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translational proteomics

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https://www.readbyqxmd.com/read/29351515/understanding-key-mechanisms-of-exercise-induced-cardiac-protection-to-mitigate-disease-current-knowledge-and-emerging-concepts
#1
Bianca C Bernardo, Jenny Y Y Ooi, Kate L Weeks, Natalie L Patterson, Julie R McMullen
The benefits of exercise on the heart are well recognized, and clinical studies have demonstrated that exercise is an intervention that can improve cardiac function in heart failure patients. This has led to significant research into understanding the key mechanisms responsible for exercise-induced cardiac protection. Here, we summarize molecular mechanisms that regulate exercise-induced cardiac myocyte growth and proliferation. We discuss in detail the effects of exercise on other cardiac cells, organelles, and systems that have received less or little attention and require further investigation...
January 1, 2018: Physiological Reviews
https://www.readbyqxmd.com/read/29348854/acid-ceramidase-and-its-inhibitors-a-de-novo-drug-target-and-a-new-class-of-drugs-for-killing-glioblastoma-cancer-stem-cells-with-high-efficiency
#2
Ninh B Doan, Hisham Alhajala, Mona M Al-Gizawiy, Wade M Mueller, Scott D Rand, Jennifer M Connelly, Elizabeth J Cochran, Christopher R Chitambar, Paul Clark, John Kuo, Kathleen M Schmainda, Shama P Mirza
Glioblastoma remains the most common, malignant primary cancer of the central nervous system with a low life expectancy and an overall survival of less than 1.5 years. The treatment options are limited and there is no cure. Moreover, almost all patients develop recurrent tumors, which typically are more aggressive. Therapeutically resistant glioblastoma or glioblastoma stem-like cells (GSCs) are hypothesized to cause this inevitable recurrence. Identifying prognostic biomarkers of glioblastoma will potentially advance knowledge about glioblastoma tumorigenesis and enable discovery of more effective therapies...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348603/comprehensive-list-of-sumo-targets-in-caenorhabditis-elegans-and-its-implication-for-evolutionary-conservation-of-sumo-signaling
#3
Krzysztof Drabikowski, Jacqueline Ferralli, Michal Kistowski, Jacek Oledzki, Michal Dadlez, Ruth Chiquet-Ehrismann
Post-translational modification by small ubiquitin-related modifier (SUMO) is a key regulator of cell physiology, modulating protein-protein and protein-DNA interactions. Recently, SUMO modifications were postulated to be involved in response to various stress stimuli. We aimed to identify the near complete set of proteins modified by SUMO and the dynamics of the modification in stress conditions in the higher eukaryote, Caenorhabditis elegans. We identified 874 proteins modified by SUMO in the worm. We have analyzed the SUMO modification in stress conditions including heat shock, DNA damage, arsenite induced cellular stress, ER and osmotic stress...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29344888/perseus-a-bioinformatics-platform-for-integrative-analysis-of-proteomics-data-in-cancer-research
#4
Stefka Tyanova, Juergen Cox
Mass spectrometry-based proteomics is a continuously growing field marked by technological and methodological improvements. Cancer proteomics is aimed at pursuing goals such as accurate diagnosis, patient stratification, and biomarker discovery, relying on the richness of information of quantitative proteome profiles. Translating these high-dimensional data into biological findings of clinical importance necessitates the use of robust and powerful computational tools and methods. In this chapter, we provide a detailed description of standard analysis steps for a clinical proteomics dataset performed in Perseus, a software for functional analysis of large-scale quantitative omics data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29343059/top-down-characterization-of-heavily-modified-histones-using-193-nm-ultraviolet-photodissociation-uvpd-mass-spectrometry
#5
Sylvester M Greer, Jennifer S Brodbelt
The characterization of protein post-translational modifications (PTMs) remains a significant challenge for traditional bottom-up proteomics methods owing to the lability of PTMs and the difficulty of mapping combinatorial patterns of PTMs based on analysis of small peptides. These shortcomings have accelerated interest in top-down MS/MS methods which focus on analysis of intact proteins. Mapping all protein PTMs simultaneously requires the ability to obtain extensive sequence coverage to allow confident localization of the modifications...
