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proteomics pathway analysis

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https://www.readbyqxmd.com/read/28805685/re-adaption-on-earth-after-spaceflights-affects-the-mouse-liver-proteome
#1
Viktoria Anselm, Svetlana Novikova, Victor Zgoda
Harsh environmental conditions including microgravity and radiation during prolonged spaceflights are known to alter hepatic metabolism. Our studies have focused on the analysis of possible changes in metabolic pathways in the livers of mice from spaceflight project "Bion-M 1". Mice experienced 30 days of spaceflight with and without an additional re-adaption period of seven days compared to control mice on Earth. To investigate mice livers we have performed proteomic profiling utilizing shotgun mass spectrometry followed by label-free quantification...
August 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28804911/chronic-ethanol-metabolism-inhibits-hepatic-mitochondrial-superoxide-dismutase-via-lysine-acetylation
#2
Mohammed A Assiri, Samantha R Roy, Peter S Harris, Hadi Ali, Yongliang Liang, Colin T Shearn, David J Orlicky, James R Roede, Matthew D Hirschey, Donald S Backos, Kristofer S Fritz
BACKGROUND: Chronic ethanol consumption is a major cause of liver disease worldwide. Oxidative stress is a known consequence of ethanol metabolism and is thought to contribute significantly to alcoholic liver disease (ALD). Therefore, elucidating pathways leading to sustained oxidative stress and downstream redox imbalances may reveal how ethanol consumption leads to ALD. Recent studies suggest that ethanol metabolism impacts mitochondrial antioxidant processes through a number of proteomic alterations, including hyperacetylation of key antioxidant proteins...
August 14, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28803608/identification-of-simvastatin-regulated-targets-associated-with-jnk-activation-in-du145-human-prostate-cancer-cell-death-signaling
#3
Eun Joo Jung, Ky Hyun Chung, Choong Won Kim
In this study, our results showed that the c-Jun N-terminal kinase (JNK) activation was associated with the enhancement of docetaxel-induced cytotoxicity by simvastatin in DU145 human prostate cancer cells. To better understand the basic molecular mechanisms, we investigated simvastatin-regulated targets during simvastatin-induced cell death in DU145 cells using two-dimensional (2D) proteomic analysis. Thus, vimentin, Ras-related protein Rab-1B (RAB1B), cytoplasmic hydroxymethylglutaryl-CoA synthase (cHMGCS), thioredoxin domain-containing protein 5 (TXNDC5), heterogeneous nuclear ribonucleoprotein K (hnRNP K), N-myc downstream-regulated gene 1 (NDRG1) and isopentenyl-diphosphate Delta-isomerase 1 (IDI1) protein spots were identified as simvastatin-regulated targets involved in DU145 cell death signaling pathways...
August 11, 2017: BMB Reports
https://www.readbyqxmd.com/read/28803590/differential-protein-analysis-of-serum-exosomes-post-intravenous-immunoglobulin-therapy-in-patients-with-kawasaki-disease
#4
Li Zhang, Qi-Fang Song, Jing-Jie Jin, Ping Huang, Zhou-Ping Wang, Xiao-Fei Xie, Xiao-Qiong Gu, Xue-Juan Gao, Hong-Ling Jia
BACKGROUND: Kawasaki disease, which is characterised by systemic vasculitides accompanied by acute fever, is regularly treated by intravenous immunoglobulin to avoid lesion formation in the coronary artery; however, the mechanism of intravenous immunoglobulin therapy is unclear. Hence, we aimed to analyse the global expression profile of serum exosomal proteins before and after administering intravenous immunoglobulin. METHODS: Two-dimensional electrophoresis coupled with mass spectrometry analysis was used to identify the differentially expressed proteome of serum exosomes in patients with Kawasaki disease before and after intravenous immunoglobulin therapy...
August 14, 2017: Cardiology in the Young
https://www.readbyqxmd.com/read/28803361/toxoplasma-gondii-and-neospora-caninum-induce-different-host-cell-responses-at-proteome-wide-phosphorylation-events-a-step-forward-for-uncovering-the-biological-differences-between-these-closely-related-parasites
#5
Mariwan M M Al-Bajalan, Dong Xia, Stuart Armstrong, Nadine Randle, Jonathan M Wastling
Toxoplasma gondii and Neospora caninum are closely related intracellular protozoan parasites and tissue cyst-forming Coccidia of the phylum Apicomplexa. There are remarkable similarities between the morphology, genomes and transcriptomes of both parasites. Toxoplasma is zoonotic, with a wide host range and is mainly transmitted horizontally between its definitive host, the cat, and its intermediate hosts. Neospora causes disease within a narrow host range and with reduced virulence potential to the hosts. The dog is the definitive host of Neospora and its epidemiology in cattle mainly depends on vertical transmission...
