LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Back to previous search Search history
Advanced search

Your last searches

  1. AU="Nir Friedman"
  2. AU="Le Jeune, Sylvain"
  3. AU="Phillips, Catherine L"
  4. AU="Galindo-Riera, Natalia"
  5. AU="Daniel, Roy Thomas"
  6. AU="Hesselink, Matthijs K C"
  7. AU=Kwong Kenneth K
  8. AU="Quintero, Luis"
  9. AU=Johnson Benjamin W.

Search results

Result 1 - 10 of total 37

Search options

  1. Article ; Online: Quantifying changes in the T cell receptor repertoire during thymic development

    Francesco Camaglia / Arie Ryvkin / Erez Greenstein / Shlomit Reich-Zeliger / Benny Chain / Thierry Mora / Aleksandra M Walczak / Nir Friedman

    eLife, Vol

    2023  Volume 12

    Abstract: One of the feats of adaptive immunity is its ability to recognize foreign pathogens while sparing the self. During maturation in the thymus, T cells are selected through the binding properties of their antigen-specific T-cell receptor (TCR), through the ... ...

    Abstract One of the feats of adaptive immunity is its ability to recognize foreign pathogens while sparing the self. During maturation in the thymus, T cells are selected through the binding properties of their antigen-specific T-cell receptor (TCR), through the elimination of both weakly (positive selection) and strongly (negative selection) self-reactive receptors. However, the impact of thymic selection on the TCR repertoire is poorly understood. Here, we use transgenic Nur77-mice expressing a T-cell activation reporter to study the repertoires of thymic T cells at various stages of their development, including cells that do not pass selection. We combine high-throughput repertoire sequencing with statistical inference techniques to characterize the selection of the TCR in these distinct subsets. We find small but significant differences in the TCR repertoire parameters between the maturation stages, which recapitulate known differentiation pathways leading to the CD4+ and CD8+ subtypes. These differences can be simulated by simple models of selection acting linearly on the sequence features. We find no evidence of specific sequences or sequence motifs or features that are suppressed by negative selection. These results favour a collective or statistical model for T-cell self non-self discrimination, where negative selection biases the repertoire away from self recognition, rather than ensuring lack of self-reactivity at the single-cell level.
    Keywords thymic selection ; immune repertoires ; statistical analysis ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle

    Haiyue Liu / Roberto Arsiè / Daniel Schwabe / Marcel Schilling / Igor Minia / Jonathan Alles / Anastasiya Boltengagen / Christine Kocks / Martin Falcke / Nir Friedman / Markus Landthaler / Nikolaus Rajewsky

    Molecular Systems Biology, Vol 19, Iss 10, Pp n/a-n/a (2023)

    2023  

    Abstract: Abstract RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation. To date, little is known about time‐dependent kinetic rates during dynamic processes. Here, we present SLAM‐ ... ...

    Abstract Abstract RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation. To date, little is known about time‐dependent kinetic rates during dynamic processes. Here, we present SLAM‐Drop‐seq, a method that combines RNA metabolic labeling and alkylation of modified nucleotides in methanol‐fixed cells with droplet‐based sequencing to detect newly synthesized and preexisting mRNAs in single cells. As a first application, we sequenced 7280 HEK293 cells and calculated gene‐specific kinetic rates during the cell cycle using the novel package Eskrate. Of the 377 robust‐cycling genes that we identified, only a minor fraction is regulated solely by either dynamic transcription or degradation (6 and 4%, respectively). By contrast, the vast majority (89%) exhibit dynamically regulated transcription and degradation rates during the cell cycle. Our study thus shows that temporally regulated mRNA degradation is fundamental for the correct expression of a majority of cycling genes. SLAM‐Drop‐seq, combined with Eskrate, is a powerful approach to understanding the underlying mRNA kinetics of single‐cell gene expression dynamics in continuous biological processes.
    Keywords cell cycle ; mRNA kinetics ; single cells ; temporal regulation ; transcription and degradation ; Biology (General) ; QH301-705.5 ; Medicine (General) ; R5-920
    Subject code 612
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: Genetic screen of the yeast environmental stress response dynamics uncovers distinct regulatory phases

    Jenia Gutin / Daphna Joseph‐Strauss / Amit Sadeh / Eli Shalom / Nir Friedman

    Molecular Systems Biology, Vol 15, Iss 8, Pp n/a-n/a (2019)

    2019  

    Abstract: Abstract Cells respond to environmental fluctuations by regulating multiple transcriptional programs. This response can be studied by measuring the effect of environmental changes on the transcriptome or the proteome of the cell at the end of the ... ...

