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Proteomics

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https://www.readbyqxmd.com/read/28627733/response-of-renal-tubular-cells-to-differential-types-and-doses-of-calcium-oxalate-crystals-integrative-proteome-network-analysis-and-functional-investigations
#1
Arada Vinaiphat, Siripat Aluksanasuwan, Juthatip Manissorn, Suchitra Sutthimethakorn, Visith Thongboonkerd
We have previously identified changes in the cellular proteome of renal tubular cells induced by low-dose (100 μg/ml) and high-dose (1,000 μg/ml) calcium oxalate monohydrate (COM) and dihydrate (COD) crystals. However, the functional significance of such expression data remained unclear. In this study, we performed comparative analyses and functional investigations of four proteomic datasets to define potential mechanisms by which renal tubular cells responded to differential crystal types and doses. The data showed that high-dose induced greater changes than low-dose, whereas COM induced more changes than COD...
June 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28627015/small-proteins-encoded-by-unannotated-orfs-are-rising-stars-of-the-proteome-confirming-shortcomings-in-genome-annotations-and-current-vision-of-an-mrna
#2
REVIEW
Vivian Delcourt, Antanas Staskevicius, Michel Salzet, Isabelle Fournier, Xavier Roucou
Short ORF-encoded peptides and small proteins in eukaryotes have been hiding in the shadow of large proteins for a long time. Recently, improved identifications in MS-based proteomics and ribosome profiling resulted in the detection of large numbers of small proteins. The variety of functions of small proteins is also emerging. It seems to be the right time to reflect on why small proteins remained invisible. In addition to the obvious technical challenge of detecting small proteins, they were mostly forgotten from annotations and they escaped detection because they were not sought...
June 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28621911/different-roles-of-cd4-cd8-and-%C3%AE-%C3%AE-t-lymphocytes-in-naive-and-vaccinated-chickens-during-s-enteritidis-infection
#3
Zuzana Sekelova, Ondrej Polansky, Hana Stepanova, Radek Fedr, Marcela Faldynova, Ivan Rychlik, Lenka Vlasatikova
Lymphocytes represent the key antigen-specific leukocyte subpopulation. Despite their importance in mounting an immune response, an unbiased description of proteins expressed by chicken lymphocytes has not been presented. In this study we therefore intravenously infected chickens with Salmonella Enteritidis, sorted CD4, CD8 and γδ T-lymphocytes from the spleen by flow cytometry and determined the proteome of each population by LC-MS/MS. CD4 T-lymphocyte characteristic proteins included ubiquitin SUMO-like domain and BAR domain containing proteins...
June 16, 2017: Proteomics
https://www.readbyqxmd.com/read/28618117/itraq-based-proteomics-of-sunflower-cultivars-differing-in-resistance-to-parasitic-weed-orobanche-cumana
#4
Chong Yang, Ling Xu, Na Zhang, Faisal Islam, Wenjian Song, Luyang Hu, Dan Liu, Xiaonan Xie, Weijun Zhou
Orobanche cumana is an obligate root parasite causing severe damage to many economically important crops, including sunflowers worldwide. For efficient control measures, it is necessary to understand the resistant mechanism during interaction at molecular level. The present study emphasizes on comparative proteomics to investigate the mechanistic basis of compatible and incompatible interaction of O. cumana with resistant (JY207) and susceptible (TK0409) sunflowers. More than 3500 proteins were identified from two cultivars by iTRAQ analysis...
June 15, 2017: Proteomics
https://www.readbyqxmd.com/read/28613014/raising-the-list-of-sirt7-targets-to-a-new-level
#5
Nicolas G Simonet, Alejandro Vaquero
Sirtuins are crucial proteins involved in sensing and coordinating the response to different forms of stress, mainly through NAD(+) -dependent deacetylation of proteins. For that reason, sirtuins are directly involved in many human pathologies including cancer, diabetes, cardiovascular and neurodegenerative diseases. SirT7, one of the less well-understood sirtuins, has been associated with ribosome biogenesis, gene expression, metabolism and cancer. Despite the wide range of these functions, only a handful of targets for SirT7 have so far been described...
