 185–198.
Simanavicius M., Juskaite K., Verbickaite A., Jasiulionis M., Tamosiunas P.L., Petraityte-Burneikiene R., Zvirbliene A., Ulrich R.G., Kucinskaite-Kodze I. Detection of rat hepatitis E virus, but not human pathogenic hepatitis E virus genotype 1-4 infections in wild rats from Lithuania. Vet Microbiol. 2018 ; 221:129-133.
Janulaitiene M, Gegzna V, Baranauskiene L, Bulavaite A, Simanavicius M., Pleckaityte M. Phenotypic characterization of Gardnerella vaginalis subgroups suggests differences in their virulence potential. PLoS One, 2018, 3(7):e0200625.
Dalgėdienė I., Lučiūnaitė A., Žvirblienė A. Activation of Macrophages by Oligomeric Proteins of Different Size and Origin. Mediators of Inflammation, 2018. ID 7501985
Tankovic J., Timinskas A., Janulaitienė M., Zilnytė M., Baudel J.-L., Maury E., Žvirblienė A., Plečkaitytė M. Gardnerella vaginalis bacteremia associated with severe acute encephalopathy in a young female patient. Anaerobe. 2017, 47: 132–134.
Janulaitienė M7., Paliulytė V., Grincevičienė Š., Zakarevičienė J., Vladisauskienė A., Marcinkutė A., Plečkaitytė M. Prevalence and distribution of Gardnerella vaginalis subgroups in women with and without bacterial vaginosis. BMC Infect. Dis. 2017, 17:394. DOI 10.1186/s12879-017-2501-y.
Janulaitiene M, Paliulyte V, Grinceviciene S, Zakareviciene J, Vladisauskiene A, Marcinkute A, Pleckaityte M: Prevalence and distribution of Gardnerella vaginalis subgroups in women with and without bacterial vaginosis. BMC Infectious Diseases 2017, 17:9.
Bulavaite A, Lasickiene R, Tamosiunas PL, Simanavicius M, Sasnauskas K, Zvirbliene A: Synthesis of human parainfluenza virus 4 nucleocapsid-like particles in yeast and their use for detection of virus-specific antibodies in human serum. Applied Microbiology and Biotechnology 2017, 101:2991–3004.
Mickiene G, Dalgediene I, Dapkunas Z, Zvirblis G, Pesliakas H, Kaupinis A, Valius M, Mistiniene E, Pleckaityte M: Construction, Purification, and Characterization of a Homodimeric Granulocyte Colony-Stimulating Factor. Molecular Biotechnology 2017, 59:374–384.
Kanopka A: Cell survival: Interplay between hypoxia and pre-mRNA splicing. Experimental Cell Research 2017, 356:187–191.
Kailasan S, Garrison J, Ilyas M, Chipman P, McKenna R, Kantola K, Soderlund-Venermo M, Kucinskaite-Kodze I, Zvirbliene A, Agbandje-McKenna M: Mapping Antigenic Epitopes on the Human Bocavirus Capsid. Journal of Virology 2016, 90:4670–4680.
Kucinskaite-Kodze I, Pleckaityte M, Bremer CM, Seiz PL, Zilnyte M, Bulavaite A, Mickiene G, Zvirblis G, Sasnauskas K, Glebe D, Zvirbliene A: New broadly reactive neutralizing antibodies against hepatitis B virus surface antigen. Virus Research 2016, 211:209–221.
Tamosiunas PL, Petraityte-Burneikiene R, Bulavaite A, Marcinkeviciute K, Simutis K, Lasickiene R, Firantiene R, Emuzyte R, Zvirbliene A, Sasnauskas K: Yeast-generated virus-like particles as antigens for detection of human bocavirus 1-4 specific antibodies in human serum. Applied Microbiology and Biotechnology 2016, 100:4935–4946.
Bulavaite A, Lasickiene R, Vaitiekaite A, Sasnauskas K, Zvirbliene A: Synthesis of human parainfluenza virus 2 nucleocapsid protein in yeast as nucleocapsid-like particles and investigation of its antigenic structure. Applied Microbiology and Biotechnology 2016, 100:4523–4534.
Butkyte S, Ciupas L, Jakubauskiene E, Vilys L, Mocevicius P, Kanopka A, Vilkaitis G: Splicing-dependent expression of microRNAs of mirtron origin in human digestive and excretory system cancer cells. Clinical Epigenetics 2016, 8:11.
Stucki D, Brites D, Jeljeli L, Coscolla M, Liu QY, Trauner A, Fenner L, Rutaihwa L, Borrell S, Luo T, et al: Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nature Genetics 2016, 48:1535–1543.
Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, Blum MGB, Ruch-Gerdes S, Mokrousov I, Aleksic E, et al: Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nature Genetics 2015, 47: 242.
