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Invited speakers

Neoantigen discovery & proteomics development at International Centre for Cancer Vaccine Science

Ostatnia modyfikacja: 
środa, 2 czerwca 2021 roku, 13:03

Sperker: Dr Sachin Kote

Talk: "Neoantigen discovery & proteomics development at International Centre for Cancer Vaccine Science"

Time: 11.06.2021, 9:00 am

Venue: Online in the "IFB seminars" group of MsTeams. Group password: ypidr3d.


I am acting team leader of the chemical biology group at the International Centre for Cancer Vaccine Science (ICCVS). I am currently leading the neoantigen discovery/immunopeptidomics projects and proteomics development at ICCVS, University of Gdansk, Poland (www.iccvs.ug.edu.pl) since 2018.

I have specialized in peptidomics, proteomics, and cancer vaccine science. I have been working in the field of proteomics concerning health, environment, and safety for the past 12 years. I started my research career as a research project assistant in the proteomics laboratory at the National Chemical Laboratory (NCL), India. Herein, I have developed a strong interest in proteomics, mass spectrometry (MS), and biomarker discovery. Afterward, I moved to Italy for doctoral studies focusing on invitro and invivo nano-bio-interactions, biomarker findings upon nano-exposure, and nanotoxicology using advanced proteomics tools. I have completed my doctoral studies with an excellent Ph.D. award from the University of Salento, Lecce, Italy. Later on, I moved to north Italy for my first postdoctoral studies at the Istituto Italiano di Tecnologia (IIT), Genova, Italy. During my tenure, I developed biological/protein nanoparticles for the safe delivery of nanomedicine applications. In the second but very challenging project, I have developed a dissolution test for risk assessment nanomaterials. I am proud to say that our development of dissolution test is included in the nano-regulatory guidelines i.e., The Organization for Economic Co-operation and Development (OECD, ENV/JM/MONO, 2020, 9) guidelines. These guidelines are applicable in 36 industrialized countries in North and South America, Europe, Asia, and the Pacific.

Additionally, I have a background in Bioinformatics, Clinical Research & Clinical Data Management (CRCDM), and Diploma in Medical Laboratory Technology (DMLT).

Academic basic research vs. big pharma R&D- similarities and differences based on my career transition from postdoc to early drug discovery at GlaxoSmithKline

Ostatnia modyfikacja: 
środa, 2 czerwca 2021 roku, 12:53


Speaker: dr Maja Firczuk

Talk: "Academic basic research vs. big pharma R&D- similarities and differences based on my career transition from postdoc to early drug discovery at GlaxoSmithKline" 

Time: 7 may 2021, 9:00 am.

Venue: Online in the "IFB seminars" group of MS Teams. Group password: ypidr3d.  


I have completed all my higher education at MWB in Gdansk. I have gained an extensive expertise in biochemistry during my PhD on Hsp70 protein systems, in the group of prof. Marszalek. In 2007 I have started postdoctoral research in systems biology of eukaryotic mRNA translation pathway, first at University on Manchester then at Warwick University. In 2018 I decided to have a career change and moved to work as a biochemist in early drug discovery at GSK.

In my talk I want to share learnings form my career journey and give you an overview of drug discovery process.

Immunopathogensis of dengue; lessons for COVID-19?

Ostatnia modyfikacja: 
środa, 2 czerwca 2021 roku, 12:55


Speaker: prof. Neelika Malavige (Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Sri Lanka)

Talk: „Immunopathogensis of dengue; lessons for COVID-19?”

Time: 12 March 2021, 9:00 am

Venue: Online in the "IFB seminars" group of MS Teams. Group password: ypidr3d.

prof. Neelika MalavigeNeelika Malavige is a Professor and Head of the Department of Immunology and Molecular Medicine at University of Sri Jayewardenepura, a Director of Centre for Dengue Research and an academic visitor at the MRC Human Immunology Unit, University of Oxford. She is also a member of Executive Committee of the International Society of Infectious Diseases.   

Neelika has obtained medical training and qualifications through University of Colombo, Sri Lanka, Royal College of Physicians, UK and European Academy of Allergology and Clinical Immunology. She did her PhD at the University of Oxford, investigating immune responses to Varicella Zoster virus, having received a Commonwealth Scholarship. She is currently both a scientist and a practising clinician with interest in infectious diseases and allergies. Neelika has obtained research funding of around $ 2 mln and with that support she set up and developed the Centre for Dengue Research at the University of Sri Jayewardenepura. 

