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Our mission is to create the atmosphere for sharing integrative approaches to understand life and disease. The communication of researchers from different fields is a key.
Eli Eisenberg. An alternate route to complexity: Trade-off between transcriptome plasticity and genome evolution in cephalopods
RNA editing by adenosine deamination is well-positioned to diversify proteomes, but it is infrequently used for this purpose. We show that extensive recoding by RNA editing is an invention of the behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites, enriched in the nervous system and targets excitability and neuronal morphology. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms that accumulate in protein coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a novel strategy for neural complexity.
Tel Aviv University, Israelhttps://www.integrativebio.com.ua
Vaida Bankauskaite: European Research Council Funding Schemes
The presentation will include description of the ERC grant schemes: Starting Grant, Consolidator and Advanced Grant. It will cover the evaluation criteria, evaluation panel structure and review procedure at the ERC. Furthermore, the presentation will contain information on how to apply to the ERC. Finally, few hints on how to prepare the application will be given.
Dr Vaida Bankauskaite Scientific Officer at ERC Life Sciences
Setting things up and meeting each other. Get together in the great conference room.
The Scientific Fair: Welcome
The Scientific Fair represents a networking event for Research, Educational, and Commercial projects/companies/ideas in the fields related to the conference topics. The format of event is: 1 - Welcome - 5 min 2 - Introductory lecture 1 - 25 min 3 - Introductory lecture 2 - 40 min Discovering novel medicines in Ukraine by Sergey Zozulya, Vice President of Biology Bienta/Enamine Ltd., Kyiv, Ukraine 2 - Series of 3-5 min pitches - appr. 1 hr 3 - Free discussion, networking, and opportunity to present a stand, materials, presentations - appr. 2 hrs The list of pitches will be announced later. If you wish to join the Scientific Fair as a presenter please email to nika.biph[at]gmail.com.
The Scientific Fair
Sergey Zozulya: Discovering novel medicines in Ukraine
There is a growing trend towards downsizing of the internal discovery at big pharma. Most of the major pharmaceutical and biotech companies are considering outsourcing as a core strategy for developing their discovery pipelines. Nowadays, focused and cost-efficient Contract Research Organisations (CRO) offer greater flexibility and diversity for pharma R&D efforts. Bienta is a trademark for preclinical biology services department of Enamine, the world’s largest supplier of novel drug-like molecules for drug discovery research located in Kyiv, Ukraine. Bienta is operating as a CRO providing high-throughput pharmacological screening and comprehensive bioanalytical support of drug discovery projects, including in vitro ADMET (absorption, distribution, metabolism, excretion, toxicity) testing, pharmacokinetics, as well as toxicity and efficacy studies in animals. Tight integration with the world-class organic chemistry powerhouse allows Bienta to provide seamless and cost-efficient support throughout drug discovery and early development stages – starting with novel molecules and assay development and ending with validated, optimized drug candidates.
The Scientific Fair
Vice President of Biology Bienta/Enamine Ltd., Kyiv, Ukrainehttp://bienta.net
The Scientific Fair
Christian Popp: Max-Delbrück-Center Graduate School and MDC-NYU Exchange Programme
The MDC Graduate School has been established in cooperation with the Humboldt-Universität zu Berlin (HU), the Freie Universität Berlin (FU), and the Charité - Universitätsmedizin Berlin medical faculty. It provides a framework of structured training for doctoral researchers in the areas of Cardiovascular and Metabolic Research, Cancer Biology and Immunology, Neuroscience, Developmental Biology, Medical Systems Biology and Bioinformatics, as well as Structural Biology, Imaging and Biophysics and currently hosts over 350 PhD researchers. The MDC-NYU Exchange Program is a special program embedded in the MDC Graduate School. It is a joint endeavor between the Berlin Institute for Medical Systems Biology (MDC/BIMSB) and the Center for Genomics and Systems Biology (NYU). PhD students carry out joint research projects of partner labs in New York and Berlin. Links: https://www.mdc-berlin.de/ https://www.mdc-berlin.de/2893/de/training/phd_program https://www.mdc-berlin.de/bimsb https://www.mdc-berlin.de/14187058/en/bimsb/phd_program
The Scientific Fair
Christian Popp completed his PhD in Epigenetics at the Babraham Institute in Cambridge UK under the supervision of Wolf Reik. After a three year excursion into industry working for QIAGEN, he joined the University of Hong Kong for a postdoc in stem cell biology and epigenetic memory. He now works as science project manager at the MDC/BIMSB and is responsible for the NYU Exchange program and various other projects run at the MDC/BIMSB.https://www.mdc-berlin.de/14187058/en/bimsb/phd_program
Alyona Borovskaya: KAU – Research University of a new type
Kyiv Academic University is a pilot project of a new type intensive research university in Ukraine, involving student to the research activity on the early stage of their carrier. KAU combines the strong scientific potential of the most effective institutes of the National Academy of Sciences with the individual approach in high education for master students. Personal support for the scientific career of talented youth from elementary school to PhD level is the key idea of KAU. Study process is based on the system, which is successfully applied in such world leading schools, as CalTech and MIT.
The Scientific Fair
Oleksii Shershnov: Medical Company ILAYA. Regenerative Medicine
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Olena Yemets: BioLabTech Ltd: Our way of fostering excellence in Life Sciences’ research and practice
The advanced research and accurate diagnostics are possible if performed with high quality equipment, reagents and by skilled personnel. For more than ten years Biolabtech team strives to provide our customers with the most up-to-date and reliable solutions and tools from the world leading manufacturers such as Thermo Fisher Scientific, Cytocell, Zymo Research. In addition, our continued trainings, seminars and workshops serve to reinforce our customer’s awareness and practical skills in advanced techniques of Molecular Biology, Genetics, and Cell Technology.