June 14, 2017: Proteomics
https://www.readbyqxmd.com/read/28613012/clinical-implications-of-compounds-designed-to-inhibit-ecm-modifying-metalloproteinases
#6
REVIEW
Sabrina Amar, Dmitriy Minond, Gregg B Fields
Remodeling of the extracellular matrix (ECM) is crucial in development and homeostasis, but also has a significant role in disease progression. Two metalloproteinase families, the matrix metalloproteinases (MMPs) and a disintegrin and metalloproteases (ADAMs), participate in the remodeling of the ECM, either directly or through the liberation of growth factors and cell surface receptors. The correlation of MMP and ADAM activity to a variety of diseases has instigated numerous drug development programs. However, broad-based and Zn(2+) -chelating MMP and ADAM inhibitors have fared poorly in the clinic...
June 14, 2017: Proteomics
https://www.readbyqxmd.com/read/28612519/glucosyltransferase-dependent-and-independent-effects-of-tcdb-on-the-proteome-of-hep-2-cells
#7
Jelena Erdmann, Johannes Junemann, Anke Schröder, Ingo Just, Ralf Gerhard, Andreas Pich
Toxin B (TcdB) of the nosocomial pathogen C. difficile has been reported to exhibit a glucosyltransferase dependent and independent effect on treated HEp-2 cells at toxin concentration above 0.3 nM. In order to investigate and further characterize both effects epithelial cells were treated with wild type TcdB and glucosyltransferase-deficient TcdBNXN and their proteomes were analyzed by LC-MS. Triplex SILAC labeling was used for quantification. Identification of 5212 and quantification of 4712 protein groups was achieved...
June 14, 2017: Proteomics
https://www.readbyqxmd.com/read/28608649/high-coverage-proteomics-reveals-methionine-auxotrophy-in-deinococcus-radiodurans
#8
Yanxia Zhou, Pan Shen, Qiuyan Lan, Chen Deng, Yao Zhang, Yanchang Li, Wei Wei, Yihao Wang, Na Su, Fuchu He, Qiong Xie, Zhitang Lyu, Dong Yang, Xu Ping
Deinococcus radiodurans is a robust bacterium best known for its capacity to resist to radiation. In this study, the SDS-PAGE coupled with high-precision LC-MS/MS was used to study the D. radiodurans proteome. A total of 1951 proteins were identified which covers 63.18% protein coding genes. Comparison of the identified proteins to the key enzymes in amino acid biosyntheses from KEGG database showed the methionine biosynthesis is incomplete while other amino acid biosynthesis are complete, which indicated methionine auxotrophy in D...
June 13, 2017: Proteomics
https://www.readbyqxmd.com/read/28597999/a-rapid-and-easy-protein-n-terminal-profiling-strategy-using-n-succinimidyloxycarbonylmethyl-tris-2-4-6-trimethoxyphenyl-phosphonium-bromide-tmpp-labeling-and-stagetip
#9
Yanchang Li, Zhiqiang Wang, Wenjing Zhou, Kun Zhang, Jie Ma, Feilin Wu, Jianguo Ji, Xuechuan Hong, Zixin Deng, Simin He, Ping Xu
Protein N-terminal profiling is crucial when characterizing biological functions and provides proteomic evidences for genome reannotations. However, most of the current N-terminal enrichment approaches involve multiple chemical derivatizations and chromatographic separation processes which are time consuming and can contribute to N-terminal peptide losses. In this study, a fast, one-step approach utilizing TMPP derivatization and StageTip separation was developed to enhance N-terminal peptide enrichment and analysis...
June 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28590090/motile-hepatocellular-carcinoma-cells-preferentially-secret-sugar-metabolism-regulatory-proteins-via-exosomes
#10
Jing Zhang, Shaohua Lu, Ye Zhou, Kun Meng, Zhipeng Chen, Yizhi Cui, Yunfeng Shi, Qing-Yu He, Tong Wang
Exosomes are deliverers of critically functional proteins, capable of transforming target cells in numerous cancers, including hepatocellular carcinoma (HCC). We hypothesize that the motility of HCC cells can be featured by comparative proteome of exosomes. Hence, we performed the super-SILAC-based MS analysis on the exosomes secreted by three human HCC cell lines, including the non-motile Hep3B cell, and the motile 97H and LM3 cells. Over 1400 exosomal proteins were confidently quantified in each MS analysis with highly biological reproducibility...
