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Immunology and Regenerative Biology Colloquium

Date:
16
Wednesday
November
2022
Lecture / Seminar
Time: 14:00-15:00
Title: H3K9me and heterochromatin in genome stability, chromatin positioning and cell fate
Location: Max and Lillian Candiotty Building
Lecturer: Prof. Susan M. Gasser
Organizer: Department of Immunology and Regenerative Biology

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    Special guest semianr with Dr. Asaf Zviran

    Date:
    17
    Sunday
    July
    2022
    Lecture / Seminar
    Time: 14:00-15:00
    Title: Ultra-sensitive detection and monitoring of solid cancers using whole-genome mutation integration
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Dr. Asaf Zviran
    Organizer: Azrieli Institute for Systems Biology
    Abstract: Early detection of recurrence and monitoring of Molecular Residual Disease (MRD) ... Read more Early detection of recurrence and monitoring of Molecular Residual Disease (MRD) post-surgery is critical for clinical decision-making to tailor personalized treatments across solid cancers. C2i Genomics has developed an ultra-sensitive whole-genome ctDNA test, allowing extremely accurate and sensitive monitoring of patients with solid tumors. Here we present results from applying whole-genome sequencing (WGS) and identification of ctDNA across a variety of adult and pediatric solid tumors. We integrate a genome-wide mutation and copy number monitoring approach coupled with advanced signal processing and Artificial Intelligence (AI) for measuring the tumor load from low-input blood samples (~1mL of plasma) with ultra-sensitive detection. The increased sensitivity allowed clinical detection of tumor fraction down to 5*10-5 and recurrence detection sensitivity achieving >65% at the first two months after definitive treatment, enabling earlier clinical intervention for high-risk patients.
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    Genetic Factors & Long Range Circuit Dynamics Underlying Memory Processing-ZOOM

    Date:
    28
    Tuesday
    June
    2022
    Lecture / Seminar
    Time: 15:00-16:00
    Lecturer: Prof. Priya Rajasethupathy
    Organizer: Department of Brain Sciences
    Details: Zoom Link: https://weizmann.zoom.us/j/95406893197?pwd=REt5L1g3SmprMUhrK3dpUDJVeH ... Read more Zoom Link: https://weizmann.zoom.us/j/95406893197?pwd=REt5L1g3SmprMUhrK3dpUDJVeHlrZz09 Meeting ID: 954 0689 3197 Password: 750421
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    Abstract: How do fleeting molecules and dynamic neural codes enable the conversion of tr ... Read more How do fleeting molecules and dynamic neural codes enable the conversion of transient stimuli into lasting internal representations? And are there unique strategies to achieve memory on different time scales. Our lab addresses these questions by bridging functional genomics with systems neuroscience to provide cross-disciplinary insights. On one hand, we perform genetic mapping in outbred mice for unbiased discovery of genes, cell types, and circuits relevant for memory across different time scales. In parallel, we develop and apply methodologies to record and manipulate high resolution neural activity from these relevant circuits in the behaving animal. In today’s talk, I will discuss how these approaches have led to new insights into the genetic contributions and long-range circuit dynamics that facilitate both short- and long- term memory.  Zoom Link: https://weizmann.zoom.us/j/95406893197?pwd=REt5L1g3SmprMUhrK3dpUDJVeHlrZz09 Meeting ID: 954 0689 3197 Password: 750421
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    Mechanisms driving genome catastrophes in cancer

    Date:
    22
    Wednesday
    June
    2022
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Max and Lillian Candiotty Building
    Lecturer: Prof. Ofer Shoshani
    Organizer: Dwek Institute for Cancer Therapy Research
    Details: Meeting URL: https://weizmann.zoom.us/j/5065402023?pwd=a3Z6KzRCU0xJaUFoM2Y5emZwZ ... Read more Meeting URL: https://weizmann.zoom.us/j/5065402023?pwd=a3Z6KzRCU0xJaUFoM2Y5emZwZm1oZz09
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    Systems Biology & Immunology Symposium - the two worlds of Nir Friedman

    Date:
    02
    Monday
    May
    2022
    Conference
    Time: 08:00
    Location: David Lopatie Conference Centre
    Organizer: Department of Systems Immunology

