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Proteomics

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https://www.readbyqxmd.com/read/30650262/a-novel-core-attachment-based-method-to-identify-dynamic-protein-complexes-based-on-gene-expression-profiles-and-ppi-networks
#1
Qianghua Xiao, Ping Luo, Min Li, Jianxin Wang, Fang-Xiang Wu
Cellular functions are always performed by protein complexes. At present, many approaches have been proposed to identify protein complexes from protein-protein interaction (PPI) networks. Some approaches focus on detecting local dense sub-graphs in PPI networks which are regarded as protein complex cores, then identify protein complexes by including local neighbors. However, from gene expression profiles at different time points or tissues we know that proteins are dynamic. Therefore, identifying dynamic protein complexes should become very important and meaningful...
January 16, 2019: Proteomics
https://www.readbyqxmd.com/read/30650255/analysis-of-the-preserved-amino-acid-bias-in-peptide-profiles-of-iron-age-teeth-from-a-tropical-environment-enable-sexing-of-individuals-using-amelogenin-mrm
#2
Valerie C Wasinger, Darren Curnoe, Sonia Bustamante, Raynold Mendoza, Rasmi Shoocongdej, Lewis Adler, Andy Baker, Kanoknart Chintakanon, Ceridwen Boel, Paul S C Tacon
We describe the first dental proteomic profiles of Iron Age individuals (c2000-1000 years B.P), collected from the site of Long Long Rak rock shelter (LLR) in northwest Thailand. A bias toward the preservation of the positively charged aromatic, and polar amino acids is observed. It is evident that the 212 proteins identified (2 peptide, FDR <1%) comprise a palimpsest of alterations that occurred both ante-mortem and post-mortem. Conservation of amino acids within the taphonomically resistant crystalline matrix enabled the identification of both X and Y chromosome linked amelogenin peptides...
January 16, 2019: Proteomics
https://www.readbyqxmd.com/read/30648817/proteome-profile-and-genome-refinement-of-the-tomato-pathogenic-bacterium-clavibacter-michiganensis-subsp-michiganensis
#3
F Christopher Peritore-Galve, David J Schneider, Yong Yang, Theodore W Thannhauser, Christine D Smart, Paul Stodghill
No abstract text is available yet for this article.
January 16, 2019: Proteomics
https://www.readbyqxmd.com/read/30637940/identification-of-rabbit-oviductal-fluid-proteins-involved-in-pre-fertilization-processes-by-quantitative-proteomics
#4
Hans Yu, Lena Hackenbroch, Florian R L Meyer, Judith Reiser, Ebrahim Razzazi-Fazeli, Katharina Nöbauer, Urban Besenfelder, Claus Vogl, Gottfried Brem, Corina Mayrhofer
Oviductal fluid (ODF) proteins modulate and support reproductive processes in the oviduct. In the present study, we identified proteins involved in the biological events that precede fertilization in the rabbit ODF proteome, isolated from the ampulla and isthmus of the oviduct at different time points within 8 hours after intrauterine insemination. We used a workflow that integrates lectin affinity capture with stable-isotope dimethyl labelling prior to nanoLC-MS/MS analysis. In total, over 400 ODF proteins, including 214 lectin enriched glycoproteins, were identified and quantified...
January 13, 2019: Proteomics
https://www.readbyqxmd.com/read/30633445/analyzing-cysteine-site-neighbors-in-proteins-to-reveal-dimethyl-fumarate-targets
#5
Arianna Carolina Rosa, Elisa Benetti, Margherita Gallicchio, Valentina Boscaro, Luigi Cangemi, Chiara Dianzani, Gianluca Miglio
This work proposes a novel approach by which to consistently classify cysteine sites in proteins in terms of their reactivity toward dimethyl fumarate (DMF) and fumarate. Dimethyl fumarate-based drug products have been approved for use as oral treatments for psoriasis and relapsing-remitting multiple sclerosis. The adduction of DMF and its (re)active metabolites to certain cysteine residues in proteins is thought to underlie their effects. However, only a few receptors for these compounds have been discovered to date...
