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Journal of Proteomics

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https://www.readbyqxmd.com/read/28343001/comprehensive-functional-analysis-of-large-lists-of-genes-and-proteins
#1
Bernhard Mlecnik, Jérôme Galon, Gabriela Bindea
The interpretation of high dimensional datasets resulting from genomic and proteomic experiments in a timely and efficient manner is challenging. ClueGO software is a Cytoscape App that extracts representative functional biological information for large lists of genes or proteins. The functional enrichment analysis is based on the latest publicly available data from multiple annotation and ontology resources that can be automatically accessed through ClueGO. Predefined settings for the selection of the terms are provided to facilitate the analysis...
March 22, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28336332/how-to-use-and-integrate-bioinformatics-tools-to-compare-proteomic-data-from-distinct-conditions-a-tutorial-using-the-pathological-similarities-between-aortic-valve-stenosis-and-coronary-artery-disease-as-a-case-study
#2
Fábio Trindade, Rita Ferreira, Beatriz Magalhães, Adelino Leite-Moreira, Inês Falcão-Pires, Rui Vitorino
Nowadays we are surrounded by a plethora of bioinformatics tools, powerful enough to deal with the large amounts of data arising from proteomic studies, but whose application is sometimes hard to find. Therefore, we used a specific clinical problem - to discriminate pathophysiology and potential biomarkers between two similar cardiovascular diseases, aortic valve stenosis (AVS) and coronary artery disease (CAD) - to make a step-by-step guide through four bioinformatics tools: STRING, DisGeNET, Cytoscape and ClueGO...
March 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28336331/are-neutral-loss-and-internal-product-ions-useful-for-top-down-protein-identification
#3
Kaijie Xiao, Fan Yu, Houqin Fang, Bingbing Xue, Yan Liu, Yunhui Li, Zhixin Tian
Neutral loss and internal product ions have been found to be significant in both peptide and protein tandem mass spectra and they have been proposed to be included in database search and for protein identification. In addition to common canonical b/y ions in collision-based dissociation or c/z ions in electron-based dissociation, inclusion of neutral loss and internal product ions would certainly make better use of tandem mass spectra data; however, their ultimate utility for protein identification with false discovery rate control remains unclear...
March 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28323242/investigation-of-the-indigenous-fungal-community-populating-barley-grains-secretomes-and-xylanolytic-potential
#4
Abida Sultan, Jens C Frisvad, Birgit Andersen, Birte Svensson, Christine Finnie
The indigenous fungal species populating cereal grains produce numerous plant cell wall-degrading enzymes including xylanases, which could play important role in plant-pathogen interactions and in adaptation of the fungi to varying carbon sources. To gain more insight into the grain surface-associated enzyme activity, members of the populating fungal community were isolated, and their secretomes and xylanolytic activities assessed. Twenty-seven different fungal species were isolated from grains of six barley cultivars over different harvest years and growing sites...
March 18, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28323244/itraq-based-differential-proteomic-analysis-in-mongolian-gerbil-brains-chronically-infected-with-toxoplasma-gondii
#5
Lin Lv, Yapei Wang, Weili Feng, Jorge A Hernandez, Wanyi Huang, Yuxiang Zheng, Xue Zhou, Shumei Lv, Yajun Chen, Zi-Guo Yuan
The aim of our study was to detect differentially regulated proteins and specific signaling pathways in Mongolian gerbil brains during chronic Toxoplasma gondii (T.gondii) PRU strain infection. We use a iTRAQ-based strategy to detecte 4935 proteins, out of which 110 proteins were differentially expressed (>/=2.0-fold, p value <0.05) when the brain of gerbils infected with T.gondii was compared to control brain tissues. We confirmed the authenticity and the accuracy of iTRAQ results through quantitative real-time PCR and western blot (WB), which was consistent with mass spectrometry analysis...