January 18, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29338241/characterization-of-macrophage-endogenous-s-nitrosoproteome-using-a-cysteine-specific-phosphonate-adaptable-tag-in-combination-with-tio2-chromatography
#6
Maria Ibañez-Vea, Honggang Huang, Xabier Martinez de Morentin, Estela Perez, Maria Gato, Miren Zuazo, Hugo Arasanz, Joaquin Fernandez-Irigoyen, Enrique Santamaría, Gonzalo Fernandez-Hinojal, Martin R Larsen, David Escors, Grazyna Kochan
Protein S-nitrosylation is a cysteine post-translational modification mediated by nitric oxide. An increasing number of studies highlight S-nitrosylation as an important regulator of signaling involved in numerous cellular processes. Despite of the significant progress in the development of redox proteomic methods, identification and quantification of endogeneous S-nitrosylation using high-throughput mass spectrometry-based methods is a technical challenge as this modification is highly labile. To overcome this drawback most methods induce S-nitrosylation chemically in proteins using nitrosylating compounds before analysis, with the risk of introducing non-physiological S-nitrosylation...
January 17, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29337910/network-based-methods-for-identifying-key-active-proteins-in-the-extracellular-electron-transfer-process-in-shewanella-oneidensis-mr-1
#7
Dewu Ding, Xiao Sun
Shewanella oneidensis MR-1 can transfer electrons from the intracellular environment to the extracellular space of the cells to reduce the extracellular insoluble electron acceptors (Extracellular Electron Transfer, EET). Benefiting from this EET capability, Shewanella has been widely used in different areas, such as energy production, wastewater treatment, and bioremediation. Genome-wide proteomics data was used to determine the active proteins involved in activating the EET process. We identified 1012 proteins with decreased expression and 811 proteins with increased expression when the EET process changed from inactivation to activation...
January 16, 2018: Genes
https://www.readbyqxmd.com/read/29336995/a-search-for-molecular-mechanisms-underlying-male-idiopathic-infertility
#8
REVIEW
An Bracke, Kris Peeters, Usha Punjabi, David Hoogewijs, Sylvia Dewilde
Infertility affects approximately 15% of the couples wanting to conceive. In 30 - 40% of the cases the aetiology of male infertility remains unknown and is called idiopathic male infertility. When assisted reproductive technologies are used to obtain pregnancy, an adequate (epi)genetic diagnosis of male infertility is of major importance to evaluate if a genetic abnormality will be transmitted to the offspring. In addition, there is need for better diagnostic seminal biomarkers to assess the success rates of these assisted reproductive technologies...
December 27, 2017: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/29331577/a-novel-encystation-specific-protein-kinase-regulates-chitin-synthesis-in-entamoeba-invadens
#9
Sintu Kumar Samanta, Sneha Susan Varghese, Deepak Krishnan, Mithu Baidya, Digant Nayak, Sumanta Mukherjee, Sudip K Ghosh
Phosphorylation is an important post-translational modification of proteins and is involved in the regulation of a variety of cellular events. The proteome of Entamoeba invadens, the reptilian counterpart of Entamoeba histolytica consists of an overwhelming number of putative protein kinases, and some may have a role to play in Entamoeba encystation. In this study, we have identified a novel protein kinase named as EiCSpk (Entamoeba invadenscyst specific protein kinase) which expressed almost exclusively during encystation...
January 10, 2018: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/29331515/mhc-class-i-loaded-ligands-from-breast-cancer-cell-lines-a-potential-hla-i-typed-antigen-collection
#10
Dmitri V Rozanov, Nikita D Rozanov, Kami Chiotti, Ashok Reddy, Phillip A Wilmarth, Larry L David, Seung W Cha, Sunghee Woo, Pavel Pevzner, Vineet Bafna, Gregory G Burrows, Juha K Rantala, Trevor Levin, Pavana Anur, Katie Johnson-Camacho, Shaadi Tabatabaei, Daniel J Munson, Tullia C Bruno, Jill E Slansky, John W Kappler, Naoto Hirano, Sebastian Boegel, Bernard A Fox, Colt Egelston, Diana L Simons, Grecia Jimenez, Peter P Lee, Joe W Gray, Paul T Spellman
To build a catalog of peptides presented by breast cancer cells, we undertook systematic MHC class I immunoprecipitation followed by elution of MHC class I-loaded peptides in breast cancer cells. We determined the sequence of 3196 MHC class I ligands representing 1921 proteins from a panel of 20 breast cancer cell lines. After removing duplicate peptides, i.e., the same peptide eluted from more than one cell line, the total number of unique peptides was 2740. Of the unique peptides eluted, more than 1750 had been previously identified, and of these, sixteen have been shown to be immunogenic...
