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Proteomics

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https://www.readbyqxmd.com/read/28449397/differential-proteome-profiling-in-the-hippocampus-of-amnesic-mice
#1
Meghraj Singh Baghel, Mahendra Kumar Thakur
Amnesia or memory loss is associated with brain aging and several neurodegenerative pathologies including Alzheimer's disease (AD). This can be induced by a cholinergic antagonist scopolamine, but the underlying molecular mechanism is poorly understood. The present study of proteome profiling in the hippocampus could provide conceptual insights into the molecular mechanisms involved in amnesia. To reveal this, mice were administered scopolamine to induce amnesia and memory impairment was validated by novel object recognition test...
April 27, 2017: Hippocampus
https://www.readbyqxmd.com/read/28449283/physiological-responses-of-reared-sea-bream-sparus-aurata-linnaeus-1758-to-an-amyloodinium-ocellatum-outbreak
#2
M Moreira, D Schrama, F Soares, T Wulff, P Pousão-Ferreira, P Rodrigues
Amyloodiniosis represents a major bottleneck for semi-intensive aquaculture production in Southern Europe, causing extremely high mortalities. Amyloodinium ocellatum is a parasitic dinoflagellate that can infest almost all fish, crustacean and bivalves that live within its ecological range. Fish mortalities are usually attributed to anoxia, associated with serious gill hyperplasia, inflammation, haemorrhage and necrosis in heavy infestations; or with osmoregulatory impairment and secondary microbial infections due to severe epithelial damage in mild infestation...
April 27, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28449083/proteomic-response-to-linoleic-acid-hydroperoxide-in-saccharomyces-cerevisiae
#3
Patrick J O'Doherty, Alamgir Khan, Adam J Johnson, Peter J Rogers, Trevor D Bailey, Ming J Wu
Yeast AP-1 transcription factor (Yap1p) and the enigmatic oxidoreductases Oye2p and Oye3p are involved in counteracting lipid oxidants and their unsaturated breakdown products. In order to uncover the response to linoleic acid hydroperoxide (LoaOOH) and the roles of Oye2p, Oye3p, and Yap1p, we carried out proteomic analysis of the homozygous deletion mutants oye3Δ, oye2Δ, and yap1Δ alongside the diploid parent strain BY4743. The findings demonstrate that deletion of YAP1 narrowed the response to LoaOOH, as the number of proteins differentially expressed in yap1Δ was 70% of that observed in BY4743...
April 25, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28448729/proteomics-of-blood-plasma-serum-samples-stored-in-biobanks-insights-for-clinical-application
#4
Jean-Daniel Tissot, Christine Currat, Dominique Sprumont
No abstract text is available yet for this article.
April 27, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28448538/combined-lipidomic-and-proteomic-analysis-of-isolated-human-islets-exposed-to-palmitate-reveals-time-dependent-changes-in-insulin-secretion-and-lipid-metabolism
#5
Kirsten Roomp, Hjalti Kristinsson, Domitille Schvartz, Kumari Ubhayasekera, Ernest Sargsyan, Levon Manukyan, Azazul Chowdhury, Hannes Manell, Venkata Satagopam, Karlfried Groebe, Reinhard Schneider, Jonas Bergquist, Jean-Charles Sanchez, Peter Bergsten
Studies on the pathophysiology of type 2 diabetes mellitus (T2DM) have linked the accumulation of lipid metabolites to the development of beta-cell dysfunction and impaired insulin secretion. In most in vitro models of T2DM, rodent islets or beta-cell lines are used and typically focus is on specific cellular pathways or organs. Our aim was to, firstly, develop a combined lipidomics and proteomics approach for lipotoxicity in isolated human islets and, secondly, investigate if the approach could delineate novel and/ or confirm reported mechanisms of lipotoxicity...
