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Molecular & Cellular Proteomics: MCP

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https://www.readbyqxmd.com/read/27895139/human-spermatozoa-quantitative-proteomic-signature-classifies-normo-and-asthenozoospermia
#1
Mayank Saraswat, Sakari Joenväärä, Tushar Jain, Anil Kumar Tomar, Ashima Sinha, Sarman Singh, Savita Yadav, Risto Renkonen
Scarcely understood defects lead to asthenozoospermia which results in poor fertility outcomes. Incomplete knowledge of these defects hinders the development of new therapies and reliance on interventional therapies, such as in vitro fertilization, increases. Sperm cells, being transcriptionally and translationally silent, necessitate the proteomic approach to study the sperm function. We have performed a differential proteomics analysis of human sperm and seminal plasma and identified and quantified 667 proteins in sperm and 429 proteins in seminal plasma dataset which were used for further analysis...
November 28, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27890865/csf-pr-2-0-an-interactive-literature-guide-to-quantitative-cerebrospinal-fluid-mass-spectrometry-data-from-neurodegenerative-disorders
#2
Astrid Guldbrandsen, Yehia Farag, Ann C Kroksveen, Eystein Oveland, Ragnhild R Lereim, Jill A Opsahl, Kjell-Morten Myhr, Frode S Berven, Harald Barsnes
The rapidly growing number of biomedical studies supported by mass spectrometry based quantitative proteomics data has made it increasingly difficult to obtain an overview of the current status of the research field. A better way of organizing the biomedical proteomics information from these studies and making it available to the research community is therefore called for. In the presented work, we have investigated scientific publications describing the analysis of the cerebrospinal fluid proteome in relation to multiple sclerosis, Parkinsons disease and Alzheimers disease...
November 27, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27879288/multi-omics-analysis-of-serum-samples-demonstrates-reprogramming-of-organ-functions-via-systemic-calcium-mobilization-and-platelet-activation-in-metastatic-melanoma
#3
Besnik Muqaku, Martin Eisninger, Samuel M Meier, Ammar Tahir, Tobias Prokop, Sebastian Haferkamp, Astrid Slany, Albrecht Reichle, Christopher Gerner
Pathophysiologies of cancer-associated syndroms such as cachexia are poorly understood and no routine biomarkers have been established, yet. Using shotgun proteomics, known marker molecules including PMEL, CRP, SAA and CSPG4 were found deregulated in patients with metastatic melanoma. Targeted analysis of 58 selected proteins with multiple reaction monitoring was applied for independent data verification. In three patients, two of which suffered from cachexia, a tissue damage signature was determined, consisting of nine proteins, PLTP, CD14, TIMP1, S10A8, S10A9, GP1BA, PTPRJ, CD44 and C4A, as well as increased levels of glycine and asparagine, and decreased levels of polyunsaturated phosphatidylcholine concentrations, as determined by targeted metabolomics...
November 22, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27864322/e-coli-proteome-microarrays-identified-the-substrates-of-clpyq-protease
#4
Chih-Hsuan Tsai, Yu-Hsuan Ho, Tzu-Cheng Sung, Whei-Fen Wu, Chien-Sheng Chen
Proteolysis is a vital mechanism to regulate the cellular proteome in all kingdoms of life, and ATP-dependent proteases play a crucial role within this process. In Escherichia coli, ClpYQ is one of the primary ATP-dependent proteases. In addition to function with removals of abnormal peptides in the cells, ClpYQ degrades regulatory proteins if necessary and thus let cells adjust to various environmental conditions. In E. coli, SulA, RcsA, RpoH and TraJ as well as RNase R, have been identified as natural protein substrates of ClpYQ...
November 18, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27852749/quantitative-proteomic-analysis-of-replicative-and-non-replicative-forms-reveals-important-insights-into-chromatin-biology-of-trypanosoma-cruzi
#5
Teresa Cristina Leandro de Jesus, Simone Guedes Calderano, Francisca Nathalia de Luna Vitorino, Ricardo Pariona Llanos, Mariana de Camargo Lopes, Christiane Bezerra de Araújo, Otavio Henrique Thiemann, Marcelo da Silva Reis, Maria Carolina Elias, Julia Pinheiro Chagas da Cunha
Chromatin associated proteins are key regulators of many important processes in the cell. Trypanosoma cruzi, a protozoa flagellate that causes Chagas disease, alternates between replicative and non-replicative forms accompanied by a shift on global transcription levels and by changes in its chromatin architecture. Here, we investigated the T. cruzi chromatin proteome using three different protocols and compared it between replicative (epimastigote) and non-replicative (trypomastigote) forms by high-resolution mass spectrometry...