Volodymyr Kravchenko: «NanoMedTech» LLC
NanoMedTech LLC is private research and development company. The main direction of company is designing of innovative drugs and diagnostic systems. We use modern analytical, microscopic, molecular biology and genetic equipment to ensure the high level of our research. The method of scanning electron microscopy with the use of high performance system allows us to focus on research and characterization of nanomaterials and biological objects with spatial resolution from 1 nm. Another direction of our company is genetic research. Modern Laboratory equipped with Next Generation Sequencing System, which gives us the possibility to explore different aims in genetics, molecular biology, biotechnology and medicine. Also, laboratory of molecular nanobiotechnology discover functions and utilization of specific biological nanovesicles – exosomes, hich have a great potential for applications as biomarkers for diagnostic, and for therapy of multiple diseases.
The Scientific Fair
Szabolcs Kokeny: Illumina Signed Distributor Agreement in Ukraine
IMG is announced as the new Channel Partner in Ukraine In spring 2017, Illumina has signed a distribution agreement with life science reagents supplier Integrated Medical Group (IMG) to distribute the firm's genomics research products in Ukraine. Illumina has made its products available on the Ukrainian market for more than 5 years but the new distributorship allows researchers to order reagents from within the country and provides them with local customer care. IMG will distribute Illumina’s full range of reagents for genomics research, particularly, next-generation sequencing in Ukraine. From now on, researchers and practitioners can take advantage of direct sales and support from Illumina, bypassing third-country mediators. Thus the industry-acclaimed products and applications based on DNA sequencing have become more affordable to Ukrainian customers.
The Scientific Fair
The Scientific Fair
Szabolcs Kokeny, PhD. Channel Partner Manager, Illuminahttps://www.illumina.com/
The Scientific Fair
Dmytro Simonov: Science in Ukrainian Society: Lost in Translation
During the past few decades the vacuum between Ukrainian scientific community and all the rest society is clearly visible. But now situation is changing and there are people and organizations that are trying to built communications between scientists and the rest of Ukrainian society. Although primary objective of Innovation House is to create friendly environment for innovations development, we understand perfectly well that science is the irreplaceable foundation for any considerable innovation. Therefore, efforts of Innovation House are aimed at science and scientific worldview promotion.
The Scientific Fair
The Scientific Fair
Michael Tulsky: Fundamental Production: From Fundamental Science to Society and Back
The Scientific Fair
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Hedwig Deubzer: Translational Neuroblastoma Research
Translational Neuroblastoma Research My laboratory pursues Translational Neuroblastoma Research. We focus on mechanisms that drive uncontrolled proliferation, mediate therapy resistance, block neuronal differentiation and promote the invasion-metastasis cascade by applying systems biology concepts to a solid basis of high-throughput molecular profiling data. Preclinical neuroblastoma models include primary neuroblastoma cell cultures, organoids and patient-derived xenografts. All research projects are directed towards providing a basis for decision-making in the rational development of novel therapeutics for the treatment of high-risk neuroblastoma patients. Drug development aspects addressed include target identification, proof of concept, tumor selectivity, extended target validation, biochemical and mechanistic cell-based assay development.
Charité Universitätsmedizin Berlin, Germany
Sergiy Klymenko: Fundamental research in clinical oncology
There are important advances made in cancer research recently based on recombinant DNA technology, genomics and protein chemistry. However, progress toward cancer prevention or cure has not been as rapid as many would like. We need to facilitate the application of fundamental scientific discoveries in clinical settings. The clinical experience of translating basic science into medical practice will be discussed in this talk.
National Research Center for Radiation Medicine, Ukraine
Oksana Sulaieva: Understanding molecular biology of thyroid cancer
High thyroid stimulating hormone (TSH) and BRAF mutations are thought to be factors promoting progression of papillary thyroid carcinoma (PTC). However, there is no data about relations between functional profile and BRAF mutation among patients with different morphological features of PTC. In this study we explored the relations between serum TSH, free T3 and T4, morphological characteristics of PTC in both BRAF positive and BRAF negative patients.
Ukrainian Research and Practical Centre of Endocrine Surgery, Ukraine
Yakov Vitrenko: Illumina platforms, solutions and pipelines for small- and mid-scale labs focusing on oncogenetics
An expanding next-generation sequencing (NGS) oncology portfolio is helping Illumina drive the revolution in cancer genomics. Our NGS technologies are among the most trusted in the world. Our sample-to-data solutions deliver high-quality, reproducible results to speed the discovery and analysis of cancer-related variants—and potentially transform the cancer care cycle. The use of Illumina benchtop instruments, such as MiSeq and NextSeq in conjunction with oncogenetic panels makes NGS affordable for any size lab.
Application scientist for Illumina NGS platforms, IMG, Kyiv, Ukrainehttp://im-group.com.ua/en/
Dimitri Zubov & Roman Vasyliev: Ukrainian biomedicinal tissue-engineered product for treatment of bone critical sized defects and AVN: manufacturing and first-in-human clinical outcomes
Based on our preclinical and pilot clinical results on use of multipotent mesenchymal stem/stromal cells (MSCs) in traumatology, our aim was to develop 3D tissue-engineered bone equivalent (3D-TEBE) technology for restoration of AVN and bone defects both in civil patients and combat related casualties. Methods. To fabricate 3D-TEBE we used devitalized allogeneic/xenogeneic bone (blocks and chips) seeded with autologous cultured cells: bone marrow-derived MSCs alone or in mix with periosteum progenitor cells (PPCs, 3:1), or with PPCs and peripheral blood endothelial progenitor cells (EPCs, 3:1:1) depending on bone defect size. Quality assurance of cell seeded 3D-TEBE was done via combined staining with FDA/PI and histological analysis. New bone formation was assessed by the radiographic examination. Results. Eighteen patients had the AVN III/IV by Steinberg, 11 of them had cystic bone reconstruction sites. In 8 patients, AVN corresponded to stage IV/V with subchondral fracture and deformation of the femoral head (26 patients in total). In AVN patients bone structure restoration was observed in 94.4% and endoprosthesis surgery was no more actual for 90.9%. Bone integrity was successfully restored in 39 combat related casualties (42 critical sized bone defects). FDA/PI staining, and histological analysis of 3D-TEBE samples showed their regular seeding with viable cells. Histological analysis of 3D-TEBE biopsies 3 months after transplantation showed their intensive remodeling and immature bone tissue formation. Conclusions. The 3D-TEBE transplantation is able to restore bone integrity and greatly reduce, as compared with conventional cure methods, patient’s rehabilitation period.