March 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28323243/proteomics-of-facs-sorted-heterogeneous-corynebacterium-glutamicum-populations
#6
Andreas Harst, Stefan P Albaum, Tanja Bojarzyn, Christian Trötschel, Ansgar Poetsch
The metabolic status of individual cells in microbial cultures can differ, being relevant for biotechnology, environmental and medical microbiology. However, it is hardly understood in molecular detail due to limitations of current analytical tools. Here, we demonstrate that FACS in combination with proteomics can be used to sort and analyze cell populations based on their metabolic state. A previously established GFP reporter system was used to detect and sort single Corynebacterium glutamicum cells based on the concentration of branched chain amino acids (BCAA) using FACS...
March 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28315483/functional-proteomic-analysis-of-corticosteroid-pharmacodynamics-in-rat-liver-relationship-to-hepatic-stress-signaling-energy-regulation-and-drug-metabolism
#7
Vivaswath S Ayyar, Richard R Almon, Debra C DuBois, Siddharth Sukumaran, Jun Qu, William J Jusko
Corticosteroids (CS) are anti-inflammatory agents that cause extensive pharmacogenomic and proteomic changes in multiple tissues. An understanding of the proteome-wide effects of CS in liver and its relationships to altered hepatic and systemic physiology remains incomplete. Here, we report the application of a functional pharmacoproteomic approach to gain integrated insight into the complex nature of CS responses in liver in vivo. An in-depth functional analysis was performed using rich pharmacodynamic (temporal-based) proteomic data measured over 66h in rat liver following a single dose of methylprednisolone (MPL)...
March 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28315482/modes-of-antibacterial-action-of-curcumin-under-dark-and-light-conditions-a-toxicoproteomics-approach
#8
Ilya Shlar, Samir Droby, Victor Rodov
Curcumin is a potent natural food-grade antimicrobial compound. Exposure to light further enhances its antimicrobial capacity. Proteomic methods were used in this study for investigating the mechanistic aspects of the antibacterial curcumin effects in the dark and upon illumination. Escherichia coli cells exposed to water-dispersible curcumin-methyl-β-cyclodextrin inclusion complex under dark and light conditions were compared with the non-treated cells kept under the same illumination regimes. Curcumin treatment in the dark evoked adaptive responses aimed at mitigation of oxidative stress, DNA protection, proteostasis, modulation of redox state via changing NADH level, and gasotransmitter (H2S and NH3) biosynthesis...
March 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28286321/synaptic-proteome-changes-in-the-hypothalamus-of-mother-rats
#9
Edina Brigitta Udvari, Katalin Völgyi, Péter Gulyássy, Diána Dimén, Viktor Kis, János Barna, Éva Rebeka Szabó, Gert Lubec, Gábor Juhász, Katalin Adrienna Kékesi, Árpád Dobolyi
To establish synaptic proteome changes associated with motherhood, we isolated synaptosome fractions from the hypothalamus of mother rats and non-maternal control females at the 11th postpartum day. Proteomic analysis by two-dimensional differential gel electrophoresis combined with mass spectrometric protein identification established 26 significant proteins, 7 increasing and 19 decreasing protein levels in the dams. The altered proteins are mainly involved in energy homeostasis, protein folding, and metabolic processes suggesting the involvement of these cellular processes in maternal adaptations...
March 9, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28286320/earwax-a-neglected-body-secretion-or-a-step-ahead-in-clinical-diagnosis-a-pilot-study
#10
Engy Shokry, Anselmo Elcana de Oliveira, Melissa Ameloti Gomes Avelino, Mariana Moreira de Deus, Nelson Roberto Antoniosi Filho
This work combines the advantages of volatile metabolites profiling as a young growing research field with a non-invasive sampling technique using earwax "a neglected body secretion" for detection and monitoring of biomarkers for diabetes mellitus (types 1 and 2). Earwax samples were collected from 26 diabetic patients of both types, analyzed by headspace gas chromatography mass spectrometry and confronted to the volatile earwax composition of 33 healthy individuals. Data mining analysis was conducted using different models to discriminate the healthy individuals from the diabetic patients and to discriminate between both types of diabetes as well...