November 16, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27852748/quantitative-gtpase-affinity-purification-identifies-rho-family-protein-interaction-partners
#6
Florian E Paul, Henrik Zauber, Laura von Berg, Oliver Rocks, Oliver Daumke, Matthias Selbach
Although Rho GTPases are essential molecular switches involved in many cellular processes, an unbiased experimental comparison of their interaction partners was not yet performed. Here, we develop quantitative GTPase affinity purification (qGAP) to systematically identify interaction partners of six Rho GTPases (Cdc42, Rac1, RhoA, RhoB, RhoC, RhoD) depending on their nucleotide loading state. The method works with cell line or tissue-derived protein lysates in combination with SILAC-based or label free quantification, respectively...
November 16, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27852747/enzyme-kinetics-for-complex-system-enables-accurate-determination-of-specificity-constants-of-numerous-substrates-in-a-mixture-by-proteomics-platform
#7
Zhenzhen Deng, Jiawei Mao, Yan Wang, Hanfa Zou, Mingliang Ye
Many important experiments in proteomics including protein digestion, enzyme substrate screening, enzymatic labeling, etc., involve the enzymatic reactions in a complex system where numerous substrates coexists with an enzyme. However, the enzyme kinetics in such a system remains unexplored and poorly understood. Herein, we derived and validated the kinetics equations for the enzymatic reactions in complex system. We developed an iteration approach to depict the enzymatic reactions in complex system. It was validated by 630 time course points from 24 enzymatic reaction experiments and was demonstrated to be a powerful tool to simulate the reactions in the complex system...
November 16, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27836980/proteome-profiling-outperforms-transcriptome-profiling-for-co-expression-based-gene-function-prediction
#8
Jing Wang, Zihao Ma, Steven A Carr, Philipp Mertins, Hui Zhang, Zhen Zhang, Daniel W Chan, Matthew J C Ellis, R Reid Townsend, Richard D Smith, Jason E McDermott, Xian Chen, Amanda G Paulovich, Emily S Boja, Mehdi Mesri, Christopher R Kinsinger, Henry Rodriguez, Karin D Rodland, Daniel C Liebler, Bing Zhang
Co-expression of mRNAs under multiple conditions is commonly used to infer co-functionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for co-expression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein co-expression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC)...
November 11, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27834735/extracellular-protein-phosphorylation-the-neglected-side-of-the-modification
#9
Eva Klement, Katalin F Medzihradszky
The very existence of extracellular phosphorylation has been questioned for a long time, although casein phosphorylation was discovered a century ago. In addition, several modification sites localized on secreted proteins or on extracellular or lumenal domains of transmembrane proteins have been catalogued in large scale phosphorylation analyses, though in most such studies this aspect of cellular localization was not considered. Our review presents examples when additional analyses were performed on already public datasets that revealed a wealth of information about this "neglected side" of the modification...
November 10, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27834734/nano-liquid-chromatography-orbitrap-ms-based-quantitative-proteomics-reveals-differences-between-the-mechanisms-of-action-of-carnosic-acid-and-carnosol-in-colon-cancer-cells
#10
Alberto Valdés, Virginia García-Cañas, Konstantin A Artemenko, Carolina Sim Oacute, Jonas Bergquist, Alejandro Cifuentes
Carnosic acid (CA) and carnosol (CS) are two structurally related diterpenes present in rosemary herb (Rosmarinus officinalis). Although several studies have demonstrated that both diterpenes can scavenge free radicals and interfere in cellular processes such as cell proliferation, they may not necessarily exert the same effects at the molecular level. In this work, a shotgun proteomics study based on stable isotope dimethyl labeling (DML) and nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) has been performed to identify the relative changes in proteins and to gain some light on the specific molecular targets and mechanisms of action of CA and CS in HT-29 colon cancer cells...