Dimitri ZUBOV, PhD, Senior Research Associate Leading Researcher, Сytogenetics laboratory, Cell & Tissue Technologies Unit State Institute of Genetic and Regenerative Medicine of National Academy of Medical Sciences of Ukraine Head of Biotechnology Laboratory ilaya.regeneration, Medical company ilaya, Kiev, Ukraine TERMIS, ISCT member Roman VASYLIEV, Researcher Сytogenetics laboratory, Cell & Tissue Technologies Unit State Institute of Genetic and Regenerative Medicine of National Academy of Medical Sciences of Ukraine Chief Biologist of the Medical company ilaya, Kiev, Ukraine TERMIS, ISSCR, ISCT member
Svitlana Drozdovska: Integrative genetic variants in Ukrainian athletes
Genetics has a great influence over components of the athletic performance such as strength, power, endurance, muscle fibre size and composition, flexibility, neuromuscular coordination, temperament and other phenotypes. Despite a relatively high heritability of athlete status, the search for genetic variants contributing to predisposition to success in certain types of sport has been a challenging task. The effect of genetic markers depends on either ethnic or specific factors of population, such as gene-gene and gene-environment interaction. The aim of the study was to investigate the association of gene polymorphisms with athlete status in Ukrainians.
Maria Obolenska: The tissue-specific triggers of IFNa neurotoxicity: bioinformatics prediction and experimental verification
The high-dose IFNA therapy is accompanied by side effects with largely undefined mechanisms of IFNA neurotoxicity. Our previous genome-wide search in rat and mouse genomes for genes containing in their promoters interferon stimulated response elements revealed new putative target genes of IFNA - Pick1, Grin3a and Gabra2, that encode correspondingly the protein kinase C binding protein which regulates the intracellular trafficking of glutamate AMPA receptor, and subunits of NMDA and GABA receptors. The goal of the study was to evaluate Pick1, Grin3a, Gabra2 mRNAs abundances and NMDA and glutamate receptors activity in mouse brain after administration of IFNA.
Lunch & Posters Discussion
ORPHEUS workshop: Supervisors’ role in success of doctoral school
Gisela Zimmermann: DAAD Research grants & DAAD-Programmes for International Cooperation with German Universities
The talk will provide a brief survey of DAAD funding opportunities for research exchange and cooperative academic projects.
DAAD Information Centre Kievhttp://www.daad.org.ua
Maksym Pogorielov. Horizon 2020 proposal: steps from idea to successful submission
Horizon 2020 proposal: steps from idea to successful submission Horizon 2020 is the biggest EU funding programme for research and innovation running from 2014 to 2020 with a €80 billion budget. Ukrainian scientists have complete access to all instruments of H2020 since 2015. Only 79 project from Ukraine supported in 2016 (for comparison – UK received 5937 projects). Current seminar aimed increasing awareness about Horizon 2020 among Ukrainian scientists and development professional competences, including topic selection, partner search and proposal writing.
Mikhail Gelfand: Three-dimensional structure and functional state of chromatin: who is the driver?
Recent advances in large-scale experimental techniques, such as RNA-Seq, ChIP-Seq, HiC and others, provide data for integrated analysis of chromatin 3D state, epigenetic markers, and gene expression. Not surprisingly, these turned out to be highly interlinked. Contacting chromatin regions tend to carry similar histone modifications and gene expression in such regions tends to be correlated. On a finer scale, topologically associating domains (TADs) also seem to depend on histone modifications and transcription. Indeed, TADs are enriched in repressive chromatin markers, wheres inter-TAD regions are enriched in active markers and highly transcribed genes. Moreover, differences in TAD structure between cell lines are accompanied by corresponding differences in transcription. These observations seem to indicate that gene active expression is the driving force behind formation of the TAD structure. Finally, there are preliminary indications that regions forming many distant contacts are also enriched in active markers and actively transcribed genes.
Institute for Information Transmission Problems, Russiahttp://www.rtcb.iitp.ru/mg_e.htm
Bartek Wilczynski: Integrating gene expression and chromatin structure for better models of gene regulation
We know that the the eukaryotic mRNA coding sequences reside on chromosomes inside a nucleus. Recent decades have brought us a wealth of information both on regulation of gene transcription as well as regulation of the chromatin state. However, usually these two issues are studied separately: either one is interested in particular chromatin effects or one studies transcription factor binding pertaining to a particular factor or a gene. Recently, due to the development of next-generation sequencing, we have seen a deluge of genomic data describing, transcription, protein binding, histone modification and (most recently) chromosomal contacts on a genome-wide scale for multiple cell types. In my talk I will discuss our recent efforts to computationally integrate these datasets and improve our understanding of regulatory processes.
