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Vilnius University Life Sciences Center. Annual Report 2019

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Vilnius University Life Sciences Center. Annual Report 2019 Life Sciences Center Life Sciences Center Center Sciences Life | Annual Report 2020 Annual Report CONTACT iNfOrmATiON Life Sciences Center Vilnius University Saulėtekio Ave 7, LT-10257 Vilnius, Lithuania Phone: +370 5 223 4435 / +370 5 223 4426 Email: [email protected] www.gmc.vu.lt/en/ Annual Report 2020 CONTENTS FOREWORD | 3 RESEARCH DESCRIPTIONS | 4 Biomolecular Structure & Function | 6 Cell & Molecular Biology | 30 Ecosystems & Biodiversity | 48 Molecular Biotechnologies | 56 Molecular Mechanisms of Disease | 68 Neurobiology | 80 OPEN ACCESS CORE FACILITIES | 86 FACTS & FIGURES | 95 Staff and Students I 96 Financing Sources I 96 International Advisory Council I 97 International Grants I 98 National Projects I 101 Partnership Highlights I 104 Graduate School I 106 Doctoral Theses 2020 I 107 Bachelor and Master Studies I 108 Student Scholarships I 110 Contribution to Overcome COVID-19 Pandemic I 111 International Awards I 114 National Awards I 116 Vilnius University Awards I 118 Scientific Events I 119 Guests I 121 Invited Speakers I 122 Community Events I 123 Public Engagement I 124 Publications in 2020 I 126 List of Patents I 133 Cooperation I 134 Names Index I 136 FOREWORD Year 2020 was both challenging and inspiring. Unexperi- enced in modern times, the deadly pandemic spread fast across the globe reaching Lithuania in early March. Initially it seemed the paralysis and major disruption of the most of our academic activities at the Life Sciences Center of Vilnius University are imminent. In mid-March when the Government announced nationwide quarantine, the lectures and student lab practices were halted and the access to research laboratories was re- stricted. In these circumstances, our community demonstrated strong determination and resilience not to let the academic life stop. Within several days the remote forms of lectures started, and the access to experimental facilities were renewed for stu- dents graduating in 2020. At the beginning of COVID-19 pandemic, Lithuania as other countries experienced a shortage of COVID-19 testing capaci- ties. Within a week, the Temporary Diagnostic Testing Labo- ratory was set up at the Life Sciences Center. After recruiting a team of volunteers and obtaining appropriate certificates from the Government, the PCR-based testing started in April. Throughout the year, more than 20 000 samples with nearly 3 000 diagnosed SARS-Cov-2-positive were tested in our Center. Giant Jamboree which this year was carried out remotely. For During the pandemic, our community members were actively the second time our students won the Grand Prize of the iGEM consulting the Ministry of Health of the Republic of Lithuania as competition. This historic victory proves again and again the well as the President. On request from the Ministry of Health, creativity and academic energy of the students at the Life Sci- the scientists at the Life Sciences Center prepared and validated ences Center. The President the Republic of Lithuania awarded the group testing protocols for COVID-19 patients. For the first our students the historical presidential flag. time the testing of surfaces was developed to track the asymp- We are very proud of our women researchers at the Life tomatic COVID-19 patients. First experimental tests of work- Sciences Center. This year two of them, Dr Rima Bydvytytė and places at the Life Sciences Center revealed the effectiveness Dominyka Dapkutė were granted L’Oréal-UNESCO Baltic For Wo- of the methodology to prevent the infection in organisations men in Science fellowships. Women are becoming more and and public spaces. This contactless technique was later adop- more active in seeking for management positions at the Life ted for COVID-19 testing in kindergartens. For significant contri- Sciences Center. Dr Eglė Lastauskienė was appointed the Di- butions in the fight against OC VID-19 the Life Sciences Center rector of the Institute of Biosciences, which is our major oper- community was awarded letters of gratitude by the Senate and ational unit involved in studies. This appointment reflects the Rector of Vilnius University and honorable awards by the Presi- efforts of our community to ensure gender equality in top man- dent and the Government of the Republic of Lithuania. agement positions at the Life Sciences Center. One of the most important academic events in 2020 was I wish to thank all our academic community for the aca- signing of the agreement between Vilnius University Life Sci- demic year full of unseen challenges. This year will remind us ences Center and the European Molecular Biology Laboratory that all challenges may also provide opportunities to realise our (EMBL). The Life