    Enteroviruses hijack lipid droplets to build their replication factories

    Date:
    12
    Tuesday
    April
    2022
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Orly Laufman
    Organizer: Department of Biomolecular Sciences
    Abstract: Positive-strand RNA viruses including corona, zika and dengue are a major threat ... Read more Positive-strand RNA viruses including corona, zika and dengue are a major threat to public health. A critical step in the life cycle of all positive-strand RNA viruses is the replication of their genome on cellular membranes called replication compartments. However, the mechanisms underlying the formation of the replication compartments are not well understood. Enteroviruses are positive-strand RNA viruses that cause diverse medical complications in humans including myocarditis, meningitis and paralysis. Combining biochemistry, molecular and cellular biology approaches, we discovered that enteroviruses hijack lipid storage organelles called lipid droplets and use the lipids stored within them to generate their replication compartments. I will describe the sophisticated viral mechanisms involved in the hijack of lipid droplets and the channeling of their content to promote virus replication. Our studies illuminate the mechanisms by which positive-strand RNA viruses rewire host organelles and lipid metabolism and provide a snapshot into the complex replication program of these viruses.
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    New advances at the G-INCPM Bioinformatics unit

    Date:
    07
    Thursday
    April
    2022
    Lecture / Seminar
    Time: 09:00-10:00
    Location: ZOOM
    Lecturer: Dr. Danny Ben-Avraham
    Organizer: Department of Life Sciences Core Facilities

    The multi-scale structure of chromatin in the nucleus

    Date:
    14
    Monday
    March
    2022
    Colloquium
    Time: 11:00-12:00
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof. Yuval Garini
    Organizer: Faculty of Chemistry
    Abstract: The DNA in a human cell which is ~2 meters long is packed in a ~10 μm radius nu ... Read more The DNA in a human cell which is ~2 meters long is packed in a ~10 μm radius nucleus. It is immersed in a condensed soup of proteins, RNA and enzymes and it is highly dynamic, while it must stay organized to prevent chromosome entanglement and for ensuring proper genome expression. Studying this nanometer – micrometer scale structure requires to use both high spatial and temporal resolutions and we combine comprehensive live-cell and molecular methods. I will discuss the latest findings on the chromatin organization, the role of lamin A that we found to be of major importance and the functionality of the structure, both for physical properties, and for its functionality on gene expression.
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    Azrieli Institute for Systems Biology, guest seminar with Ahmed H. Badran

    Date:
    18
    Tuesday
    January
    2022
    Lecture / Seminar
    Time: 17:00-18:00
    Title: Teaching Old Machines New Activities: Engineering Cellular Protein Translation for New-to-Nature Functions
    Lecturer: Ahmed H. Badran, PhD
    Organizer: Azrieli Institute for Systems Biology

    MicroEco2 Microbial Ecology Symposium for Young Researchers

    Date:
    09
    Thursday
    December
    2021
    Conference
    Time: 08:00
    Location: David Lopatie Conference Centre
    Organizer: Azrieli Institute for Systems Biology

    The epigenetic landscape of cancer-associated fibroblasts

    Date:
    30
    Tuesday
    November
    2021
    Lecture / Seminar
    Time: 10:00-10:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Coral Halperin
    Organizer: Department of Biomolecular Sciences
    Abstract: Cancer cells recruit and rewire normal cells in their microenvironment to suppor ... Read more Cancer cells recruit and rewire normal cells in their microenvironment to support and protect them by creating a pro-tumorigenic tumor microenvironment (TME). We lack an overarching view of how, despite being genomically stable, stromal cells in the tumor microenvironment are heterogeneously reprogrammed across time and space to promote the evolution of aggressive disease. Recent work by us and others has shown that fibroblasts in the tumor microenvironment are transcriptionally rewired to become protumorigenic cancer associated fibroblasts (CAFs). Here we hypothesize that CAFs are epigenetically modified and that these modifications lead to deregulation of signaling pathways and transcriptional circuitries that support tumorigenic growth in the neoplastic cells. We applied a sensitive method of whole genome bisulfide sequencing on a model of triple-negative breast cancer in mice to evaluate the methylome profile of CAFs compared to normal mammary fibroblasts (NMFs). We detected global changes in DNA methylation as well as distinct changes in promoter methylation between NMFs and breast CAFs in mice. These changes inversely correlated with transcriptional changes between CAFs and NMFs. We characterized potential regulators of this process, and tested their expression in CAFs in human breast cancer patients, to confirm relevance of our findings to human disease. Our findings suggest that epigenetic alterations contribute to the transcriptional rewiring of fibroblasts to CAFs. This work presents a comprehensive map of DNA-methylation in CAFs, and reveals a previously unknown facet of the dynamic plasticity of the stroma.
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    Special Guest seminar

