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Proteomics

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https://www.readbyqxmd.com/read/29150981/systematic-proteomic-analysis-of-protein-methylation-in-prokaryotes-and-eukaryotes-revealed-distinct-substrate-specificity
#1
Min Zhang, Jun-Yu Xu, Hao Hu, Bang-Ce Ye, Minjia Tan
The studies of protein methylation mainly focus on lysine and arginine residues due to their diverse roles in essential cellular processes from gene expression to signal transduction. Nevertheless, atypical protein methylation occurring on amino acid residues, such as glutamine and glutamic acid, was largely neglected until recently. In addition, the systematic analysis for the distribution of methylation on different amino acids in various species is still lacking, which hinders our understanding of its functional roles...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29150924/comprehensive-profiling-of-lysine-acetylome-in-baculovirus-infected-silkworm-bombyx-mori-cells
#2
Dongbing Hu, Shengjie Xue, Cui Zhao, Ming Wei, Huihui Yan, Yanping Quan, Wei Yu
Bombyx mori is one of the key lepidopteran model species, and is economically important for silk production and proteinaceous drug expression. Baculovirus and insect host are important natural biological models for studying host-pathogen interactions. The impact of Bombyx mori nucleopolyhedrovirus (BmNPV) infection on the proteome and acetylome of Bombyx mori ovarian (BmN) cells were explored to facilitate a better understanding of infection-driven interactions between BmNPV and host in vitro. The proteome and acetylome were profiled through 6-plex Tandem mass tag (TMT) labelling-based quantitative proteomics...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29150671/urothelial-cancer-proteomics-provides-both-prognostic-and-functional-information
#3
Guillermo de Velasco, Lucia Trilla-Fuertes, Angelo Gamez-Pozo, Maria Urbanowicz, Gustavo Ruiz-Ares, Juan M Sepúlveda, Guillermo Prado-Vazquez, Jorge M Arevalillo, Andrea Zapater-Moros, Hilario Navarro, Rocio Lopez-Vacas, Ray Manneh, Irene Otero, Felipe Villacampa, Jesus M Paramio, Juan Angel Fresno Vara, Daniel Castellano
Traditionally, bladder cancer has been classified based on histology features. Recently, some works have proposed a molecular classification of invasive bladder tumors. To determine whether proteomics can define molecular subtypes of  muscle invasive urothelial cancer (MIUC) and allow evaluating the status of biological processes and its clinical value. 58 MIUC patients who underwent curative surgical resection at our institution between 2006 and 2012 were included. Proteome was evaluated by high-throughput proteomics in routinely archive FFPE tumor tissue...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150651/comprehensive-functional-enrichment-analysis-of-male-infertility
#4
Seyed Morteza Razavi, Marjan Sabbaghian, Mahdi Jalili, Adeleh Divsalar, Olaf Wolkenhauer, Ali Salehzadeh-Yazdi
Spermatogenesis is a multifactorial process that forms differentiated sperm cells in a complex microenvironment. This process involves the genome, epigenome, transcriptome, and proteome to ensure the stability of the spermatogonia and supporting cells. The identification of signaling pathways linked to infertility has been hampered by the inherent complexity and multifactorial aspects of spermatogenesis. Systems biology is a promising approach to unveil underlying signaling pathways and genes and identify putative biomarkers...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150633/ketamine-s-antidepressant-effect-is-mediated-by-energy-metabolism-and-antioxidant-defense-system
#5
Katja Weckmann, Michael J Deery, Julie A Howard, Renata Feret, John M Asara, Frederik Dethloff, Michaela D Filiou, Jamie Iannace, Christiana Labermaier, Giuseppina Maccarrone, Christian Webhofer, Larysa Teplytska, Kathryn Lilley, Marianne B Müller, Christoph W Turck
