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Journal of Proteomics

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https://www.readbyqxmd.com/read/29038038/global-proteome-and-phosphoproteome-dynamics-indicate-novel-mechanisms-of-vitamin-c-induced-dormancy-in-mycobacterium-smegmatis
#1
Claudia Albeldas, Naadir Ganief, Bridget Calder, Kehilwe C Nakedi, Shaun Garnett, Andrew J M Nel, Jonathan M Blackburn, Nelson C Soares
Vitamin C has been found to affect mycobacteria in multiple ways, including increasing susceptibility to antimicrobial drugs, inducing dormancy, and having a bactericidal effect. However, the regulatory events mediating vitamin C related adaptations remain largely elusive. Ser/Thr/Tyr protein phosphorylation plays an important regulatory role in mycobacteria, contributing to environmental adaptation, including dormancy and drug resistance. This study utilised the model organism, Mycobacterium smegmatis, and TiO2 phosphopeptide enrichment combined with mass spectrometry-based proteomics methods to elucidate the mycobacterial signalling and regulatory response to sub-lethal concentrations of vitamin C...
October 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29037750/environmental-toxicology-and-omics-a-question-of-sex
#2
Xuefang Liang, April Feswick, Denina Simmons, Christopher J Martyniuk
Molecular initiating events and downstream transcriptional/proteomic responses provide valuable information for adverse outcome pathways, which can be used predict the effects of chemicals on physiological systems. There has been a paucity of research that addresses sex-specific expression profiling in toxicology and due to cost, time, and logistical considerations, sex as a variable has not been widely considered. In response to this deficiency, federal agencies in the United States, Canada, and Europe have highlighted the importance of including sex as a variable in scientific investigations...
October 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29032071/comparing-intestinal-versus-diffuse-gastric-cancer-using-a-peff-oriented-proteomic-pipeline
#3
Helisa Helena Wippel, Marlon Dias Mariano Santos, Milan Avila Clasen, Louise Ulrich Kurt, Fabio Cesar Sousa Nogueira, Carlos Eduardo Carvalho, Thaís Messias McCormick, Guilherme Pinto Bravo Neto, Lysangela Ronalte Alves, Maria da Gloria da Costa Carvalho, Paulo Costa Carvalho, Juliana de Saldanha da Gama Fischer
Gastric cancer is the fifth most common malignant neoplasia and the third leading cause of cancer death worldwide. Mac-Cormick et al. recently showed the importance of considering the anatomical region of the tumor in proteomic gastric cancer studies; more differences were found between distinct anatomical regions than when comparing healthy versus diseased tissue. Thus, failing to consider the anatomical region could lead to differential proteins that are not disease specific. With this as motivation, we compared the proteomic profiles of intestinal and diffuse adenocarcinoma from the same anatomical region, the corpus...
October 11, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28993202/temporal-expression-profiling-of-plasma-proteins-reveals-oxidative-stress-in-early-stages-of-type-1-diabetes-progression
#4
Chih-Wei Liu, Lisa Bramer, Bobbie-Jo Webb-Robertson, Kathleen Waugh, Marian J Rewers, Qibin Zhang
Blood markers other than islet autoantibodies are greatly needed to indicate the pancreatic beta cell destruction process as early as possible, and more accurately reflect the progression of Type 1 Diabetes Mellitus (T1D). To this end, a longitudinal proteomic profiling of human plasma using TMT-10plex-based LC-MS/MS analysis was performed to track temporal proteomic changes of T1D patients (n=11) across 9 serial time points, spanning the period of T1D natural progression, in comparison with those of the matching healthy controls (n=10)...
October 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28988882/gender-proteomics-i-which-proteins-in-non-sexual-organs
#5
Elisabetta Gianazza, Ingrid Miller, Uliano Guerrini, Luca Palazzolo, Chiara Parravicini, Ivano Eberini
Differences related to gender have long been neglected but recent investigations show that they are widespread and may be recognized with all types of omics approaches, both in tissues and in biological fluids. Our review compiles evidence collected with proteomics techniques in our species, mainly focusing on baseline parameters in non-sexual organs in healthy men and women. Data from human specimens had to be replaced with information from other mammals every time invasive procedures of sample procurement were involved...
