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Post Doctoral Fellow - Livestock Genomic Analysis (Bioinformatics) in Livestock Genetics program. (Photo credit: ILRI)
JBI Award –Translation Bioinformatics
Peter Van Loo
Co-authors: Silje Nordgard, Ole Christian Lingjærde, Hege Russnes, Inga Rye, Wei Sun, Victor Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume, Charles Perou,Anne-Lise Børresen-Dale, Vessela Kristensen
Tiffani Williams creates new algorithmic tools for reconstructing the Tree of Life, which depicts the evolutionary connections among the world's species. As a scientist in bioinformatics and high-performance computing, she is working with a multidisciplinary team to build the Open Tree of Life. This project will produce the first comprehensive draft tree of all 1.8 million named species and enable community-driven updates and revisions to the tree. She has been a Radcliffe Institute Fellow, has been funded by the National Science Foundation, and has published in Science, Evolutionary Bioinformatics, and the Journal of Computational Biology. By helping identify how species are related to each other, Williams is providing a framework for a new understanding of the diversity of life and its implications in areas such as ecological health, environmental change, and human disease.
Christopher L. Barrett, Executive Director, Virginia Bioinformatics Institute/Professor of Computer Science, Virginia Tech. Dr. Barrett’s talk entitled “Massively Interactive Systems: Thinking and Deciding in the Age of Big Data"
Abstract: This talk discusses advanced computationally assisted reasoning about large interaction-dominated systems. Current questions in science, from the biochemical foundations of life to the scale of the world economy, involve details of huge numbers and levels of intricate interactions. Subtle indirect causal connections and vastly extended definitions of system boundaries dominate the immediate future of scientific research. Beyond sheer numbers of details and interactions, the systems are variously layered and structured in ways perhaps best described as networks. Interactions include, and often co-create, these morphological and dynamical features, which can interact in their own right. Such “massively interacting” systems are characterized by, among other things, large amounts of data and branching behaviors. Although the amount of associated data is large, the systems do not even begin to explore their entire phase spaces. Their study is characterized by advanced computational methods. Major methodological revisions seem to be indicated.
Heretofore unavailable and rapidly growing basic source data and increasingly powerful computing resources drive complex system science toward unprecedented detail and scale. There is no obvious reason for this direction in science to change. The cost of acquiring data has historically dominated scientific costs and shaped the research environment in terms of approaches and even questions. In the several years, as the costs of social data, biological data and physical data have plummeted on a per-unit basis and as the volume of data is growing exponentially, the cost drivers for scientific research have clearly shifted from data generation to storage and analytical computation-based methods. The research environment is rapidly being reshaped by this change and, in particular, the social and bio–sciences are revolutionized by it. Moreover, the study of socially– and biologically–coupled systems (e.g., societal infrastructures and infectious disease public health policy analysis) is in flux as computation-based methods begin to greatly expand the scope of traditional problems in revolutionary ways.
How does this situation serve to guide the development of “information portal technology” for complex system science and for decision support? An example of an approach to detailed computational analysis of social and behavioral interaction with physical and infrastructure effects in the immediate aftermath of a devastating disaster will be described in this context.
An international team led by Dr Claudia Pommerenke and Dr Cord Uphoff of the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH has identified three cell lines suitable as model system for SARS-CoV-2 research. The scientists published their findings in the renowned journal PLOS ONE (doi.org/10.1371/journal.pone.0255622). Dr Pommerenke is active in the department of Bioinformatics and Databases, Dr Uphoff works in the department of Human and Animal Cell Cultures at the DSMZ.
Cell lines are obtained from cancer cells and are established model systems in basic research. In corona research, these model systems are also used to investigate the penetration of the virus into the cell as well as the subsequent reproduction and release of virus particles, in particular under the influence of medicinal products. Until now, the scientific focus was on three cell lines, one of which stems from monkeys. "The choice of a suitable cell line is the prerequisite of basic research, because findings from animal cells can only partially be transferred to human cells and therefore to humans", stresses Dr Cord Uphoff of the Leibniz-Institute DSMZ. Together with his colleagues, the cell biologist has examined more than 300 human cancer cell lines for their suitability as model systems.
ACE-2 receptor insufficient as model system
Researchers of the DSMZ and of the Helmholtz Centre for Infection Research (HZI) were able to show that the presence of the surface proteins ACE2 and TMPRSS2 in itself is not pivotal for allowing SARS-CoV-2 to penetrate into the cell. Changes in the composition of the surface proteins, for instance by exchange of amino acids, could also have a significant impact on the uptake of the coronavirus into the cell. Other parameters such as available resources within a cell, its intrinsic immunity or pending apoptosis have to be considered as well.
