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https://www.readbyqxmd.com/read/28808994/monitoring-dynamic-changes-of-the-cell-surface-glycoproteome-by-quantitative-proteomics
#1
Mathias Kalxdorf, Hans Christian Eberl, Marcus Bantscheff
The analysis of the cell surface accessible proteome provides invaluable information about cellular identity, cellular functions, and interactions. Cell surface labeling in combination with quantitative proteomics enables the unbiased identification and quantification of cell surface proteins. We describe a fast, efficient, and robust protocol for the enrichment of the N-linked plasma membrane glycoproteome and subsequent analysis by mass spectrometry. Precise and multiplexed quantification of relative changes of cell surface protein presentation is enabled by an isobaric labeling strategy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28806774/fibroblast-growth-factor-receptor-1-mediates-internalization-of-pathogenic-spotted-fever-rickettsiae-into-host-endothelium
#2
Abha Sahni, Jignesh Patel, Hema P Narra, Casey L C Schroeder, David H Walker, Sanjeev K Sahni
Rickettsial infections continue to cause serious morbidity and mortality in severe human cases around the world. Host cell adhesion and invasion is an essential requisite for intracellular growth, replication, and subsequent dissemination of pathogenic rickettsiae. Heparan sulfate proteoglycans [HSPGs] facilitate the interactions between fibroblast growth factor(s) and their tyrosine kinase receptors resulting in receptor dimerization/activation and have been implicated in bacterial adhesion to target host cells...
2017: PloS One
https://www.readbyqxmd.com/read/28804941/proteomic-analysis-to-unravel-the-effect-of-heat-stress-on-gene-expression-and-milk-synthesis-in-bovine-mammary-epithelial-cells
#3
Lian Li, Yiru Wang, Chengmin Li, Genlin Wang
Heat stress can play a negative effect on milk yield and composition of dairy cattle, leading to immeasurable economic loss. The basic components of the mammary gland are the alveoli; these alveolar mammary epithelial cells reflect the milk producing ability of dairy cows. In this study, we exposed bovine mammary epithelial cells to heat stress and compared them to a control group using isobaric tags for relative and absolute quantitation combined with liquid chromatography coupled with tandem mass spectrometry...
August 14, 2017: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/28802577/how-fast-fast-folding-proteins-fold-in-silico
#4
Yuan-Ping Pang
In reported microcanonical molecular dynamics simulations, fast-folding proteins CLN025 and Trp-cage autonomously folded to experimentally determined native conformations. However, the folding times of these proteins derived from the simulations were more than 4-10 times longer than their experimental values. This article reports autonomous folding of CLN025 and Trp-cage in isobaric-isothermal molecular dynamics simulations with agreements within factors of 0.69-1.75 between simulated and experimental folding times at different temperatures...
August 9, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28802015/identification-and-characterization-of-metformin-on-peptidomic-profiling-in-human-visceral-adipocytes
#5
Yao Gao, XingYun Wang, FangYan Huang, XianWei Cui, Yun Li, Xing Wang, Yan Cao, PengFei Xu, KaiPeng Xie, RanRan Tang, Le Zhang, ChenBo Ji, LiangHui You, XiRong Guo
OBJECTIVES: To gain insight into the effect of metformin on losing weight from peptidomic perspective and to screen potential active peptides for reducing fat lipid deposition. METHODS: After determining the proper concentration of metformin on human primary visceral adipocytes, we constructed a comparative peptidomic profiling between control and metformin treatment group (n = 3) using a stable isobaric labeling strategy involving tandem mass tag reagents, followed by liquid chromatography tandem mass spectrometry...
August 12, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28800743/an-itraq-based-proteomic-analysis-reveals-dysregulation-of-neocortical-synaptopodin-in-lewy-body-dementias
#6
Arnab Datta, Yuek Ling Chai, Jing Min Tan, Jasinda H Lee, Paul T Francis, Christopher P Chen, Siu Kwan Sze, Mitchell K P Lai
Lewy body dementias are the second most common cause of neurodegenerative dementia in the elderly after Alzheimer's disease (AD). The two clinical subgroups of Lewy body dementias, namely, dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD), are differentiated by the chronology of cognitive symptoms relative to parkinsonism. At present, there remains a debate on whether DLB and PDD are separate disease entities, or fall within the same spectrum of Lewy body dementias. In this study, we compared the detergent-soluble proteome via an 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) analysis of pooled lysates from the prefrontal cortex (BA9) of DLB (n = 19) and PDD (n = 21) patients matched a priori for amyloid (total Aβ42) burden, semi-quantitative scores for Lewy bodies and neurofibrillary tangles together with age-matched control (n = 21) subjects...
