1,720,983 research outputs found
Signaling for death: tyrosine phosphorylation in the response to glucose deprivation
Get PDFThe shift from oxidative phosphorylation to aerobic glycolysis in cancer has focused attention on the altered metabolism of cancer cells as a means of therapeutic intervention. Metabolic dysregulation in cancer was first proposed by Warburg in the 1930s, and this topic remains an active area of research. While previous studies have explored the connection between cellular signaling and metabolism, many have focused on a small subset of components within a complex network of proteins, enzymes, and biochemical signals. In a recent article published in Molecular Systems Biology, Graham et al (2012) endeavor to better understand the relationship between metabolism and signaling at the network level. Although the question of how cancer cells respond to glucose starvation posited by the authors is relatively simple, the answer ends up being unexpectedly complex. To answer this question, the authors use mass spectrometry and other biochemical profiling techniques to demonstrate a connection between glucose levels, reactive oxygen species (ROS), and alterations in phosphotyrosine-mediated signaling in glioblastoma cell lines
Quantitative Profiling of Lysine Acetylation Reveals Dynamic Crosstalk between Receptor Tyrosine Kinases and Lysine Acetylation
Get PDFLysine acetylation has been primarily investigated in the context of transcriptional regulation, but a role for acetylation in mediating other cellular responses has emerged. Multiple studies have described global lysine acetylation profiles for particular biological states, but none to date have investigated the temporal dynamics regulating cellular response to perturbation. Reasoning that lysine acetylation may be altered in response to growth factors, we implemented quantitative mass spectrometry-based proteomics to investigate the temporal dynamics of lysine acetylation in response to growth factor stimulation in cultured carcinoma cell lines. We found that lysine acetylation changed rapidly in response to activation of several different receptor tyrosine kinases by their respective ligands. To uncover the effects of lysine acetylation dynamics on tyrosine phosphorylation signaling networks, cells were treated with an HDAC inhibitor. This short-term pharmacological inhibition of histone deacetylase activity modulated signaling networks involving phosphorylated tyrosine and thereby altered the response to receptor tyrosine kinase activation. This result highlights the interconnectivity of lysine acetylation and tyrosine phosphorylation signaling networks and suggests that HDAC inhibition may influence cellular responses by affecting both types of post-translational modifications.National Institutes of Health (U.S.) (Grant R24DK090963)National Institutes of Health (U.S.) (Grant R01CA118705)National Institutes of Health (U.S.) (Grant U54CA112967)National Institutes of Health (U.S.) (Grant U24CA159988)National Institutes of Health (U.S.) (Grant P30CA14051
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Leveraging PhagoID to Define How Cytokines Reprogram the Phagosomal Proteome
Get PDFThe ability of phagocytosing diverse cargoes and maintaining tissue homeostasis under different immune contexts and challenges is what lends tissue resident macrophages their identity as immune sentinels. Previous studies that were aimed towards isolating and studying the macrophage phagosome suffered from certain limitations due to the highly dynamic and interactive nature of this organelle, making its proteomic analysis an especially arduous task. In a recent study, we reported the development of a novel tool called PhagoID which uses a proximity labeling-based strategy for resolving phagosomal lumen proteins with high specificity and efficiency, facilitating their identification using mass spectrometry and downstream proteomic analyses. Here, we validate the use of epigallocatechin gallate (EGCG) as a ROS scavenger capable of minimizing extracellular labeling in the case of PhagoID. Next, we adapted PhagoID to quantify the phagosome lumen proteome of fetal-derived alveolar-like macrophages (FLAMs) under the effect of type I interferon signaling.
The phagocytic activity of alveolar macrophages (AMs) is important both at baseline for routine cleaning of cellular debris, as well as to initiate a strong inflammatory responses to respiratory pathogens. We profiled the phagosomal proteome of FLAMs as a model for primary AMs and found proteins involved in the class I MHC pathway to be the only ER subset enriched in the phagosome on IFN-β activated FLAMs. Additionally, we identified the presence of proteins belonging to 3 families of interferon induced GTPases (IIGPs), including multiple GBPs and all IRGM proteins which have been well recognized for their role in cell autonomous immunity against bacterial infections like Mycobacterium tuberculosis and Chlamydia trachomatis. We also detected the enrichment of the enzyme aconitate decarboxylase (ACOD1/IRG1) involved in the production of the anti-microbial metabolite, itaconate. Going ahead, we propose the design of an itaconate biosensor targeted to the endosomal and lysosomal compartments to understand which host factors govern itaconate trafficking to phagosomes. Thus, using PhagoID enabled us to gain important insights into how IFN-β, a cytokine known for its highly context-dependent role in case of bacterial infections, can alter the phagosome proteome of AMs.Medical Scienc
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
Computer aided manual validation of mass spectrometry-based proteomic data
Get PDFAdvances in mass spectrometry-based proteomic technologies have increased the speed of analysis and the depth provided by a single analysis. Computational tools to evaluate the accuracy of peptide identifications from these high-throughput analyses have not kept pace with technological advances; currently the most common quality evaluation methods are based on statistical analysis of the likelihood of false positive identifications in large-scale data sets. While helpful, these calculations do not consider the accuracy of each identification, thus creating a precarious situation for biologists relying on the data to inform experimental design. Manual validation is the gold standard approach to confirm accuracy of database identifications, but is extremely time-intensive. To palliate the increasing time required to manually validate large proteomic datasets, we provide computer aided manual validation software (CAMV) to expedite the process. Relevant spectra are collected, catalogued, and pre-labeled, allowing users to efficiently judge the quality of each identification and summarize applicable quantitative information. CAMV significantly reduces the burden associated with manual validation and will hopefully encourage broader adoption of manual validation in mass spectrometry-based proteomics.National Institutes of Health (U.S.) (Grant R24DK090963)National Institutes of Health (U.S.) (Grant U54CA112967)National Cancer Institute (U.S.). Integrative Cancer Biology Program (Fellowship)Charles S. Krakauer FellowshipHugh Hampton Young Fellowshi
Engineered bromodomains to explore the acetylproteome
No full textMass spectrometry-based analysis of the acetylproteome has highlighted a role for acetylation in a wide array of biological processes including gene regulation, metabolism, and cellular signaling. To date, anti-acetyllysine antibodies have been used as the predominant affinity reagent for
enrichment of acetyllysine-containing peptides and proteins; however, these reagents suffer from high non-specific binding and lot-to-lot variability. Bromodomains represent potential affinity reagents for acetylated proteins and peptides, given their natural role in recognition of acetylated
sequence motifs in vivo. To evaluate their efficacy, we generated recombinant proteins representing all known yeast bromodomains. Bromodomain specificity for acetylated peptides was determined using degenerate peptide arrays, leading to the observation that different
bromodomains display a wide array of binding specificities. Despite their relatively weak affinity, we demonstrate the ability of selected bromodomains to enrich acetylated peptides from a complex biological mixture prior to mass spectrometric analysis. Finally, we demonstrate a method for improving the utility of bromodomain enrichment for mass spectrometry through engineering novel affinity reagents using combinatorial tandem bromodomain pairs.National Institutes of Health (U.S.) (Grants R24DK090963, R01CA118705, U54CA112967, R01ES015339, R01 GM104047, U24CA159988 and P30CA14051)Charles S. Krakauer FellowshipHugh Hampton Young Fellowshi
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
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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