Neelika’s current research interest involve immune responses to Dengue virus and biomarker identification; she is also running clinical trials to reduce vascular leak in severe disease. With the onset of the COVID-19 pandemic, Neelika and her team have been also investigating humoral and cellular responses to SARS-CoV2 and sequencing the viral strains.

She has published extensively on Dengue, VZV and now also on COVID-19 in prestigious journals, including Nature Communications, Scientific Reports and PLoS NeglectedTropical Diseases. She has been awarded countless excellence research awards and multiple awards for quality in research supervision. She has been involved in science popularisation, has been proclaimed a “role model” for Women in STEM and has recently won the title of “The most inspiring woman of the year” in Sri Lanka.


Oxford-AstraZeneca Covid-19 vaccine - questions and answers session

Ostatnia modyfikacja: 
piątek, 15 stycznia 2021 roku, 9:59


Speaker: Dr Adam Ritchie (Jenner Institute, Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford)

Talk: Oxford-AstraZeneca Covid-19 vaccine - questions and answers session

Time: 29 January 2021, 9:00 am

Venue: Online in the "IFB seminars" group of MS Teams. Group password: ypidr3d.

Dr Adam RitchieDr Ritchie completed his Bachelor of Science degree in Medical Microbiology and Immunology (2001) and PhD in Immunology (2005), both at the University of New South Wales in Australia. His doctoral research involved investigation of modulation of immune responses by Pseudomonas aeruginosa. After his PhD, he moved to the University of Oxford, working as a postdoctoral researcher in infection risk of blood products, which focused on malaria and variant Creutzfeldt–Jakob disease. Then, he followed with a post-doctoral research position in HIV/AIDS immunology at the Weatherall Institute for Molecular Medicine, University of Oxford as part of the Centre for HIV/AIDS Vaccine Immunology (CHAVI) consortium (2008-2012). During the time he coordinated the CHAVI002 study into individuals resistant to HIV infection in cohorts in the UK and Uganda.

From 2011 to 2017 Dr Ritchie was the Lecturer in Science and Public Policy at the Blavatnik School of Government, a new department at Oxford that he helped establish. Here he taught public policy students and policy makers how to work with scientific evidence, including preparing for and responding to pandemics.

Currently, he is working at the Jenner Institute, University of Oxford as a Senior Project Manager in Vaccine Development and is part of the Oxford COVID Vaccine Trial Group. Initially working on Rabies vaccine from 2017, he set up and manages phase I clinical trials for this vaccine in the UK and Tanzania. In 2020 his role changed due to the pandemic; he was instrumental in developing and delivering the manufacturing process for the ChAdOx1 nCoV-19 vaccine. This included setting up the Manufacturing consortium now producing the vaccine under licence with AstraZeneca, obtaining a UK government commitment of £65 million support for manufacturing, and managing £15 million of that budget.

Dr Ritchie is also actively involved in multiple non-research roles at Oxford, including as the Senior Admissions Adviser for Blavatnik School of Government, and as a Lecturer in Human Science at St Catherine’s College. He holds a Post-Graduate Diploma in Learning and Teaching in Higher Education at the University of Oxford and the Higher Education Academy (2013). He is a Senior fellow of the Higher Education Academy, and received the St Bonaventure University Medal of Honor (2012) and University of Oxford Teaching Excellence Award (2013) for his contributions to education.

Dr Ritchie has co-authored work published by Journal of Virology, Vaccine, Journal of Clinical Investigation, Retrovirology, Infection and Immunity, etc. His most recent work focusing on the COVID19 vaccine resulted in multiple papers published in The Lancet and Nature Medicine.

Regulation of gene expression through biomolecular condensation

Ostatnia modyfikacja: 
wtorek, 20 października 2020 roku, 10:41


Speaker: dr Adam Kłosin (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany)

Talk: Regulation of gene expression through biomolecular condensation

Time: 06 November 2020, 9:00 am

Venue: Online in the "IFB seminars" group of MS Teams. Group password: ypidr3d.

Adam KłosinAdam Kłosin is a postdoctoral researcher and a Marie Skłodowska-Curie Fellow at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany. In 2016 he completed his PhD in the group of Ben Lehner at the Centre for Genomic Regulation in Barcelona where he studied mechanisms of epigenetic inheritance in Caenorhabditis elegans. He then moved to Dresden to train in the arts of biological phase separation in the group of Tony Hyman. In his research he applies biophysical methods to understand various aspects of gene regulation such as transcriptional initiation and control of protein expression variability. His most recent work demonstrates a very effective mechanism for noise reduction in mammalian cells based on compartmentalisation of a protein via liquid- liquid phase separation. He is currently investigating the role of disordered protein domains in regulating interactions with the DNA in the context of transcriptional initiation.