Sciences Center became the 7th remote part- talents and energy for the benefit of society. To take advantage nership institution of EMBL. According to the agreement the of those opportunities we need to continue standing firmly on VU LSC-EMBL Partnership Institute for Genome Editing will be our basic academic values: dedication to excellence in science, established. The funding of the Partnership Institute was se- academic freedom, collegiality and inclusiveness, openness to cured from the Ministry of Education, Science and Sport to start the world and non-discrimination, respect for societal needs six research groups at the Life Sciences Center specializing in and public engagement. These values, I believe, will lead us various fields and applications of CRISPR gene editing systems. towards new success stories in 2021. This year witnessed exceptional achievements of our stu- dents at iGEM international competition in synthetic biology. Addressing an important problem of modern fish farming, which faces a high risk of fish infections our students along with their colleagues from other University departments pre- Gintaras Valinčius pared and remotely presented their project at the annual iGEM Director 3 FACTS & FIGURES RESEARCH DESCRIPTIONS Biomolecular Cell & Molecular Ecosystems & Structure & Function Biology Biodiversity Antiviral Defense Systems in Bacteria I 6 Applications of the Molecular Microbiology Animal Biodiversity, Structure and Bioelectrochemical Systems in of Prokaryotes in Biotechnology and Ecology of Populations I 48 Biopharmacy I 30 Biosensors and Bioreactors I 8 Biodiversity and Ecology of Plants, Algae Biological Modification of DNA and RNA I 10 Applied and Environmental and Fungi I 50 Microbiology I 32 Crystallography and Molecular Environmental Assessment & Ecosystem Modelling I 12 Functioning and Epigenetic Mechanisms of Development I 52 Electrochemical Biosensors for Human Stem Cells I 34 Real-World Applications I 14 Genetic and Structural Diversity of Genotoxicity of Anthropogenic and Bacteriophages I 54 Mechanisms of Flavoenzyme Redox Natural Factors I 36 Reactions I 16 Molecular Mechanisms of Cell Death and Microbial Diversity as a Source of Survival I 38 New Biocatalysts I 18 Molecular Mechanisms of Intracellular Protein Structural Bioinformatics I 20 Trafficking I 39 Protein Structure and Interactions in Phospholipid Membranes I 22 Plant Polymorphism, Genome Stability and Its Changing Factors I 40 Signalling in Prokaryotic Antiviral Defence I 24 Single-Cell Transcriptomics and Single-Molecule Studies of Protein and DNA Genomics I 42 Interactions I 26 Stem Cell Technologies for Bone Tissue Structural Biochemistry I 27 Engineering I 44 Structure and Thermodynamics for Drug Strategies in Antimicrobial Therapy and Design I 28 Protein Engineering I 46 4 OPEN ACCESS CORE FACILITIES Molecular Molecular Mechanisms of Neurobiology Biotechnologies Disease Advanced Microfluidics Technology Antibiotic Resistance and Pathogenesis I 68 Electrophysiological Brain States: Modulating for Biological and Biomedical Factors and Clinical Applications I 80 Epigenomic Studies of Human Disease I 70 Applications I 56 Molecular Signalling Pathways for Synaptic Molecular Mechanisms of Cancer Cell CRISPR-CAS Tools and Technologies I 58 Pruning I 81 Chemoresistance I 71 Biosynthesis of Chimeric and Native Neuroscience and Cellular Biophysics I 82 Genetic and Epigenetic Mechanisms of Cancer Proteins I 60 Development and Progression I 72 Role of Microbiota-Gut-Brain Axis in Development and Application of Molecular Mechanisms of Cancer Cell Neuropsychiatric Disorders I 84 Biocatalytic Systems I 62 Treatment I 74 Evaluation of the Specificity of Genome Molecular Virology: Mechanisms, Evolution, Editing Tools I 64 Antivirals I 76 Generation and Analysis of New Strategies in Fighting the CO VID-19 Antibodies I 65 Pandemic I 77 Molecular Tools for Covalent Labelling Protein Misfolding and Aggregation I 78 and Profiling of Epigenome I 66 5 BIOMOLECULAR STRUCTURE & FUNCTION VirginiJUS ŠIKŠNYS Distinguished Professor Head, Department of Protein-Nucleic Acids Interactions Institute of Biotechnology Email: [email protected] Phone: +370 5 223 4354 Antiviral Defense Systems in Bacteria Phages are the most abundant organisms in the biosphere and the major parasites of bacteria. They infect bacteria in order to replicate and usually kill bacteria when the replication is completed. In response to the phage threat, bacteria developed multiple defence barriers for countering and fighting viral attacks. In the Department of Protein-Nucleic Acids Interactions we aim to understand the structure-function relationships of enzymes and enzyme assemblies that contribute to the bacteria defence systems that target invading nucleic acids. We are particularly interested in the molecular machinery involved in the CRISPR-Cas
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