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AI (R)Evolution in Chemistry and Physics

Date:
12
Monday
February
2024
Colloquium
Time: 11:00-12:15
Title: Annual Pearlman Lecture
Location: Gerhard M.J. Schmidt Lecture Hall
Lecturer: Prof. Alexandre Tkatchenko
Organizer: Department of Molecular Chemistry and Materials Science
Contact: sarah.amzallag@weizmann.ac.il
Abstract: Learning from data has led to paradigm shifts in a multitude of disciplines, inc ... Read more Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search and generation, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding (quantum) molecules and materials? Aiming towards a unified machine learning (ML) model of molecular interactions in chemical space, I will discuss the potential and challenges for using ML techniques in chemistry and physics. ML methods can not only accurately estimate molecular properties of large datasets, but they can also lead to new insights into chemical similarity, aromaticity, reactivity, and molecular dynamics. For example, the combination of reliable molecular data with ML methods has enabled a fully quantitative simulation of protein dynamics in water (https://arxiv.org/abs/2205.08306). While the potential of machine learning for revealing insights into molecules and materials is high, I will conclude my talk by discussing the many remaining challenges.
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AI (R)Evolution in Chemistry and Physics Colloquium website

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    10x genomics User Group Meeting 2023

    Date:
    23
    Monday
    October
    2023
    Conference
    Time: 08:00
    Location: Dolfi and Lola Ebner Auditorium
    Contact: hadas.keren-shaul@weizmann.ac.il

    Systems Biology Seminar 2022-2023

    Date:
    24
    Monday
    July
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Systems Biology Seminar 2022-2023

    Date:
    10
    Monday
    July
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Localized but not Systemic Type I Interferon Therapy Improves Immune Infiltration and PD-blockade in a Mouse Melanoma Model

    Date:
    27
    Tuesday
    June
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Daniel Harari
    Organizer: Department of Biomolecular Sciences
    Contact: levana.ayvazo@weizmann.ac.il
    Abstract: Daniel Harari 1, Ron Rotkopf 2, Shlomit Reich-Zeliger 3, Mathumathi Krishnamohan ... Read more Daniel Harari 1, Ron Rotkopf 2, Shlomit Reich-Zeliger 3, Mathumathi Krishnamohan 1, Alona Dov 1, Vladislav Volchinski 1 and Gideon Schreiber 1 1. Dept. Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel 2. Bioinformatics Unit, The Weizmann Institute of Science 3. Dept. Immunology, The Weizmann Institute of Science Transcriptomic analysis of tumor biopsies from metastatic melanoma patients (SKCM-TCGA) demonstrates a profound survival advantage for approximately one-third of patients who exhibit the highest levels of intratumoral type I Interferon (IFN-I) signaling (Hazard Ratio 0.36; Pr: 4E-06), these which coincide with a sharp increase in transcripts indicating infiltration of CD4-T, CD8-T, B-cells and Macrophages to the tumors. Pathway analysis furthermore demonstrates that these patients exhibit T- and B-cell activation and a Th-1 response. To test if IFN-I signaling is central to and not simply correlating with these associated factors, we employed an adeno-associated virus (AAV) delivery system, locally expressing mouse IFNβ in B16F10 cells grafted into congenic C57BL/6 mice, this a known cold tumor model particularly hard to treat. Whereas anti-PDL1 monotherapy had no response in this model, combination therapy slowed, and in some cases cleared the mice of tumors. AAV-IFNβ monotherapy alone can slow but will not cure the mice. In sharp contrast to localized IFN delivery, systemic IFN therapy showed no beneficial effects in slowing tumor growth. To examine this more deeply, we injected the mice bilaterally with B16F10 tumors, where one tumor received AAV- IFNβ and the contralateral tumor received control. Both the injected and contralateral tumors nevertheless demonstrated a large reduction in tumor size, this effect lost when repeated using IFNAR2 knockout mice. Furthermore both the IFN-treated and contralateral tumors exhibited a large increase in CD3+CD4+ and CD3+CD4- lymphocytes. We submit that enforcing localized IFN-I signaling to a tumor in melanoma can drive immune cell infiltration, with the potential to elicit a systemic immune response, and possibly even cure, particularly when used in combination with immune checkpoint inhibitors.
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    Systems Biology Seminar 2022-2023