August 12, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28802583/cytoskeleton-and-nuclear-lamina-affection-in-recessive-osteogenesis-imperfecta-a-functional-proteomics-perspective
#6
Assunta Gagliardi, Roberta Besio, Chiara Carnemolla, Claudia Landi, Alessandro Armini, Mona Aglan, Ghada Otaify, Samia A Temtamy, Antonella Forlino, Luca Bini, Laura Bianchi
Osteogenesis imperfecta (OI) is a collagen-related disorder associated to dominant, recessive or X-linked transmission, mainly caused by mutations in type I collagen genes or in genes involved in type I collagen metabolism. Among the recessive forms, OI types VII, VIII, and IX are due to mutations in CRTAP, P3H1, and PPIB genes, respectively. They code for the three components of the endoplasmic reticulum complex that catalyzes 3-hydroxylation of type I collagen α1Pro986. Under-hydroxylation of this residue leads to collagen structural abnormalities and results in moderate to lethal OI phenotype, despite the exact molecular mechanisms are still not completely clear...
August 9, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28798222/an-integrated-approach-to-explore-composition-and-dynamics-of-cholesterol-rich-membrane-microdomains-in-sexual-stages-of-malaria-parasite
#7
Federica Fratini, Carla Raggi, Gabriella Sferra, Cecilia Birago, Anna Sansone, Felicia Grasso, Chiara Curr Agrave, Anna Olivieri, Tomasino Pace, Stefania Mochi, Leonardo Picci, Carla Ferreri, Antonella Di Biase, Elisabetta Pizzi, Marta Ponzi
Membrane microdomains that include lipid rafts, are involved in key physiological and pathological processes and participate in the entry of endocellular pathogens. These assemblies, enriched in cholesterol and sphingolipids, form highly dynamic, liquid-ordered phases that can be separated from the bulk membranes thanks to their resistance to solubilization by non-ionic detergents. To characterize complexity and dynamics of detergent-resistant membranes of sexual stages of the rodent malaria parasite Plasmodium berghei, here we propose an integrated study of raft components based on proteomics, lipid analysis and bioinformatics...
August 10, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28798160/protein-coalation-a-redox-linked-post-translational-modification
#8
Steven C Ley, Luiz Pedro S de Carvalho
Regulation of metabolic pathways by signal transduction and transcriptional cascades can alter cellular levels of metabolites. Metabolites themselves can also have regulatory activity as shown in a new study published in the Biochemical Journal Tsuchiya et al. describe a novel antibody and mass spectrometry-based method for identifying proteins that are reversibly modified with Coenzyme A (CoA). Analysis of the 'CoAlated proteome' under conditions of oxidative and metabolic stress revealed a bias towards the modification of metabolic enzymes by CoA...
August 10, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28797234/succinyl-proteome-profiling-of-dendrobium-officinale-an-important-traditional-chinese-orchid-herb-revealed-involvement-of-succinylation-in-the-glycolysis-pathway
#9
Shangguo Feng, Kaili Jiao, Hong Guo, Mengyi Jiang, Juan Hao, Huizhong Wang, Chenjia Shen
BACKGROUND: Lysine succinylation is a ubiquitous and important protein post-translational modification in various eukaryotic and prokaryotic cells. However, its functions in Dendrobium officinale, an important traditional Chinese orchid herb with high polysaccharide contents, are largely unknown. RESULTS: In our study, LC-MS/MS was used to identify the peptides that were enriched by immune-purification with a high-efficiency succinyl-lysine antibody. In total, 314 lysine succinylation sites in 207 proteins were identified...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28795660/systems-and-synthetic-biology-perspective-of-the-versatile-plant-pathogenic-and-polysaccharide-producing-bacterium-xanthomonas-campestris
#10
Sarah Schatschneider, Jessica Schneider, Jochen Blom, Fabien Létisse, Karsten Niehaus, Alexander Goesmann, Frank-Jörg Vorhölter
Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features...