Institute of Informatics, University of Warsaw, Polandhttp://regulomics.mimuw.edu.pl/~bartek/
Michal Okoniewski: Answering biological and medical questions with genomic big data
Answering biological and medical questions with genomic big data There is a group of biological and medical questions that can be answered or solved better with the use of big data approaches. The talk will present case studies of such ones: a prototype of genomic data warehouse and basics of big-data-driven nucleotide-precision RNA-seq analysis. They may lead to new types of insights, useful for medical research on the molecular level as well as in the clinical use. Such next-generation sequencing based genomics approaches are intended to bridge the gap between the large datasets and their useful interpretations in personalised medicine.
Scientific IT Services, ETH, Switzerlandhttps://www.ethz.ch/services/en/organisation/departments/it-services/people/person-detail.html?persid=207010
Dmytro Fishman: Deep Learning in Medicine and Computational Biology
Deep learning has been shown to be extremely successful in various domains from image and voice recognition to beating humans at playing games and sorting waste. A major part of this advancement is due to rich datasets available to researches in those domains. In biology the amount and the complexity of data has increased dramatically, over the past decade, making biology and medicine suitable domains for applying deep learning. At the beginning, applying even simple networks on these large amounts of biological data provided a sophisticated advantage over canonical machine learning methods. Now, new ideas were adapted from rapidly developing artificial intelligence field in order to improve the performance of deep learning models across various biological tasks, such as: genomics, medical diagnostics and biological image analysis. In this talk, we will review some of these major recent advances and discuss their potential impact on the field. The talk is based on a review paper - Computational biology - deep learning by William Jones, Kaur Alasoo, Dmytro Fishman et al. (accepted).
University of Tartu, Estonia
Alina Frolova: Integrative analysis of expression profiles in healthy and preeclampsia-affected human placenta
Preeclampsia is a multi-factorial disorder that affects 2-8% of women worldwide (Khan at al. 2006), and leading cause of maternal and perinatal mortality and morbidity. The disease is characterized by oxidative stress, elevated inflammatory response, and generalized endothelial cell dysfunction. While defective placentation is generally described as being at the root of the disease, its pathogenesis is not fully understood. Here we performed direct integration of two independent microarray datasets: third-trimester placental samples obtained after cesarean sections from preeclamptic women (n = 25) and women with uncomplicated pregnancies (n = 23) and ones from gestational age matched first-trimester pregnancies with normal uterine artery Doppler resistance indexes (n = 11).
Institute of Molecular Biology and Genetics, Ukrainehttp://sysbio.org.ua/
Anastasiia Hryhorzhevska: A Scalable Distributed Approach to Population Structure Analysis
Identification of novel disease genes is a central part of human and molecular genetics. It is a challenging task that requires large scale case-control studies, which often involve individuals from various human populations. Population structure retrieving and inferences are critical in association studies, in which population stratification can lead to inferential errors. Genotype-based clustering of individuals is an important way of summarizing the genetic similarities and differences between individuals of diverse ancestry. Typical approaches that deal with the problem consist of several time consuming pre-processing steps, such as variant filtering, LD-pruning and dimensionality reduction of genotype matrix. However, these algorithms need to be well-tuned to complete the learning process in the best possible way and considerably low computation time. Traditional parallelization strategies cannot scale with variable data sizes at runtime. To address this issue, we have developed a framework using R programming language for fine-tuning the quality-control and the classification model parameters, and a distributed computing framework for scalable stratification analysis in Apache Spark that is more effective in processing of datasets containing large number of observations (i.e. number of samples > 10, 000). Performed tests confirmed the efficiency and scalability of the presented approach. The implemented tools can also be applied to any variant data set, including data from large scale sequencing projects or custom data sets from clinical laboratories.
Lunch & Posters Discussion
Stephanie Duguez: Stratified Medicine for Motor neuron disease: identification of biomarkers specific to ALS
Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron disease with an adult onset that selectively selective degenerate the upper and lower motor neurons. It results in muscle atrophy and paralysis leading to a major disability and followed by death 3 to 5 years after the onset. Most of the cases are sporadic (approximatively 90%) while 5-10% are dominantly inherited. Its pathogenesis remains unknown, and the only drug currently available, riluzole, only modestly prolongs survival. During the last 30 years, intensive genomic research unraveled up to 30 genes associated with ALS – the most frequent being SOD1, C9ORF72, FUS, TDP43 – but all the gene mutations identified are not sufficient to explain all ALS cases. Currently, the only diagnosis and monitoring of ALS is exclusively based on clinical examination and electromyography studies, and on the exclusion of disorders mimicking ALS, such as SMA-III/IV and SBMA (spinal and bulbar muscular atrophy). In the absence of validated biomarkers, the overlapping symptoms with other diseases render ALS diagnosis often difficult, particularly early in the disease when the patient has only limited symptoms. As several studies show that motor neuron degeneration starts at the neuromuscular junction in animal models and ALS patients and as the skeletal muscle is known to have a functional secretory activity, we hypothesized that ALS muscle cells can realize vesicles such as exosomes and participate the motor neuron death. We hypothesise that altered exosome secretion influences the intercellular communication between the muscle and its environment, including motor neurons. This phenomenon occurs independently of muscle denervation and could be a key element in the disease progression.
Ulster University, Northern Irelandhttp://biomed.science.ulster.ac.uk/research-institute/stratified-medicine/staff/dr-stephanie-duguez/
William Duddy: Tailored bioinformatics tools for neuromuscular function & disease.