October 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28988881/comprehensive-proteomic-profiles-of-mouse-aapoaii-amyloid-fibrils-provide-insights-into-the-involvement-of-lipoproteins-in-the-pathology-of-amyloidosis
#6
Hiroki Miyahara, Jinko Sawashita, Eri Ishikawa, Mu Yang, Xin Ding, Yingye Liu, Naomi Hachiya, Fuyuki Kametani, Masahide Yazaki, Masayuki Mori, Keiichi Higuchi
Amyloidosis is a disorder characterized by extracellular fibrillar deposits of misfolded proteins. The amyloid deposits commonly contain several non-fibrillar proteins as amyloid-associated proteins, but their roles in amyloidosis pathology are still unknown. In mouse senile amyloidosis, apolipoprotein A-II (ApoA-II) forms extracellular amyloid fibril (AApoAII) deposits with other proteins (AApoAII-associated proteins) in many organs. We previously reported that R1.P1-Apoa2(c) mice provide a reproducible model of AApoAII amyloidosis...
October 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28988880/gender-proteomics-ii-which-proteins-in-sexual-organs
#7
Elisabetta Gianazza, Ingrid Miller, Uliano Guerrini, Luca Palazzolo, Chiara Parravicini, Ivano Eberini
In continuity with the review dealing with differences by gender in non-sexual organs [1], this review collects data on the proteomes of the sexual organs as involved in human reproduction, under both physiological and pathological conditions. It also collects data on the tissue structures and biological fluids typical of pregnancy, such as placenta and amniotic fluid, as well as what may be tested on preimplantation embryos during medically assisted reproduction. The review includes as well mention to all fluids and secretions connected with sex organs and/or reproduction, including sperm and milk, to exemplify two distinctive items in male and female physiology...
October 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28986270/integrated-physiological-and-proteomic-analysis-reveals-underlying-response-and-defense-mechanisms-of-brachypodium-distachyon-seedling-leaves-under-osmotic-stress-cadmium-and-their-combined-stresses
#8
Zhi-Wei Cheng, Zi-Yan Chen, Xing Yan, Yan-Wei Bian, Xiong Deng, Yue-Ming Yan
Drought stress, a major abiotic stress, commonly occurs in metal-contaminated environments and affects crop growth and yield. In this study, we performed the first integrated phenotypic, physiological, and proteomic analysis of Brachypodium distachyon L. seedling leaves under polyethylene glycol (PEG) mock osmotic stress, cadmium (Cd(2+)), and their combined stresses. Combined osmotic and Cd(2+) stress had more significant effects than each individual stress on seedling growth, and the physiological traits and ultrastructures of leaves...
October 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28986269/quantitative-proteomic-analysis-reveals-that-chemotaxis-is-involved-in-chlortetracycline-resistance-of-aeromonas-hydrophila
#9
Wanxin Li, Farman Ali, Qilan Cai, Zujie Yao, Lina Sun, Wenxion Lin, Xiangmin Lin
In recent years, Aeromonas hydrophila, which has been classified as a food borne pathogen, has presented with increased levels of antibiotic resistance, with the mechanisms of this resistance being poorly understood. In this study, iTRAQ coupled mass spectrometry was employed to compare differentially expressed proteins in chlortetracycline (CTC) resistant A. hydrophila relative to a control strain. Result showed that a total of 234 differential proteins including 151 down-regulated and 83 up-regulated were identified in chlortetracycline resistance strain...
October 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28982538/label-free-quantitative-proteomic-analysis-of-drought-stress-responsive-late-embryogenesis-abundant-proteins-in-the-seedling-leaves-of-two-wheat-triticum-aestivum-l-genotypes
#10
Na Li, Shuai Zhang, Yajun Liang, Yuhong Qi, Juan Chen, Weining Zhu, Linsheng Zhang
Late embryogenesis abundant (LEA) proteins are highly hydrophilic proteins with key roles in environmental stress responses. In this study, we performed the first survey of the LEA proteome in seedling leaves from two wheat genotypes subjected to drought stress, i.e., Shaanhe 6 (SH, drought-tolerant) and Zhengyin 1 (ZY, drought-sensitive). After isolating the LEA subpopulation by treating total soluble proteins with heating combined with 1% trichloroacetic acid treatment that was assessed by Western blotting of dehydrins, label-free proteomic analysis identified 38 LEA proteins or homologues belonging to seven LEA subfamilies in the two genotypes...
