Outreach activities
We are actively involved in educational and outreach activities, including lectures in schools and hospitals, articles in mass media, participation in TV and radio broadcasts.
Since 2015 we collaborate with Vilnius Gabijos gymnasium and provide a possibility for schoolchildren to work in our laboratories and learn molecular biology and immunology techniques.
https://www.lrt.lt/mediateka/irasas/1013694599/radijo-popiete-2018-06-22-14-05
https://www.youtube.com/watch?v=qLPac6QkyGI
https://www.lrt.lt/mediateka/irasas/1013707848/labas-rytas-lietuva
http://www.santaroszinios.lt/blog/bakterijos-kurias-turetume-gerbti-ir-tausoti-suzinokite-kodel/
Projects and collaborations
Grants from the Research Council of Lithuania:
MIP-039/2015 "development of new diagnostic tools for hepatitis E virus (HEV) and studies on HEV prevalence in Lithuania" (2015-2018). Coordinator - I. Kučinskaitė-Kodzė.
S-MIP-17-49 „The prevalence and distribution of virulence factors among subgroups of vaginal bacteria Gardnerella vaginalis“ (2017-2020). Coordinator - M. Plečkaitytė.
Project No. 01.2.2-LMT-K-718-01-0008 „New technologies for development of recombinant allergens“ under the Measure No. 01.2.2-LMT-K-718, 2017-2020. Coordinator – G.Žvirblis (VU), participants: M.Simanavičius, K.Juškaitė, M.Plečkaitytė, V.Rudokas, A. Žvirblienė.
National research program “Healthy ageing”, project SEN-14/2015 „Investigation of Genetic and Epigenetic Prognostic Markers for Prediction of Clinical Course of Papillary Thyroid Cancer (PTC) in Different age Groups”, 2015-2018. Coordinator - B.Žilaitienė (LSMU), participants: A. Žvirblienė, D. Stravinskienė, E.Leiputė.
Post-doctoral fellowship No. 09.3.3-LMT-K-712-02-0094 „Investigation of pneumolysin by immunoassays“ (2017-2019), I. Kučinskaitė-Kodzė.
Post-doctoral fellowship No. 09.3.3-LMT-K-712-02-0095 „Alternative pre-iRNR splicing: association between hypoxia and neurodegenerative disorders“ (2017-2019), E. Jakubauskienė.
Contracts with industrial partners:
- UAB Imunodiagnostika No. 52-1705/TPS-600000-974, 2017-2019
- UAB Imunodiagnostika No. 51-1705/TPS-600000-966, 2017-2019
- Kalon Biological Ltd. (UK)
- Abcam Ltd. (UK)
- Santa Cruz Biotechnology (USA)
- ArcDia (Finland)
Collaboration 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)
Publications 2018-2015
2018
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
2017
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 M., 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.
2016
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.
2015
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.
COMER
COMER: Protein remote homology search
COMER is a protein sequence alignment tool designed for protein remote homology detection. It accepts a multiple sequence alignment as input and converts it into the profile to search a profile database for statistically significant similarities. Version 2 harnesses the power of GPUs to conduct very fast sensitive homology searches. COMER is licensed under the GNU GP License, version 3. Please refer to the README file for instructions on how to use the software.
The following directory contains databases of COMER profiles to be searched against with COMER. Any profile from a database can be easily extracted and, e.g., searched with COMER against the database (see the `README' file in the COMER installation package).
References:
Margelevicius, M. (2020) COMER2: GPU-accelerated sensitive and specific homology searches. Bioinformatics 36(11), 3570–3572.
Margelevicius, M. (2019) Estimating statistical significance of local protein profile-profile alignments. BMC Bioinformatics 20, 419.
Margelevičius M. (2018) Low-complexity add-on scores for protein remote homology search with COMER. Bioinformatics 34(12), 2037-2045.
Margelevičius M. (2016) Bayesian nonparametrics in protein remote homology search. Bioinformatics 32(18), 2744–2752.