June 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28556466/microproteomics-with-microfluidic-based-cell-sorting-application-to-1-000-and-100-immune-cells
#11
Kie Kasuga, Yasutake Katoh, Keisuke Nagase, Kazuhiko Igarashi
Ultimately, cell biology seeks to define molecular mechanisms underlying cellular functions. However, heterogeneity within cell populations must be considered for optimal assay design and data interpretation. Although single-cell analyses are desirable for addressing this issue, practical considerations, including assay sensitivity, limit their broad application. Therefore, omics studies on small numbers of cells in defined subpopulations represent a viable alternative for elucidating cell functions at the molecular level...
May 27, 2017: Proteomics
https://www.readbyqxmd.com/read/28556443/swath-based-quantitative-proteomics-reveals-the-mechanism-of-enhanced-bombyx-mori-nucleopolyhedrovirus-resistance-in-silkworm-reared-on-uv-b-treated-mulberry-leaves
#12
Jin Hu, Wei Zhu, Yaohan Li, Qijie Guan, Haijian Yan, Jiaojiao Yu, Zhirong Fu, Xingmeng Lu, Jingkui Tian
Bombyx mori nucleopolyhedrovirus (BmNPV) is one of the most acute infectious diseases in silkworm, which has led to great economic loss in sericulture. Previous study showed that the content of secondary metabolites in mulberry leaves, particularly for moracin N, was increased after UV-B irradiation. In this study, the BmNPV resistance of silkworms reared on UV-B treated and moracin N spreaded mulberry leaves was improved. To uncover the mechanism of enhanced BmNPV resistance, silkworm midguts from UV-B treated mulberry leaves (BUM) and moracin N (BNM) groups were analyzed by SWATH-based proteomic technique...
May 27, 2017: Proteomics
https://www.readbyqxmd.com/read/28556401/quantitative-proteome-based-systematic-identification-of-sirt7-substrates
#13
Chaohua Zhang, Zichao Zhai, Ming Tang, Zhongyi Cheng, Tingting Li, Haiying Wang, Wei-Guo Zhu
SIRT7 is a class III histone deacetylase that is involved in numerous cellular processes. Only six substrates of SIRT7 have been reported thus far, so we aimed to systematically identify SIRT7 substrates using stable-isotope labeling with amino acids in cell culture (SILAC) coupled with quantitative mass spectrometry (MS). Using SIRT7(+/+) and SIRT7(-/-) mouse embryonic fibroblasts as our model system, we identified and quantified 1,493 acetylation sites in 789 proteins, of which 261 acetylation sites in 176 proteins showed ≥2-fold change in acetylation state between SIRT7(-/-) and SIRT7(+/+) cells...
May 27, 2017: Proteomics
https://www.readbyqxmd.com/read/28548456/proteomics-in-cell-division
#14
REVIEW
Zeynep Cansu Üretmen Kagıalı, Aydanur Şentürk, Nazlı Ezgi Özkan Küçük, Mohammed Haroon Qureshi, Nurhan Özlü
Cell division requires a coordinated action of the cell cycle machinery, cytoskeletal elements, chromosomes and membranes. Cell division studies have greatly benefitted from the mass spectrometry (MS)-based proteomic approaches for probing the biochemistry of highly dynamic complexes and their coordination with each other as a cell progresses into division. In this review, we first summarize a wide-range of proteomic studies that focus on the identification of sub-cellular components/protein complexes of the cell division machinery including kinetochores, mitotic spindle, midzone and centrosomes...
May 26, 2017: Proteomics
https://www.readbyqxmd.com/read/28547889/comparison-between-chaotropic-and-detergent-based-sample-preparation-workflow-in-tendon-for-mass-spectrometry-analysis
#15
Yalda A Kharaz, Danae Zamboulis, Karen Sander, Eithne Comerford, Peter Clegg, Mandy Peffers
Exploring the tendon proteome is a challenging but important task for understanding the mechanisms of physiological/pathological processes during ageing and disease and for the development of new treatments. Several extraction methods have been utilised for tendon mass spectrometry, however different extraction methods have not been simultaneously compared. In the present study we compared protein extraction in tendon with two chaotropic agents, guanidine hydrochloride (GnHCl) and urea, a detergent, RapiGest(ۛ) , and their combinations for shotgun mass spectrometry...