    Date:
    26
    Monday
    June
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Systems Biology Seminar 2022-2023

    Date:
    12
    Monday
    June
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Systems Biology Seminar 2022-2023

    Date:
    29
    Monday
    May
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Systems Biology Seminar 2022-2023

    Date:
    15
    Monday
    May
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Deciphering microbial gene functions: insights from large-scale (meta)genomics

    Date:
    09
    Tuesday
    May
    2023
    Lecture / Seminar
    Time: 11:30-12:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. David Burstein
    Organizer: Department of Plant and Environmental Sciences
    Contact: david.zeevi@weizmann.ac.il

    Systems Biology Seminar

    Date:
    01
    Monday
    May
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Systems Biology Seminar 2022-2023

    Date:
    01
    Monday
    May
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Systems Biology Seminar 2022-2023

    Date:
    27
    Monday
    March
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Systems Biology Seminar 2022-2023

    Date:
    13
    Monday
    March
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Systems Biology Seminar 2022-2023

    Date:
    16
    Monday
    January
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    The power of ONE: Immunology in the age of single cell genomics

    Date:
    05
    Thursday
    January
    2023
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Max and Lillian Candiotty Building
    Lecturer: Prof. Ido Amit
    Organizer: Dwek Institute for Cancer Therapy Research
    Contact: michal.av@weizmann.ac.il
    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 Seminar 2022-2023

    Date:
    02
    Monday
    January
    2023
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology
    Contact: esther.weindling@weizmann.ac.il

    Biosynthesis of Plant Natural Products: from the Colours of Beet to Defences in Wheat

    Date:
    27
    Tuesday
    December
    2022
    Lecture / Seminar
    Time: 11:30-12:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Guy Polturak
    Organizer: Department of Plant and Environmental Sciences
    Contact: david.zeevi@weizmann.ac.il
    Abstract: Plants produce a vast range of specialized metabolites that serve various roles, ... Read more Plants produce a vast range of specialized metabolites that serve various roles, including mediating interactions with their immediate environments and providing defence against (a)biotic stresses. The ‘omics era’ has brought a new golden age for plant specialized metabolism research, vastly accelerating the discovery of novel metabolites and our understanding of their biosynthesis, roles and regulation. Two studies exemplifying omics-driven discovery of metabolic pathways, in beet and in wheat, will be presented: 1. Betalains are red-violet and yellow pigments restricted to order Caryophyllales, which have attracted interest due to their health-promoting properties and use as food colorants. Transcriptomics-led discovery of enzymes catalyzing the last unknown step in betalain biosynthesis in red beet enabled us to heterologously produce these pigments in plants and microbes, providing a valuable platform for studying their in-planta roles and enabling their subsequent utilization as reporter genes and plant transformation markers. 2. Wheat is one of the most widely grown crops in the world but is susceptible to numerous pests and pathogens, leading to major annual losses. Despite its agricultural importance, current knowledge of wheat chemical defenses remains very limited. Using a genome mining approach we uncovered six previously unknown pathogen-induced metabolic pathways in hexaploid bread wheat, which produce a diverse set of molecules and are encoded by biosynthetic gene clusters. Discovery and characterization of these cluster-encoded metabolic pathways provides key insights into the molecular basis of biotic stress responses in wheat, thus opening new potential avenues for improvement of this major food crop.
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    RNA-Lipid Nanoparticles 2.0: From Gene Silencing to Genome Editing

