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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Elliott D. SoRelle; Scott R. White; Benjamin B. Yellen; Kris C. Wood; +2 Authors

    AbstractAppropriately tailored segmentation techniques can extract detailed quantitative information from biological image datasets to characterize and better understand sample distributions. Practically, high-resolution characterization of biological samples such as cell populations can provide insights into the sources of variance in biomarker expression, drug resistance, and other phenotypic aspects, but it is still unclear what is the best method for extracting this information from large image-based datasets. We present a software pipeline and comparison of multiple image segmentation methods to extract single-cell morphological and fluorescence quantitation from time lapse images of clonal growth rates using a recently reported microfluidic system. The inputs in all pipelines consist of thousands of unprocessed images and the outputs are the detection of cell counts, chamber identifiers, and individual morphological properties of each clone over time detected through multi-channel fluorescence and bright field imaging. Our conclusion is that unsupervised learning methods for cell segmentation substantially outperform supervised statistical methods with respect to accuracy and have key advantages including individual cell instance detection and flexibility through model training. We expect this system and software to have broad utility for researchers interested in high-throughput single-cell biology.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ https://www.biorxiv....arrow_drop_down
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    https://www.biorxiv.org/conten...
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ https://www.biorxiv....arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Authors: Sebastien A. Gauthier; Rocío Pérez-González; Ajay Sharma; Fang-Ke Huang; +6 Authors

    A dysfunctional endosomal pathway and abnormally enlarged early endosomes in neurons are an early characteristic of Down syndrome (DS) and Alzheimer’s disease (AD). We have hypothesized that endosomal material can be released by endosomal multivesicular bodies (MVBs) into the extracellular space via exosomes to relieve neurons of accumulated endosomal contents when endosomal pathway function is compromised. Supporting this, we found that exosome secretion is enhanced in the brains of DS patients and a mouse model of the disease, and by DS fibroblasts. Furthermore, increased levels of the tetraspanin CD63, a regulator of exosome biogenesis, were observed in DS brains. Importantly, CD63 knockdown diminished exosome release and worsened endosomal pathology in DS fibroblasts. Taken together, these data suggest that increased CD63 expression enhances exosome release as an endogenous mechanism mitigating endosomal abnormalities in DS. Thus, the upregulation of exosome release represents a potential therapeutic goal for neurodegenerative disorders with endosomal pathology. Electronic supplementary material The online version of this article (doi:10.1186/s40478-017-0466-0) contains supplementary material, which is available to authorized users.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Acta Neuropathologica Communications
    Article
    License: CC BY
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    Acta Neuropathologica Communications
    Article . 2017 . Peer-reviewed
    License: CC BY
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DOAJ
    Article . 2017
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Acta Neuropathologica Communications
      Article
      License: CC BY
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Acta Neuropathologica Communications
      Article . 2017 . Peer-reviewed
      License: CC BY
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DOAJ
      Article . 2017
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Chen, Qian; Pollard, Thomas D.;

    We created two new mutants of fission yeast cofilin to investigate why cytokinesis in many organisms depends on this small actin-binding protein. These mutant cofilins bound actin monomers normally, but bound and severed ADP-actin filaments much slower than wild-type cofilin. Cells depending on mutant cofilins condensed nodes, precursors of the contractile ring, into clumps rather than rings. Starting from clumped nodes, mutant cells slowly assembled rings from diverse intermediate structures including spiral strands containing actin filaments and other contractile ring proteins. This process in mutant cells depended on α-actinin. These slowly assembled contractile rings constricted at a normal rate but with more variability, indicating ring constriction is not very sensitive to defects in severing by cofilin. Computer simulations of the search-capture-pull and release model of contractile ring formation predicted that nodes clump when the release step is slow, so cofilin severing of actin filament connections between nodes likely contributes to the release step. When fission yeast express mutant cofilin that is inefficient at actin filament severing, cytokinetic contractile ring formation is severely impaired, but ring contraction proceeds efficiently.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    The Journal of Cell Biology
    Article . 2011 . Peer-reviewed
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      The Journal of Cell Biology
      Article . 2011 . Peer-reviewed
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    Authors: C A, Hobbs; S J, James; A, Parsian; P A, Krakowiak; +4 Authors