March 9, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28286130/the-benefits-and-misfortunes-of-sds-in-top-down-proteomics
#11
Carolyn Kachuk, Alan A Doucette
Top-down proteomics (TDP) has great potential for high throughput proteoform characterization. With significant advances in mass spectrometry (MS) instrumentation permitting tandem MS of large intact proteins, a limitation to the widespread adoption of TDP still resides on front-end sample preparation protocols (e.g. fractionation, purification) that are amenable to MS analysis of intact proteins. Chromatographic strategies are improving but pose higher risk of sample loss. Gel-based separations (e.g. GELFrEE) may alleviate this concern but at the expense of requiring sodium dodecyl sulfate (SDS)...
March 8, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28284755/itraq-based-quantitative-proteomic-analysis-reveals-potential-virulence-factors-of-erysipelothrix-rhusiopathiae
#12
Ya Wang, Jingtao Li, Anding Zhang, Weifeng Zhu, Qiang Zhang, Zhongmin Xu, Shuxian Yan, Xiaomei Sun, Huanchun Chen, Meilin Jin
Erysipelothrix rhusiopathiae is a ubiquitous pathogen that has caused considerable economic losses to pig farmers. However, the mechanisms of E. rhusiopathiae pathogenesis remain unclear. To identify new virulence-associated factors, the differentially abundant cell wall-associated proteins (CWPs) between high- and low-virulence strains were investigated through isobaric Tags for Relative and Absolute Quantitation (iTRAQ) combined with liquid chromatography-quadrupole mass spectrometry (LC-MS/MS). In total, 100 CWPs showed significant differences in abundance...
March 8, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28274896/functional-proteomic-analyses-of-bothrops-atrox-venom-reveals-phenotypes-associated-with-habitat-variation-in-the-amazon
#13
Leijiane F Sousa, José A Portes-Junior, Carolina A Nicolau, Juliana L Bernardoni, Milton Y Nishiyama-Jr, Diana R Amazonas, Luciana A Freitas-de-Sousa, Rosa Hv Mourão, Hipócrates M Chalkidis, Richard H Valente, Ana M Moura-da-Silva
Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats (terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA2s and LAAOs...
March 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28268116/key-metabolic-traits-of-pisum-sativum-maintain-cell-vitality-during-didymella-pinodes-infection-cultivar-resistance-and-the-microsymbionts-influence
#14
Reinhard Turetschek, Getinet Desalegn, Tamara Epple, Hans-Peter Kaul, Stefanie Wienkoop
Ascochyta blight causes severe losses in field pea production and the search for resistance traits towards the causal agent Didymella pinodes is of particular importance for farmers. Various microsymbionts were reported to shape the plants' immune response. However, regardless their contribution to resistance, they are hardly included in experimental designs. Here, we first delineate the bi-directional effect of the symbionts' (rhizobia, mycorrhiza) and the leaf proteome/metabolome of two field pea cultivars with varying resistance levels towards D...
March 4, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28263888/combined-venomics-antivenomics-and-venom-gland-transcriptome-analysis-of-the-monocoled-cobra-naja-kaouthia-from-china
#15
Ning Xu, Hong-Yan Zhao, Yin Yin, Shan-Shan Shen, Lin-Lin Shan, Chuan-Xi Chen, Yan-Xia Zhang, Jian-Fang Gao, Xiang Ji
We conducted an omics-analysis of the venom of Naja kaouthia from China. Proteomics analysis revealed six protein families [three-finger toxins (3-FTx), phospholipase A2 (PLA2), nerve growth factor, snake venom metalloproteinase (SVMP), cysteine-rich secretory protein and ohanin], and venom-gland transcriptomics analysis revealed 28 protein families from 79 unigenes. 3-FTx (56.5% in proteome/82.0% in transcriptome) and PLA2 (26.9%/13.6%) were identified as the most abundant families in venom proteome and venom-gland transcriptome...