August 11, 2017: Molecular Brain
https://www.readbyqxmd.com/read/28800394/zno-101-%C3%AC-0-surface-hydroxylation-under-ambient-water-vapor
#7
John T Newberg, Chris Goodwin, Chris Arble, Yehia Khalifa, Jorge Anibal Boscoboinik, Sana Rani
The interaction of water vapor with a single crystal ZnO(101 ̅0) surface was investigated using synchrotron-based ambient pressure X-ray photoelectron spectroscopy (APXPS). Two isobaric experiments were performed at 0.3 and 0.07 Torr water vapor pressure at sample temperatures ranging from 750 K to 295 K up to a maximum of 2 % relative humidity (RH). Below 10-4 % RH the ZnO(101 ̅0) interface is covered with ~0.25 monolayers of OH groups attributed to dissociation at non-stoichiometric defect sites. At ~10-4 % RH there is sharp onset in increased surface hydroxylation attributed to reaction at stoichiometric terrace sites...
August 11, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28800123/differential-proteomic-analysis-reveals-the-effect-of-calcium-on-malus-baccata-borkh-leaves-under-temperature-stress
#8
Lijie Li, Hong Su, Huaiyu Ma, Deguo Lyu
In the cool apple-producing areas of northern China, air temperature during early spring changes in a rapid and dramatic manner, which affects the growth and development of apple trees at the early stage of the growing season. Previous studies have shown that the treatment of calcium can increase the cold tolerance of Malus baccata Borkh., a widely-used rootstock apple tree in northern China. To better understand the physiological function of calcium in the response of M. baccata to temperature stress, we analyzed the effect of calcium treatment (2% CaCl₂) on M...
August 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28792770/proteomic-analysis-of-brain-and-cerebrospinal-fluid-from-the-three-major-forms-of-neuronal-ceroid-lipofuscinosis-reveals-potential-biomarkers
#9
David E Sleat, Abla Tannous, Istvan Sohar, Jennifer A Wiseman, Haiyan Zheng, Meiqian Qian, Caifeng Zhou, Winnie Xin, Rosemary Barone, Katherine B Sims, Dirk F Moore, Peter Lobel
Clinical trials have been conducted for the neuronal ceroid lipofuscinoses (NCLs), a group of neurodegenerative lysosomal diseases that primarily affect children. While clinical rating systems will evaluate long-term efficacy, biomarkers to measure short-term response to treatment would be extremely valuable. To identify candidate biomarkers, we analyzed autopsy brain and matching CSF samples from controls and three genetically distinct NCLs due to deficiencies in palmitoyl protein thioesterase 1 (CLN1 disease), tripeptidyl peptidase 1 (CLN2 disease) and CLN3 protein (CLN3 disease)...
August 9, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28792419/interaction-of-heat-shock-protein-60-hsp60-with-microrna-in-chinese-mitten-crab-during-spiroplasma-eriocheiris-infection
#10
Ming-Xiao Ning, Yun-Ji Xiu, Jing-Xiu Bi, Yu-Han Liu, Li-Bo Hou, Zheng-Feng Ding, Wei Gu, Wen Wang, Qing-Guo Meng
Heat shock protein 60 from the Chinese mitten crab Eriocheir sinensis (EsHSP60) was previously identified in relation to Spiroplasma eriocheiris infection by isobaric tags for relative and absolute quantitation labelling followed by liquid chromatography-tandem mass spectrometry. In the present study, to validate the immune function of this protein, the cDNA of the EsHSP60 gene was cloned. Various crab tissues were assessed using real-time PCR, which showed that EsHSP60 transcription occurred in all tissues examined...
August 9, 2017: Diseases of Aquatic Organisms
https://www.readbyqxmd.com/read/28791374/corilagin-sensitizes-epithelial-ovarian-cancer-to-chemotherapy-by-inhibiting-snail%C3%A2-glycolysis-pathways
#11
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/28790852/impact-of-combined-treatment-with-nimesulide-and-cisplatin-on-oral-carcinoma-cells
#12
Aleksandra Barac, Goran Mitulovic, Seth Hallström, Sonja Zehetmayer, Matthaeus Ch Grasl, Boban M Erovic
BACKGROUND: Despite significant advances in diagnosis and therapy, the rate of survival of patients with oral cancers still remains poor as an appropriate treatment has not been found yet, due to side effects of chemo/radiotherapy. AIM: This study aimed to identify molecular mechanisms of cell death of oral cancer cells caused by treatment with a nonselective Cox-2 inhibitor in combination with a low-dose chemotherapeutic drug. METHODS: Squamous cell carcinoma (SCC) cells SCC9 and SCC25 were subjected to mono- and combination therapy with nimesulide and cisplatin...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28789995/proteome-profiling-of-s-nitrosylated-synaptosomal-proteins-by-isobaric-mass-tags
#13
Teodora Stella Wijasa, Marc Sylvester, Nahal Brocke-Ahmadinejad, Markus P Kummer, Frederic Brosseron, Volkmar Gieselmann, Michael T Heneka
No abstract text is available yet for this article.
