1,720,967 research outputs found
Microfluidic Concentration-Enhanced Cellular Kinase Activity Assay
No full textIn this paper, we reported a simple, disposable PDMS micro/nanofluidic preconcentration chip for in vitro concentration-enhanced cell kinase assays. Utilizing the preconcentration (electrokinetic trapping) directly from cell lysate (1 mM ATP) samples, we could achieve at least a 25-fold increase in reaction velocity and 65-fold enhancement in sensitivity. In addition, we shorten the assay time down to less than 10 min, with the sample volume requirements of down to 5 cells. This device could be a generic and powerful tool for diagnostics and systems biology studies at the single-cell level, if properly optimized and integrated with the cell culture microdevices.National Institutes of Health (U.S.) (R01-EB005743)National Institutes of Health (U.S.) (R01-CA119402)National Institutes of Health (U.S.) (P50-GM68672)Institute for Collaborative Biotechnologie
Co-regulation of endothelial and myogenic cell fates through intercellular crosstalk in skeletal muscle
No full textSkeletal muscle is one of the most dynamic organs in the human body, which has a vigorous potential to regenerate and adapt to environmental changes. Depending on environments, skeletal muscle enables essential life activities to survive by controlling movement and metabolism. The functional and structural adaptations of skeletal muscle crosstalk with other physiological systems enabling nutrition and oxygen delivery, and the elimination of metabolic waste products. The work in this dissertation focuses on the intercellular signals produced by myogenic cells to dynamically remodel skeletal muscle during exercise or muscle repair, and the reciprocal signals from the local niche and the systemic environment that regulate myogenic cell fate and metabolism according to physiological needs. This complex crosstalk is dissected in three specific chapters where we study the crosstalk of myogenic cells with endothelial cells and the vasculature to coordinate local niche interactions and systemic crosstalks. First, we demonstrate that an exercise-induced myokine called apelin is produced by muscle fiber and mediates intercellular signaling to endothelial cells through the apelin receptor. In addition, through a yeast one-hybrid screen of transcription factor binding to the apelin promoter, we identified the myogenic transcription factor TEA domain family member 1 (Tead1) as a regulator of Apln transcription. We observed via single-cell transcriptomic analysis of regenerating skeletal muscle that Aplnr (Apelin receptor) is enriched in muscle endothelial cells, whereas Tead1 is enriched in myogenic cells. Myofiber-specific over-expression of Tead1 suppresses apelin secretion at the whole-body level, and apelin secretion via Tead1 knock-down in muscle cells stimulates endothelial cell proliferation in co-cultures. By showing that apelin peptide supplementation in vivo enhances endothelial cell expansion following muscle injury, we conclude that paracrine crosstalk in which apelin secretion controlled by Tead1 in myogenic cells influences endothelial remodeling during skeletal muscle repair. Secondly, we show how tissue-resident support cells affect muscle progenitor activation in different metabolic environments. Skeletal muscle progenitors (SKMP) reside in close proximity to supportive cell types in the stem cell niche and dynamically interact with each other to adapt to environmental changes. Here, we studied how different niche cell types affect SKMPs in response to glycemic levels. Using co-cultures of SKMPs and niche cells, we discovered that endothelial cells synergistically enhance SKMP proliferation in a low glycemic environment, while fibroblasts and macrophages had no effect. We observed that the crosstalk between SKMPs and endothelial cells was mediated by direct cell-cell contacts independent of soluble paracrine signals. Transcriptomic analysis revealed that the endothelial alpha/beta hydrolase N-Myc Downstream Regulated1 (NDRG1) is induced by a low glycemic environment and is associated with biological adhesion. SKMPs co-cultured with Ndrg1 knock-down endothelial cells lose their synergistic functional relationship in response to glucose levels. Therefore, our findings suggest that Ndrg1 is a key mediator of endothelial cell-mediated glycemic control of SKMPs and provides a link between systemic energy levels and the skeletal muscle stem cell niche. Lastly, I developed intravital imaging to monitor muscle stem cells and vasculature.SSV-EN
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes
No full textSystematic study of cell signaling networks increasingly involves high throughput proteomics, transcriptional profiling, and automated literature mining with the aim of assembling large-scale interaction networks. In contrast, functional analysis of cell signaling usually focuses on a much smaller sets of proteins and eschews computation but focuses directly on cellular responses to environment and perturbation. We sought to combine these two traditions by collecting cellresponse measures on a reasonably large scale and then attempting to infer differences in network topology between two cell types. Human hepatocytes and hepatocellular carcinoma (HCC) cell lines were exposed to inducers of inflammation, innate immunity and proliferation in the presence and absence of small molecule drugs and multiplex biochemical measurement then performed on intra- and extracellular signaling molecules. We uncover major differences between primary and transformed hepatocytes with respect to the engagement of toll-like receptor and NF-κBdependent secretion of chemokines and cytokines that prime and attract immune cells. Overall, our results serve as a proof-of-principle for an approach to network analysis that is systematic, comparative and biochemically focused. More specifically, our data support the hypothesis that HCC cells down-regulate normal inflammatory and immune responses to avoid immune editing.National Institutes of Health (U.S.) (Grant GM68762)National Institutes of Health (U.S.) (Grant CA112967
A multipathway phosphoproteomic signaling network model of idiosyncratic and inflammatory cytokine-induced toxicity in human hepatocytes
No full textIdiosyncratic drug hepatotoxicity is a hepatotoxicity subset that occurs in a very small fraction of human patients, is poorly predicted by standard preclinical models and in clinical trials, and frequently leads to postapproval drug failure. Animal models utilizing bacterial LPS co-administration to induce an inflammatory background and hepatocyte cell culture models utilizing cytokine mix cotreatment have successfully reproduced idiosyncratic hepatotoxicity signatures for certain drugs, but the hepatocyte signaling mechanisms governing these drug-cytokine toxicity synergizes are largely unclear. Here, we summarize our efforts to computationally model the signaling mechanisms regulating inflammatory cytokine-associated idiosyncratic drug hepatotoxicity. We collected a ldquocue-signal-responserdquo (CSR) data compendium in cultured primary human hepatocytes treated with many combinations of idiosyncratic hepatotoxic drugs and inflammatory cytokine mixes (ldquocuesrdquo) and subjected this compendium to orthogonal partial-least squares regression (OPLSR) to computationally relate the measured intracellular phosphoprotein signals and hepatocellular death responses. This OPLSR model suggested that hepatocytes specify their cell death responses to toxic drug/cytokine conditions by integrating signals from four key pathways - Akt, p70 S6K, ERK, and p38. An OPLSR model focused on data from these four signaling pathways demonstrated accurate predictions of idiosyncratic drug- and cytokine-induced hepatotoxicities in a second human hepatocyte donor, suggesting that hepatocytes from different individuals have shared network control mechanisms governing toxicity responses to diverse combinations of idiosyncratic hepatotoxicants and inflammatory cytokines
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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