Genome editing in mitochondria: past, present and future

Ostatnia modyfikacja: 
piątek, 6 marca 2020 roku, 6:56

Speaker: dr Michał Mińczuk (MRC Mitochondrial Biology Unit, University of Cambridge)

Talk: Genome editing in mitochondria: past, present and future

Time: 06 March 2020, 9:00 am

Venue: Intercollegiate Faculty of Biotechnology, Abrahama 58, hall 042

MMMitochondria are essential for human life. They are complex, compartmentalised organelles that form a dynamic network throughout the cell, host crucial metabolic processes vital for energy provision, and are central to cell fate decisions. Mitochondria contain multiple copies of their own genome, the mtDNA, that encodes the core subunits of the oxidative phosphorylation system. Mutations in protein or RNA coding genes of mtDNA are the most frequent cause of mitochondrial disease. These disorders are currently incurable and effectively untreatable, with heterogeneous penetrance, presentation and prognosis. In most cases, mutant and wild-type mtDNAs coexist within a single cell, resulting in heteroplasmy. The selective elimination of mutant mtDNA, and consequent enrichment of wild-type mtDNA, can rescue pathological phenotypes in heteroplasmic cells. In our work, we have developed mitochondrially targeted zinc finger-nucleases (mtZFNs) for degradation of mutant mtDNA through site-specific DNA cleavage. We have successfully used mtZFNs to target and cleave mtDNA harbouring disease-associated point mutations or large-scale deletions in vitro. More recently, we exploited a unique mouse model that recapitulates common molecular features of heteroplasmic mtDNA disease in cardiac tissue: the m.5024C>T tRNAAla mouse. Through application of mtZFN delivered systemically by adeno-associated virus (AAV), we induced specific elimination of mutant mtDNA across the heart, coupled to a reversion of molecular and biochemical phenotypes. These recent findings constitute proof of principle that mtDNA heteroplasmy correction using programmable nucleases could provide a therapeutic route for heteroplasmic mitochondrial diseases of diverse genetic origin.


Towards a HIV cure: in which cells is the virus hiding and how to inactivate integrated HIV genomes

Ostatnia modyfikacja: 
wtorek, 3 marca 2020 roku, 9:46

Speaker: prof. dr Ben Berkhout (Laboratory of Experimental Virology, Amsterdam UMC)

Talk: Towards a HIV cure: in which cells is the virus hiding and how to inactivate integrated HIV genomes

Time: 03 April 2020, 9:00 am

Venue: Intercollegiate Faculty of Biotechnology, Abrahama 58, hall 042

BBWe can successfully treat HIV-infected individuals with multiple antiviral drugs, but we cannot cure them as the virus hides in certain cells from which it rebounds after therapy is stopped. A better description of this cellular reservoir has been the Holy Grail of HIV cure research for many years. We could confirm that HIV DNA is quite profoundly enriched in a very small subset of T cells that express the CD32a marker. This is surprising as CD32a is abundantly expressed and functional as Fcgamma receptor on e.g. B cells, but there is a very small T cell subset that also express this surface marker. Thus, cure approaches should be directed towards these CD32a-positive T cells. We developed the CRISPR-Cas technology for a direct attack on the integrated HIV DNA genome. The underlying mechanism of HIV inactivation will be discussed. We propose to develop CD32a-targeting lentiviral vectors that encode these optimized CRISPR-Cas reagents.