October 2, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28970103/systems-analysis-of-singly-and-multiply-o-glycosylated-peptides-in-the-human-serum-glycoproteome-via-ethcd-and-hcd-mass-spectrometry
#11
Yong Zhang, Xinfang Xie, Xinyuan Zhao, Fang Tian, Jicheng Lv, Wantao Ying, Xiaohong Qian
Human serum has been intensively studied to identify biomarkers via global proteomic analysis. The altered O-glycoproteome is associated with human pathological state including cancer, inflammatory and degenerative diseases and is an attractive source of disease biomarkers. Because of the microheterogeneity and macroheterogeneity of O-glycosylation, site-specific O-glycosylation analysis in human serum is still challenging. Here, we developed a systematic strategy that combined multiple enzyme digestion, multidimensional separation for sample preparation and high-resolution tandem MS with Byonic software for intact O-glycopeptide characterization...
September 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28970102/the-proteome-speciation-of-an-immortalized-cystic-fibrosis-cell-line-new-perspectives-on-the-pathophysiology-of-the-disease
#12
Puglia Michele, Landi Claudia, Gagliardi Assunta, Breslin Loretta, Armini Alessandro, Brunetti Jlenia, Pini Alessandro, Bianchi Laura, Bini Luca
Cystic Fibrosis (CF) is a recessively inherited disease caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. CFTR has a pivotal role in the onset of CF, and several proteins are involved in its homeostasis. To study CFTR interactors at protein species level, we used a functional proteomics approach combining 2D-DIGE, mass spectrometry and enrichment analysis. A human bronchial epithelial cell line with cystic fibrosis (CFBE41o-) and the control (16HBE14o-) were used for the comparison...
September 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28966053/proteome-analysis-in-dystrophic-mdx-mouse-muscle-reveals-a-drastic-alteration-of-key-metabolic-and-contractile-proteins-after-chronic-exercise-and-the-potential-modulation-by-anti-oxidant-compounds
#13
Tania Gamberi, Tania Fiaschi, Elisa Valocchia, Alessandra Modesti, Paola Mantuano, Jean-Francois Rolland, Francesca Sanarica, Annamaria De Luca, Francesca Magherini
Weakness and fatigability are typical features of Duchenne muscular dystrophy patients and are aggravated in dystrophic mdx mice by chronic treadmill exercise. In the present study, we describe, the pattern of differentially abundant spots that is associated to the worsening of dystrophy phenotype induced by chronic exercise. Our proteomic analysis pointed out 34 protein spots with different abundance between sedentary and exercised mdx mice. These proteins belong mostly to glucose metabolism, energy production and sarcomere structure categories...
September 28, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28942014/a-flow-through-nanoporous-alumina-trypsin-bioreactor-for-mass-spectrometry-peptide-fingerprinting
#14
Marcus Kjellander, Erika Billinger, Harisha Ramachandraiah, Mats Boman, Sara Bergström Lind, Gunnar Johansson
Mass spectrometry-based proteomics benefits from efficient digestion of protein samples. In this study, trypsin was immobilized on nanoporous anodized alumina membranes to create an enzyme reactor suitable for peptide mass fingerprinting. The membranes were derivatized with 3-aminopropyltriethoxysilane and the amino groups were activated with carbonyldiimidazole to allow coupling of porcine trypsin via ε-amino groups. The function was assessed using the artificial substrate Nα-Benzoyl-L-arginine 4-nitroanilide hydrochloride, bovine ribonuclease A and a human plasma sample...
September 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28939340/use-of-ribosomal-proteins-as-biomarkers-for-identification-of-flavobacterium-psychrophilum-by-maldi-tof-mass-spectrometry
#15
Clara Fernández-Álvarez, Yolanda Torres-Corral, Ysabel Santos
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) is a rapid methodology for identification of bacteria that is increasingly used in diagnostic laboratories. This work aimed at evaluating the potential of MALDI-TOF-MS for identification of the main serotypes of Flavobacterium psychrophilum isolated from salmonids, and its discrimination from closely related Flavobacterium spp. A mass spectra library was constructed by analysing 70 F. psychrophilum strains representing the serotypes O1, O2a, O2b and O3, including reference and clinical isolates...