    Date:
    24
    Wednesday
    November
    2021
    Lecture / Seminar
    Time: 11:00
    Title: “Origin, evolution and domestication of the budding yeast S. cerevisiae”
    Location: Zoom: https://weizmann.zoom.us/j/99054616059?pwd=Vis4a1BQSnB1aUhJQ1hwN0ZwRzBqQT09 Meet ing ID: 9905 4616 059 Pas sword: 599698
    Lecturer: Prof. Gianni Liti
    Organizer: Azrieli Institute for Systems Biology

    Systematic Discovery and Characterization of Microbial Toxins

    Date:
    16
    Tuesday
    November
    2021
    Lecture / Seminar
    Time: 11:30-12:30
    Title: Guest seminar
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Asaf Levy
    Organizer: Department of Plant and Environmental Sciences
    Details: Host: David Zeevi
    Abstract: Microbes use protein toxins to kill competitors and to infect host cells. Discov ... Read more Microbes use protein toxins to kill competitors and to infect host cells. Discovering new toxins and describing their function is important to understand processes in microbial ecology and host-microbe interactions. Moreover, the toxins can be used in various applications, including drugs, pesticides, vaccines, potent enzymes, etc. We study toxins in the lab by combining large-scale computational genomics and molecular microbiology. In the talk, I will tell two recent stories from the lab on microbial toxins and their secretion systems. The first study is about the mysterious extracellular contractile injection system. This toxin delivery system evolved from a phage into a molecular weapon employed by bacteria against eukaryotic cells. In the second study, I will tell about the exciting group of polymorphic toxins. These are large toxin proteins that undergo recombination to create large diversity of antimicrobial toxins. We developed methods to discover toxins from both groups, study the ecological role of the toxins, and their molecular function. These approaches led to discovery of over 30 novel microbial toxins that we study in the lab.
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    A role for SINE-encoded RNA in neuronal regeneration?

    Date:
    15
    Tuesday
    June
    2021
    Lecture / Seminar
    Time: 10:00-10:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Indrek Koppel
    Organizer: Department of Biomolecular Sciences
    Details: Via zoom: https://weizmann.zoom.us/j/95718660413?pwd=MjFpUVBJVnNWZGpYb3FJeG1jNSt5QT09
    Abstract: B2 small noncoding RNAs are transcribed from short interspersed nuclear elements ... Read more B2 small noncoding RNAs are transcribed from short interspersed nuclear elements (SINEs), which are high copy number transposable elements in the mouse genome. B2 RNAs are upregulated upon cellular stress and may repress mRNA synthesis or affect protein translation. Surprisingly, we observed global upregulation of polyadenylated B2 RNAs in sensory neuron ganglia following periperal nerve injury. Interestingly, similar induction was not seen in optic nerve injury, a model of central nervous system injury. In this talk, I will discuss our efforts to understand the possible involvement of B2 RNAs (and their corresponding human Alu RNA analogs) in neuronal regeneration.
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    Zoom Lecture: “NMR of RNA: dynamics or in-cells”

    Date:
    06
    Thursday
    May
    2021
    Lecture / Seminar
    Time: 09:15-10:15
    Lecturer: Prof. Katja Petzold
    Organizer: Department of Molecular Chemistry and Materials Science
    Abstract: Zoom Lecture: https://weizmann.zoom.us/j/98819686427?pwd=algvMEJUNHdvaFppNS9x ... Read more Zoom Lecture: https://weizmann.zoom.us/j/98819686427?pwd=algvMEJUNHdvaFppNS9xVzlTUkhYQT09 Passcode: 551107 Many functions of RNA depend on rearrangements in secondary structure that are triggered by external factors, such as protein or small molecule binding. These transitions can feature on one hand localized structural changes in base-pairs or can be presented by a change in chemical identity of e.g. a nucleo-base tautomer. We use and develop R1ρ-relaxation-dispersion NMR methods for characterizing transient structures of RNA that exist in low abundance (populations
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    Computational protein design: basic research and applications