Ben Berkhout studied molecular biology at the Leiden University (1976-1981), and obtained his PhD in 1986 at the same university on a research project concerning the regulation of gene expression in RNA bacteriophages, in particular translational control by means of RNA structure. He performed postdoctoral research at the Dana Farber Cancer Institute of the Harvard Medical School in the field of molecular immunology (1986-1989) and initiated HIV-1 research at the National Institutes of Health, Bethesda (Department of Molecular Microbiology, 1989-1991). Ben Berkhout initiated a molecular virology research line in 1991 upon his return to the Netherlands and he has been at the Academic Medical Center (AMC) of the University of Amsterdam since then. He became Head of the Laboratory of Experimental Virology and was appointed as Professor of Human Retrovirology in 2002. Ben Berkhout is editor-in-chief of Virus Research, editor for several journals (Retrovirology, Journal of Biomedical Science, Journal of Biological Chemistry, Virology Journal) and editorial board member for many more. He successfully supervised 46 PhD students and was a member of 131 other PhD thesis committees. Ben Berkhout has published over 520 peer-reviewed manuscripts on diverse topics concerning HIV-1 replication (mechanism of transcription, reverse transcription, RNA-regulated functions), virus evolution (both as a research tool and the underlying molecular mechanisms of drug-resistance), virus discovery (human coronavirus NL63), new antiviral therapeutic strategies (RNA interference, CRISPR-Cas) and HIV-1 vaccine design (improved Env protein immunogen design and conditional live-attenuated HIV-1). His work received >18,800 citations and he has an H-index of 67. Ben Berkhout received the Retrovirology Prize 2008 for his pioneering research on the structure and function of the HIV-1 RNA genome.


How photoheterotrophic bacteria can challenge our understanding of carbon cycle

Ostatnia modyfikacja: 
czwartek, 20 lutego 2020 roku, 6:54

Speaker: dr Katarzyna Piwosz (Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, Trebon)

Talk: How photoheterotrophic bacteria can challenge our understanding of carbon cycle

Time: 28 February 2020, 9:00 am

Venue: Intercollegiate Faculty of Biotechnology, Abrahama 58, hall 042

KaisaMy main scientific interest is on ecology of aquatic microorganisms. Aquatic microorganisms: bacteria, algae and heterotrophic protists, are the key players in energy transfer and element cycling in freshwater and marine habitats. These processes are vital for sustaining aquatic ecosystem and the entire biosphere. My research includes investigation of diversity, distribution, dynamics and activity of bacteria, algae and heterotrophic protists in their natural environments. I graduated from the University of Gdansk in Poland. I did my first scientific project for my master thesis at the Institute of Oceanology of the Polish Academy of Sciences. I studied diversity and distribution of algae dwelling in the Arctic Ocean. During hours spent counting different algal species under a microscope, I noticed a plethora of tiny, tiny cells that neither my supervisor, nor any other ecologists could name. This is how I became fascinated with the smallest of microorganisms, for which high quality light microscopy was not enough. Looking for the possibility to identify those cells, I read about use of molecular methods to study microbial diversity. However, to learn these techniques, I had to move to Germany, where I joined Max Planck Research School at Max Planck Institute for Marine Microbiology in Bremen (Marmic). Studying at Marmic and working on my second master thesis at the Alfred Wegener Institute for Polar and Marine Research in Bremerhaven, I learned all the theory and practice I needed to pursue my doctoral study. I returned to the Institute of Oceanology PAS, and, in cooperation with the University of Zurich, I studied small algae and protists in the Baltic Sea. The phylogenetic diversity of algae and protists in the Baltic Sea turned out to be incredible, with thousands of species present in the Gulf of Gdańsk over a year. I discovered groups of protists that no one expected to be present in the Baltic. After I accomplished my PhD, I returned to Polar Regions to answer the question from my first master project: who were the tiny tiny cells in my samples :)

During my work, I participated in scientific cruises to the Baltic Sea, Arctic Ocean and Adriatic Sea. I successfully managed five international scientific projects. I was awarded fellowships and stipends from the EMBL, FEMS, the Director of the Institute of Baltic Sea Research, Warnemünde, Swiss Foundation for Hydrobiology & Limnology, and the University of Zurich, and received four awards from the Director of National Marine Fisheries Research Institute for the publications record. I have been appointed the Ambassador for Poland by the International Society for Microbial Ecology (https://www.isme-microbes.org/). Presently I am a researcher in Institute of Microbiology of Czech Academy of Sciences. My work concentrates on role of photoheterotrophic bacteria in freshwater carbon cycle. There are two known types of photoheterotrophic bacteria: rhodopsin containing and bacteriochlorophylls containing. The former seems to be abundant but slow growing, while the letter are more rare (but still they can make up to 40% of all bacterial abundance) but fast growing, and my current focus lies on them. In my talk, I will present my research on ecology of the bacteriochlorophylls containing photoheterotrophic bacteria in freshwaters: their diversity, seasonal dynamics, activity and interaction with other microbes.  