January 11, 2019: Proteomics
https://www.readbyqxmd.com/read/30632700/redox-proteomic-analysis-reveals-oxidative-modifications-of-proteins-by-increased-levels-of-intracellular-reactive-oxygen-species-during-hypoxia-adaptation-of-aspergillus-fumigatus
#6
Elena Shekhova, Lia Ivanova, Thomas Krüger, Maria C Stroe, Juliane Macheleidt, Olaf Kniemeyer, Axel A Brakhage
At the site of infection, the human fungal pathogen Aspergillus fumigatus faces abrupt changes in oxygen concentrations. An increasing number of studies have demonstrated that elevated production of intracellular reactive oxygen species (ROS) under low oxygen conditions plays a regulatory role in modulating cellular responses for adaptation to hypoxia. To learn more about this process in A. fumigatus, we determined intracellular ROS production during hypoxia. Our results confirmed increased amounts of intracellular ROS in A...
January 11, 2019: Proteomics
https://www.readbyqxmd.com/read/30632691/optimising-size-exclusion-chromatography-for-extracellular-vesicle-enrichment-and-proteomic-analysis-from-clinically-relevant-samples
#7
Rebecca E Lane, Darren Korbie, Matt Trau, Michelle M Hill
The field of extracellular vesicle (EV) research has rapidly expanded in recent years, with particular interest in their potential as circulating biomarkers. Proteomic analysis of EVs from clinical samples is complicated by the low abundance of EV proteins relative to highly abundant circulating proteins such as albumin and apolipoproteins. To overcome this, size exclusion chromatography (SEC) has been proposed as a method to enrich EVs whilst depleting protein contaminants, however, the optimal SEC parameters for EV proteomics have not been thoroughly investigated...
January 11, 2019: Proteomics
https://www.readbyqxmd.com/read/30632670/proteomic-analysis-of-endothelial-cells-exposed-to-ultrasmall-nanoparticles-reveals-disruption-in-paracellular-and-transcellular-transport
#8
Jacob Kuruvilla, Narges Bayat, Susana Cristobal
The large interactive surfaces of nanoparticles increase the opportunities to develop nanoparticles for vascular targeting. Proteomic analysis of endothelial cells exposed to nanoparticles reveals the cellular response and turns the focus into the impairment of the endothelial permeability. Here, we combined quantitative proteomics and transcriptome sequencing to evaluate the effects of exposure to sub-lethal concentrations of TiO2 -USNPs and TiO2 -NPs on human dermal microvascular endothelial cells. Endothelial cells react to preserve the semi-permeable properties that are essential for vascular tissue fluid homeostasis, vascular development and angiogenesis...
January 11, 2019: Proteomics
https://www.readbyqxmd.com/read/30628183/large-scale-analysis-of-redox-sensitive-conditionally-disordered-protein-regions-reveals-their-widespread-nature-and-key-roles-in-high-level-eukaryotic-processes
#9
Gábor Erdős, Bálint Mészáros, Dana Reichmann, Zsuzsanna Dosztányi
Recently developed quantitative redox proteomic studies enable the direct identification of redox-sensing cysteine residues that regulate the functional behavior of target proteins in response to changing levels of reactive oxygen species (ROS). At the molecular level, redox regulation can directly modify the active sites of enzymes, although a growing number of examples indicate the importance of an additional underlying mechanism that involves conditionally disordered proteins. These proteins alter their functional behavior by undergoing a disorder-to-order transition in response to changing redox conditions...
January 9, 2019: Proteomics
https://www.readbyqxmd.com/read/30592560/does-intrinsic-disorder-in-proteins-favors-their-interaction-with-lipids
#10
Evgenia Deryusheva, Ekaterina Nemashkalova, Marie Galloux, Charels-Adrien Richard, Jean-François Eléouët, Denis Kovacs, Karo Van Belle, Peter Tompa, Vladimir N Uversky, Sergei Permyakov
Intrinsically disordered proteins (IDPs) are implicated in a range of human diseases, some of which are associated with ability of certain IDPs to bind lipids. Although the presence of solvent-exposed hydrophobic regions in IDPs should favor their interactions with low-molecular-weight hydrophobic/amphiphilic compounds, this hypothesis has not been systematically explored as of yet. In this study, analysis of the DisProt database with regard to the presence of lipid-binding IDPs (LBIDPs) reveals that they comprise at least 15% of DisProt entries...