August 10, 2017: Microbiology
https://www.readbyqxmd.com/read/28794502/proteomics-phosphoproteomics-of-left-ventricular-biopsies-from-patients-with-surgical-coronary-revascularization-and-pigs-with-coronary-occlusion-reperfusion-remote-ischemic-preconditioning
#11
Nilgün Gedik, Marcus Krüger, Matthias Thielmann, Eva Kottenberg, Andreas Skyschally, Ulrich H Frey, Elke Cario, Jürgen Peters, Heinz Jakob, Gerd Heusch, Petra Kleinbongard
Remote ischemic preconditioning (RIPC) by repeated brief cycles of limb ischemia/reperfusion reduces myocardial ischemia/reperfusion injury. In left ventricular (LV) biopsies from patients undergoing coronary artery bypass grafting (CABG), only the activation of signal transducer and activator of transcription 5 was associated with RIPC's cardioprotection. We have now used an unbiased, non-hypothesis-driven proteomics and phosphoproteomics approach to analyze LV biopsies from patients undergoing CABG and from pigs undergoing coronary occlusion/reperfusion without (sham) and with RIPC...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28792668/comparative-transcriptomic-and-proteomic-analyses-reveal-a-flug-mediated-signalling-pathway-relating-to-asexual-sporulation-of-antrodia-camphorata
#12
Hua-Xiang Li, Zhen-Ming Lu, Qing Zhu, Jin-Song Gong, Yan Geng, Jin-Song Shi, Zheng-Hong Xu, Yan-He Ma
Medicinal mushroom Antrodia camphorata sporulate large numbers of arthroconidia in submerged fermentation, which is rarely reported in basidiomycetous fungi. Nevertheless, the molecular mechanisms underlying this asexual sporulation (conidiation) remain unclear. Here, we used comparative transcriptomic and proteomic approaches to elucidate possible signalling pathway relating to the asexual sporulation of A. camphorata. First, 104 differentially expressed proteins and 2586 differential cDNA sequences during the culture process of A...
August 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28791374/corilagin-sensitizes-epithelial-ovarian-cancer-to-chemotherapy-by-inhibiting-snail%C3%A2-glycolysis-pathways
#13
Luoqi Jia, Jiayi Zhou, Hongbo Zhao, Hongyan Jin, Minzhi Lv, Naiqing Zhao, Zhizhong Zheng, Yiling Lu, Yanlin Ming, Yinhua Yu
We identified that corilagin is a major component extracted from a well-known hepatoprotective and antiviral medicinal herb, Phyllanthus niruri L with antitumor activity. Our previous study found that corilagin inhibited the growth of ovarian cancer cells via the TGF-β/AKT/ERK signaling pathways. Recently, we demonstrated that corilagin enhanced the sensitivity of ovarian cancer cells to chemotherapy. Ovarian cancer cell lines, SKOv3ip, Hey and HO-8910PM-Snail, were treated with different concentrations of corilagin in combination with paclitaxel and carboplatin...
August 7, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28791255/quantitative-proteomic-analysis-reveals-changes-in-the-benchmark-corynebacterium-pseudotuberculosis-biovar-equi-exoproteome-after-passage-in-a-murine-host
#14
Wanderson M Silva, Rodrigo D De Oliveira Carvalho, Fernanda A Dorella, Edson L Folador, Gustavo H M F Souza, Adriano M C Pimenta, Henrique C P Figueiredo, Yves Le Loir, Artur Silva, Vasco Azevedo
Corynebacterium pseudotuberculosis biovar equi is the etiologic agent of ulcerative lymphangitis. To investigate proteins that could be related to the virulence of this pathogen, we combined an experimental passage process using a murine model and high-throughput proteomics with a mass spectrometry, data-independent acquisition (LC-MS(E)) approach to identify and quantify the proteins released into the supernatants of strain 258_equi. To our knowledge, this approach allowed characterization of the exoproteome of a C...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28781988/multiple-response-regression-analysis-links-magnetic-resonance-imaging-features-to-de-regulated-protein-expression-and-pathway-activity-in-lower-grade-glioma
#15
Michael Lehrer, Anindya Bhadra, Visweswaran Ravikumar, James Y Chen, Max Wintermark, Scott N Hwang, Chad A Holder, Erich P Huang, Brenda Fevrier-Sullivan, John B Freymann, Arvind Rao
BACKGROUND AND PURPOSE: Lower grade gliomas (LGGs), lesions of WHO grades II and III, comprise 10-15% of primary brain tumors. In this first-of-a-kind study, we aim to carry out a radioproteomic characterization of LGGs using proteomics data from the TCGA and imaging data from the TCIA cohorts, to obtain an association between tumor MRI characteristics and protein measurements. The availability of linked imaging and molecular data permits the assessment of relationships between tumor genomic/proteomic measurements with phenotypic features...