September 19, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28918933/structural-proteomics-topology-and-relative-accessibility-of-plant-lipid-droplet-associated-proteins
#16
Pascale Jolivet, Laure Aymé, Alexandre Giuliani, Frank Wien, Thierry Chardot, Yann Gohon
Lipid droplets are the major stock of lipids in oleaginous plant seeds. Despite their economic importance for oil production and biotechnological issues (biofuels, lubricants and plasticizers), numerous questions about their formation, structure and regulation are still unresolved. To determine water accessible domains of protein coating at lipid droplets surface, a structural proteomic approach has been performed. This technique relies on the millisecond timescale production of hydroxyl radicals by the radiolysis of water using Synchrotron X-ray white beam...
September 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28918200/profiling-the-short-linear-non-disulfide-bond-containing-peptidome-from-the-venom-of-the-scorpion-tityus-obscurus
#17
Nathalia Baptista Dias, Bibiana Monson de Souza, Fernando Kamimura Cocchi, Hipócrates M Chalkidis, Valquíria Abrão Coronado Dorce, Mario Sergio Palma
Many scorpion accidents occur in the Brazilian Amazonian region and are frequently caused by Tityus obscurus. Approximately 5% of the crude venom of this species is composed of short linear, non-disulfide-bridged peptides, which have not been intensively investigated. As a consequence, only a few of these peptides have been structurally and functionally characterized to date. In the present paper, the peptide fraction of the venom was subjected to peptide profiling using an LCMS-IT-TOF/MS and MS(n) system. The analysis detected 320 non-disulfide bond-containing peptides (NDBPs), of which twenty-seven had their sequences assigned; among them, thirteen peptides were characterized, constituting novel toxins in T...
September 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28887210/can-half-marathon-affect-overall-health-the-yin-yang-of-sport
#18
Luca Dalle Carbonare, Marcello Manfredi, Giuseppe Caviglia, Eleonora Conte, Elisa Robotti, Emilio Marengo, Samuele Cheri, Francesco Zamboni, Daniele Gabbiani, Michela Deiana, Daniela Cecconi, Federico Schena, Monica Mottes, Maria Teresa Valenti
Physical activity improves overall health and counteracts metabolic pathologies. Adipose tissue and bone are important key targets of exercise; the prevalence of diseases associated with suboptimal physical activity levels has increased in recent times as a result of lifestyle changes. Mesenchymal stem cells (MSCs) differentiation in either osteogenic or adipogenic lineage is regulated by many factors. Particularly, the expression of master genes such as RUNX2 and PPARγ2 is essential for MSC commitment to osteogenic or adipogenic differentiation, respectively...
September 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28887209/thyroid-associated-orbitopathy-and-tears-a-proteomics-study
#19
Edina Kishazi, Marianne Dor, Simone Eperon, Aurélie Oberic, Mehrad Hamedani, Natacha Turck
To date, Thyroid-Associated Orbitopathy (TAO), an autoimmune inflammatory disease affecting the eye, remains poorly characterised and its diagnosis challenging. The aim of this study was to investigate the tears of the TAO patients in order to identify potential biomarkers. Two independent quantitative Tandem Mass Tag™ 6-plex experiments were done. After in-solution digestion and isoelectric fractionation, the 12 fractions were analysed with a LTQ Orbitrap Velos coupled to a liquid chromatography. Raw files were searched against Swiss-Prot-AC database using Proteome Discoverer software, with a false discovery rate of 1% at peptide and protein levels...
September 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28887208/proteomic-comparison-of-three-clinical-diarrhoeagenic-drug-resistant-escherichia-coli-isolates-grown-on-chromagar%C3%A2-stec-media
#20
John Bosco Kalule, Suereta Fortuin, Bridget Calder, Lourens Robberts, Karen H Keddy, Andrew Nel, Shaun Garnett, Mark Nicol, Digby F Warner, Nelson C Soares, Jonathan M Blackburn
Shiga-toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) are key diarrhoea-causing foodborne pathogens. We used proteomics to characterize the virulence and antimicrobial resistance protein profiles of three clinical pathogenic E. coli isolates (two EPEC [one resistant to ciprofloxacin] and one STEC) cultured on CHROMagar™STEC solid media after minimal laboratory passage. We identified 4767 unique peptides from 1630 protein group across all three clinical E. coli strains...
September 5, 2017: Journal of Proteomics
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