December 28, 2018: Proteomics
https://www.readbyqxmd.com/read/30592551/toward-standardization-of-mesenchymal-stromal-cell-derived-extracellular-vesicles-for-therapeutic-use-a-call-for-action
#11
Santiago Roura, Antoni Bayes-Genis
Extracellular vesicles (EVs), which include a variety of nano-sized membrane-encapsulated particles, are released to the extracellular microenvironment by the vast majority of cells and carry lipids, proteins, mRNA, and miRNA or non-coding RNA. Increasing evidence suggests the great versatility and potential of EV-based applications in humans. In this issue, van Balkom et al. explore and compare the reported proteomic signature of mesenchymal stromal cell (MSC)-derived small EVs. In particular, their paper offers a valuable approach and point of view on MSC-EV manufacturing and therapeutic potential...
December 28, 2018: Proteomics
https://www.readbyqxmd.com/read/30585401/absolute-quantification-of-all-identified-plasma-proteins-from-swath-data-for-biomarker-discovery
#12
Shawn J Rice, Xin Liu, Jianhong Zhang, Chandra P Belani
The current state of proteomics requires a choice between targeted and global discovery methods. We have established and optimized a method that combines targeted and data-independent acquisition for absolute quantification of all identified plasma proteins in a single Sequential Window Acquisition of all THeoretical fragment ions (SWATH) acquisition run using a panel of Spike-In Standards (SIS). We compared the Absolute Quantification (AQ) of SWATH and Multiple-Reaction Monitoring-High Resolution (MRM-HR) acquisition methods using the 100 protein PlasmaDive SIS panel spiked into non-depleted human plasma...
December 25, 2018: Proteomics
https://www.readbyqxmd.com/read/30582284/exosomes-derived-from-human-primary-and-metastatic-colorectal-cancer-cells-contribute-to-functional-heterogeneity-of-activated-fibroblasts-by-reprogramming-their-proteome
#13
Alin Rai, David W Greening, Maoshan Chen, Rong Xu, Hong Ji, Richard J Simpson
Cancer-associated fibroblasts (CAFs) are a heterogeneous population of activated fibroblasts that constitute a dominant cellular component of the tumour microenvironment (TME) performing distinct functions. Here, we investigated the role of tumour-derived exosomes in activating quiescent fibroblasts into distinct functional subtypes. Proteomic profiling and functional dissection revealed that early (SW480) and late-stage (SW620) colorectal cancer (CRC) cell-derived exosomes both activated normal quiescent fibroblasts (α-SMA- , CAV+ , FAP+ , VIM+ ) into CAF-like fibroblasts (α-SMA+ , CAV- FAP+ , VIM+ )...
December 23, 2018: Proteomics
https://www.readbyqxmd.com/read/30578658/vero-cell-proteomic-changes-induced-by-zika-virus-infection
#14
Kathleen K M Glover, Ang Gao, Ali Zahedi-Amiri, Kevin M Coombs
The re-emergence, and recent spread of Zika virus (ZIKV), has raised significant global concerns due to lack of information in patient diagnosis and management. Thus, in addition to gaining more basic information about ZIKV biology, appropriate interventions and management strategies are being sought to control ZIKV-associated diseases and its spread. This study's objective was to identify host cell proteins that are significantly dysregulated during ZIKV infection. We used SOMAScan® , a novel aptamer-based assay, to simultaneously screen >1300 host proteins to detect ZIKV-induced host protein dysregulation at multiple time points during infection...
December 22, 2018: Proteomics
https://www.readbyqxmd.com/read/30578603/ms-rescue-a-computational-pipeline-to-increase-the-quality-and-yield-of-immunopeptidomics-experiments
#15
Massimo Andreatta, Annalisa Nicastri, Xu Peng, Gemma Hancock, Lucy Dorrell, Nicola Ternette, Morten Nielsen
Liquid chromatography tandem mass spectrometry (LC-MS/MS) has become the standard platform for the characterization of immunopeptidomes, the collection of peptides naturally presented by MHC molecules to the cell surface. The protocols and algorithms used for immunopeptidomics data analysis are based on tools developed for traditional bottom-up proteomics, that address the identification of peptides generated by tryptic digestion. Such algorithms are generally not tailored to the specific requirements of MHC ligand identification and, as a consequence, immunopeptidomics datasets suffer from dismissal of informative spectral information and high false discovery rates...