    Date:
    22
    Monday
    March
    2021
    Colloquium
    Time: 11:00-12:00
    Location: https://weizmann.zoom.us/j/98063488104?pwd=N3VqTC9sU1A4RHVDZ1dhOGVxbU1iUT09
    Lecturer: Prof. Sarel Fleishman
    Organizer: Faculty of Chemistry
    Abstract: Until very recently, the accuracy of protein-design calculations was considered ... Read more Until very recently, the accuracy of protein-design calculations was considered too low to enable the design of large proteins of complex fold. As a result, enzyme and binder optimization has relied on random or semi-rational mutagenesis and high-throughput screening. Our lab is developing a unique approach that combines structural bioinformatics analyses with atomistic design calculations to dramatically increase the accuracy of design calculations. Using this strategy, we have developed several general and completely automated methods for optimizing protein stability and activity. I will briefly discuss the fundamentals of this strategy and show case studies of large and complex proteins that we and our collaborators have optimized. Our lab’s long-term and still-unmet research goal is to enable the completely automated design of any biomolecular activity, and I will focus on our current research directions including the design of new enzymes and binders.
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    MicroEco 2020

    Date:
    06
    Wednesday
    January
    2021
    -
    07
    Thursday
    January
    2021
    Conference
    Time: 08:00
    Location: David Lopatie Conference Centre

    Understanding the distinctive neuronal epigenome

    Date:
    01
    Tuesday
    December
    2020
    Lecture / Seminar
    Time: 14:00
    Lecturer: Prof. Harrison Gabel
    Organizer: Department of Brain Sciences
    Details: Zoom link to join: https://weizmann.zoom.us/j/96608033618?pwd=SEdJUkR2ZzRBZ3laUU ... Read more Zoom link to join: https://weizmann.zoom.us/j/96608033618?pwd=SEdJUkR2ZzRBZ3laUUdGbWR1VFJTdz09 Meeting ID: 966 0803 3618 Password: 564068 Host: Dr. Rita Schmidt rita.schmidt@weizmann.ac.il tel: 9070
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    Abstract: Recent discoveries indicate that the genomes of mammalian neurons are enriched f ... Read more Recent discoveries indicate that the genomes of mammalian neurons are enriched for unique epigenetic modifications, including exceptionally high levels of non-CG DNA methylation. In my seminar, I will present our studies defining how a distinctive DNA methylation landscape is established in neurons and exploring how this methylation is read out to control critical gene expression programs. I will discuss the role of gene expression and genome architecture in shaping genomic profiles of non-CG methylation and highlight emerging mechanistic insights into how non-CG methylation and the Rett syndrome protein, MeCP2, work together to control transcription. Finally, I will outline growing evidence that disruption of this regulatory pathway contributes to neurodevelopmental disorders. Zoom link to join: https://weizmann.zoom.us/j/96608033618?pwd=SEdJUkR2ZzRBZ3laUUdGbWR1VFJTdz09 Meeting ID: 966 0803 3618 Password: 564068 Host: Dr. Rita Schmidt rita.schmidt@weizmann.ac.il tel: 9070
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    Reversing personalized medicine

    Date:
    10
    Thursday
    September
    2020
    Lecture / Seminar
    Time: 13:30-14:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Prof. Gal Markel
    Organizer: Department of Immunology and Regenerative Biology
    Details: the link for the lecture's zoom room https://weizmann.zoom.us/j/5065402023?pwd= ... Read more the link for the lecture's zoom room https://weizmann.zoom.us/j/5065402023?pwd=a3Z6KzRCU0xJaUFoM2Y5emZwZm1oZz09
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    Abstract: Personalized medicine in oncology is focused on fitting drugs to the appropriat ... Read more Personalized medicine in oncology is focused on fitting drugs to the appropriate patients, mainly by identifying unique mutations in tumor genomics and development of highly selective drugs. The main challenge is that the relevant populations grow smaller, while development costs are constant, leading to significant reduction in effective drug development. The immune system provides personalized anti cancer response, and immune checkpoint inhibitors enable decent responses over a wide array of tumors. The outstanding challenge is that efficacy is observed in less than a third of the patients. Here we explore strategies to alter the patient in a way that will enable standard of care immunotherapy to exert its full potential, i.e. fitting the patients to the existing immunotherapeutic medications.
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    The power of ONE: Immunology in the age of single cell genomics