May 26, 2017: Proteomics
https://www.readbyqxmd.com/read/28544771/quantitative-proteomic-analysis-of-host-epithelial-cells-infected-by-salmonella-enterica-serovar-typhimurium
#16
Linlu Qi, Mo Hu, Jiaqi Fu, Yanhua Liu, Mei Wu, Kaiwen Yu, Xiaoyun Liu
Systems-level analyses have the capability to offer new insight into host-pathogen interactions on the molecular level. Using Salmonella infection of host epithelial cells as a model system, we previously analyzed intracellular bacterial proteome as a window into pathogens' adaptations to their host environment (Infect. Immun. 2015; J. Proteome Res. 2017). Herein we extended our efforts to quantitatively examine protein expression of host cells during infection. In total, we identified more than 5,000 proteins with 194 differentially regulated proteins upon bacterial infection...
May 25, 2017: Proteomics
https://www.readbyqxmd.com/read/28544614/proteomic-profiling-of-the-hypothalamus-in-two-mouse-models-of-narcolepsy
#17
Sausan Azzam, Daniela Schlatzer, David Nethery, Dania Saleh, Xiaolin Li, Afaf Akladious, Mark R Chance, Kingman P Strohl
Narcolepsy is a disabling neurological disorder of sleepiness linked to the loss of neurons producing orexin neuropeptides in the hypothalamus. Two well characterized phenotypic mouse models of narcolepsy, loss-of-function (orexin-knockout) and progressive loss of orexin (orexin/ataxin-3) exist. The open question is whether the proteomics signatures of the hypothalamus would be different between the two models. To address this gap, we utilized a label-free proteomics approach and conducted a hypothalamic proteome analysis by comparing each disease model to that of wild type...
May 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28544375/proteomic-analysis-of-hair-shafts-from-monozygotic-twins-expression-profiles-and-genetically-variant-peptides
#18
Pei-Wen Wu, Katelyn E Mason, Blythe P Durbin-Johnson, Michelle Salemi, Brett S Phinney, David M Rocke, Glendon J Parker, Robert H Rice
Forensic association of hair shaft evidence with individuals is currently assessed by comparing mitochondrial DNA haplotypes of reference and casework samples, primarily for exclusionary purposes. Present work tests and validates more recent proteomic approaches to extract quantitative transcriptional and genetic information from hair samples of monozygotic twin pairs, which would be predicted to partition away from unrelated individuals if the datasets contain identifying information. Protein expression profiles and polymorphic, genetically variant hair peptides were generated from 10 pairs of monozygotic twins...
May 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28544705/sma3s-a-universal-tool-for-easy-functional-annotation-of-proteomes-and-transcriptomes
#19
Carlos S Casimiro-Soriguer, Antonio Muñoz-Mérida, Antonio J Pérez-Pulido
The current cheapening of next-generation sequencing has led to an enormous growth in the number of sequenced genomes and transcriptomes, allowing wet labs to get the sequences from their organisms of study. To make the most of these data, one of the first things that should be done is the functional annotation of the protein-coding genes. But it used to be a slow and tedious step that can involve the characterization of thousands of sequences. Sma3s is an accurate computational tool for annotating proteins in an unattended way...
May 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28523650/ubiquitin-specific-peptidase-5-mediates-histidine-rich-protein-hpn-induced-cell-apoptosis-in-hepatocellular-carcinoma-through-p14-p53-signaling
#20
Yi Liu, Wei-Mao Wang, Li-Yi Zou, Li Li, Lu Feng, Ming-Zhu Pan, Min-Yi Lv, Ying Cao, Hua Wang, Hsiang-Fu Kung, Jian-Xin Pang, Wei-Ming Fu, Jin-Fang Zhang
Hpn is a small histidine-rich cytoplasmic protein from Helicobacter pylori and has been recognized as a high-risk factor for several cancers including gastric cancer, colorectal cancer, and MALT lymphoma. However, the relationship between Hpn and cancers remains elusive. In this study, we discovered that Hpn protein effectively suppressed cell growth and induced apoptosis in hepatocellular carcinoma (HCC). A two-dimensional gel electrophoresis and mass spectrometry-based comparative proteomics was performed to find the molecular targets of Hpn in HCC cells...
May 18, 2017: Proteomics
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