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  1. Article ; Online: Super-resolved trajectory-derived nanoclustering analysis using spatiotemporal indexing

    Tristan P. Wallis / Anmin Jiang / Kyle Young / Huiyi Hou / Kye Kudo / Alex J. McCann / Nela Durisic / Merja Joensuu / Dietmar Oelz / Hien Nguyen / Rachel S. Gormal / Frédéric A. Meunier

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 16

    Abstract: Abstract Single-molecule localization microscopy techniques are emerging as vital tools to unravel the nanoscale world of living cells by understanding the spatiotemporal organization of protein clusters at the nanometer scale. Current analyses define ... ...

    Abstract Abstract Single-molecule localization microscopy techniques are emerging as vital tools to unravel the nanoscale world of living cells by understanding the spatiotemporal organization of protein clusters at the nanometer scale. Current analyses define spatial nanoclusters based on detections but neglect important temporal information such as cluster lifetime and recurrence in “hotspots” on the plasma membrane. Spatial indexing is widely used in video games to detect interactions between moving geometric objects. Here, we use the R-tree spatial indexing algorithm to determine the overlap of the bounding boxes of individual molecular trajectories to establish membership in nanoclusters. Extending the spatial indexing into the time dimension allows the resolution of spatial nanoclusters into multiple spatiotemporal clusters. Using spatiotemporal indexing, we found that syntaxin1a and Munc18-1 molecules transiently cluster in hotspots, offering insights into the dynamics of neuroexocytosis. Nanoscale spatiotemporal indexing clustering (NASTIC) has been implemented as a free and open-source Python graphic user interface.
    Keywords Science ; Q
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Tau forms synaptic nano-biomolecular condensates controlling the dynamic clustering of recycling synaptic vesicles

    Shanley F. Longfield / Mahdie Mollazade / Tristan P. Wallis / Rachel S. Gormal / Merja Joensuu / Jesse R. Wark / Ashley J. van Waardenberg / Christopher Small / Mark E. Graham / Frédéric A. Meunier / Ramón Martínez-Mármol

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 20

    Abstract: Abstract Neuronal communication relies on the release of neurotransmitters from various populations of synaptic vesicles. Despite displaying vastly different release probabilities and mobilities, the reserve and recycling pool of vesicles co-exist within ...

    Abstract Abstract Neuronal communication relies on the release of neurotransmitters from various populations of synaptic vesicles. Despite displaying vastly different release probabilities and mobilities, the reserve and recycling pool of vesicles co-exist within a single cluster suggesting that small synaptic biomolecular condensates could regulate their nanoscale distribution. Here, we performed a large-scale activity-dependent phosphoproteome analysis of hippocampal neurons in vitro and identified Tau as a highly phosphorylated and disordered candidate protein. Single-molecule super-resolution microscopy revealed that Tau undergoes liquid-liquid phase separation to generate presynaptic nanoclusters whose density and number are regulated by activity. This activity-dependent diffusion process allows Tau to translocate into the presynapse where it forms biomolecular condensates, to selectively control the mobility of recycling vesicles. Tau, therefore, forms presynaptic nano-biomolecular condensates that regulate the nanoscale organization of synaptic vesicles in an activity-dependent manner.
    Keywords Science ; Q
    Subject code 571
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Microscopy Image Browser

    Ilya Belevich / Merja Joensuu / Darshan Kumar / Helena Vihinen / Eija Jokitalo

    PLoS Biology, Vol 14, Iss 1, p e

    A Platform for Segmentation and Analysis of Multidimensional Datasets.

    2016  Volume 1002340

    Abstract: Understanding the structure-function relationship of cells and organelles in their natural context requires multidimensional imaging. As techniques for multimodal 3-D imaging have become more accessible, effective processing, visualization, and analysis ... ...

    Abstract Understanding the structure-function relationship of cells and organelles in their natural context requires multidimensional imaging. As techniques for multimodal 3-D imaging have become more accessible, effective processing, visualization, and analysis of large datasets are posing a bottleneck for the workflow. Here, we present a new software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data, which is freely available from a dedicated website. The open-source environment enables modification and insertion of new plug-ins to customize the program for specific needs. We provide practical examples of program features used for processing, segmentation and analysis of light and electron microscopy datasets, and detailed tutorials to enable users to rapidly and thoroughly learn how to use the program.
    Keywords Biology (General) ; QH301-705.5
    Subject code 004
    Language English
    Publishing date 2016-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Ancestral SARS-CoV-2, but not Omicron, replicates less efficiently in primary pediatric nasal epithelial cells.