    Background: Most non-syndromic congenital heart defects (CHD) are caused by a complex interaction between maternal lifestyle factors, environmental exposures, and maternal and fetal genetic variants. Maternal periconceptional intake of folic acid containing vitamin supplements is reported to decrease the risk of CHD. The 677C→T and 1298A→C polymorphisms in the methylenetetrahydrofolate reductase (MTHFR) gene decrease enzyme activity. Objective: To examine the relation between CHD and maternal and fetal MTHFR polymorphisms Methods: 375 nuclear families were studied. The transmission/disequilibrium test was used to test for transmission distortion in complete triads. A log-linear approach was used to test for associations between CHD and maternal and offspring polymorphisms, and to estimate independently the contributions of maternal and fetal variants to relative risks. Haplotype frequencies were estimated and a haplotype transmission disequilibrium test carried out. Results: The 1298C allele was transmitted less often than expected (p = 0.0013). There was no distortion in the transmission of the 677T allele, neither was there evidence of a parent of origin effect in the transmission of either of the single nucleotide polymorphisms. The 677C–1298C haplotype was also transmitted less often than expected (p = 0.0020). The relative risk associated with inheriting one copy of the 1298C allele was 0.64 (95% confidence interval, 0.48 to 0.87) and the that associated with inheriting two copies of the 1298C allele, 0.38 (0.21 to 0.70). Conclusions: The apparent protective effect of the MTHFR 1298C allele against CHD could have several explanations and further study is needed.

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    Europe PubMed Central
    Other literature type . 2006
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    Journal of Medical Genetics
    Article . 2005 . Peer-reviewed
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      Europe PubMed Central
      Other literature type . 2006
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      Journal of Medical Genetics
      Article . 2005 . Peer-reviewed
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    Authors: Weiwei Xu; M.M. Fahd Qadir; Daniela Nasteska; Paula Mota de Sa; +31 Authors

    Summary: Male mice lacking the androgen receptor (AR) in pancreatic β cells exhibit blunted glucose-stimulated insulin secretion (GSIS), leading to hyperglycemia. Testosterone activates an extranuclear AR in β cells to amplify glucagon-like peptide-1 (GLP-1) insulinotropic action. Here, we examined the architecture of AR targets that regulate GLP-1 insulinotropic action in male β cells. Testosterone cooperates with GLP-1 to enhance cAMP production at the plasma membrane and endosomes via: (1) increased mitochondrial production of CO2, activating the HCO3−-sensitive soluble adenylate cyclase; and (2) increased Gαs recruitment to GLP-1 receptor and AR complexes, activating transmembrane adenylate cyclase. Additionally, testosterone enhances GSIS in human islets via a focal adhesion kinase/SRC/phosphatidylinositol 3-kinase/mammalian target of rapamycin complex 2 actin remodeling cascade. We describe the testosterone-stimulated AR interactome, transcriptome, proteome, and metabolome that contribute to these effects. This study identifies AR genomic and non-genomic actions that enhance GLP-1-stimulated insulin exocytosis in male β cells.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Oxford University Re...arrow_drop_down
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    Cell Reports
    Article . 2022
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    Cell Reports
    Article . 2023
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      Cell Reports
      Article . 2022
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      Cell Reports
      Article . 2023
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    Authors: Rei Bufi; Ron Korstanje;

    The mouse is the most commonly used mammalian model to study disease, including kidney disease. However, close attention needs to be paid to the differences and effects of genetic background. The default choice of most investigators is to use C57BL/6 mice, but not all C57BL/6 mice are the same. Ever since the C57BL/6 line was first established, differences in the genetic background have risen between substrains, which have major implications in the phenotypes expressed in kidney disease. Furthermore, considering that C57BL/6 substrains are relatively resistant to kidney damage, there can be major benefits in selecting other mouse inbred strains when studying kidney disease. These strains can show more similar responses regarding kidney damage as in humans, and results may therefore translate better to human application. Genetically diverse mice, such as the Diversity Outbred mice, allow investigators to study kidney phenotypes with comparable levels of genetic diversity as seen in humans, which yield results that more closely reflect the variation in human disease outcomes due to genetic variation. Hence, embracing the genetic diversity that is present in mice can lead to better translational research methods. Investigators need to always take into consideration that genetic background is a variable that can alter results significantly, and optimization of translational research asks for careful strain selection and more rigorous reporting of the genetic background that is being used in experiment.