January 10, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29330519/large-scale-aggregation-analysis-of-eukaryotic-proteins-reveals-an-involvement-of-intrinsically-disordered-regions-in-protein-folding
#11
Eri Uemura, Tatsuya Niwa, Shintaro Minami, Kazuhiro Takemoto, Satoshi Fukuchi, Kodai Machida, Hiroaki Imataka, Takuya Ueda, Motonori Ota, Hideki Taguchi
A subset of the proteome is prone to aggregate formation, which is prevented by chaperones in the cell. To investigate whether the basic principle underlying the aggregation process is common in prokaryotes and eukaryotes, we conducted a large-scale aggregation analysis of ~500 cytosolic budding yeast proteins using a chaperone-free reconstituted translation system, and compared the obtained data with that of ~3,000 Escherichia coli proteins reported previously. Although the physicochemical properties affecting the aggregation propensity were generally similar in yeast and E...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29324744/qcloud-a-cloud-based-quality-control-system-for-mass-spectrometry-based-proteomics-laboratories
#12
Cristina Chiva, Roger Olivella, Eva Borràs, Guadalupe Espadas, Olga Pastor, Amanda Solé, Eduard Sabidó
The increasing number of biomedical and translational applications in mass spectrometry-based proteomics poses new analytical challenges and raises the need for automated quality control systems. Despite previous efforts to set standard file formats, data processing workflows and key evaluation parameters for quality control, automated quality control systems are not yet widespread among proteomics laboratories, which limits the acquisition of high-quality results, inter-laboratory comparisons and the assessment of variability of instrumental platforms...
2018: PloS One
https://www.readbyqxmd.com/read/29322920/investigation-and-identification-of-functional-post-translational-modification-sites-associated-with-drug-binding-and-protein-protein-interactions
#13
Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi, Tzong-Yi Lee
BACKGROUND: Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of proteins, thereby modifying the functions of proteins. The improved throughput of mass spectrometry (MS) or MS/MS technology has not only brought about a surge in proteome-scale studies, but also contributed to a fruitful list of identified PTMs. However, with the increase in the number of identified PTMs, perhaps the more crucial question is what kind of biological mechanisms these PTMs are involved in...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29319931/metaproteomics-of-colonic-microbiota-unveils-discrete-protein-functions-among-colitic-mice-and-control-groups
#14
Clara Moon, Gregory S Stupp, Andrew I Su, Dennis W Wolan
Metaproteomics can greatly assist established high-throughput sequencing methodologies to provide systems biological insights into the alterations of microbial protein functionalities correlated with disease-associated dysbiosis of the intestinal microbiota. Here, we utilized the well-characterized murine T cell transfer model of colitis to find specific changes within the intestinal luminal proteome associated with inflammation. MS proteomic analysis of colonic samples permitted the identification of ∼10,000-12,000 unique peptides that corresponded to 5,610 protein clusters identified across three groups, including the colitic Rag1-/- T cell recipients, isogenic Rag1-/- controls, and wild-type mice...
January 10, 2018: Proteomics
https://www.readbyqxmd.com/read/29317198/rhodomyrtone-rom-is-a-membrane-active-compound
#15
Jongkon Saising, Minh Thu Nguyen, Thomas Härtner, Patrick Ebner, Abdulla Al Mamun Bhuyan, Anne Berscheid, Melanie Muehlenkamp, Sina Schäkermann, Nimerta Kumari, Martin E Maier, Supayang P Voravuthikunchai, Julia Bandow, Florian Lang, Heike Brötz-Oesterhelt, Friedrich Götz
Particularly in Asia medicinal plants with antimicrobial activity are used for therapeutic purpose. One such plant-derived antibiotic is rhodomyrtone (Rom) isolated from Rhodomyrtus tomentosa leaves. Rom shows high antibacterial activity against a wide range of Gram-positive bacteria, however, its mode of action is still unclear. Reporter gene assays and proteomic profiling experiments in Bacillus subtilis indicate that Rom does not address classical antibiotic targets like translation, transcription or DNA replication, but acts at the cytoplasmic membrane...