    Date:
    25
    Sunday
    December
    2022
    Lecture / Seminar
    Time: 11:00-12:00
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Dan Peer
    Organizer: Department of Molecular Chemistry and Materials Science
    Contact: ana.naamat@weizmann.ac.il
    Abstract: Accumulating work points out relevant genes and signaling pathways hampered in h ... Read more Accumulating work points out relevant genes and signaling pathways hampered in human disorders as potential candidates for therapeutics. Developing nucleic acid-based tools to manipulate gene expression, such as siRNAs, mRNA and genome editing strategies, open up opportunities for personalized medicine. Yet, although major progress was achieved in developing RNA targeted delivery carriers, mainly by utilizing monoclonal antibodies (mAbs) for targeting, their clinical translation has not occurred. In part because of massive development and production requirements and high batch-to-batch variability of current technologies, which relies on chemical conjugation. Here we present a self-assembled modular platform that enables to construct theoretically unlimited repertoire of RNA targeted carriers. The platform self-assembly is based on a membrane-anchored lipoprotein, incorporated into RNA-loaded novel, unique lipid nanoparticles that interact with the antibody Fc domain. We show that a simple switch of 8 different mAbs, redirects specific uptake of siRNAs by diverse leukocyte subsets in vivo. The platform therapeutic potential is demonstrated in an inflammatory bowel disease model, by targeting colon macrophages to reduce inflammatory symptoms, and in Mantle Cell Lymphoma xenograft model, by targeting cancer cells to induce cell death and improve survival. In addition, I will discuss novel approach for delivering modified mRNA to specific cell types in vivo utilizing this platform. I will also share some data on mRNA vaccines for COVID19 and Finally, I will share new data showing very high efficiency genome editing in glioma and metastatic ovarian cancer. This modular delivery platform can serve as a milestone in turning precision medicine feasible.
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    Using genomics to investigate radiation-related thyroid cancer following the Chernobyl accident in 1986

    Date:
    13
    Tuesday
    December
    2022
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Max and Lillian Candiotty Building
    Lecturer: Stephen J. Chanock, M.D.
    Organizer: Dwek Institute for Cancer Therapy Research
    Contact: michal.av@weizmann.ac.il
    Details: https://weizmann.zoom.us/j/5065402023?pwd=a3Z6KzRCU0xJaUFoM2Y5emZwZm1oZz09

    M.Sc thesis defense: "Self-Integrating Memories Based on Guided Nanowires"

    Date:
    24
    Thursday
    November
    2022
    Lecture / Seminar
    Time: 11:00-12:00
    Location: Helen and Milton A. Kimmelman Building
    Lecturer: Omri Ron
    Organizer: Department of Molecular Chemistry and Materials Science
    Contact: ana.naamat@weizmann.ac.il
    Abstract: Neuromorphic computing designs have an important role in the modern ‘big data ... Read more Neuromorphic computing designs have an important role in the modern ‘big data’ era, as they are suitable for processing large amount of information in short time, eliminating the von Neumann (VN) bottleneck. The neuromorphic hardware, taking its inspiration from the human brain, is designed to be used for artificial intelligence tasks via physical neural networks, such as speech or image recognition, bioinformatics, visual art processing and much more. The memristor (memory + resistor), is one of the promising building blocks for this hardware, as it mimics the behavior of a human synapse, and can be used as an analog non-volatile memory. The memristor has been proven as a viable memory element and has been used for constructing resistive random access memory (RRAM) as a replacement for current VN hardware. However, the mechanism of operation and the conducting bridge formation mechanisms in electrochemical metallization memristors still require further investigation. A planar single-nanowire (NW) based memristor is a good solution for elucidating the mechanism of operation, thanks to the high localization of switching events, allowing in-situ investigation as well as post-process analysis. Our group, which has developed the guided-growth approach to grow guided planar NWs on different substrates, has used this method to integrate guided epitaxial NWs into functional devices such as field-effect transistors (FETs), photodetectors and even address decoders. However, the guided-growth approach has not been used for creating memristors up to date. In this work, I successfully synthesized guided NWs of two metal-oxides on flat and faceted sapphire substrates – ZnO and β-Ga2O3 were successfully grown in the VLS mechanism as surface guided NWs. I successfully grew planar guided β-Ga2O3 NWs on six different sapphire substrates, for the first time as far as we know. We characterized the newly grown β-Ga2O3 NWs with SEM, TEM, EDS and Raman spectroscopy. The monoclinic NWs grew along surprising directions on the flat sapphire surfaces and I demonstrated a new mode of growth – epitaxy favored growth on a faceted surface, when graphoepitaxy is also possible. I created electrochemical metallization memristors with the obtained NWs and successfully demonstrated the effect of resistive switching for β-Ga2O3 guided NW based devices. With the abovementioned achievements, we expanded the guided-growth approach on flat and faceted sapphire surfaces, and opened the opportunity for creating surface guided-NW based neuromorphic hardware.
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    Immunology and Regenerative Biology Colloquium