    Date:
    02
    Thursday
    July
    2020
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Prof. Ido Amit
    Organizer: Dwek Institute for Cancer Therapy Research

    Frontiers in Systems Biology

    Date:
    09
    Tuesday
    June
    2020
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Lacra Bintu
    Organizer: Azrieli Institute for Systems Biology

    Cancer Research Club - Prof Dan Landau: Novel genomics perspectives on cancer evolution: from basic principles to therapeutic optimization

    Date:
    04
    Thursday
    June
    2020
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Prof. Dan Landau
    Organizer: Department of Immunology and Regenerative Biology

    Frontiers in Systems Biology

    Date:
    05
    Tuesday
    May
    2020
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Nassos Typas
    Organizer: Azrieli Institute for Systems Biology

    Frontiers in Systems Biology

    Date:
    21
    Tuesday
    April
    2020
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology

    Azrieli Institute for Systems Biology

    Date:
    04
    Wednesday
    March
    2020
    Lecture / Seminar
    Time: 14:00-15:00
    Title: “Does host-pathogen coevolution explain extraordinary genetic diversity”
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Dieter Ebert
    Organizer: Azrieli Institute for Systems Biology

    The Biological Age Concept: Predicting Healthspan and Lifespan using Genomics, Epigenomics and Proteomics from Saliva and Plasma

    Date:
    27
    Thursday
    February
    2020
    Lecture / Seminar
    Time: 14:00-15:00
    Title: Guest Talk with Prof Jaap Goudsmit
    Lecturer: Prof. Jaap Goudsmit
    Organizer: Department of Molecular Cell Biology
    Details: The Biological Age Concept: Predicting Healthspan and Lifespan using Genomics, E ... Read more The Biological Age Concept: Predicting Healthspan and Lifespan using Genomics, Epigenomics and Proteomics from Saliva and Plasma Jaap Goudsmit, MD, PhD Departments of Immunology & Infectious Diseases and Epidemiology, Harvard T.H. Chan School of Public Health The moment the first age-related disease manifests itself defines healthspan, like the moment of death does for lifespan. Lifespan and healthspan are impacted by mutations in a set of genetic loci as well as series of events afterwards impacting epigenetic changes downregulating the transcription of DNA to RNA (DNAm) or the translation of RNA to protein (microRNAs). Age, like sex, impacts lifespan most during life as a marker independent from individual age-related diseases. The length of the period after the healthspan ends is characterized by a stochastic accumulation of morbidities that each in combination or on their own can shorten lifespan. Biological age can be viewed as a metric defining the link between healthspan and lifespan. The best algorithm for biological age includes a combination of organ system markers including a marker for deterioration of the brain, which we call “Biosystem Age”, calibrated on the stringency of predicting lifespan independent of chronological age. Biosystem Age predicts healthspan as well as individual age-related diseases better than chronological age and has a very specific age-related microRNA signature. We propose that each change of events or genetic pathway during life that at first hand appears to be associated with disease or death rates is heavily influenced by Biosystem Age. We plan to test whether immune responsiveness to vaccines declining with age is dependent of Biosystem Age.
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    Assurance of Clonality Next-Generation Single-Cell Dispensing in Cell Line Development and Single-Cell Genomics

    Date:
    24
    Monday
    February
    2020
    Lecture / Seminar
    Time: 10:00-11:00
    Title: Presentation & ‘Cytena f.sight’ hands-on
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Adrian Zambrano
    Organizer: Department of Life Sciences Core Facilities

    Language of Evolution and Evolution of Language

    Date:
    23
    Sunday
    February
    2020
    -
    24
    Monday
    February
    2020
    Conference
    Time: 08:00
    Location: David Lopatie Conference Centre

    The Genomics of Fasting and Inflammation Reveals Dynamic Cooperativity Between Transcription Factors