Most bioinformatics tools and data resources are designed to have wide application, whereas more tailored approaches can provide analyses that are adapted to specific pathologies or tissue types. We have developed several systems biology tools for neuromuscular research, accessible through the Sys-Myo website: http://sys-myo.rhcloud.com/. These tools include: (i) CellWhere - when given a list of genes/proteins, CellWhere returns a network map of gene functional associations overlaid onto a schema of the cell and its subcellular compartments. CellWhere can be used to help formulate mechanistic hypotheses and to screen data for proteins that may be at specific cell compartments. (ii) Muscle Gene Sets - public transcriptomic data are used to create lists of genes that were differentially expressed across muscle experiments and pathologies, to be used for gene enrichment testing. (iii) The Dystrophin Interactome - this tool combines public functional association data with new proteomic experimental data on the binding partners of Dystrophin, enabling exploration of the interactions of this important muscle protein with other cellular components. (iv) MyoMiner - this database summarizes gene co-expression across previous microarray studies of muscle tissues and pathologies, potentially yielding a new empirically-derived definition of functional gene clusters in muscle.
Ulster University, Northern Irelandhttp://biomed.science.ulster.ac.uk/research-institute/stratified-medicine/staff/dr-william-duddy/
Paweł Łabaj: Are we ready for personalised medicine? – urban microbiome perspective
Małopolska Center of Biotechnology, Jagiellonian University, Kraków, Poland; APART Fellow of Austrian Academy of Sciences, Vienna, Austria; Chair of Bioinformatics RG, Boku University Vienna, Austria; MetaSUB International Consortium.http://bioinf.boku.ac.at%20
ELIXIR: safeguarding the results of life science research in Europe
ELIXIR organisation is a European intergovernmental organisation that is made up of life scientists, computer scientists and support personnel. ELIXIR main goal is to help researchers take advantage of the huge amounts of data now produced in life science, so that they can gain new insights into how living organisms work in health and disease. In order to accomplish this goal, ELIXIR brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers. ELIXIR includes 21 member countries and over 180 research organisations. In this talk we are going to focus on means in which ELIXIR is contributing to life science research and how researchers can make use of these resources. Also we will discuss how other countries and Ukraine in particular can become an ELIXIR member.
Markiyan Samborskyy: Evolution of Illumina sequencing technologies and implications of reads quality and length changes for downstream data analysis.
Over the last decade there was a massive growth of the throughput of Illumina sequencing instruments, which initially was accompanied with improvement in both reads length and quality with decreasing error rates. Reads length peaked at 250 bps with average error rates at 0.05 – 0.1% achieved by MiSEQ and HiSEQ 2500 instruments in rapid run mode. Unfortunately those quality and read length trends had reversed after 2014 due to inherent limitations of the technology combined with further push to increase the raw sequence throughput and decrease the costs of manufacture.
The introduction of the two channel imaging and reduction of the read length and accuracy due to decreased dephasing compensation dynamic range when compared with four channel imaging (HiSeq and MiSeq instruments). Two channel imaging is present in NextSeq, MiniSeq and NovaSeq systems and allows to halve the number of images taken (and running time) per basepair of raw output while increasing the error rate by 3-10 fold and limiting usable read length to 130-150bp. .
The development of patterned flowcells using the ExAmp chemistry based on Recombinant Polymerase Amplification and increase of the input library quality requirements in the HiSeqX, HiSeq3000, HiSeq4000 and NovaSeq instruments. Those instruments have a much narrower input library concentration range. . Also ExAmp chemistry has higher incidence of index hopping, which can affect multiplexed RNAseq and CHIPseq analysis, unless the mitigation measure in form of dual unique indexing is taken. [3,4]
DNA Sequencing Facility, Department of Biochemistry, University of Cambridge, Cambridge, UK
(cancelled) Nikolaus Rajewsky: Regulatory RNAs & Single Cell Sequencing
Regulatory RNAs & Single Cell Sequencing In the first part of my talk I will discuss circular RNAs (circRNAs). circRNAs have recently emerged as an interesting, large class of animal RNAs with mostly unknown function. I will present loss-of-function data in mouse brain independently for two circular RNAs and describe our understanding of the molecular and functional consequences. In the second part of my talk I will present projects where we employ massively parallel, high-throughput single-cell RNA sequencing. I will present (a) the perhaps first “complete” cell/lineage atlas of a complex animal (b) (collaboration with Zinzen lab) a “virtual embryo” where we have sequenced each cell of the drosophila embryo at stage 6 and reconstructed gene expression for 8,000 genes per cell in 3-D, (c) data about single-cell sequencing of an animal germline which reveal spatial organization of functional classes of RNA.
Max Delbrück Centre for Molecular Medicine / Berlin Institute for Medical Systems Biology, Germanyhttps://www.mdc-berlin.de/1151037/en/research/research_teams/systems_biology_of_gene_regulatory_elements
Eugene Koonin: Metagenomic discovery of new viruses and antivirus defense systems
Jan Barciszewski: New catalytic RNA-based strategy for mitochondria transformation and gene regulation
New catalytic RNA-based strategy for mitochondria transformation and gene regulation K.Rolle1, E.Wyszko1, P.Głodowicz1, A. Dietrich2, J.Barciszewski1 1Institute of Bioorganic Chemistry of the Polish Academy of Sciences Noskowskiego 12/14, 61-704 Poznań,2Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général 12 Zimmer, 67084 Strasbourg, France Genetic information in eukaryotic cells is encoded within nucleus and mitochondria in non-plant organisms as well as in mitochondria and chloroplasts in plants. The phenotype of an organism is a function of all genomes expression and communication between them. Mitochondria are a factors of the energy production through oxidative phosphorylation and fatty acid beta-oxidation. They play a key role in the redox status of the cell and in signaling cascades with reactive oxygen species. Mutations in the human mitochondrial DNA result in disorders with neurological and myopatic deficits. Because of the lack oft he cures, to combat them a specific and direct regulation of a pathogenic gene or ist products is needed. The aim of the work was to develop a new and efficient tool to down regulate mitochondrial genes in human with specific catalytic ribozymes. To get that, first we designed and proved the concept in plant mitochodria. We showed that, the tRNA-like structure from the 3’ end of the Turnip yellow mosaic virus (TYMV) genomic RNA, can drive a cargo RNA into mitochondria in plant. As an initial approach for mitochondrial strategies, a transcript with trans-cleaving hammerhead ribozyme attached to the tRNA-like shuttle was expressed in transformed plants and imported into the organelles with the first directed knockdown of a mitochondrial RNA in eukaryote. With our pioneering ribozyme-based aprroach we designed the constructs with hammerhead ribozymes against atp 9 and matR mRNA sequences and introduced them into Arabidopis thaliana.. Ribozymes, designed to cleave inside both the atp9 and matR reading frame, were then driven into the organelles as “passenger” molecules with a tRNA-like shuttle. With this innovative approach for the first time we generated the mitochondrial loss-of-function plant, followed by the functional characteristics of mitochondrial gene. We showed that the matR locus encodes a mitochondrial protein, which is associated with various pre-RNAs, and that reduction in MatR expression affects the processing of a number of group II introns in Arabidopsis mitochondria.