2017: PloS One
https://www.readbyqxmd.com/read/28448532/a-selected-reaction-monitoring-mass-spectrometric-assessment-of-biomarker-candidates-diagnosing-large-cell-neuroendocrine-lung-carcinoma-by-the-scaling-method-using-endogenous-references
#6
Tetsuya Fukuda, Masaharu Nomura, Yasufumi Kato, Hiromasa Tojo, Kiyonaga Fujii, Toshitaka Nagao, Yasuhiko Bando, Thomas E Fehniger, György Marko-Varga, Haruhiko Nakamura, Harubumi Kato, Toshihide Nishimura
Selected reaction monitoring mass spectrometry (SRM-MS) -based semi-quantitation was performed to assess the validity of 46 selected candidate proteins for specifically diagnosing large-cell neuroendocrine lung carcinoma (LCNEC) and differentiating it from other lung cancer subtypes. The scaling method was applied in this study using specific SRM peak areas (AUCs) derived from the endogenous reference protein that normalizes all SRM AUCs obtained for the candidate proteins. In a screening verification study, we found that seven out of the 46 candidate proteins were statistically significant for the LCNEC phenotype, including 4F2hc cell surface antigen heavy chain (4F2hc/CD98) (p-ANOVA ≤ 0...
2017: PloS One
https://www.readbyqxmd.com/read/28448054/lipid-droplet-isolation-for-quantitative-mass-spectrometry-analysis
#7
Kathrin Rösch, Marcel Kwiatkowski, Hartmut Schlüter, Eva Herker
Lipid droplets are vital to the replication of a variety of different pathogens, most prominently the Hepatitis C Virus (HCV), as the putative site of virion morphogenesis. Quantitative lipid droplet proteome analysis can be used to identify proteins that localize to or are displaced from lipid droplets under conditions such as virus infections. Here, we describe a protocol that has been successfully used to characterize the changes in the lipid droplet proteome following infection with HCV. We use Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) and thus label the complete proteome of one population of cells with "heavy" amino acids to quantitate the proteins by mass spectrometry...
April 17, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28448026/lerlic-ms-ms-for-in-depth-characterization-and-quantification-of-glutamine-and-asparagine-deamidation-in-shotgun-proteomics
#8
Xavier Gallart-Palau, Aida Serra, Siu Kwan Sze
Characterization of protein deamidation is imperative to decipher the role(s) and potentialities of this protein posttranslational modification (PTM) in human pathology and other biochemical contexts. In order to perform characterization of protein deamidation, we have recently developed a novel long-length electrostatic repulsion-hydrophilic interaction chromatography-tandem mass spectrometry (LERLIC-MS/MS) method which can separate the glutamine (Gln) and asparagine (Asn) isoform products of deamidation from model compounds to highly complex biological samples...
April 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447668/functional-characterization-of-a-multi-cancer-risk-locus-on-chr5p15-33-reveals-regulation-of-tert-by-znf148
#9
Jun Fang, Jinping Jia, Matthew Makowski, Mai Xu, Zhaoming Wang, Tongwu Zhang, Jason W Hoskins, Jiyeon Choi, Younghun Han, Mingfeng Zhang, Janelle Thomas, Michael Kovacs, Irene Collins, Marta Dzyadyk, Abbey Thompson, Maura O'Neill, Sudipto Das, Qi Lan, Roelof Koster, Rachael S Stolzenberg-Solomon, Peter Kraft, Brian M Wolpin, Pascal W T C Jansen, Sara Olson, Katherine A McGlynn, Peter A Kanetsky, Nilanjan Chatterjee, Jennifer H Barrett, Alison M Dunning, John C Taylor, Julia A Newton-Bishop, D Timothy Bishop, Thorkell Andresson, Gloria M Petersen, Christopher I Amos, Mark M Iles, Katherine L Nathanson, Maria Teresa Landi, Michiel Vermeulen, Kevin M Brown, Laufey T Amundadottir
Genome wide association studies (GWAS) have mapped multiple independent cancer susceptibility loci to chr5p15.33. Here, we show that fine-mapping of pancreatic and testicular cancer GWAS within one of these loci (Region 2 in CLPTM1L) focuses the signal to nine highly correlated SNPs. Of these, rs36115365-C associated with increased pancreatic and testicular but decreased lung cancer and melanoma risk, and exhibited preferred protein-binding and enhanced regulatory activity. Transcriptional gene silencing of this regulatory element repressed TERT expression in an allele-specific manner...