    Date:
    09
    Sunday
    February
    2020
    Lecture / Seminar
    Time: 15:00-16:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Dr. Ido Goldstein
    Organizer: Life Sciences

    Insights into human evolution from a new high-coverage Neandertal genome and thousands of present-day human ones

    Date:
    04
    Tuesday
    February
    2020
    Lecture / Seminar
    Time: 11:30-12:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Fabrizio Mafessoni
    Organizer: Department of Plant and Environmental Sciences
    Details: Hosts: Prof. Avi Levy

    Next Gen Immunology 2020

    Date:
    02
    Sunday
    February
    2020
    -
    05
    Wednesday
    February
    2020
    Conference
    Time: 08:00
    Location: Michael Sela Adutitorium
    Organizer: Azrieli Institute for Systems Biology

    New Approaches for Structure Determination of Protein Complexes by Mass Spectrometry

    Date:
    13
    Monday
    January
    2020
    Colloquium
    Time: 11:00-12:15
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof. Vicki Wysocki
    Organizer: Faculty of Chemistry
    Abstract: Characterization of the overall topology and inter-subunit contacts of protein c ... Read more Characterization of the overall topology and inter-subunit contacts of protein complexes, and their assembly/disassembly and unfolding pathways, is critical because protein complexes regulate key biological processes, including processes important in understanding and controlling disease. Tools to address structural biology problems continue to improve. Native mass spectrometry (nMS) and associated technologies such as ion mobility are becoming an increasingly important component of the structural biology toolbox. When the mass spectrometry approach is used early or mid-course in a structural characterization project, it can provide answers quickly using small sample amounts and samples that are not fully purified. Integration of sample preparation/purification with effective dissociation methods (e.g., surface-induced dissociation), ion mobility, and computational approaches provide a MS workflow that can be enabling in biochemical, synthetic biology, and systems biology approaches. Native MS can determine whether the complex of interest exists in a single or in multiple oligomeric states and can provide characterization of topology/intersubunit connectivity, and other structural features. Beyond its strengths as a stand-alone tool, nMS can also guide and/or be integrated with other structural biology approaches such as NMR, X-ray crystallography, and cryoEM.
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    Adaptation of bacteria with CRISPR and adaptation on a rugged fitness landscape

    Date:
    06
    Monday
    January
    2020
    Lecture / Seminar
    Time: 14:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Marija Vucelja
    Organizer: Department of Physics of Complex Systems
    Abstract: I will tell you two stories of adaptation of populations aided and enriched by s ... Read more I will tell you two stories of adaptation of populations aided and enriched by statistical physics approaches. The first story is about the adaptation of bacteria with CRISPR. CRISPR-Cas is a famous biology buzz word, due to its applications to gene editing. However, CRISPR-Cas is also a prokaryote immune system. It works as a “library” of previous infections. This library contains snippets of exogenous genetic material. With a new infection, the library is consulted, and if a match is found, the attempt will be made to neutralize the intruding genome. Bacteria use CRISPR-Cas as an immune system against phages and plasmids. Such immunity is hereditary and dynamic — it can be gained and lost during the lifetime of the single bacteria. Also, the process of acquiring snippets when exposed to the same phage is stochastic, and the same strain bacteria in a population contain different CRISPR loci content and thus variable immunity to the phage. We use dynamical systems approaches to predict the shape of this diverse distribution of CRISPR loci content within a bacterial population as a function of two crucial parameters — the rate of acquisition and the immunity to the phage. The second story is about adaptation on a rugged fitness landscape. A crude measure of adaption to a new environment called fitness. Often one defines fitness as the expected growth rate. The higher the fitness, the more thriving is a population. What happens over long times for a population with a finite genome — when all beneficial, fitness mutations, are exhausted? Contrary to expectations, the experiments show that fitness does not reach a plateau. Here we introduce a spin-glass microscopic model, where a genome can be represented as a spin configuration, and individual spins are genes. The fitness plays the role of minus the Hamiltonian of the system. We use numerical approaches and estimates to study hopping between metastable states on a rugged fitness landscape. We show that with gene interactions (interacting spins), double beneficial mutations (flipping of pairs of spins) can lead to a slow, logarithmic increase of fitness in a wide class of cases.
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    Adaptation of bacteria with CRISPR and adaptation on a rugged fitness landscape