November 10, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27834733/quantitative-proteomics-reveals-fundamental-regulatory-differences-in-oncogenic-hras-and-idh1-driven-astrocytoma
#11
Sophia Doll, Anatoly Urisman, Juan A Oses-Prieto, David Arnott, Alma L Burlingame
Glioblastoma multiformes (GBMs) are high-grade astrocytomas and the most common brain malignancies. Primary GBMs are often associated with disturbed RAS signaling, and expression of oncogenic HRAS results in a malignant phenotype in glioma cell lines. Secondary GBMs arise from lower-grade astrocytomas, have slower progression than primary tumors, and contain IDH1 mutations in over 70% of cases. Despite significant amount of accumulating genomic and transcriptomic data, the fundamental mechanistic differences of gliomagenesis in these two types of high-grade astrocytoma remain poorly understood...
November 10, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27803151/proteome-scale-binary-interactomics-in-human-cells
#12
Sam Lievens, José Van der Heyden, Delphine Masschaele, Leentje De Ceuninck, Ioanna Petta, Surya Gupta, Veronic De Puysseleyr, Virginie Vauthier, Irma Lemmens, Dries J H De Clercq, Dieter Defever, Nele Vanderroost, Anne-Sophie De Smet, Sven Eyckerman, Serge Van Calenbergh, Lennart Martens, Karolien De Bosscher, Claude Libert, David E Hill, Marc Vidal, Jan Tavernier
Because proteins are the main mediators of most cellular processes they are also prime therapeutic targets. Identifying physical links among proteins and between drugs and their protein targets is essential in order to understand the mechanisms through which both proteins themselves and the molecules they are targeted with act. Thus, there is a strong need for sensitive methods that enable mapping out these biomolecular interactions. Here we present a robust and sensitive approach to screen proteome-scale collections of proteins for binding to proteins or small molecules using the well validated MAPPIT (Mammalian Protein-Protein Interaction Trap) and MASPIT (Mammalian Small Molecule-Protein Interaction Trap) assays...
December 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27799293/global-dynamic-proteome-study-of-a-pellicle-forming-acinetobacter-baumannii-strain
#13
Takfarinas Kentache, Ahmed Ben Abdelkrim, Thierry Jouenne, Emmanuelle De, Julie Hardouin
Since several decades, many bacteria, among which A. baumannii, have shown their ability to colonize the upper surface of static liquids, forming a biofilm at the air-liquid interface named pellicle. Despite the ubiquity of these pellicles in both natural and artificial environments, few studies have investigated this biofilm type. The present data set provides the first description of the whole proteome of A. baumannii cells grown as pellicle, using a label-free mass spectrometry approach. Results accord with the general findings reporting that sessile bacteria are far more resistant to detrimental conditions than their planktonic counterparts, by the accumulation of stress proteins...
October 31, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27784728/quantitative-protein-profiling-of-chlamydia-trachomatis-growth-forms-reveals-defense-strategies-against-tryptophan-starvation
#14
Ole Østergaard, Frank Follmann, Anja W Olsen, Niels H Heegaard, Peter Andersen, Ida Rosenkrands
Chlamydia trachomatis is one of the most common sexually transmitted bacterial pathogens in humans. The infection is often asymptomatic and can lead to chronic manifestations. The infectious elementary body and the replicating reticulate body are the two growth forms in the normal developmental cycle. Under the influence of interferon-γ, the normal cycle is disrupted because of tryptophan degradation, leading to a third persistent form, the aberrant reticulate body.For the genital strain C. trachomatis D/UW-3/CX we established a quantitative, label-free proteomic approach, and identified in total 655 out of 903 (73%) predicted proteins, allowing the first quantitative comparison of all three growth forms...
December 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27777341/identification-of-novel-biomarkers-for-behcet-disease-diagnosis-using-huprot-array-approach
#15
Chao-Jun Hu, Jian-Bo Pan, Guang Song, Xiao-Ting Wen, Zi-Yan Wu, Si Chen, Wen-Xiu Mo, Feng-Chun Zhang, Jiang Qian, Heng Zhu, Yong-Zhe Li
Behcet disease (BD) is a chronic systemic vasculitis and considered as an autoimmune disease. Although rare, BD can be fatal due to ruptured vascular aneurysms or severe neurological complications. To date, no known biomarker has been reported for this disease, making it difficult to diagnosis in the clinics. To undertake this challenge, we employed the HuProt arrays, each comprised of~20,000 unique human proteins, to identify BD-specific autoantibodies using a Two-Phase strategy established previously. In Phase I, we profiled the autoimmunity on the HuProt arrays with 75 serum samples collected from 40 BD patients, 15 diagnosed autoimmune patients who suffer from Takayasu arteritis (TA; N=5)), ANCA associated vasculitis(AAV; N=5), and Sjogren's syndrome(SS; N=5), and 20 healthy subjects, and identified 20 candidate autoantigens that were significantly associated with BD...
