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translational proteomics

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https://www.readbyqxmd.com/read/28079188/proteome-response-of-chicken-embryo-fibroblast-cells-to-recombinant-h5n1-avian-influenza-viruses-with-different-neuraminidase-stalk-lengths
#1
Yongtao Li, Fan Ming, Huimin Huang, Kelei Guo, Huanchun Chen, Meilin Jin, Hongbo Zhou
The variation on neuraminidase (NA) stalk region of highly pathogenic avian influenza H5N1 virus results in virulence change in animals. In our previous studies, the special NA stalk-motif of H5N1 viruses has been demonstrated to play a significant role in the high virulence and pathogenicity in chickens. However, the molecular mechanisms underlying the pathogenicity of viruses with different NA stalk remain poorly understood. This study presents a comprehensive characterization of the proteome response of chicken cells to recombinant H5N1 virus with stalk-short NA (rNA-wt) and the stalkless NA mutant virus (rSD20)...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078386/early-differences-in-islets-from-prediabetic-nod-mice-combined-microarray-and-proteomic-analysis
#2
Inne Crèvecoeur, Valborg Gudmundsdottir, Saurabh Vig, Fernanda Marques Câmara Sodré, Wannes D'Hertog, Ana Carolina Fierro, Leentje Van Lommel, Conny Gysemans, Kathleen Marchal, Etienne Waelkens, Frans Schuit, Søren Brunak, Lut Overbergh, Chantal Mathieu
AIMS/HYPOTHESIS: Type 1 diabetes is an endocrine disease where a long preclinical phase, characterised by immune cell infiltration in the islets of Langerhans, precedes elevated blood glucose levels and disease onset. Although several studies have investigated the role of the immune system in this process of insulitis, the importance of the beta cells themselves in the initiation of type 1 diabetes is less well understood. The aim of this study was to investigate intrinsic differences present in the islets from diabetes-prone NOD mice before the onset of insulitis...
January 12, 2017: Diabetologia
https://www.readbyqxmd.com/read/28077444/protein-interactions-during-the-flavivirus-and-hepacivirus-life-cycle
#3
Gisa Gerold, Janina Bruening, Bettina Weigel, Thomas Pietschmann
Protein-protein interactions govern biological functions in cells, in the extracellular milieu and at the border between cells and extracellular space. Viruses are small intracellular parasites and thus rely on protein interactions to produce progeny inside host cells and to spread from cell to cell. Usage of host proteins by viruses can have severe consequences e.g. apoptosis, metabolic disequilibria or altered cell proliferation and mobility. Understanding protein interactions during virus infection can thus educate us on viral infection and pathogenesis mechanisms...
January 11, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28076774/chromatographic-efficiency-and-selectivity-in-top-down-proteomics-of-histones
#4
Yiyang Zhou, Ximo Zhang, Luca Fornelli, Philip D Compton, Neil Kelleher, Mary J Wirth
Histones are involved in epigenetic control of a wide variety of cellular processes through their multiple post-translational modifications. Their strongly cationic nature makes them challenging to separate with reversed-phase liquid chromatography coupled to mass spectrometry (RPLC-MS), where trifluoroacetic acid is avoided due to adduct formation. Columns with higher resolution are needed. In this work, RPLC-MS is performed on a histone sample using difluoroacetic acid and a 20-min gradient. Columns with C18 surfaces are compared for two different types of particle morphologies: 1) fully porous particles of 5μm in diameter, 2) superficially porous particles of 3μm in diameter with a shell of 0...
December 23, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28069893/alga-pras-algal-protein-annotation-suite-a-database-of-comprehensive-annotation-in-algal-proteomes
#5
Atsushi Kurotani, Yutaka Yamada, Tetsuya Sakurai
Algae are smaller organisms than land plants and offer clear advantages in research over terrestrial species in terms of rapid production, short generation time, and varied commercial applications. Thus, studies investigating the practical development of effective algal production are important and will improve our understanding of both, aquatic and terrestrial plants. In this study, we estimated multiple physicochemical and secondary structural properties of protein sequences, the predicted presence of post-translational modification (PTM) sites, and subcellular localization using a total of 510,123 protein sequences from the proteomes of 31 algae and three plant species...