    Date:
    17
    Thursday
    November
    2022
    Lecture / Seminar
    Time: 10:00-11:00
    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
    Contact: efrat.shema@weizmann.ac.il

    iSCAR seminar

    Date:
    10
    Thursday
    November
    2022
    Lecture / Seminar
    Time: 09:00-10:00
    Title: "Genome Stability in Reproduction and Aging: new insights from C. elegans"
    Location: Max and Lillian Candiotty Building
    Lecturer: Prof. Bjorn Schumacher
    Organizer: Department of Immunology and Regenerative Biology
    Contact: karina.yaniv@weizmann.ac.il

    “The immune system of bacteria: Beyond CRISPR”

    Date:
    08
    Tuesday
    November
    2022
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Prof. Rotem Sorek
    Organizer: Department of Biomolecular Sciences
    Contact: levana.ayvazo@weizmann.ac.il
    Abstract: The arms race between bacteria and phages led to the development of sophisticate ... Read more The arms race between bacteria and phages led to the development of sophisticated anti-phage defense systems, including CRISPR-Cas and restriction systems. We have recently reported that the microbial pan-genome contains many new defense systems whose function was so far unexplored. The talk will describe the functions of recently discovered new anti-phage systems. These include systems that utilize secondary metabolites for intracellular or as chemical defense against phages. Surprisingly, our studies show that bacterial defense from phage gave rise to key components in the eukaryotic immune system.
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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
    Contact: sandra.britton@weizmann.ac.il
    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
    Contact: naomi.moses@weizmann.ac.il
    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
    Contact: michal.av@weizmann.ac.il
    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
    Contact: s.jung@weizmann.ac.il

    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
    Contact: levana.ayvazo@weizmann.ac.il
    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
    Contact: dan.ben-avraham@weizmann.ac.il
    Gallery: New advances at the G-INCPM Bioinformatics unit Gallery
    New advances at the G-INCPM Bioinformatics unit Lecture / Seminar website

    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
    Contact: sarah.amzallag@weizmann.ac.il
    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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    The multi-scale structure of chromatin in the nucleus Colloquium website

    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
    Contact: sandra.britton@weizmann.ac.il

    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
    Contact: noa.barak@weizmann.ac.il
    MicroEco2 Microbial Ecology Symposium for Young Researchers Conference website

    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
    Contact: levana.ayvazo@weizmann.ac.il
    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
    Contact: evi.ben-ami@weizmnn.ac.il

    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
    Contact: david.zeevi@weizmann.ac.il
    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
    Contact: levana.ayvazo@weizmann.ac.il
    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
    Contact: ana.naamat@weizmann.ac.il
    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
    Contact: sarah.amzallag@weizmann.ac.il
    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
    Contact: microeco2020@gmail.com
    MicroEco 2020 Conference website

    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
    Contact: Ingrid.lehrer@weizmann.ac.il

    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
    Contact: hilla.kriskin@weizmann.ac.il