Fewer than 50% of all patients with major depressive disorder (MDD) treated with currently available antidepressants (ADs) show full remission. Moreover, about one third of the patients suffering from MDD does not respond to conventional ADs and develop treatment-resistant depression (TRD). Ketamine, a non-competitive, voltage-dependent N-Methyl-D-aspartate receptor (NMDAR) antagonist, has been shown to have a rapid antidepressant effect, especially in patients suffering from TRD. Hippocampi of ketamine-treated mice were analysed by metabolome and proteome profiling to delineate ketamine treatment-affected molecular pathways and biosignatures...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150517/multi-omics-reveal-the-lifestyle-of-the-acidophilic-mineral-oxidizing-model-species-leptospirillum-ferriphilum-t
#6
Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150433/tyrosine-phosphorylation-of-munc18-1-inhibits-synaptic-transmission-by-preventing-snare%C3%A2-assembly
#7
Marieke Meijer, Bernhard Dörr, Hanna Ca Lammertse, Chrysanthi Blithikioti, Jan Rt van Weering, Ruud Fg Toonen, Thomas H Söllner, Matthijs Verhage
Tyrosine kinases are important regulators of synaptic strength. Here, we describe a key component of the synaptic vesicle release machinery, Munc18-1, as a phosphorylation target for neuronal Src family kinases (SFKs). Phosphomimetic Y473D mutation of a SFK phosphorylation site previously identified by brain phospho-proteomics abolished the stimulatory effect of Munc18-1 on SNARE complex formation ("SNARE-templating") and membrane fusion in vitro Furthermore, priming but not docking of synaptic vesicles was disrupted in hippocampal munc18-1-null neurons expressing Munc18-1Y473D Synaptic transmission was temporarily restored by high-frequency stimulation, as well as by a Munc18-1 mutation that results in helix 12 extension, a critical conformational step in vesicle priming...
November 17, 2017: EMBO Journal
https://www.readbyqxmd.com/read/29150244/proteomic-analysis-of-follicular-fluid-from-tropically-adapted-goats
#8
Alexandre R Paula Junior, Mauricio F van Tilburg, Marina D P Lobo, Ana C O Monteiro-Moreira, Renato A Moreira, Carlos H S Melo, Joanna M G Souza-Fabjan, Airton A Araújo, Luciana M Melo, Dárcio I A Teixeira, Arlindo A Moura, Vicente J F Freitas
The present study was conducted to characterize the major proteome of ovarian follicular fluid from locally-adapted, "Canindé" goats in the northeast of Brazil. Eight estrous cycling goats received a hormonal treatment consisting of medroxyprogesterone acetate, D-cloprostenol and FSH. Fluid was collected by laparoscopy from small (<3mm), medium (3-4mm) and large (>4mm) follicles and then, proteins were analyzed by 2-D SDS-PAGE and tandem mass spectrometry. Thirty-six proteins were identified in the goat follicular fluid, including albumin, immunoglobulins, ceruloplasmin, complement factor B, alpha-1B-glycoprotein precursor, serotransferrin, complement C3 and serpins, among others...
November 6, 2017: Animal Reproduction Science
https://www.readbyqxmd.com/read/29149817/high-density-lipoprotein-hdl-dysfunction-and-future-of-hdl
#9
Sibel Ertek
Although high density lipoprotein cholesterol (HDL-C) levels are inversely proportional to cardiovascular risk in many studies, recent pharmacological interventional studies with HDL-C raising strategies did not show a benefit in terms of vascular events. The HDL particle is heterogenous with anti-atherogenic functions and non-vascular effects. Many factors affect HDL components and may either cause compositional changes, post-translational modifications of proteins, or alter lipids and other cargo molecules; generally these factors cause more than one of these changes, resulting in functional differences...
November 16, 2017: Current Vascular Pharmacology
https://www.readbyqxmd.com/read/29149599/autophagosomal-content-profiling-reveals-an-lc3c-dependent-piecemeal-mitophagy-pathway
#10
François Le Guerroué, Franziska Eck, Jennifer Jung, Tatjana Starzetz, Michel Mittelbronn, Manuel Kaulich, Christian Behrends
Autophagy allows the degradation of cytosolic endogenous and exogenous material in the lysosome. Substrates are engulfed by double-membrane vesicles, coined autophagosomes, which subsequently fuse with lysosomes. Depending on the involvement of specific receptor proteins, autophagy occurs in a selective or nonselective manner. While this process is well understood at the level of bulky cargo such as mitochondria and bacteria, we know very little about individual proteins and protein complexes that are engulfed and degraded by autophagy...