January 9, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28069826/endostatin-inhibits-androgen-independent-prostate-cancer-growth-by-suppressing-nuclear-receptor-mediated-oxidative-stress
#6
Joo Hyoung Lee, Minsung Kang, Hong Wang, Gurudatta Naik, James A Mobley, Guru Sonpavde, W Timothy Garvey, Victor M Darley-Usmar, Selvarangan Ponnazhagan
Androgen-deprivation therapy has been identified to induce oxidative stress in prostate cancer (PCa), leading to reactivation of androgen receptor (AR) signaling in a hormone-refractory manner. Thus, antioxidant therapies have gained attention as adjuvants for castration-resistant PCa. Here, we report for the first time that human endostatin (ES) prevents androgen-independent growth phenotype in PCa cells through its molecular targeting of AR and glucocorticoid receptor (GR) and downstream pro-oxidant signaling...
January 9, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28063982/proteomic-analysis-of-lysine-succinylation-of-the-human-pathogen-histoplasma-capsulatum
#7
Longxiang Xie, Juan Li, Wanyan Deng, Zhaoxiao Yu, Wenjie Fang, Min Chen, Wanqing Liao, Jianping Xie, Weihua Pan
: Histoplasma capsulatum, the causative agent of histoplasmosis (also called "Darling's disease"), can affect both immunocompetent and immunocompromised hosts. Post-translational protein modification by lysine succinylation (Ksuc) is a frequent occurrence in eukaryote and prokaryote. Recently, the roles of succinylation and its regulatory enzymes in regulating metabolic pathway in bacteria, mammalian and fungus were highlighted. Here, we report the first global profiling of lysine succinylation, with 463 modification sites in 202 proteins from H...
January 4, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28057602/formin-like-1-expression-is-increased-on-cd4-t-lymphocytes-in-spontaneous-autoimmune-uveitis
#8
Roxane L Degroote, Patrizia B Uhl, Barbara Amann, Angela M Krackhardt, Marius Ueffing, Stefanie M Hauck, Cornelia A Deeg
: The membrane protein expression repertoire of cells changes in course of activation. In equine recurrent uveitis (ERU), a spontaneous autoimmune disease in horses with relapsing and ultimately blinding inner eye inflammation, CD4+ T lymphocytes are the crucial pathogenic cells activated in the periphery directly prior to an inflammatory episode. In order to find relevant changes in the membrane proteome associated to disease, we sorted CD4+ lymphocytes and compared protein abundance from the generated proteome datasets of both healthy horses and ERU cases...
January 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28049741/integrating-omics-and-alternative-splicing-reveals-insights-into-grape-response-to-high-temperature
#9
Jianfu Jiang, Xinna Liu, Guotian Liu, Chonghuai Liu, Shaohua Li, Lijun Wang
Heat stress is one of the primary abiotic stresses that limit crop production. Grape is a cultivated fruit with high economic value throughout the world, with its growth and development often influenced by high temperature. Alternative splicing (AS) is a widespread phenomenon increasing transcriptome and proteome diversity. We conducted high temperature treatments (35oC, 40oC and 45oC) on grapevines (Vitis vinifera), and assessed transcriptomic (especially AS) and proteomic changes in leaves. We found that nearly 70% of the genes were alternatively spliced under high temperature...
January 3, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28045055/personalised-proteome-analysis-by-means-of-protein-microarrays-made-from-individual-patient-samples
#10
Syafrizayanti, Smiths S Lueong, Cuixia Di, Jonas V Schaefer, Andreas Plückthun, Jörg D Hoheisel
DNA sequencing has advanced to a state that permits studying the genomes of individual patients as nearly a matter of routine. Towards analysing a tissue's protein content in a similar manner, we established a method for the production of microarrays that represent full-length proteins as they are encoded in individual specimens, exhibiting the particular variations, such as mutations or splice variations, present in these samples. From total RNA isolates, each transcript is copied to a specific location on the array by an on-chip polymerase elongation reaction, followed by in situ cell-free transcription and translation...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28040467/proteomic-profile-of-susceptible-and-multidrug-resistant-clinical-isolates-of-escherichia-coli-and-klebsiella-pneumoniae-using-label-free-and-immunoproteomic-strategies
#11
Sandra Magalhães, Miguel Aroso, Inês Roxo, Sónia Ferreira, Frederico Cerveira, Elmano Ramalheira, Rita Ferreira, Rui Vitorino
Infectious diseases caused by multidrug-resistant (MDR) Enterobacteriaceae have exponentially increased in the past decade, and are a major concern in hospitals. In the first part of the work, we compared the proteome profile of MDR and susceptible clinical isolates of Escherichia coli and Klebsiella pneumoniae in order to identify possible biological processes associated with drug resistance and susceptible phenotypes, using a label-free approach. In the second part, we used an immunoproteomics approach to identify immunoreactive proteins in the same isolates...