January 6, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29316319/protein-profile-in-aspergillus-nidulans-recombinant-strains-overproducing-heterologous-enzymes
#16
Mariane Paludetti Zubieta, Fabiano Jares Contesini, Marcelo Ventura Rubio, Any Elisa de Souza Schmidt Gonçalves, Jaqueline Aline Gerhardt, Rolf Alexander Prade, André Ricardo de Lima Damasio
Filamentous fungi are robust cell factories and have been used for the production of large quantities of industrially relevant enzymes. However, the production levels of heterologous proteins still need to be improved. Therefore, this article aimed to investigate the global proteome profiling of Aspergillus nidulans recombinant strains in order to understand the bottlenecks of heterologous enzymes production. About 250, 441 and 424 intracellular proteins were identified in the control strain Anid_pEXPYR and in the recombinant strains Anid_AbfA and Anid_Cbhl respectively...
January 8, 2018: Microbial Biotechnology
https://www.readbyqxmd.com/read/29313810/proteome-wide-lysine-acetylation-identification-in-developing-rice-oryza-sativa-seeds-and-protein-co-modification-by-acetylation-succinylation-ubiquitination-and-phosphorylation
#17
Xiaoxi Meng, Yuanda Lv, Hana Mujahid, Mariola J Edelmann, Han Zhao, Xiaojun Peng, Zhaohua Peng
Protein lysine acetylation is a highly conserved post-translational modification with various biological functions. However, only a limited number of acetylation sites have been reported in plants, especially in cereals, and the function of non-histone protein acetylation is still largely unknown. In this report, we identified 1003 lysine acetylation sites in 692 proteins of developing rice seeds, which greatly extended the number of known acetylated sites in plants. Seven distinguished motifs were detected flanking acetylated lysine...
December 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29313205/distinguishing-sulfotyrosine-containing-peptides-from-their-phosphotyrosine-counterparts-using-mass-spectrometry
#18
Guangming Chen, Yixiang Zhang, Jonathan C Trinidad, Charles Dann
Sulfotyrosine and phosphotyrosine are two post-translational modifications present in higher eukaryotes. A simple and direct mass spectrometry method to distinguish between these modifications is crucial to advance our understanding of the sulfoproteome. While sulfation and phosphorylation are nominally isobaric, the accurate mass of the sulfuryl moiety is 9.6 mDa less than the phosphoryl moiety. Based on this difference, we have used an Orbitrap Fusion Lumos mass spectrometer to characterize, resolve, and distinguish between sulfotyrosine and phosphotyrosine modifications using a set of model peptides...
January 8, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29310484/pathology-proteomics-and-the-pathway-to-personalised-medicine
#19
Ping Jin, Jiang Lan, Kui Wang, Mark S Baker, Canhua Huang, Edouard C Nice
As we move from a discovery to a translational phase in proteomics, with a focus on developing validated clinical assays to assist personalized medicine, there is a growing need for strong bidirectional interactions with the clinical pathology community. Thus, while on one hand the proteomics community will provide candidate biomarkers to assist in diagnosis, prognosis, surveillance, identification of individualized patient medication and development and validation of new assays for diagnostic use, on the other the pathology community will assist with specific tissue identification and selection (e...
January 8, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29301501/inhibition-of-neddylation-facilitates-cell-migration-through-enhanced-phosphorylation-of-caveolin-1-in-pc3-and-u373mg-cells
#20
Sung Yeon Park, Jong-Wan Park, Gun-Woo Lee, Lan Li, Yang-Sook Chun
BACKGROUND: Protein neddylation is a post-translational modification by a covalent conjugation with the neural precursor cell expressed, developmentally downregulated 8 (NEDD8). Although this process has been reported to participate in diverse cellular signaling, little is known about its role in cancer cell migration. Given a recent proteomics report showing that NEDD8 is downregulated in prostate cancer tissues versus normal prostate tissues, we tested the possibility that neddylation plays a role in cancer evolution, and then tried to identify target proteins of the neddylation...
January 5, 2018: BMC Cancer
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