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29149484/comparative-analysis-of-proteomes-between-diabetic-and-normal-human-sperm-insights-into-the-effects-of-diabetes-on-male-reproduction-based-on-the-regulation-of-mitochondria-related-proteins
#11
Tian An, Yue-Fen Wang, Jia-Xian Liu, Yan-Yun Pan, Yu-Fei Liu, Zhong-Chen He, Fang-Fang Mo, Jun Li, Li-Hua Kang, Yu-Jie Gu, Bo-Han Lv, Si-Huan Gao, Guang-Jian Jiang
This study sought to identify sources of the reduced fertility of men with type 2 diabetes mellitus. Significant reductions in semen volume, sperm concentration, and total sperm count were observed in diabetic individuals, while transmission electron microscopy revealed that the structure of mitochondria in the tail of sperm from diabetic patients was damaged. Proteins potentially associated with these sperm defects were identified using proteomics. Isobaric tagging for relative and absolute quantitation labeling and high-performance liquid chromatography-tandem mass spectrometry allowed us to identify 357 proteins significantly differentially expressed in diabetic versus control semen (>1...
November 17, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/29149247/quantitative-proteomic-profiling-of-bovine-follicular-fluid-during-follicle-development
#12
Rodrigo de Andrade Ferrazza, Elizabeth Moreira Dos Santos Schmidt, Monika Mihm Carmichael, Fabiana Ferreira de Souza, Richard Burchmore, Roberto Sartori, Peter David Eckersall, João Carlos Pinheiro Ferreira
Bovine follicular fluid (FF) constitutes the microenvironment of follicles and includes various biologically active proteins. We performed a study involving 18 healthy non-lactating Holstein cows to determine the protein expression profile of FF at key-stages of follicular development. Follicles were individually aspirated in vivo at pre-deviation (F1∼7.0mm); deviation (F1∼8.5mm); post-deviation (F1∼12.0mm); and pre-ovulatory stages of follicle development, which were confirmed by measurement of follicular estradiol and progesterone concentrations...
November 15, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29148792/proteomic-markers-of-the-functional-sperm-population-in-bovines-1-comparison-of-low-and-high-density-spermatozoa-following-cryopreservation
#13
Olivier D'Amours, Gilles Frenette, Sylvie Bourassa, Ezequiel Calvo, Patrick Blondin, Robert Sullivan
Mammalian semen contains a heterogeneous population of sperm cells. This heterogeneity results from variability in the complex processes of cell differentiation in the testis, biochemical modifications undergone by spermatozoa during transit along the male reproductive tract, interactions with secretions from accessory sex glands at ejaculation, and, in the context of reproductive technologies, in the ability of ejaculated spermatozoa to resist damage associated with freeze-thaw procedures. When submitted to density gradient centrifugation, ejaculated spermatozoa distribute themselves into two distinct populations: a low-density population characterized by low motility parameters, and a high-density population with high motility characteristics...
November 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29148239/metabolic-signature-of-microvescicles-from-umbilical-cord-mesenchimal-stem-cells-of-preterm-and-term-infants
#14
Maurizio Bruschi, Laura Santucci, Silvia Ravera, Martina Bartolucci, Andrea Petretto, Daniela Calzia, Gianmarco Ghiggeri, Luca A Ramenghi, Giovanni Candiano, Isabella Panfoli
PURPOSE: Microvesicles, 200-1000 nm bodies budding from the cell plasma membrane, are a promising source of biomarkers. This study aimed at comparing the proteome of Microvesicles collected by ultracentrifugation from cultured Mesenchymal Stem Cells from Human Umbilical Cord of Preterm newborns(<34-weeks gestational age) in comparison to infants at Term(≥37 weeks). This discovery study was designed to establish the signature of prematurity. EXPERIMENTAL DESIGN: Orbitrap mass spectrometry, statistical, bioinformatics and biochemical analyses were employed...
November 16, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29148229/proteomics-of-diabetes-obesity-and-related-disorders
#15
EDITORIAL
Robert Moulder, Domitille Schvartz, David R Goodlett, Loïc Dayon
No abstract text is available yet for this article.