Simanaviciene V, Popendikyte V, Gudleviciene Z, Zvirbliene A: Different DNA methylation pattern of HPV16, HPV18 and HPV51 genomes in asymptomatic HPV infection as compared to cervical neoplasia. Virology 2015, 484:227–233.
Simanaviciene V, Gudleviciene Z, Popendikyte V, Dekaminaviciute D, Stumbryte A, Rubinaite V, Zvirbliene A: Studies on the Prevalence of Oncogenic HPV Types Among Lithuanian Women With Cervical Pathology. Journal of Medical Virology 2015, 87:461–471.
Gudleviciene Z, Stumbryte A, Jukne G, Simanaviciene V, Zvirbliene A: Distribution of human papillomavirus type 16 variants in Lithuanian women with cervical cancer. Medicina-Lithuania 2015, 51:328–335.
Pleckaityte M, Bremer CM, Gedvilaite A, Kucinskaite-Kodze I, Glebe D, Zvirbliene A: Construction of polyomavirus-derived pseudotype virus-like particles displaying a functionally active neutralizing antibody against hepatitis B virus surface antigen. BMC Biotechnology 2015, 15.
Gedvilaite A, Kucinskaite-Kodze I, Lasickiene R, Timinskas A, Vaitiekaite A, Ziogiene D, Zvirbliene A: Evaluation of Trichodysplasia Spinulosa-Associated Polyomavirus Capsid Protein as a New Carrier for Construction of Chimeric Virus-Like Particles Harboring Foreign Epitopes. Viruses-Basel 2015, 7:4204–4229.
Zilnyte M, Venclovas C, Zvirbliene A, Pleckaityte M: The Cytolytic Activity of Vaginolysin Strictly Depends on Cholesterol and Is Potentiated by Human CD59. Toxins 2015, 7:110–128.
Jakubauskiene E, Vilys L, Makino Y, Poellinger L, Kanopka A: Increased Serine-Arginine (SR) Protein Phosphorylation Changes Pre-mRNA Splicing in Hypoxia. Journal of Biological Chemistry 2015, 290:18079–18089.
Jakubauskiene E, Peciuliene I, Vilys L, Mocevicius P, Vilkaitis G, Kanopka A: Gastrointestinal tract tumors and cell lines possess differential splicing factor expression and tumor associated mRNA isoform formation profiles. Cancer Biomarkers 2015, 15:575–581.
Department of Biothermodynamics and Drug Design
The Department of Biothermodynamics and Drug Design (DBDD) was established in 2006 based on the former Laboratory of Recombinant Proteins. The DBDD designs novel chemical compounds for therapeutic purposes. The efficiency of both naturally occurring and synthetic compounds is evaluated by structural biothermodynamics and molecular modeling methods.
Department of Bioinformatics
In Bioinformatics Laboratory we mainly deal with protein sequences and their three-dimensional structures. There are two main directions of our research:
Methods development. We aim at improving computational methods for sequence comparison and protein structure prediction (mainly in comparative modeling) as well as methods for assessment of protein structure quality.
Application of computational methods to biological problems. Most often we use computational methods to characterize structure and interactions of both individual proteins and their complexes. In these studies we tend to focus on proteins/protein complexes that function in DNA metabolism including DNA replication, recombination and repair. Our objective is to make inferences regarding structural and functional features, molecular mechanisms, interactions, etc. that can be tested experimentally. Most of such studies are joint collaborations with experimentalists.
Sector of Applied Biocatalysis
Sector of Applied Biocatalysis was established in 2007 as a group of Industrial Biotechnology in conjunction with the start of the National Programme on the Development of Industrial Biotechnology in Lithuania 2007-2010. In October 2010 the group was transformed into the Sector of Applied Biocatalysis and is headed by Inga Matijošytė (Ph.D. in biochemistry and biocatalysis from Delft University of Technology, The Netherlands, 2008).
Sector‘s research is directed towards the search for enzymes with new functionalities and their development towards applied biocatalysis. The limited number of suitable and well characterized biocatalysts delays the progress in the application of enzymes in the synthesis of compounds for materials, pharmaceuticals and chemicals.
Sector of Applied Biocatalysis seeks to identify biocatalysts with novel activities by screening for enzymes, development of biocatalyst and application of biocatalyst.
The research focuses on developing of biocatalytic systems employing enzymes from two main classes: oxidoreductases and hydrolases (laccases, lipases, alcohol oxidases, xylanases, etc.). We have variety of bacterial and yeast expression systems. Also, we also have long lasting experience in developing immobilization systems (carrier and carrier-free). Recently, the sector is orienting the research towards dicrovery of new novel biocatalytic routes for high-added value products from bio-based raw materials – biopolymers (polyols, polyurethanes, etc.).