December 21, 2018: Proteomics
https://www.readbyqxmd.com/read/30578591/intact-glycopeptide-analysis-of-influenza-a-h1n1-09-neuraminidase-revealing-the-effects-of-host-and-glycosite-location-on-site-specific-glycan-structures
#16
Bojing Zhu, Jiechen Shen, Ting Zhao, Haihai Jiang, Tianran Ma, Jie Zhang, Liuyi Dang, Ni Gao, Yingwei Hu, Yi Shi, Shisheng Sun
Influenza H1N1 virus has posed serious threat to human health. The glycosylation of neuraminidase (NA) could affect the infectivity and virulence of influenza virus, but detailed site-specific glycosylation information of NA is still missing. In this study, intact glycopeptide analysis was performed on an influenza NA (A/H1N1/California/2009) that was expressed in human 293T and insect Hi-5 cells. Our data indicated that three of four potential N-linked glycosylation sites were glycosylated, including one partial glycosylation site from both cell lines...
December 21, 2018: Proteomics
https://www.readbyqxmd.com/read/30561828/oncogenic-regulation-of-extracellular-vesicle-proteome-and-heterogeneity
#17
REVIEW
Dongsic Choi, Cristiana Spinelli, Laura Montermini, Janusz Rak
Mutational and epigenetic driver events profoundly alter intercellular communication pathways in cancer. This effect includes deregulated release, molecular composition, and biological activity of extracellular vesicles (EVs), membranous cellular fragments ranging from a few microns to less than 100 nanometers in diameter and filled with bioactive molecular cargo (proteins, lipids and nucleic acids). While EVs are usually classified on the basis of their physical properties and biogenetic mechanisms recent analyses of their proteome suggest a larger than expected molecular diversity, a notion that is also supported by multicolour nano-flow cytometry and other emerging technology platforms designed to analyze single EVs...
December 18, 2018: Proteomics
https://www.readbyqxmd.com/read/30557447/analysing-the-secretome-of-gut-microbiota-as-the-next-strategy-for-early-detection-of-colorectal-cancer
#18
REVIEW
Putri-Intan-Hafizah Megat Mohd Azlan, Siok-Fong Chin, Teck Yew Low, Neoh Hui-Min, Rahman Jamal
Dysbiosis of gut microbiome can contribute to inflammation, and subsequently initiation and progression of colorectal cancer (CRC). Throughout these stages, various proteins and metabolites are secreted to the external environment by microorganisms or the hosts themselves. Studying these proteins may help enhance our understanding of the host-microorganism relationship or they may even serve as useful biomarkers for CRC. However, secretomic studies of gut microbiome of CRC patients, until now, are scarcely performed...
December 17, 2018: Proteomics
https://www.readbyqxmd.com/read/30556651/ucp2-overexpression-redirects-glucose-into-anabolic-metabolic-pathways
#19
Annapoorna Sreedhar, Teresa Cassell, Parker Smith, Daiwei Lu, Hyung W Nam, Andrew N Lane, Yunfeng Zhao
Uncoupling protein 2 (UCP2) is often upregulated in cancer cells. The UCP2 upregulation is positively correlated with enhanced proliferation, tumorigenesis, and metabolic alterations, thus suggesting that UCP2 upregulation could play a key role in sensing metabolic changes to promote tumorigenesis. To determine the global metabolic impact of UCP2 upregulation, we used 13 C6 glucose as a source molecule to 'trace' the metabolic fate of carbon atoms derived from glucose. UCP2 overexpression in skin epidermal cells enhanced the incorporation of 13 C-label to pyruvate, TCA cycle intermediates, nucleotides, and amino acids, suggesting that UCP2 upregulation reprograms cellular metabolism towards macromolecule synthesis...
December 17, 2018: Proteomics
https://www.readbyqxmd.com/read/30537342/towards-the-molecular-deciphering-of-pomacea-canaliculata-immunity-first-proteomic-analysis-of-circulating-hemocytes
#20
Federica Boraldi, Francesco D Lofaro, Alice Accorsi, Eric Ross, Davide Malagoli, F Boraldi, F D Lofaro
Pomacea canaliculata is a freshwater snail with interesting biological features that include invasiveness, human parasite hosting and adult regeneration. Its immune system may represent the target for strategies aimed at controlling the spread of the snail population and its hosting of the human parasite Angiostrongylus cantonensis. Moreover, immune functions likely have a role in the snail's ability to wound heal and regenerate. Despite its importance in multiple processes, very little is known about the molecular basis of P...
December 10, 2018: Proteomics
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