    Yanshan Zhu / Keng Yih Chew / Melanie Wu / Anjana C Karawita / Georgina McCallum / Lauren E Steele / Ayaho Yamamoto / Larisa I Labzin / Tejasri Yarlagadda / Alexander A Khromykh / Xiaohui Wang / Julian D J Sng / Claudia J Stocks / Yao Xia / Tobias R Kollmann / David Martino / Merja Joensuu / Frédéric A Meunier / Giuseppe Balistreri /
    Helle Bielefeldt-Ohmann / Asha C Bowen / Anthony Kicic / Peter D Sly / Kirsten M Spann / Kirsty R Short

    PLoS Biology, Vol 20, Iss 8, p e

    2022  Volume 3001728

    Abstract: Children typically experience more mild symptoms of Coronavirus Disease 2019 (COVID-19) when compared to adults. There is a strong body of evidence that children are also less susceptible to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) ... ...

    Abstract Children typically experience more mild symptoms of Coronavirus Disease 2019 (COVID-19) when compared to adults. There is a strong body of evidence that children are also less susceptible to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection with the ancestral viral isolate. However, the emergence of SARS-CoV-2 variants of concern (VOCs) has been associated with an increased number of pediatric infections. Whether this is the result of widespread adult vaccination or fundamental changes in the biology of SARS-CoV-2 remain to be determined. Here, we use primary nasal epithelial cells (NECs) from children and adults, differentiated at an air-liquid interface to show that the ancestral SARS-CoV-2 replicates to significantly lower titers in the NECs of children compared to those of adults. This was associated with a heightened antiviral response to SARS-CoV-2 in the NECs of children. Importantly, the Delta variant also replicated to significantly lower titers in the NECs of children. This trend was markedly less pronounced in the case of Omicron. It is also striking to note that, at least in terms of viral RNA, Omicron replicated better in pediatric NECs compared to both Delta and the ancestral virus. Taken together, these data show that the nasal epithelium of children supports lower infection and replication of ancestral SARS-CoV-2, although this may be changing as the virus evolves.
    Keywords Biology (General) ; QH301-705.5
    Subject code 610
    Language English
    Publishing date 2022-08-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  5. Article ; Online: GORAB scaffolds COPI at the trans-Golgi for efficient enzyme recycling and correct protein glycosylation

    Tomasz M. Witkos / Wing Lee Chan / Merja Joensuu / Manuel Rhiel / Ed Pallister / Jane Thomas-Oates / A. Paul Mould / Alex A. Mironov / Christophe Biot / Yann Guerardel / Willy Morelle / Daniel Ungar / Felix T. Wieland / Eija Jokitalo / May Tassabehji / Uwe Kornak / Martin Lowe

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 18

    Abstract: COPI is recruited to the membrane by binding to Arf GTPases. Here the authors find that GORAB, a trans-Golgi protein, promotes COPI recruitment by forming membrane domains that also contain the COPI-interacting protein Scyl1, which is required for ... ...

    Abstract COPI is recruited to the membrane by binding to Arf GTPases. Here the authors find that GORAB, a trans-Golgi protein, promotes COPI recruitment by forming membrane domains that also contain the COPI-interacting protein Scyl1, which is required for efficient glycosylation of cargo proteins.
    Keywords Science ; Q
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    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: GORAB scaffolds COPI at the trans-Golgi for efficient enzyme recycling and correct protein glycosylation

    Tomasz M. Witkos / Wing Lee Chan / Merja Joensuu / Manuel Rhiel / Ed Pallister / Jane Thomas-Oates / A. Paul Mould / Alex A. Mironov / Christophe Biot / Yann Guerardel / Willy Morelle / Daniel Ungar / Felix T. Wieland / Eija Jokitalo / May Tassabehji / Uwe Kornak / Martin Lowe

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 18

    Abstract: COPI is recruited to the membrane by binding to Arf GTPases. Here the authors find that GORAB, a trans-Golgi protein, promotes COPI recruitment by forming membrane domains that also contain the COPI-interacting protein Scyl1, which is required for ... ...

    Abstract COPI is recruited to the membrane by binding to Arf GTPases. Here the authors find that GORAB, a trans-Golgi protein, promotes COPI recruitment by forming membrane domains that also contain the COPI-interacting protein Scyl1, which is required for efficient glycosylation of cargo proteins.
    Keywords Science ; Q
    Language English
    Publishing date 2019-01-01T00:00:00Z
    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.

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