December 28, 2016: Research in Microbiology
https://www.readbyqxmd.com/read/28039739/what-computational-non-targeted-mass-spectrometry-based-metabolomics-can-gain-from-shotgun-proteomics
#12
REVIEW
Hamid Hamzeiy, Jürgen Cox
Computational workflows for mass spectrometry-based shotgun proteomics and untargeted metabolomics share many steps. Despite the similarities, untargeted metabolomics is lagging behind in terms of reliable fully automated quantitative data analysis. We argue that metabolomics will strongly benefit from the adaptation of successful automated proteomics workflows to metabolomics. MaxQuant is a popular platform for proteomics data analysis and is widely considered to be superior in achieving high precursor mass accuracies through advanced nonlinear recalibration, usually leading to five to ten-fold better accuracy in complex LC-MS/MS runs...
December 28, 2016: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28039451/high-throughput-proteome-analysis-reveals-targeted-trpm8-degradation-in-prostate-cancer
#13
Swapna Asuthkar, Lusine Demirkhanyan, Samuel Robert Mueting, Alejandro Cohen, Eleonora Zakharian
The Ca2+-permeable ion channel TRPM8 is a hallmark of the prostate epithelium. We recently discovered that TRPM8 is an ionotropic testosterone receptor. This finding suggested that testosterone-induced TRPM8 activity regulates Ca2+ homeostasis in the prostate epithelium. Since androgens are significantly implicated in prostate cancer development, the role of the novel testosterone receptor TRPM8 in cancer was assessed in our study. Although TRPM8 mRNA levels increase at the early prostate cancer stages, we found that it is not proportionally translated into TRPM8 protein levels...
December 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/28036160/bile-acids-a-potential-role-in-the-pathogenesis-of-pharyngeal-malignancy
#14
Zachary Shellman, Adil Aldhahrani, Bernard Verdon, Michael Mather, Vinidh Paleri, Janet Wilson, Jeffery Pearson, Chris Ward, Jason Powell
OBJECTIVE: Gastro-oesophageal reflux disease is thought to be a risk factor for head and neck malignancies. Bile acids are one of the principle components of gastric refluxate and have previously been implicated in the development of oesophageal and bowel malignancies. There is clear evidence that bile acids reflux into the laryngopharynx. Despite this, the carcinogenic properties of bile acids in this area are yet to be fully identified. We therefore investigated the potential role of bile acids in pharyngeal malignancy, through the highly conserved process of epithelial-mesenchymal transition (EMT)...
December 30, 2016: Clinical Otolaryngology
https://www.readbyqxmd.com/read/28036087/label-free-quantitative-proteomic-analysis-of-harmless-and-pathogenic-strains-of-infectious-microalgae-prototheca-spp
#15
Jayaseelan Murugaiyan, Murat Eravci, Christoph Weise, Uwe Roesler
Microalgae of the genus Prototheca (P.) spp are associated with rare algal infections of invertebrates termed protothecosis. Among the seven generally accepted species, P. zopfii genotype 2 (GT2) is associated with a severe form of bovine mastitis while P. blaschkeae causes the mild and sub-clinical form of mastitis. The reason behind the infectious nature of P. zopfii GT2, while genotype 1 (GT1) remains non-infectious, is not known. Therefore, in the present study we investigated the protein expression level difference between the genotypes of P...