May 2, 2017: Nature Communications
https://www.readbyqxmd.com/read/28447619/little-cigars-are-more-toxic-than-cigarettes-and-uniquely-change-the-airway-gene-and-protein-expression
#10
Arunava Ghosh, Sabri H Abdelwahab, Steven L Reeber, Boris Reidel, Abigail J Marklew, Andrew J Garrison, Shernita Lee, Hong Dang, Amy H Herring, Gary L Glish, Mehmet Kesimer, Robert Tarran
Little cigars (LCs) are regulated differently than cigarettes, allowing them to be potentially targeted at youth/young adults. We exposed human bronchial epithelial cultures (HBECs) to air or whole tobacco smoke from cigarettes vs. LCs. Chronic smoke exposure increased the number of dead cells, lactate dehydrogenase release, and interleukin-8 (IL-8) secretion and decreased apical cilia, cystic fibrosis transmembrane conductance regulator (CFTR) protein levels, and transepithelial resistance. These adverse effects were significantly greater in LC-exposed HBECs than cigarette exposed cultures...
April 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28447382/quantitative-proteomic-analysis-of-ezh2-inhibition-in-acute-myeloid-leukemia-reveals-the-targets-and-pathways-that-precede-the-induction-of-cell-death
#11
Jarrod J Sandow, Giuseppe Infusini, Aliaksei Z Holik, Gabriela Brumatti, Tessa V Averink, Paul G Ekert, Andrew I Webb
PURPOSE: Chromosomal translocation of the Mixed Lineage Leukemia (MLL) locus generates fusion proteins that drive acute myeloid leukemia (AML) resulting in atypical histone methyltransferase activity and alterations in the epigenetic regulation of gene expression. Targeting histone regulators, such as Enhancer of Zeste Homologue 2 (EZH2), has shown promise in AML. Profiling differential protein expression following inhibition of epigenetic regulators in AML may help to identify novel targets for therapeutics...
April 26, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28446914/constructing-integrated-networks-for-identifying-new-secondary-metabolic-pathway-regulators-in-grapevine-recent-applications-and-future-opportunities
#12
Darren C J Wong, José Tomás Matus
Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Whereas, some studies have used gene co-expression networks to find common pathways and putative targets for transcription factors related to development and metabolism, others have defined networks of primary and secondary metabolites for characterizing the main metabolic differences between cultivars throughout fruit ripening...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28446771/monitoring-global-protein-thiol-oxidation-and-protein-s-mycothiolation-in-mycobacterium-smegmatis-under-hypochlorite-stress
#13
Melanie Hillion, Jörg Bernhardt, Tobias Busche, Martina Rossius, Sandra Maaß, Dörte Becher, Mamta Rawat, Markus Wirtz, Rüdiger Hell, Christian Rückert, Jörn Kalinowski, Haike Antelmann
Mycothiol (MSH) is the major low molecular weight (LMW) thiol in Actinomycetes. Here, we used shotgun proteomics, OxICAT and RNA-seq transcriptomics to analyse protein S-mycothiolation, reversible thiol-oxidations and their impact on gene expression in Mycobacterium smegmatis under hypochlorite stress. In total, 58 S-mycothiolated proteins were identified under NaOCl stress that are involved in energy metabolism, fatty acid and mycolic acid biosynthesis, protein translation, redox regulation and detoxification...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446769/identification-of-key-proteins-and-pathways-in-cadmium-tolerance-of-lactobacillus-plantarum-strains-by-proteomic-analysis
#14
Qixiao Zhai, Yue Xiao, Jianxin Zhao, Fengwei Tian, Hao Zhang, Arjan Narbad, Wei Chen
Our previous study confirmed the protective potential of Lactobacillus plantarum (L. plantarum) strains in alleviation of cadmium (Cd) toxicity in vivo and demonstrated that the observed protection largely depended on the tolerance of the strains to Cd-induced stress. It was also observed that there were significant intra-species differences in Cd tolerance of L. plantarum strains. In this study, we investigated the mechanism of Cd induced stress response of L. plantarum strains using the isobaric tags for relative and absolute quantitation (iTRAQ) based comparative proteomics...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446709/control-of-mitochondrial-biogenesis-and-function-by-the-ubiquitin-proteasome-system
#15
REVIEW
Piotr Bragoszewski, Michal Turek, Agnieszka Chacinska
Mitochondria are pivotal organelles in eukaryotic cells. The complex proteome of mitochondria comprises proteins that are encoded by nuclear and mitochondrial genomes. The biogenesis of mitochondrial proteins requires their transport in an unfolded state with a high risk of misfolding. The mislocalization of mitochondrial proteins is deleterious to the cell. The electron transport chain in mitochondria is a source of reactive oxygen species that damage proteins. Mitochondrial dysfunction is linked to many pathological conditions and, together with the loss of cellular protein homeostasis (proteostasis), are hallmarks of ageing and ageing-related degeneration diseases...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28446668/serine-235-is-the-primary-ns5a-hyper-phosphorylation-site-responsible-for-hcv-replication
#16
Shih-Chin Hsu, Chieh-Wen Lo, Ting-Chun Pan, Kuan-Ying Lee, Ming-Jiun Yu
The non-structural protein 5A (NS5A) of the hepatitis C virus (HCV) is a phosphoprotein with two phosphorylation states: hypo- and hyper-phosphorylation. Genetic mutation studies have demonstrated a cluster of serine residues responsible for NS5A hyper-phosphorylation and functions in viral replication and assembly; however, the phosphorylation levels and potential interactions among the serine residues are unclear. We used three specific antibodies to measure NS5A phosphorylation at S222, S235, and S238 that were identified in our previous proteomics study...