Institute of Bioorganic Chemistry, Polandhttps://www.ibch.poznan.pl/structure/department-of-epigenetics-2/
Siegfried Labeit: Molecular Medicine of the gigantic muscle protein titin filament
Titin is the largest known protein with a molecular mass of up to 4,200,000 kDa. Its giant filamentous polypeptide chain forms an intrasarcomeric Z-disc to M-line spanning structure. Within the sarcomere, titin senses strain signals and provides biomechanical feedback to the myocyte. Recent progress indicates that mutations in the titin gene are a frequent cause for hereditary myopathies. In this presentation, recent progress on titin´s medical genetics and potentially emerging treatment strategies will be discussed.
University of Heidelberg, Germany
Oksana Piven: Adhesion proteins more than just cardiomyocytes coupling
Adhesion proteins more than just cardiomyocytes coupling The structural integrity of the heart is necessary for its function and is maintained by the intercalated discs (IDs) that comprise the end-to-end connections between myocytes. IDs consist of three main junctional complexes: adherens junctions (AJs), gap junctions and desmosomes. Each of these junctional complexes is extremely important for maintenance of normal mechanical and electrical coupling between cardiomyocytes, and therefore for normal heart function. In the heart, the AJs are comprised predominantly of N-cadherin, which is highly expressed in the developing and mature myocardium. Classical cadherins are transmembrane proteins that mediate specific cell–cell adhesion. At the cytoplasmic side of the junction, either b-catenin or plakoglobin can interact directly with a core region within the C-terminus of the cadherin cytoplasmic domain. The N-terminal ortion of b-catenin or plakoglobin interacts with a-catenin, which links this complex to the cytoskeleton. Wide known that intercellular adhesion is important for the development of any multicellular organism, but here we would like discuss other function of adherens junctions proteins in embryonic and adult heart. In our work we have focused on signalling function of b- and a-E – catenin. Beta –catenin is main transcriptional co-activator of canonical Wnt –signalling and in such way it involved in cells differentiation and proliferation control. Signalling function of a-E catenin recovered during last decades, it was shown that last one can regulate a few important signalling passway including canonical Wnt, Hippo, Hedgehog and NF-κB. Thus signalling function of b-catenin in heart is controversial and signalling function of a-E catenin is fur from understood. With conditional knockout mice using we have focused on signalling function of a E-catenin an b-catenin function in heart development and maturation. We observed the adult heart maturation delay in mice with b-catenin haploinsufficiency. Moreover, we registered fetal genes up-regulation in mutant mice together with canonical Wnt down-regulation. Our data suggest that canonical Wnt and b-catenin is highly important for new born heart maturation and terminal differentiation of cardiomyocytes. We also recovered that even basal level of canonical Wnt activity is critically important for adult heart adaptation for stress. This data supported by other experiments where we registered heart enlarged hypertrophy and heart failure in mice with a-E catenin missing. In these mice we registered higher level of b-catenin and Yap dependent transcription.
Institute of Molecular Biology and Genetics, Ukraine
Adrian Karmazyn: A New U.S.-Based Biotechnology Initiative in Support of Ukrainian Biotech
Special Advisor for Strategic Communications and Development U.S.-Ukraine Foundation
Lunch & Poster Discussion
Alex Shcheglovitov: Using iPSC-derived neurons and organoids for studying human cortical development, synapses, and synaptopathies
Using iPSC-derived neurons and organoids for studying human cortical development, synapses, and synaptopathies In my presentation, I will discuss our recent progress in the generation of human cortical neurons and organized neuronal networks from induced pluripotent stem cells.
University of Utah, USAhttp://www.shcheglovitov.com/
Svitlana Kurinna: miRNAs as new regulators of regeneration
Many patients suffer from insufficient wound healing following injuries, large-area burns, chronic diabetic sores, and aging skin fragility. The development of efficient strategies for the improvement of cutaneous repair requires understanding of the mechanisms underlying normal and impaired wound healing. Many factors can interfere with one or more phases of the cutaneous healing process, thus causing improper or impaired wound healing in patients. Recent data implicates microRNAs (miRs) as one such factor involved in wound repair. Because of the short sequence (~20 nt) and the tissue-specific activity, miRs are targets for oligonucleotide-based RNA silencing therapy. The accessibility of the skin allows local miR manipulation. Our previous work identified an important function of miR-29s in regulating desmosomes in normal and hyper-proliferative epidermis. miR-29s also regulate collagen production by fibroblasts and are a new therapeutic target in the Phase I clinical trial for cutaneous sclerosis. However, the regulation and functions of miR-29s in homeostatic and regenerating epidermis remain largely unknown. The in vivo function of miRs depends on the tissue-specific expression of RNA targets. We are using fluorescently labeled miR-29 antisense oligonucleotides with enhanced in vivo activity to track their delivery into wounds, and test the ability of antisense miR-29s to improve cutaneous wound healing. The results of this project will help developing a new miR-based approach for treatment of cutaneous wounds. In addition, it will open new avenues for the use of modified antisense oligonucleotides as a therapy for non-healing wounds and other types of skin diseases.