November 16, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29148176/differential-proteomic-analysis-reveals-protein-networks-and-pathways-that-may-contribute-to-helicobacter-pylori-fkbp-type-ppiase-associated-gastric-diseases
#16
Yanmei Zhu, Yuehua Gong, Aodi Li, Moye Chen, Dan Kang, Jun Liu, Yuan Yuan
PURPOSE: Though Helicobacter pylori (H. pylori) has been classified as class I carcinogen, key virulence factor generated by H. pylori that causes gastric cancer remains to be fully determined. Recently, we identified a gastric cancer-associated H. pylori gene, peptidylprolyl isomerase-FK506 binding protein (PPIase-FKBP), and showed that PPIase-FKBP was capable of inducing oncogenic transformation of gastric epithelial cells. But its mechanism was unclear. EXPERIMENTAL DESIGN: We carried out a comparative proteomic analysis of human gastric epithelial cells that either express PPIase-FKBP or green fluorescent protein (GFP) using two-dimensional (2-D) gel electrophoresis and then matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS/MS)...
November 16, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29148164/protein-profiling-of-non-model-plant-cuminum-cyminum-by-gel-based-proteomic-approach
#17
Uzma Zaman, Henning Urlaub, Atiya Abbasi
INTRODUCTION: Cumin (Cuminum cyminum), a popular spice has been widely used in traditional medicine to cure various ailments. Despite the existence of scientific literature about its pharmacological properties, no successful proteome profiling has yet been attempted. OBJECTIVE: To optimise extraction of cumin proteins and analyse its profile by shotgun proteomics, using one-dimensional electrophoresis coupled with nano-ESI-LC-MS/MS. METHODOLOGY: As a first step, we have compared three extraction protocols for total proteins extraction from cumin...
November 16, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/29147916/integrative-analysis-of-proteomics-data-to-obtain-clinically-relevant-markers
#18
Nathan Salomonis
The analysis of proteomics data can be significantly challenging. Beyond the technical challenges of accurately identifying and quantifying peptides, identifying the most biologically coherent set of biomarkers can be a particularly daunting step. In this chapter, we will review a series of methods implemented in the software AltAnalyze that can be used to normalize proteomics peptide counts, identify a minimal set of the most distinguishing morbidity-associated biomarkers, and connect up these results to known pathways and interacting protein and regulatory networks...
November 18, 2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29147852/enhanced-peptide-detection-toward-single-neuron-proteomics-by-reversed-phase-fractionation-capillary-electrophoresis-mass-spectrometry
#19
Sam B Choi, Camille Lombard-Banek, Pablo Muñoz-LLancao, M Chiara Manzini, Peter Nemes
The ability to detect peptides and proteins in single cells is vital for understanding cell heterogeneity in the nervous system. Capillary electrophoresis (CE) nanoelectrospray ionization (nanoESI) provides high-resolution mass spectrometry (HRMS) with trace-level sensitivity, but compressed separation during CE challenges protein identification by tandem HRMS with limited MS/MS duty cycle. Here, we supplemented ultrasensitive CE-nanoESI-HRMS with reversed-phase (RP) fractionation to enhance identifications from protein digest amounts that approximate to a few mammalian neurons...
November 16, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29147069/expression-profiling-of-long-noncoding-rna-splice-variants-in-human-microvascular-endothelial-cells-lipopolysaccharide-effects-in-vitro
#20
Imran H Chowdhury, Hema P Narra, Abha Sahni, Kamil Khanipov, Casey L C Schroeder, Jignesh Patel, Yuriy Fofanov, Sanjeev K Sahni
Endothelial cell interactions with lipopolysaccharide (LPS) involve both activating and repressing signals resulting in pronounced alterations in their transcriptome and proteome. Noncoding RNAs are now appreciated as posttranscriptional and translational regulators of cellular signaling and responses, but their expression status and roles during endothelial interactions with LPS are not well understood. We report on the expression profile of long noncoding (lnc) RNAs of human microvascular endothelial cells in response to LPS...
2017: Mediators of Inflammation
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