April 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28446534/proteomics-analysis-of-tissue-samples-reveals-changes-in-mitochondrial-protein-levels-in-parathyroid-hyperplasia-over-adenoma
#17
Gurler Akpinar, Murat Kasap, Nuh Zafer Canturk, Mehin Zulfigarova, Eylül Ece Islek, Sertac Ata Guler, Turgay Simsek, Zeynep Canturk
BACKGROUND/AIM: To unveil the pathophysiology of primary hyperparathyroidism, molecular details of parathyroid hyperplasia and adenoma have to be revealed. Such details will provide the tools necessary for differentiation of these two look-alike diseases. Therefore, in the present study, a comparative proteomic study using postoperative tissue samples from the parathyroid adenoma and parathyroid hyperplasia patients was performed. MATERIALS AND METHODS: Protein extracts were prepared from tissue samples (n=8 per group)...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28446324/-research-advance-of-microparticles-in-hypercoagulation-of-hemolytic-anemia-review
#18
Xie Su, Peng Cheng, Dong-Hong Deng
Microparticles (MP) are small membrane vesicles released from many different cell types in response to cellular activation or apoptosis, which have the procoagulant effect. Hemolytic anemia(HA) is a type of anemia that have a short life expectancy of red blood cells due to the destruction which exceed the hematopoietic compensatory capacity of bone marrow. Sickle cell anemia(SCD), thalassemia and paroxysmal nocturnal hemoglobinuria(PNH) are all characterized by hypercoagulation and thromboembolism (TE). Research shows that MP can promote the formation of hypercoagulative state which in turn increases the risk of thromboembolism in HA...
April 2017: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/28445954/a-clinically-feasible-multiplex-proteomic-immunoassay-as-a-novel-functional-diagnostic-for-pancreatic-ductal-adenocarcinoma
#19
Kian-Huat Lim, Emma Langley, Feng Gao, Jingqin Luo, Lin Li, Gary Meyer, Phillip Kim, Sharat Singh, Vladamir M Kushnir, Dayna S Early, Daniel K Mullady, Steven A Edmundowicz, Sachin Wani, Faris M Murad, Dengfeng Cao, Riad R Azar, Andrea Wang-Gillam
To date, targeted therapy for pancreatic ductal adenocarcinoma (PDAC) remains largely unsuccessful in the clinic. Current genomics-based technologies are unable to reflect the quantitative, dynamic signaling changes in the tumor, and require larger tumor samples that are difficult to obtain in PDAC patients. Therefore, a highly sensitive functional tool that can reliably and comprehensively inform intra-tumoral signaling events is direly needed to guide treatment decision. We tested the utility of a highly sensitive proteomics-based functional diagnostic platform, Collaborative Enzyme Enhanced Reactive-immunoassay (CEERTM), on fine-needle aspiration (FNA) samples obtained from 102 patients with radiographically-evident pancreatic tumors...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445788/an-emerging-role-for-the-ribosome-as-a-nexus-for-post-translational-modifications
#20
REVIEW
Deniz Simsek, Maria Barna
The ribosome is one of life's most ancient molecular machines that has historically been viewed as a backstage participant in gene regulation, translating the genetic code across all kingdoms of life in a rote-like fashion. However, recent studies suggest that intrinsic components of the ribosome can be regulated and diversified as a means to intricately control the expression of the cellular proteome. In this review, we discuss advances in the characterization of ribosome post-translational modifications (PTMs) from past to present...
April 22, 2017: Current Opinion in Cell Biology
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