    Date:
    06
    Monday
    January
    2020
    Lecture / Seminar
    Time: 14:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Marija Vucelja
    Organizer: Department of Physics of Complex Systems
    Abstract: I will tell you two stories of adaptation of populations aided and enriched by s ... Read more I will tell you two stories of adaptation of populations aided and enriched by statistical physics approaches. The first story is about the adaptation of bacteria with CRISPR. CRISPR-Cas is a famous biology buzz word, due to its applications to gene editing. However, CRISPR-Cas is also a prokaryote immune system. It works as a “library” of previous infections. This library contains snippets of exogenous genetic material. With a new infection, the library is consulted, and if a match is found, the attempt will be made to neutralize the intruding genome. Bacteria use CRISPR-Cas as an immune system against phages and plasmids. Such immunity is hereditary and dynamic — it can be gained and lost during the lifetime of the single bacteria. Also, the process of acquiring snippets when exposed to the same phage is stochastic, and the same strain bacteria in a population contain different CRISPR loci content and thus variable immunity to the phage. We use dynamical systems approaches to predict the shape of this diverse distribution of CRISPR loci content within a bacterial population as a function of two crucial parameters — the rate of acquisition and the immunity to the phage. The second story is about adaptation on a rugged fitness landscape. A crude measure of adaption to a new environment called fitness. Often one defines fitness as the expected growth rate. The higher the fitness, the more thriving is a population. What happens over long times for a population with a finite genome — when all beneficial, fitness mutations, are exhausted? Contrary to expectations, the experiments show that fitness does not reach a plateau. Here we introduce a spin-glass microscopic model, where a genome can be represented as a spin configuration, and individual spins are genes. The fitness plays the role of minus the Hamiltonian of the system. We use numerical approaches and estimates to study hopping between metastable states on a rugged fitness landscape. We show that with gene interactions (interacting spins), double beneficial mutations (flipping of pairs of spins) can lead to a slow, logarithmic increase of fitness in a wide class of cases.
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    How ancient genomes aid in tracing human mobility and disease

    Date:
    02
    Thursday
    January
    2020
    Lecture / Seminar
    Time: 11:30-12:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Michal Feldman
    Abstract: Recent technological advances such as next-generation sequencing and new capture ... Read more Recent technological advances such as next-generation sequencing and new capture and sampling techniques have enabled the retrieval of genomic information from archaeological human remains, even from regions previously known to have poor conditions for DNA preservation, such as the Near East. I will describe two studies in which these methods helped us in recording the past by tracing human mobility and disease. In the first study, we retrieved a high-coverage Y. pestis genome from the remains of a 6th century victim of the Justinianic Plague, the first of three historic pandemics caused by Y. pestis. The results confirmed a central or south Asian origin of the strain and demonstrated its presence in rural south Germany where no historical source records it. In a second study, genome-wide data was reconstructed from human remains recovered from the ancient seaport of Ashkelon, identified as “Philistine” during the Iron Age. The comparison of Bronze and Iron Age individuals was used to address whether the cultural transition observed in the archaeological record was mirrored by a foreign genetic influx.
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    The LSCF Bioinformatics Unit Achievements & Challenges

    Date:
    02
    Thursday
    January
    2020
    Lecture / Seminar
    Time: 09:00-10:00
    Title: LSCF departmental seminar
    Location: Max and Lillian Candiotty Building
    Lecturer: Dr. Dena Leshkowitz
    Organizer: Department of Life Sciences Core Facilities

    5th round of Systems Biology Innovative Student-Awards Series

    Date:
    16
    Sunday
    September
    2018
    Conference
    Time: 09:30-14:00
    Location: Botnar auditorium, Belfer Bldg.
    Organizer: Azrieli Institute for Systems Biology

    From Statistical Mechanics to Cancer Genomics

    Date:
    16
    Tuesday
    May
    2017
    -
    17
    Wednesday
    May
    2017
    Retreat
    Time: 09:00 - 18:00
    Location: Weissman Auditorium, Physics Building
    Organizer: Department of Physics of Complex Systems

    System Biology Symposium

    Date:
    15
    Sunday
    January
    2017
    Retreat
    Time: 00:00
    Location: Ein-Gedi
    Organizer: Department of Computer Science and Applied Mathematics