John L. Wallace
John L. Wallace. Hydrogen sulfide to the rescue: Trials and tribulations of translational research
Hydrogen sulfide to the rescue: Trials and tribulations of translational research Ulceration of the gastrointestinal tract by nonsteroidal anti-inflammatory drugs (NSAIDs) remains a major health problem. We have exploited the powerful protective and repair-promoting effects of hydrogen sulfide to design new NSAIDs that are safe in the GI tract. Translating our basic science research to clinical use has been exciting but very challenging.
John L. Wallace
Arnold Martin: From Sample to Insight: Simplify your lab life with Zymo Research
Today’s methods for DNA and RNA analyses get more and more sensitive. This in turn leads to the need of extraction methods which fulfill the highest standard of DNA and RNA purification. In this talk we will focus on simple solutions for the isolation of high quality DNA and RNA and we will also give an overview of methods to analyze methylated DNA.
Zymo Research Europe GmbH, Freiburg Germany
Alexander V. Zholos. Species differences in receptor-operated TRPC4 channels
The ever-growing number of sequenced animal genomes provides a wealth of information concerning not only evolutionary relations, but also molecular structure-function relations. In this talk, our recent work on receptor-operated TRPC4 channel expressed in intestinal myocytes of rodents will be discussed in the context of the role of certain naturally occurring structural differences of these channel proteins, as well as the potential issues concerning using animal models for translational research.
Taras Shevchenko National University of Kyiv, Ukraine
Bohdan Ostash. Codon usage bias as a regulatory device: lessons from GC-rich genomes
Many amino acids are encoded by more than one codon (referred to as synonymous), and so different nucleotide sequences may specify the same polypeptide. Synonymous codons are used unevenly within and across genomes, leading to codon usage bias (CUB). CUB creates a layer of auxiliary genetic information which may have significant phenotypic outcome, such as (but not limited to) altered protein folding, timing and rate of protein synthesis. In this talk I will outline different computational biology approaches that my research team applies to GC-rich genomes of Streptomyces in hope to gain new insights into origin and functional meaning of CUB. Advantages and challenges that streptomycete codon biases offer are given in comparison to popular models such as yeasts and E. coli. I will conclude the talk with description of our new research directions inspired by studies of Streptomyces CUB.
Ivan Franko National University of Lviv, Ukrainehttp://bioweb.franko.lviv.ua/genetic/teachers_/ostash.php
Oleksandr Yushchuk. Evolution of glycopeptide and moenomycin antibiotic biosynthesis pathways in bacteria
Bacterial cell wall (peptidoglycan) is one of the most successful targets for antibiotic intervention. Nowadays, when we face an unprecedented rise of multidrug resistant bacteria, cell wall active antibiotics remain the line of last defense. Humankind desperately needs new classes of antibiotics to avoid the disasters of pre-antibiotic era, and much effort is spent to develop novel compounds that act on peptidoglycan. In my talk I will present the use of molecular phylogenetic approaches to elucidate the evolution of genes for two important classes of peptidoglycan inhibitors, glycopeptides and moenomycins. Prospects of use of obtained insights for screening and generation of novel antibiotics will be outlined.
Ivan Franko National University of Lviv, Ukrainehttp://bioweb.franko.lviv.ua/genetic/post-grad_/yushchuk.php
Oleh Lushchak. From small observation to big discovery
It is always difficult to predict exciting results for great paper. More and more rich labs are using screening strategy to get ideas. These screens are time-consuming and expensive way to discover something new. There is also another way to big discoveries but they require step-by-step development of the project based on small observation the experimenter had noticed. Within my talk I will present the story built on the interesting observed unexpected phenotype. I will go through the experiments made within time period of about 5 years to show the main milestones and decisions we have made. Even when all data was generated one additional experiment forced us to look on these data completely from unexpected side.
Vasyl Stefanyk Precarpathian National University, Ukrainehttp://biochem.if.ua/index.php?option=com_content&view=article&id=124%3Alushchak-o&catid=2%3Alector2
Victoria Novitska: V-table© – an interactive tool to explore virus diversity providing a structured overview on a viral world.
Viruses are highly diverse biologic entities. They do not share a single gene, nor do they have a common origin. Viruses differ extremely in terms of genome and capsid size, as well as in host range. Taxonomy of viruses is currently undergoing massive changes, including taxa reassignment, renaming and creating new taxa of higher level from the lower ones. The number of new viral taxa is constantly growing and each new one presents another example of pushing the limits and balancing at the edge of survival by co-evolving with a host. To explore and understand the limits of different viral characteristics we first applied categorization according to the type of genome and host, as most fundamental. It allowed creation of small manageable groups related by content, instead of a long alphabetical list of all viruses. Viral family is the highest level of virus taxonomy, covering most of viral species currently recognized by International Committee on Taxonomy of Viruses. Each viral family has its unique set of characteristics and is used as unit of information in V-table. The interactive database of viruses allows observing trends in viral diversity by grouping viruses of particular type of genome and host further according to the type of capsid symmetry, size of genome and capsid. The structure of V-table is based on placing viruses with similar characteristics of genome and capsid near each other to reveal trends in viral diversity and simplify learning virology. The new approach in understanding virosphere is to combine viral taxonomy, phylogeny and molecular characteristics.