May 2017: Oncoscience
https://www.readbyqxmd.com/read/28780297/respiration-disruption-and-detoxification-at-the-protein-expression-levels-in-the-pacific-oyster-crassostrea-gigas-under-zinc-exposure
#16
Jie Meng, Wen-Xiong Wang, Li Li, Guofan Zhang
The Pacific oyster (Crassostrea gigas) can accumulate high levels of zinc (Zn) without obvious toxicity, but the related molecular mechanisms are largely unknown. In the present study, C. gigas were exposed to excess Zn for 9days and the differentially expressed proteins (DEPs) were examined using the isobaric tags for relative and absolute quantitation (iTRAQ) method. In total, 2667 proteins containing at least two peptides and detected in both replicates were used for proteomic analysis. Among these DEPs, 332 were up-regulated and 282 were down-regulated...
July 26, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28780132/commentary-on-comprehensive-molecular-characterization-of-papillary-renal-cell-carcinoma-cancer-genome-atlas-research-network-n-engl-j-med-2016-jan-14-374-2-135-45
#17
Byron H Lee
BACKGROUND: Papillary renal-cell carcinoma, which accounts for 15%-20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation, and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. METHODS: We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis...
August 2, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28777931/biallelic-mutations-in-mrps34-lead-to-instability-of-the-small-mitoribosomal-subunit-and-leigh-syndrome
#18
Nicole J Lake, Bryn D Webb, David A Stroud, Tara R Richman, Benedetta Ruzzenente, Alison G Compton, Hayley S Mountford, Juliette Pulman, Coralie Zangarelli, Marlene Rio, Nathalie Bodaert, Zahra Assouline, Mingma D Sherpa, Eric E Schadt, Sander M Houten, James Byrnes, Elizabeth M McCormick, Zarazuela Zolkipli-Cunningham, Katrina Haude, Zhancheng Zhang, Kyle Retterer, Renkui Bai, Sarah E Calvo, Vamsi K Mootha, John Christodoulou, Agnes Rötig, Aleksandra Filipovska, Ingrid Cristian, Marni J Falk, Metodi D Metodiev, David R Thorburn
The synthesis of all 13 mitochondrial DNA (mtDNA)-encoded protein subunits of the human oxidative phosphorylation (OXPHOS) system is carried out by mitochondrial ribosomes (mitoribosomes). Defects in the stability of mitoribosomal proteins or mitoribosome assembly impair mitochondrial protein translation, causing combined OXPHOS enzyme deficiency and clinical disease. Here we report four autosomal-recessive pathogenic mutations in the gene encoding the small mitoribosomal subunit protein, MRPS34, in six subjects from four unrelated families with Leigh syndrome and combined OXPHOS defects...
August 3, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28777577/proteomic-analysis-of-human-angiogenin-interactions-reveals-cytoplasmic-pcna-as-a-putative-binding-partner
#19
Demetra S M Chatzileontiadou, Martina Samiotaki, Annika N Alexopoulou, Marina Cotsiki, George Panayotou, Melina Stamatiadi, Nikolaos A A Balatsos, Demetres D Leonidas, Maria Kontou
Human Angiogenin (hAng) is a member of the ribonuclease A superfamily and a potent inducer of neovascularization. Herein, protein interactions of hAng in the nucleus and cytoplasm of the human umbilical vein cell line EA.hy926, have been investigated by mass spectroscopy. Data are available via ProteomeXchange with identifiers PXD006583 and PXD006584. The first gel-free analysis of hAng immunoprecipitates revealed many statistically significant potential hAng-interacting proteins involved in crucial biological pathways...
August 4, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28777000/quantitative-proteomics-reveal-temporal-proteomic-changes-in-signaling-pathways-during-bv2-mouse-microglial-cell-activation
#20
Jongmin Woo, Dohyun Han, Joseph Inje Wang, Joonho Park, Hyunsoo Kim, Youngsoo Kim
The development of systematic proteomic quantification techniques in systems biology research has enabled one to perform an in-depth analysis of cellular systems. In this study, we have developed a systematic proteomic approach that encompasses the spectrum from global to targeted analysis on a single platform. We have applied this technique to an activated microglia cell system to examine changes in the intracellular and extracellular proteomes. Microglia become activated when their homeostatic microenvironment is disrupted...
August 4, 2017: Journal of Proteome Research
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