Website:        Centre Algatech                 About me               Our Team     


Cold atmospheric pressure plasma – new challenges, new hopes

Ostatnia modyfikacja: 
czwartek, 20 lutego 2020 roku, 6:52

Speaker: prof. Paweł Pohl (Wrocław University of Science and Technology)

Talk: Cold atmospheric pressure plasma – new challenges, new hopes

Time: 13 March 2020, 09:00 am

Venue: Intercollegiate Faculty of Biotechnology, Abrahama 58, hall 042

pohlScientific interests: analytical chemistry, atomic spectrometry, optical emission spectrometry, trace analysis, elemental analysis, speciation analysis, food and environmental analytics, spectroscopic diagnostics. 

Plasma (the 4th state of matter) is an ionized gas generated by different processes, including electric discharges or nuclear reactions, and characterized by very high temperatures, i.e., 100,000 K and much more. Natural examples of plasmas are the sun, lightnings on earth, or temporary electrical discharges. Cold atmospheric pressure plasmas (CAPPs) are just partially ionized gases, and ionization degrees in this case are very small (>>0.01%). Such plasmas can be sustained at atmospheric pressure and operated at room temperature, and are characterized by relatively low temperature, or more precisely, several temperatures that are arranged in the following line: Te (electron temperature)>>Texc (excitation temperature of atoms)>Trot (rotational temperature of molecules)@Tg (kinetic temperature of gas molecules, being from few to less than 103 oC). In addition, being sustained under atmospheric pressure, CAPP is a rich source of different species, including high energy electrons, ions, excited atoms and molecules, radicals, e.g., O3, NO, NO2, NH, OH, H, UV radiation, and heat. Temperature behavior of CAPP (called non-equilibrium or non-thermal plasma, NTP) in addition to the presence of a “cocktail” of species both determine its features and phenomenal applications. The content and the type of species in CAPP may significantly vary for different sources, and hence, can be modified for specific purposes and applications, showing its great flexibility and diversity. In other words, the concentration and the inherent composition of CAPP can be designed for different intended applications. Some of these applications, including spectrochemical analysis, metallic nanoparticles synthesis, and microorganisms inactivation, will be presented in this lecture, although, it should be noted that the number of possible uses of CAPP is much higher, and go beyond human’s imagination.



RNA decay and surveillance in human mitochondria

Ostatnia modyfikacja: 
wtorek, 3 grudnia 2019 roku, 11:24

Speaker: dr hab. Roman Szczęsny (IBB PAN)

Talk: RNA decay and surveillance in human mitochondria

Time: 06 December 2019, 09:00 am

Venue: Intercollegiate Faculty of Biotechnology, Abrahama 58, hall 042

rszDr Roman Szczesny graduated from the University of Warsaw in 2004 and joined a PhD programme at the Institute of Biochemistry and Biophysics, PAS. In his thesis he showed that human RNA helicase SUV3 is an essential enzyme for decay and surveillance of mitochondrial RNA (mtRNA). He also described cell death pathways that are activated upon SUV3 silencing. During that time he received several scholarships to work in France and Finland. After obtaining his PhD, he continued to work on mtRNA decay. He supervised the project that led to the identification of the long sought mitochondrial ribonuclease – PNPase, and the discovery of new structures named D-foci where mtRNA degradation occurs. In 2009 he joined Andrzej Dziembowski’s laboratory where he studied mechanisms responsible for RNA surveillance. Having established his group at the Institute of Biochemistry and Biophysics PAS in Warsaw he continues his research into the metabolism of human mitochondrial RNA. His main focus is unraveling mitochondrial gene expression regulation by identification and functional analysis of novel factors engaged in the process. In his research he combines molecular biology, biochemistry and high-throughput methods, including genome-wide siRNA screenings, which provide broad insight into various steps of mitochondrial gene regulation.

Mitochondria are organelles present in most eukaryotic cells that play a vital role in maintaining cellular homeostasis. The function of these organelles depends on the crosstalk between two genomes: nuclear and mitochondrial. Most of the proteins present in mitochondria are encoded in the nuclear genome and are imported into mitochondria upon synthesis in the cytoplasm. Nevertheless, 13 proteins encoded within the mitochondrial genome are essential for human as they are key components of the respiratory complexes. Since human mitochondria seem to have limited possibilities to regulate gene expression by altering the transcription initiation rate, posttranscriptional processes, including RNA degradation, are of great importance for proper mitochondrial and cellular homeostasis. The machinery responsible for mitochondrial RNA decay in humans had remained unknown for many years. We have contributed significantly to the identification and description of the RNA-degradation pathways in human mitochondria. This process, its actors, as well as the consequences of its dysfunction on cellular homeostasis, will be presented.