    Abstract Abstract Cells respond to environmental fluctuations by regulating multiple transcriptional programs. This response can be studied by measuring the effect of environmental changes on the transcriptome or the proteome of the cell at the end of the response. However, the dynamics of the response reflect the working of the regulatory mechanisms in action. Here, we utilized a fluorescent stress reporter gene to track the dynamics of protein production in yeast responding to environmental stress. The response is modulated by changes in both the duration and rate of transcription. We probed the underlying molecular pathways controlling these two dimensions using a library of ~1,600 single‐ and double‐mutant strains. Dissection of the effects of these mutants and the interactions between them identified distinct modulators of response duration and response rate. Using a combination of mRNA‐seq and live‐cell microscopy, we uncover mechanisms by which Msn2/4, Mck1, Msn5, and the cAMP/PKA pathway modulate the response of a large module of stress‐induced genes in two discrete regulatory phases. Our results and analysis show that transcriptional stress response is regulated by multiple mechanisms that overlap in time and cellular location.
    Keywords budding yeast ; dynamics of transcriptional response to stress ; genetic interactions ; Msn2 and Msn4 ; signaling pathways ; Biology (General) ; QH301-705.5 ; Medicine (General) ; R5-920
    Subject code 570
    Language English
    Publishing date 2019-08-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Conserved degronome features governing quality control associated proteolysis

    Bayan Mashahreh / Shir Armony / Kristoffer Enøe Johansson / Alon Chappleboim / Nir Friedman / Richard G. Gardner / Rasmus Hartmann-Petersen / Kresten Lindorff-Larsen / Tommer Ravid

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 13

    Abstract: How misfolded proteins are selected by the ubiquitin-conjugating system for elimination is largely unknown. Here, the authors identify conserved features of proteome-derived degradation signals, including amino acid and structural preferences, that ... ...

    Abstract How misfolded proteins are selected by the ubiquitin-conjugating system for elimination is largely unknown. Here, the authors identify conserved features of proteome-derived degradation signals, including amino acid and structural preferences, that trigger quality-control-associated proteolysis.
    Keywords Science ; Q
    Language English
    Publishing date 2022-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma

    Miriam I. Rosenberg / Erez Greenstein / Martin Buchkovich / Ayelet Peres / Eric Santoni-Rugiu / Lei Yang / Martin Mikl / Zalman Vaksman / David L. Gibbs / Dan Reshef / Amy Salovin / Meredith S. Irwin / Arlene Naranjo / Igor Ulitsky / Pedro A. de Alarcon / Katherine K. Matthay / Victor Weigman / Gur Yaari / Jessica A. Panzer /
    Nir Friedman / John M. Maris

    Cell Reports, Vol 42, Iss 8, Pp 112879- (2023)

    2023  

    Abstract: Summary: Neuroblastoma is a lethal childhood solid tumor of developing peripheral nerves. Two percent of children with neuroblastoma develop opsoclonus myoclonus ataxia syndrome (OMAS), a paraneoplastic disease characterized by cerebellar and brainstem- ... ...

    Abstract Summary: Neuroblastoma is a lethal childhood solid tumor of developing peripheral nerves. Two percent of children with neuroblastoma develop opsoclonus myoclonus ataxia syndrome (OMAS), a paraneoplastic disease characterized by cerebellar and brainstem-directed autoimmunity but typically with outstanding cancer-related outcomes. We compared tumor transcriptomes and tumor-infiltrating T and B cell repertoires from 38 OMAS subjects with neuroblastoma to 26 non-OMAS-associated neuroblastomas. We found greater B and T cell infiltration in OMAS-associated tumors compared to controls and showed that both were polyclonal expansions. Tertiary lymphoid structures (TLSs) were enriched in OMAS-associated tumors. We identified significant enrichment of the major histocompatibility complex (MHC) class II allele HLA-DOB∗01:01 in OMAS patients. OMAS severity scores were associated with the expression of several candidate autoimmune genes. We propose a model in which polyclonal auto-reactive B lymphocytes act as antigen-presenting cells and drive TLS formation, thereby supporting both sustained polyclonal T cell-mediated anti-tumor immunity and paraneoplastic OMAS neuropathology.
    Keywords CP: Cancer ; CP: Immunology ; Biology (General) ; QH301-705.5
    Subject code 610
    Language English
    Publishing date 2023-08-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: Condition‐specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response

    Jenia Gutin / Amit Sadeh / Ayelet Rahat / Amir Aharoni / Nir Friedman

    Molecular Systems Biology, Vol 11, Iss 10, Pp n/a-n/a (2015)

    2015  

    Abstract: Abstract Cells must quickly respond and efficiently adapt to environmental changes. The yeast Saccharomyces cerevisiae has multiple pathways that respond to specific environmental insults, as well as a generic stress response program. The later is ... ...