We strive to meet scientific challenges in combination with application-oriented research. Therefore, close collaboration with industrial partners resulted in several research oriented projects.
We have skills and experience, possess tools and capacities to develop biocatalytic solutions for specific needs. Please contact us if you need:
- screening for enzymes (environmental samples, enzyme and strain collections, metagenomic and expression libraries, development of screening systems, etc.);
- development of biocatalyst (gene engineering, development of analytical systems, protein purification, development of expression systems, etc.);
- application of biocatalyst (immobilization, recycling, proof of principal, activity/selectivity, stability, reaction media, improved efficiency of bioconversions, quality analysis of products obtained by biocatalysis, etc.);
- application of Green Chemistry principles in technologies and processes.
V. Malūnavičius, G. Druteika, M. Sadauskas, A. Veteikytė, I. Matijošytė, E. Lastauskiene, A. Gegeckas, R. Gudiukaite. Usage of GD-95 and GD-66 lipases as fusion partners leading to improved chemiric enzyme LipGD95-GD66. Int. J. Biol. Macromol. 2018, in press, DOI: 10.1016/j.ijbiomac.2018.07.002.
M. Šulcienė, B. Kolvenbach, E. Ammann, I. Matijošytė. Towards an affordable enzymatic production of biopolyols – Comparing the immobilization of lipases by two optimized techniques. Int. J. Biol. Macromol. 2018, 116, 1049-1055
Veteikytė, R. Šiekštelė, B. Tvaska, I. Matijošytė. Sequential application of waste whey as a medium component for Klyuveromyces lactis cultivation and a co-feeder for lipase immobilization by CLEA method. Applied Microbiology and Biotechnology. 2017, 101:3617-3626.
Melvydas, I. Bruzauskaitė, G. Gedminienė, R. Šiekštelė. A Novel Saccharomyces cerevisiae killer strain secreting the X factor related to killer activity and inhibition of S. cerevisiae K1, K2 and K28 killer toxins. Indian Journal of Microbiology. 2016, 56(3): 335-343.
Gruškienė, V. Kairys, I. Matijošytė. CLEA-based immobilization of methylotropic yeast alcohol oxidase: influence on storage stability and reaction efficiency. Org. Process Res. Dev., 2015, 19 (12): 2025-2033.
Šiekštelė, A. Veteikytė, B. Tvaska, I. Matijošytė. 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., 2015, 42: 1309-1317
Šulcienė, A. Karalius, I. Matijošytė. Chemo-enzymatic route for the production of biopolyol from rapeseed oil. Curr. Org. Chem. 2014, 18: 3037-3043
Kleinaitė, V. Jaška, B. Tvaska, I. Matijošytė. A cleaner approach for biolubricant production using biodiesel as a starting material. J. Clean Prod., 2014, 75:40-44
Veteikytė A., Aštrauskaitė M., Gruškienė R., Tekorienė R., Matijošytė I., "Secondary alcohol oxidase activity identified in genus of Pseudomonas isolated from the oil polluted soil“. Agricult. Biotechnol., 2013, 2 (2): 89-95
A. Tromp, I. Matijošytė, R.A. Sheldon, I.W.C.E. Arends, M.T. Kreutzer, J.A. Moulijn, S. de Vries, “Mechanism of laccase/TEMPO oxidation of benzyl alcohol”. ChemCatChem., 2010 (2): 827-833
Visits funded by Lithuanian Science Council
- Conference “Multistep Enzyme Catalyzed Processes Congress (MECP2014).“ N° SF3-25 (N° VIZ-KON-1011). Poster: I. Matijošytė, A. Karalius, M. Šulcienė “Biopolyol production by a two step chemo-enzymatic synthesis”. 6-11 April 2014, Madrid, Spain.
- 6th International Congress on Biocatalysis (Biocat 2012). N° VIZIT-4-KON-381. Poster: I. Matijošytė, E. Kleinaitė, R. Šiekštelė, B. Pudžiuvytė „Novel lipase from Serratia sp. for biolubricant production“. 2-6 September 2012, Hamburg, Germany.
- Symposium on Biocatalysis and Biotransformations (Biotrans2011), N° KEL-007/2011. Poster: I. Matijošytė, M. Aštrauskaitė, A. Veteikytė, R. Gruškienė, E. Kleinaitė “A novel biocatalyst for oxidation of secondary alcohols“. 2-6 October 2010, Sicily, Italy.
Projects and cooperation
- COST Action CM1303: Systems Biocatalysis, duration 2014.09.15 - 2017.11.19.