CL-14, CL-40 and CAL-51 for corona research
After bioinformatic analyses, the scientists chose 29 cell lines to be exposed to SARS-CoV-2. This took place at the HZI, in the biological protection grade 3 laboratory of Dr Ulfert Rand. "Freely available data bases such as in this case the Cancer Cell Line Encyclopedia make this form of screening possible", explains bioinformatician Dr Claudia Pommerenke of the Leibniz-Institute DSMZ. "For academic staff, it means saving time and resources. They can start immediately with laboratory tests."
The results of these lab tests were however unexpected: The majority of cell lines that - due to the presence of ACE2- and TMPRSS2-receptors - should have been infected by the corona virus did not even react to it, while eleven cell lines produced only low amounts of infectious virus. Only three cell lines showed high levels of uptake, reproduction and release of corona virus particles. These were the cell lines CL-14 and CL-40 (human colon cancer cells) and CAL-51 (human breast cancer cells). "Due to their characteristics, these three cell lines are ideally suited as model system in corona research. We have done a very good job in characterising these cells, which are located in the collection of the Leibniz Institute DSMZ. They are available to order by scientists worldwide", summarizes Cord Uphoff.
More than 860 cell lines in the DSMZ collection of human and animal cell cultures
The collection of the Leibniz-Institute DSMZ contains more than 860 cell lines of human and animal origin, including the LL-100 panel. This comprises 100 different cancer cell lines from 22 tumour entities of human leukaemia and lymphoma.
Original publication
Pommerenke C., Rand U., Uphoff C., Nagel S., Zaborski M., Hauer V., Kaufmann M., Meyer C., Denkmann S., Riese P., Eschke K., Kim Y., Safranko Z.M., Kurolt I.C., Markotic A., Cicin-Sain L., Steenpass L. (2021) Identification of cell lines CL-14, CL-40 and CAL-51 as suitable models for SARS-CoV-2 infection studies. PLoS One. 2021 Aug 2;16(8):e0255622.
doi: 10.1371/journal.pone.0255622. eCollection 2021.
Press contact:
PhDr. Sven-David Müller, Head of Public Relations, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH
Phone: ++49 (0)531/2616-300
Mail: press(at)dsmz.de
About the Leibniz Institute DSMZ
The Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures is the world's most diverse collection of biological resources (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). Microorganisms and cell cultures are collected, investigated and archived at the DSMZ. As an institution of the Leibniz Association, the DSMZ with its extensive scientific services and biological resources has been a global partner for research, science and industry since 1969. The DSMZ is the first registered collection in Europe (Regulation (EU) No. 511/2014) and certified according to the quality standard ISO 9001:2015. As a patent depository, it offers the only possibility in Germany to deposit biological material in accordance with the requirements of the Budapest Treaty. In addition to scientific services, research is the second pillar of the DSMZ. The institute, located on the Science Campus Braunschweig-Süd, accommodates more than 75,000 cultures and biomaterials and has around 200 employees. www.dsmz.de ... pr-gateway.de/t/406353
Figure 2 from Evolution of Cellular Inclusions in Bietti’s Crystalline Dystrophy Published in Ophthalmology and Eye Diseases
JBI Award –Translation Bioinformatics
Peter Van Loo
Co-authors: Silje Nordgard, Ole Christian Lingjærde, Hege Russnes, Inga Rye, Wei Sun, Victor Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume, Charles Perou,Anne-Lise Børresen-Dale, Vessela Kristensen
Steve Conlan is Professor of Molecular and Cell Biology and head of Reproductive Biology and Gynaecological Oncology research at Swansea University’s College of Medicine.
Professor Conlan is also Director of Swansea University’s £22 Million Centre for NanoHealth where his interests centre around the characterisation of cellular interactions at the nanoscale.
His research focuses on the application of molecular, cellular and nano biology approaches to understanding gynaecological pathologies and he holds an honorary consultant position in the Abertawe Bro Morgannwg NHS Board.
Describing his talk, Prof Conlan says:
"The College of Medicine through Swansea University’s Centre for NanoHealth was a pioneering member of the Texas-UK Collaborative that established the original bridge between Swansea and Texas institutes including Houston Methodist Research Institute, Rice University, University of Houston and Texas A&M.
Eight years on this talk will highlight our ongoing strategic links in biomedical research including e-Health, bioinformatics, nanotoxicology, cancer epigenomics, and nano-characterisation, as well as the burgeoning area of regenerative medicine.
The talk will also highlight parallels in biomedical research innovation between Texas and Wales, where the Institute of Life Science at Swansea’s College of Medicine, continues to pave the way."
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