August 5, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28780297/respiration-disruption-and-detoxification-at-the-protein-expression-levels-in-the-pacific-oyster-crassostrea-gigas-under-zinc-exposure
#14
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/28762069/optimized-experimental-workflow-for-tandem-mass-spectrometry-molecular-networking-in-metabolomics
#15
Florent Olivon, Fanny Roussi, Marc Litaudon, David Touboul
New omics sciences generate massive amounts of data, requiring to be sorted, curated, and statistically analyzed by dedicated software. Data-dependent acquisition mode including inclusion and exclusion rules for tandem mass spectrometry is routinely used to perform such analyses. While acquisition parameters are well described for proteomics, no general rule is currently available to generate reliable metabolomic data for molecular networking analysis on the Global Natural Product Social Molecular Networking platform (GNPS)...
July 31, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28758227/standardization-approaches-in-absolute-quantitative-proteomics-with-mass-spectrometry
#16
REVIEW
Francisco Calderón-Celis, Jorge Ruiz Encinar, Alfredo Sanz-Medel
Mass spectrometry-based approaches have enabled important breakthroughs in quantitative proteomics in the last decades. This development is reflected in the better quantitative assessment of protein levels as well as to understand post-translational modifications and protein complexes and networks. Nowadays, the focus of quantitative proteomics shifted from the relative determination of proteins (ie, differential expression between two or more cellular states) to absolute quantity determination, required for a more-thorough characterization of biological models and comprehension of the proteome dynamism, as well as for the search and validation of novel protein biomarkers...
July 31, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28755911/itraq-proteomic-analysis-of-the-interactions-between-bombyx-mori-nuclear-polyhedrosis-virus-and-silkworm
#17
Wei-Tao Dong, Long-Fei Xiao, Jun-Jie Hu, Xin-Xu Zhao, Ji-Xing Liu, Yong Zhang
The silkworm hemolymph is an important defense system against bacteria and viruses. In this study, silkworms were infected with Bombyx mori nuclear polyhedrosis virus to investigate the subsequent immune response at the protein level. Proteomes were analyzed before and after infection using isobaric tags for relative and absolute quantitation and LC-MS. A total of 456 differentially expressed proteins were identified, of which 179 were upregulated and 193 were downregulated. Changes in expression were validated by western blot for several proteins...
July 26, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28752479/quantitative-proteomic-analysis-of-optimal-cutting-temperature-oct-embedded-core-needle-biopsy-of-lung-cancer
#18
Xiaozheng Zhao, Kenneth E Huffman, Junya Fujimoto, Jamie Rodriguez Canales, Luc Girard, Guangjun Nie, John V Heymach, Igacio I Wistuba, John D Minna, Yonghao Yu
With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT...
July 27, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28752295/nmr-based-metabolomics-reveals-the-metabolite-profiles-of-vibrio-parahaemolyticus-under-ferric-iron-stimulation
#19
Jun Zhou, Chenyang Lu, Dijun Zhang, Chennv Ma, Xiurong Su
Vibrio parahaemolyticus is a halophilic bacterium endemic to coastal areas, and its pathogenicity has caused widespread seafood poisoning. In our previous research, the protein expression of V. parahaemolyticus in Fe(3+) medium was determined using isobaric tags for relative and absolute quantitation (iTRAQ). Here, nuclear magnetic resonance (NMR) was used to detect changes in the V. parahaemolyticus metabolome. NMR spectra were obtained using methanol-water extracts of intracellular metabolites from V. parahaemolyticus under various culture conditions, and 62 metabolites were identified, including serine, arginine, alanine, ornithine, tryptophan, glutamine, malate, NAD(+), NADP(+), oxypurinol, xanthosine, dCTP, uracil, thymine, hypoxanthine, and betaine...
August 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28752099/expressions-profiles-of-the-proteins-associated-with-carbohydrate-metabolism-in-rat-liver-regeneration
#20
Li Yin, Cuifang Chang, Cunshuan Xu
Liver has a very amazing ability to regenerate from the remnant liver after injury or partial hepatectomy (PH). Carbohydrate metabolism plays a critical role in regeneration. Many signaling pathways are involved in the metabolism process. We analyzed the changes of proteins at 0-36 h after PH in rats using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with LC-MS/MS-based quantitative proteomics strategy. The results showed that 110 proteins and 5 signaling pathways related to carbohydrate metabolism in rat LR changed significantly...
2017: BioMed Research International
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