    Abstract Abstract Cells must quickly respond and efficiently adapt to environmental changes. The yeast Saccharomyces cerevisiae has multiple pathways that respond to specific environmental insults, as well as a generic stress response program. The later is regulated by two transcription factors, Msn2 and Msn4, that integrate information from upstream pathways to produce fast, tunable, and robust response to different environmental changes. To understand this integration, we employed a systematic approach to genetically dissect the contribution of various cellular pathways to Msn2/4 regulation under a range of stress and growth conditions. We established a high‐throughput liquid handling and automated flow cytometry system and measured GFP levels in 68 single‐knockout and 1,566 double‐knockout strains that carry an HSP12‐GFP allele as a reporter for Msn2/4 activity. Based on the expression of this Msn2/4 reporter in five different conditions, we identified numerous genetic and epistatic interactions between different components in the network upstream to Msn2/4. Our analysis gains new insights into the functional specialization of the RAS paralogs in the repression of stress response and identifies a three‐way crosstalk between the Mediator complex, the HOG MAPK pathway, and the cAMP/PKA pathway.
    Keywords budding yeast ; genetic interactions ; Msn2 and Msn4 ; signaling pathways ; transcriptional response to stress ; Biology (General) ; QH301-705.5 ; Medicine (General) ; R5-920
    Subject code 570
    Language English
    Publishing date 2015-10-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: Fine-Resolution Mapping of TF Binding and Chromatin Interactions

    Jenia Gutin / Ronen Sadeh / Nitzan Bodenheimer / Daphna Joseph-Strauss / Avital Klein-Brill / Adi Alajem / Oren Ram / Nir Friedman

    Cell Reports, Vol 22, Iss 10, Pp 2797-

    2018  Volume 2807

    Abstract: Summary: Transcription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput ...

    Abstract Summary: Transcription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput automation. Here, we describe SLIM-ChIP (short-fragment-enriched, low-input, indexed MNase ChIP), which combines enzymatic fragmentation of chromatin and on-bead indexing to address these desiderata. SLIM-ChIP reproduces a high-resolution binding map of yeast Reb1 comparable with existing methods, yet with less input material and full compatibility with high-throughput procedures. We demonstrate the robustness and flexibility of SLIM-ChIP by probing additional factors in yeast and mouse. Finally, we show that SLIM-ChIP provides information on the chromatin landscape surrounding the bound transcription factor. We identify a class of Reb1 sites where the proximal −1 nucleosome tightly interacts with Reb1 and maintains unidirectional transcription. SLIM-ChIP is an attractive solution for mapping DNA binding proteins and charting the surrounding chromatin occupancy landscape at a single-cell level. : Mapping transcription factors binding to DNA by chromatin immunoprecipitation sequencing is a key step in studying transcriptional programs. Gutin et al. introduce SLIM-ChIP, a simple, automation compatible protocol, that provides insights about the chromatin landscape at the bound sites. Using this protocol, they discover promoter architectures that enforce unidirectional transcription. Keywords: Reb1, CTCF, ChIP-seq, chromatin, transcription factor, DNA-binding, promoter directionality, nucleosomes
    Keywords Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2018-03-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Article ; Online: Selective flexible packaging pathways of the segmented genome of influenza A virus

    Ivan Haralampiev / Simon Prisner / Mor Nitzan / Matthias Schade / Fabian Jolmes / Max Schreiber / Maria Loidolt-Krüger / Kalle Jongen / Jasmine Chamiolo / Niklaas Nilson / Franziska Winter / Nir Friedman / Oliver Seitz / Thorsten Wolff / Andreas Herrmann

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 13

    Abstract: The mechanism underlying packaging of the 8 segments of the influenza virus genome into virions is not well understood. Here, the authors use a multiplexed FISH assay to monitor the 8 segments in parallel in infected cells suggesting bundling routes ... ...

    Abstract The mechanism underlying packaging of the 8 segments of the influenza virus genome into virions is not well understood. Here, the authors use a multiplexed FISH assay to monitor the 8 segments in parallel in infected cells suggesting bundling routes during the packaging process.
    Keywords Science ; Q
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  9. Article ; Online: Correction

    Naomi Habib / Tommy Kaplan / Hanah Margalit / Nir Friedman

    PLoS Computational Biology, Vol 7, Iss

    A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval.

    2011  Volume 5

    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2011-05-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  10. Article ; Online: Selective flexible packaging pathways of the segmented genome of influenza A virus

    Ivan Haralampiev / Simon Prisner / Mor Nitzan / Matthias Schade / Fabian Jolmes / Max Schreiber / Maria Loidolt-Krüger / Kalle Jongen / Jasmine Chamiolo / Niklaas Nilson / Franziska Winter / Nir Friedman / Oliver Seitz / Thorsten Wolff / Andreas Herrmann

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 13

    Abstract: The mechanism underlying packaging of the 8 segments of the influenza virus genome into virions is not well understood. Here, the authors use a multiplexed FISH assay to monitor the 8 segments in parallel in infected cells suggesting bundling routes ... ...

    Abstract The mechanism underlying packaging of the 8 segments of the influenza virus genome into virions is not well understood. Here, the authors use a multiplexed FISH assay to monitor the 8 segments in parallel in infected cells suggesting bundling routes during the packaging process.
    Keywords Science ; Q
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top