- Sciex Junior Researchers‘ Felloship programos projektas IMMOZYME (k 13.101), University of Applied Sciences and Arts Northwestern, Basel, Switzerland, 2013.10.01-2014.04.01
- Project „Development of innovative biotechnology for oil base lubricant production“ (BIOLUBRICANT) under Industrial Biotechnology development programme for in Lithuania for 2011 – 2013. Project partners JSC Biocentras (www.biocentras.lt), duration 2011-2013.
- Project „The development of innovative biocatalytic stain remover“ (FASTREMOVE), under Industrial Biotechnology development programme for in Lithuania for 2011 – 2013. Project partners: SC NAUJOJI RINGUVA (www.ringuva.lt), duration 2012-2013.
- Project „Design and evaluation of ageing-resistant biodegradable esters with controllable flammability“ (BIOSKALESTER) under Industrial Biotechnology development programme for in Lithuania for 2007 – 2009, duration 2008-2010
- Project „The search for new biofuel components and investigation of second generation biofuel production technologies“ (BIOTEKA) under Industrial Biotechnology development programme for in Lithuania for 2007 – 2009, duration 2007-2009.
- Project „Investigation of immobilization of biocatalysts and their application in biotechnological processes“ (BIOKATALIMA) under Industrial Biotechnology development programme for in Lithuania for 2007 – 2009, duration 2007-2009.
Inovation voucher (funded by MITA) :
- Inovation voucher N° K-824-01-049 (2017/6 mėn), customer AC Pienas LT.
- Inovation voucher N° 31V- (2014/6 month), customer JSC Akses.
- Inovation voucher N° 43V-255 (2014/6 month), customer JSC Noventus.
- Inovation voucher N° 43V-10 (2013/6 month), customer JSC Lutora.
- Inovation voucher N° 31V-224 (2012/6 month), customer JSC Chemopolis.
- Inovation voucher N° 31V-105 (2011/6 month), customer JSC Nuostolių valdymas.
- Inovation voucher N° 31V-39 (2011/6 month), customer JSC PET group.
- Inovation voucher N° 31V-38 (2011/6 month), customer JSC Biocentras.
- Inovation voucher N° 31V- 72 (2010/3 month), customer JSC Naujoji Ringuva.
Contractual R&D projects with:
- JSC Bioenergy LT
- SC Amilina
- JSC Biorro
- AC Pienas LT
- Lithuanian University of Health Sciences
- JC Naujoji Ringuva „Enzymes and their application in detergents“ N° B1-560000-153
Scientific collaborations with:
- University of Torino (IT)
- Delft University of Technology (NL)
- Leiden University (NL)
- University of Applied Sciences and Arts Northwestern Switzerland (CHE)
- Latvian State Institute of Wood Chemistry (LV)
- JSC Probiosanus
- JSC Vita Baltic
Students of the year 2017-2018:
Žymantas Venckus (VU Microbiology and biotechnology)
Mantas Baliukynas (VU VU Microbiology and biotechnology)
Gabija Aleknavičiūtė (VU Molecular biology)
Jokūbas Krutkevičius (VU VU Microbiology and biotechnology)
Justinas Babinskas (VU Chemistry)
Marius Petkus (VU VU Microbiology and biotechnology)
Since the establishment of the Sector more than 20 thesis by undergraduate and postgraduate students were prepared.
Sector of Microtechnologies
The basic principle of droplet microfluidics is easy to appreciate: highly monodisperse aqueous droplets are generated in an inert carrier oil in microfluidic channels on a chip and each droplet functions as an independent microreactor. Hence, each droplet is the functional equivalent of a well (or tube), yet the volume of droplet is roughly a thousand to a million times smaller. Such massive reduction in reaction volume provides huge savings in reagents cost when performing large numbers of reactions in parallel. Furthermore, unlike the conventional microtiter plates or valve-based microfluidics, droplets are intrinsically scalable: the number of reaction ‘wells’ is not limited by the physical dimensions of the chip but scales linearly with the emulsion volume. Different microfluidic modules can be employed to manipulate droplets in sophisticated, yet highly controllable manner. Large numbers of droplets (>10^9) can be generated at astonishingly high rates (>20,000 droplets per second), their size tuned precisely, new reagents introduced into pre-formed droplets at defined time points, droplet split and sorted, therefore opening new opportunities for single-cell -omics field. Many useful microfluidic 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. We are working at fulfilling this demand by bringing higher throughput, reduced reagent cost, scalability and single-molecule resolution for diverse set of quantitative experiments in cell biology and biomedicine.
Group of Amyloid Research
We study effects of environmental factors such as temperature, pressure, pH, ions, macromolecular crowding, and the presence of different organic solvents, ligands and biomolecules on aggregation kinetics, thermodynamic stability, and structural properties of amyloid-like fibrils. We believe only comprehensive knowledge of all factors may give genuine understanding of mechanisms of amyloid self-replication and thus proteinaceous infectivity.