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    Kidney International
    Article . 2022 . Peer-reviewed
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      Kidney International
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    Authors: Yi-An Yang; Alexander Chong; Jeongmin Song;

    Salmonella enterica serovar Typhi (S. Typhi) and S. Paratyphi, namely typhoidal Salmonellae, are the cause of (para) typhoid fever, which is a devastating systemic infectious disease in humans. In addition, the spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR) S. Typhi in many low and middle-income countries poses a significant risk to human health. While currently available typhoid vaccines and therapeutics are efficacious, they have some limitations. One important limitation is the lack of controlling individuals who chronically carry S. Typhi. However, due to the strict host specificity of S. Typhi to humans, S. Typhi research is hampered. As a result, our understanding of S. Typhi pathogenesis is incomplete, thereby delaying the development and improvement of prevention and treatment strategies. Nonetheless, to better combat and contain S. Typhi, it is vital to develop a vaccine and therapy for controlling both acutely and chronically infected individuals. This review discusses how scientists are trying to combat typhoid fever, why it is so challenging to do so, which approaches show promise, and what we know about the pathogenesis of S. Typhi chronic infection.

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    Vaccines
    Article . 2018 . Peer-reviewed
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    Vaccines
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      Vaccines
      Article . 2018 . Peer-reviewed
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      Vaccines
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    Authors: Matthew D. Taylor; Matthew D. Taylor; Tiago D. Fernandes; Tiago D. Fernandes; +6 Authors

    The role of T cell memory in sepsis is poorly understood. Recent work has demonstrated that mice exposed to frequent antigenic stimulation, in contrast to laboratory mice, better recapitulate the human T cell repertoire. This difference may profoundly alter responses to inflammatory insults. We induced isolated T cell memory by inoculating C57Bl/6 mice with an anti-CD3ϵ activating antibody, a process we term “immune education.” These mice were subjected to the cecal ligation and puncture (CLP) model of sepsis and responses were compared to those of isotype-treated controls. CLP-induced increases in 1) CD4 T cell production and serum levels of IFNγ, 2) CD8 T cell granzyme B levels, and 3) innate cell function were all more pronounced in educated mice than in control mice. Immune education increased CLP-induced liver injury and decreased survival. The differences in responses to CLP were not recapitulated in mice with either isolated CD4 or isolated CD8 T cell memory. Relative to controls, CLP in educated CD8−/− mice (isolated CD4 memory) increased monocyte-derived dendritic cells. Combined CD4 and CD8 memory did not increase monocyte-derived dendritic cells; this combination recapitulated increases in neutrophil and inflammatory monocyte numbers in educated wild-type mice. Induction of T cell memory prior to CLP alters immune responses, organ function, and survival. Both CD4 and CD8 memory T cells play important and independent roles in this response. These findings have profound implications for the development of murine models of human inflammatory disorders such as infection and sepsis.

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    Frontiers in Immunology
    Article . 2020
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    Frontiers in Immunology
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    Frontiers in Immunology
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      Frontiers in Immunology
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    Authors: Christodoulou, Joan; Stokes, Lynissa R.; Bantjes, Jason; Tomlinson, Mark; +5 Authors

    Author(s): Christodoulou, Joan; Stokes, Lynissa R; Bantjes, Jason; Tomlinson, Mark; Stewart, Jackie; Rabie, Stephan; Gordon, Sarah; Mayekiso, Andile; Rotheram-Borus, Mary Jane | Abstract: BackgroundIn high-income countries, individual- and community-level factors are associated with increased contact with the criminal justice system. However, little is known about how these factors contribute to the risk of arrest in South Africa, which has one of the highest rates of arrests globally. We examine both individual- and community-level factors associated with arrests among young men living in the townships of Cape Town.MethodsData were collected from a stratified community sample of 906 young men aged 18-29 years old living in 18 township neighborhoods. Communities with high and low rates of arrest were identified. Logistic regression models were used to assess which individual-level (such as substance use and mental health status) and community-level (such as infrastructure and presence of bars and gangs) factors predict arrests.ResultsSignificant predictors of arrests were substance use, gang activity, being older, more stressed, and less educated. Living in communities with better infrastructure and in more recently established communities populated by recent immigrants was associated with having a history of arrests.ConclusionsWhen considering both individual- and community-level factors, substance use and gang violence are the strongest predictors of arrests among young men in South Africa. Unexpectedly, communities with better infrastructure have higher arrest rates. Community programs are needed to combat substance use and gang activity as a pathway out of risk among South African young men.Trial registrationClinicalTrials.gov registration #NCT02358226, registered Nov 24, 2014.