Tatiana Yakushkina: Evolutionary models with lethal mutations
Next generation sequencing is the key method for identifying genetic disorders on population scale
Using genomic tools like SNP microarrays in whole genome association studies and Next Generation Sequencing (NGS), markers and actionable genetic targets have been identified for common complex diseases, like various types of cancer, neuronal disorders or metabolic and heart diseases. These marker panels can now be used for improving diagnostic procedures, patient stratification, outcome prediction and to optimize individualized treatment strategies. In addition, we know more than 7000 rare diseases affecting all together about 7% of the total population. The WHO estimates that over 300.000.000 individuals are globally affected, predominantly children and newborns. Due to their low population penetrance (>0.05%) these disorders are very difficult to diagnose. Even in countries with a well-developed healthcare system like the USA, it takes on average 7.6 years (in UK 5.6 years) to identify rare diseases, far too long especially for newborns, that account for over 50% of the cases. Whole genome and exome sequencing, as well as sequencing large panels with known target regions can significantly speed up the identification and characterization of these rare diseases and open new options for therapy selection. These technologies supply the input of large global databases that will continuously improve and speed up the development of diagnostic and treatment procedures, using the combined resources of the global research community.
Senior product specialist, Illumina, Munich, Germany.https://www.illumina.com/
Klas Udekwu: AMR in the Built Environment Mobilome, The Stockholm Subway
Using a combination of classical microbiology and NGS, we studied the colistin resistant fraction of the BE microbiome in 20 Stockholm subway stations. This talk will highlight the methodology and partial results of a longitudinal dataset currently being assembled.
Stockholm University, Sweden
Lunch & Posters Discussion
Pavel Gol’din. Heterochrony as a driver of cetacean evolution
Fully aquatic cetaceans (whales and dolphins) evolved from semi-aquatic ancestors nearly 45 million years ago and gave a broad diversity of forms. Much of this development can be explained as heterochronies, with paedomorphosis leading as to diminishing, as to increase in body size, and peramorphosis expressing itself in bizarre structures. Initially, paedomorphosis could develop as a factor facilitating suction feeding or social interactions, whereas peramorphosis could be driven by sexual selection. A possible genomic mechanism for heterochrony may be positive selection in regulatory genes.
Schmalhausen Institute of Zoology, Ukrainehttp://www.izan.kiev.ua/eng/deps/depmorph/goldin.htm
Eugene Koonin. Evolutionary principles and concepts in the postgenomic era
The Modern Synthesis of Evolutionary Biology solidified in the 1950s, years before even the idea let alone the practice of deciphering evolutionary mechanisms and reconstructing the history of life by direct comparison of genome sequences entered the mind of evolutionary biologists. However, since the late 1990s, evolutionary genomics has been coming of age. What is the standing of the Modern Synthesis in light of evolutionary genomics? Have our concepts of evolution changed substantially? Do we need a ‘Postmodern Synthesis’? I will argue that, although the tenets of the Modern Synthesis have not been rejected, genome analysis dramatically expands the range of major evolutionary mechanisms and relevant phenomena, and changes evolutionary thinking, indeed calling for a new level of generalization. Somewhat paradoxically, it was the advent of comparative genomics, and more specifically, the drastic difference in genomic architectures of prokaryotes and eukaryotes, that brought to fore the essentiality of the population-genetic theory (largely developed by Fisher, Wright and Haldane already in the 1930s) for understanding the processes and results of evolution. As Michael Lynch paraphrased the famous motto of Dobzhansky, “Nothing in evolution makes sense except in the light of population genetics”. Indeed, comparative genomics provides ample material for testing evolutionary models that replace vague notions of selection and adaptation with concrete regimes of evolution and evolutionary parameter values. No less important, genomics has opened a widening window into the evolution of microbes and viruses that remained completely hidden in the days of the Modern Synthesis and has not contributed to the formulation of its concepts. Microbial and virus genomics reveal new evolutionary dynamics, engendered by horizontal gene flow, and the enormity of the evolutionary effects of host-parasite coevolution that was a key factor of major evolutionary transitions. The ‘Postmodern Synthesis’ of Evolutionary Biology is still in the making, but I will try to provide a general outline of its essential components.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USAhttps://www.ncbi.nlm.nih.gov/research/groups/koonin/
Poster Prize & Goodbye
Informal meetings, sightseeing walk-together, and departure
The day of departure is a good chance to walk around Kyiv, meet people, talk about impressions, discuss possible projects, and get home.
For researchers driven by passion
to solve the riddles of life and disease
- Students, PhD Students – 100 Euro
- Academy – 150 Euro
- Industry – 200 Euro
- One-day Tickets are available (you can see prices by pressing ‘Registration’ button).
- Discounts are possible for an excellent motivation letter.
- Registration & abstracts submission deadline: Spt 16, 2017
- Registration WITHOUT abstracts submission deadline: Oct 1, 2017
- Before submitting an abstract please register.
- Number of places is limited. Discounts are possible.
Registration fee covers the participation in all conference activities, conference materials, coffee-breaks and lunches.
It does NOT cover accommodation and transport costs.
If you cannot afford the full registration fee, please send a motivation letter and we may be able to offer a discount. Your motivation letter must be in English, contain information about who you are, what project(s) you are working on, your vision of this conference mission, why you need to get there, and the fee which you could afford. If you would like to be a volunteer during the conference, please mention it in your letter. Please, email your letter to Dr. Veronika Gurianova nika.biph[at]gmail.com.
– or –
GENERAL INFORMATIONAL PARTNER
Integrative Biology & Medicine will take place in Kyiv, at the Great Conference Hall of the National Academy of Sciences of Ukraine.
Address: Volodymyrska Street 55, Kyiv, Ukraine