October 24, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27777340/multi-omics-evidence-for-inheritance-of-energy-pathways-in-red-blood-cells
#16
Erin M M Weisenhorn, Thomas J van T Erve, Nicholas M Riley, John R Hess, Thomas J Raife, Joshua J Coon
Each year over 90 million units of blood are transfused worldwide. Our dependence on this blood supply mandates optimized blood management and storage. During storage, red blood cells undergo degenerative processes resulting in altered metabolic characteristics which may make blood less viable for transfusion. However, not all stored blood spoils at the same rate, a difference that has been attributed to variable rates of energy usage and metabolism in red blood cells. Specific metabolite abundances are heritable traits; however, the link between heritability of energy metabolism and red blood cell storage profiles is unclear...
December 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27770032/deficiency-in-outer-dense-fiber-1-is-a-marker-and-potential-driver-of-idiopathic-male-infertility
#17
Louise Hetherington, Elena K Schneider, David DeKretser, Charles H Muller, Hubert Hondermarck, Tony Velkov, Mark A Baker
Globally, ∼1 in 15 men of reproductive age are infertile, yet the precise mechanisms underlying their gamete failure are unknown. Although a semen analysis is performed to determine fertilizing potential, the diagnostic suitability of this analysis has been questioned in several reports, as many men, classified as infertile according to their semen analysis, subsequently turn out to be fertile. Herein, we have used a quantitative (phospho)-proteomic analysis, using enrichment on titanium dioxide followed by ion-trap mass spectrometry (LC-MS/MS), to compare the semen of infertile versus fertile males...
December 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27765818/time-resolved-analysis-of-proteome-dynamics-by-tandem-mass-tags-and-stable-isotope-labeling-in-cell-culture-tmt-silac-hyperplexing
#18
Kevin A Welle, Tian Zhang, Jennifer R Hryhorenko, Shichen Shen, Jun Qu, Sina Ghaemmaghami
Recent advances in mass spectrometry have enabled system-wide analyses of protein turnover. By globally quantifying the kinetics of protein clearance and synthesis, these methodologies can provide important insights into the regulation of the proteome under varying cellular and environmental conditions. To facilitate such analyses, we have employed a methodology that combines metabolic isotopic labeling (Stable Isotope Labeling in Cell Culture - SILAC) with isobaric tagging (Tandem Mass Tags - TMT) for analysis of multiplexed samples...
December 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27754876/salmonella-typhimurium-enzymatically-landscapes-the-host-intestinal-epithelial-cell-iec-surface-glycome-to-increase-invasion
#19
Dayoung Park, Narine Arabyan, Cynthia C Williams, Ting Song, Anupam Mitra, Bart C Weimer, Emanual Maverakis, Carlito B Lebrilla
Although gut host-pathogen interactions are glycan-mediated processes, few details are known about the participating structures. Here we employ high-resolution mass spectrometric profiling to comprehensively identify and quantitatively measure the exact modifications of native intestinal epithelial cell surface N-glycans induced by S. typhimurium infection. Sixty minutes postinfection, select sialylated structures showed decreases in terms of total number and abundances. To assess the effect of cell surface mannosylation, we selectively rerouted glycan expression on the host using the alpha-mannosidase inhibitor, kifunensine, toward overexpression of high mannose...
December 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27742740/immunoseroproteomic-profiling-in-african-american-men-with-prostate-cancer-evidence-for-an-autoantibody-response-to-glycolysis-and-plasminogen-associated-proteins
#20
Tino W Sanchez, Guangyu Zhang, Jitian Li, Liping Dai, Saied Mirshahidi, Nathan R Wall, Clayton Yates, Colwick Wilson, Susanne Montgomery, Jian-Ying Zhang, Carlos A Casiano
African American (AA) men suffer from a disproportionately high incidence and mortality of prostate cancer (PCa) compared with other racial/ethnic groups. Despite these disparities, African American men are underrepresented in clinical trials and in studies on PCa biology and biomarker discovery. We used immunoseroproteomics to profile antitumor autoantibody responses in AA and European American (EA) men with PCa, and explored differences in these responses. This minimally invasive approach detects autoantibodies to tumor-associated antigens that could serve as clinical biomarkers and immunotherapeutic agents...
December 2016: Molecular & Cellular Proteomics: MCP
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