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    PLoS ONE
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    Article . 2019
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    PLoS ONE
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      Article . 2019
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      PLoS ONE
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    Authors: Calvin S. Leung; Stephen M. Douglass; Marco Morselli; Matthew B. Obusan; +3 Authors

    SUMMARY In the eukaryotic cell, spliceosomes assemble onto pre-mRNA cotranscriptionally. Spliceosome assembly takes place in the context of the chromatin environment, suggesting that the state of the chromatin may affect splicing. The molecular details and mechanisms through which chromatin affects splicing, however, are still unclear. Here, we show a role for the histone methyltransferase Set2 and its histone modification, H3K36 methylation, in pre-mRNA splicing through high-throughput sequencing. Moreover, the effect of H3K36 methylation on pre-mRNA splicing is mediated through the chromodomain protein Eaf3. We find that Eaf3 is recruited to intron-containing genes and that Eaf3 interacts with the splicing factor Prp45. Eaf3 acts with Prp45 and Prp19 after formation of the precatalytic B complex around the time of splicing activation, thus revealing the step in splicing that is regulated by H3K36 methylation. These studies support a model whereby H3K36 facilitates recruitment of an “adapter protein” to support efficient, constitutive splicing. In Brief Leung et al. demonstrate that H3K36 trimethylation facilitates efficient pre-mRNA splicing through the association of chromodomain protein Eaf3. Eaf3 binds to methylated H3K36 at intron-containing genes to stabilize association of the splicing factor Prp45 and regulate proper cotranscriptional spliceosome assembly. Graphical Abstract

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    Cell Reports
    Article . 2019 . Peer-reviewed
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    Cell Reports
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    Cell Reports
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    Article . 2019
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      Cell Reports
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Elliott D. SoRelle; Scott R. White; Benjamin B. Yellen; Kris C. Wood; +2 Authors

    AbstractAppropriately tailored segmentation techniques can extract detailed quantitative information from biological image datasets to characterize and better understand sample distributions. Practically, high-resolution characterization of biological samples such as cell populations can provide insights into the sources of variance in biomarker expression, drug resistance, and other phenotypic aspects, but it is still unclear what is the best method for extracting this information from large image-based datasets. We present a software pipeline and comparison of multiple image segmentation methods to extract single-cell morphological and fluorescence quantitation from time lapse images of clonal growth rates using a recently reported microfluidic system. The inputs in all pipelines consist of thousands of unprocessed images and the outputs are the detection of cell counts, chamber identifiers, and individual morphological properties of each clone over time detected through multi-channel fluorescence and bright field imaging. Our conclusion is that unsupervised learning methods for cell segmentation substantially outperform supervised statistical methods with respect to accuracy and have key advantages including individual cell instance detection and flexibility through model training. We expect this system and software to have broad utility for researchers interested in high-throughput single-cell biology.

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    Authors: Sebastien A. Gauthier; Rocío Pérez-González; Ajay Sharma; Fang-Ke Huang; +6 Authors

    A dysfunctional endosomal pathway and abnormally enlarged early endosomes in neurons are an early characteristic of Down syndrome (DS) and Alzheimer’s disease (AD). We have hypothesized that endosomal material can be released by endosomal multivesicular bodies (MVBs) into the extracellular space via exosomes to relieve neurons of accumulated endosomal contents when endosomal pathway function is compromised. Supporting this, we found that exosome secretion is enhanced in the brains of DS patients and a mouse model of the disease, and by DS fibroblasts. Furthermore, increased levels of the tetraspanin CD63, a regulator of exosome biogenesis, were observed in DS brains. Importantly, CD63 knockdown diminished exosome release and worsened endosomal pathology in DS fibroblasts. Taken together, these data suggest that increased CD63 expression enhances exosome release as an endogenous mechanism mitigating endosomal abnormalities in DS. Thus, the upregulation of exosome release represents a potential therapeutic goal for neurodegenerative disorders with endosomal pathology. Electronic supplementary material The online version of this article (doi:10.1186/s40478-017-0466-0) contains supplementary material, which is available to authorized users.

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    Acta Neuropathologica Communications
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    Acta Neuropathologica Communications
    Article . 2017 . Peer-reviewed
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