December 29, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28035797/combining-hcd-and-ethcd-fragmentation-in-a-product-dependent-manner-confidently-assigns-proteome-wide-adp-ribose-acceptor-sites
#16
Vera Bilan, Mario Leutert, Paolo Nanni, Christian Panse, Michael O Hottiger
Protein ADP-ribosylation is a physiologically and pathologically important post-translational modification. Recent technological advances have improved analysis of this complex modification and have led to the discovery of hundreds of ADP-ribosylated proteins in both cultured cells and mouse tissues. Nevertheless, accurate assignment of the ADP-ribose acceptor site(s) within the modified proteins identified has remained a challenging task. This is mainly due to poor fragmentation of modified peptides. Here, using an Orbitrap Fusion Tribrid mass spectrometer, we present an optimized methodology that not only drastically improves the overall localization scores for the ADP-ribosylation acceptor sites, but also boosts ADP-ribosylated peptide identifications...
December 28, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28034645/protein-acetylation-involved-in-streptomycin-biosynthesis-in-streptomyces-griseus
#17
Yuji Ishigaki, Genki Akanuma, Minoru Yoshida, Sueharu Horinouchi, Saori Kosono, Yasuo Ohnishi
Protein acetylation, the reversible addition of an acetyl group to lysine residues, is a protein post-translational modification ubiquitous in living cells. Although the involvement of protein acetylation in the regulation of primary metabolism has been revealed, the function of protein acetylation is largely unknown in secondary metabolism. Here, we characterized protein acetylation in Streptomyces griseus, a streptomycin producer. Protein acetylation was induced in the stationary and sporulation phases in liquid and solid cultures, respectively, in S...
December 26, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/28031460/inhibitory-role-of-%C3%AE-2-6-sialylation-in-adipogenesis
#18
Tomoko Kaburagi, Yasuhiko Kizuka, Shinobu Kitazume, Naoyuki Taniguchi
Adipose tissue plays critical roles in obesity and related diseases such as diabetes and cardiovascular diseases. Previous reports suggest that glycans, the most common post-translational modifications, are involved in obesity-related diseases, but what type of glycan regulates adipogenesis during obesity remains unclear. In this study, we first quantified the mRNA levels of 167 genes (encoding 144 glycosyltransferases and 23 related enzymes) in visceral adipose tissues (VATs) from control mice and high fat diet (HFD)-induced obese mice...
December 28, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28031280/proteolytic-cleavage-of-the-immunodominant-outer-membrane-protein-rompa-in-rickettsia-rickettsii
#19
Nicholas F Noriea, Tina R Clark, David Mead, Ted Hackstadt
: Rickettsia rickettsii, the causative agent of Rocky Mountain spotted fever, contains two immunodominant proteins, rOmpA and rOmpB, in the outer membrane. Both rOmpA and rOmpB are conserved throughout spotted fever group rickettsiae as members of a family of autotransporter proteins. Previously, it was demonstrated that rOmpB is proteolytically processed with the cleavage site residing near the autotransporter domain at the carboxy-terminal end of the protein, cleaving the 168 kDa precursor into apparent 120 kDa and 32 kDa fragments...
December 28, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/28025748/patient-derived-xenograft-pdx-models-in-basic-and-translational-breast-cancer-research
#20
Lacey E Dobrolecki, Susie D Airhart, Denis G Alferez, Samuel Aparicio, Fariba Behbod, Mohamed Bentires-Alj, Cathrin Brisken, Carol J Bult, Shirong Cai, Robert B Clarke, Heidi Dowst, Matthew J Ellis, Eva Gonzalez-Suarez, Richard D Iggo, Peter Kabos, Shunqiang Li, Geoffrey J Lindeman, Elisabetta Marangoni, Aaron McCoy, Funda Meric-Bernstam, Helen Piwnica-Worms, Marie-France Poupon, Jorge Reis-Filho, Carol A Sartorius, Valentina Scabia, George Sflomos, Yizheng Tu, François Vaillant, Jane E Visvader, Alana Welm, Max S Wicha, Michael T Lewis
Patient-derived xenograft (PDX) models of a growing spectrum of cancers are rapidly supplanting long-established traditional cell lines as preferred models for conducting basic and translational preclinical research. In breast cancer, to complement the now curated collection of approximately 45 long-established human breast cancer cell lines, a newly formed consortium of academic laboratories, currently from Europe, Australia, and North America, herein summarizes data on over 500 stably transplantable PDX models representing all three clinical subtypes of breast cancer (ER+, HER2+, and "Triple-negative" (TNBC))...
December 27, 2016: Cancer Metastasis Reviews
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