March 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28263889/proteomic-analysis-of-chondromodulin-i-induced-differentiation-of-mesenchymal-stem-cells-into-chondrocytes
#16
Shuang-Chun Xing, Lian-Xin Du, Wei Zhou, Yu-Qiang Hu, Ya Feng, Hong-Feng Liang, Lin Sang, Min Qi, Li-Jie Zhai, Zhi-Qiang Wang
To identify novel proteins that might help clarify the molecular mechanisms underlying chondromodulin-I (ChM-I) induction of mesenchymal stem cells (MSCs) differentiate into chondrocytes. MSCs are triggered to differentiate into chondrocytes, which are recognized as important factors in cartilage tissue engineering. ChM-I is a glycoprotein that stimulates the growth of chondrocytes and inhibits angiogenesis in vitro. In this study, the proteomic approach was used to evaluate protein changes between undifferentiated MSCs and ChM-I-transfected MSCs...
March 2, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28254676/unveiling-antimicrobial-peptide-generating-human-proteases-using-proteasix
#17
Paulo Bastos, Fábio Trindade, Rita Ferreira, Mercedes Arguello Casteleiro, Robert Stevens, Julie Klein, Rui Vitorino
Extracting information from peptidomics data is a major current challenge, as endogenous peptides can result from the activity of multiple enzymes. Proteolytic enzymes can display overlapping or complementary specificity. The activity spectrum of human endogenous peptide-generating proteases is not fully known. Hence, the indirect study of proteolytic enzymes through the analysis of its substrates is largely hampered. Antimicrobial peptides (AMPs) represent a primordial set of immune defense molecules generated by proteolytic cleavage of precursor proteins...
February 27, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28242453/analysis-of-the-herbicidal-mechanism-of-4-hydroxy-3-methoxy-cinnamic-acid-ethyl-ester-using-itraq-and-real-time-pcr
#18
Mingyue Zhang, Ce Liu, Juan Yang, Peng Yang, Lihui Zhang, Jingao Dong
Absolute quantitation (iTRAQ) is the latest development in the new quantitative proteomics technology for high-throughput identification and quantitation of proteins. The mechanisms underlying the 4-hydroxy-3-methoxy cinnamic acid ethyl ester treatment in Arabidopsis thaliana was investigated. Deficiency-induced changes in the protein profile of A. thaliana caused by this compound were analyzed using iTRAQ and quantitative real-time PCR. A total of 2909 proteins were quantified, of which 49 and 34 proteins were upregulated and downregulated, respectively, in the experimental plants compared with the controls...
February 24, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28242452/top-down-analysis-of-immunoglobulin-g-isotypes-1-and-2-with-electron-transfer-dissociation-on-a-high-field-orbitrap-mass-spectrometer
#19
Luca Fornelli, Daniel Ayoub, Konstantin Aizikov, Xiaowen Liu, Eugen Damoc, Pavel A Pevzner, Alexander Makarov, Alain Beck, Yury O Tsybin
The increasing importance of immunoglobulins G (IgGs) as biotherapeutics calls for improved structural characterization methods designed for these large (~150kDa) macromolecules. Analysis workflows have to be rapid, robust, and require minimal sample preparation. In a previous work we showed the potential of Orbitrap Fourier transform mass spectrometry (FTMS) combined with electron transfer dissociation (ETD) for the top-down investigation of an intact IgG1, resulting in ~30% sequence coverage. Here, we describe a top-down analysis of two IgGs1 (adalimumab and trastuzumab) and one IgG2 (panitumumab) performed with ETD on a mass spectrometer equipped with a high-field Orbitrap mass analyzer...
February 24, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28242451/characterisation-of-the-bordetella-pertussis-secretome-under-different-media
#20
Laurence Don Wai Luu, Sophie Octavia, Ling Zhong, Mark Raftery, Vitali Sintchenko, Ruiting Lan
Our understanding of the Bordetella pertussis secretome remains limited including the role of different growth conditions in the secretome. In this study the secretome of L1423, a clinical isolate from the 2008-2012 Australian epidemic, cultured on Stainer-Scholte (SS) and Thalen-IJssel (THIJS) media for 12h was characterised using liquid chromatography-mass spectrometry (LC-MS/MS). In the supernatant, LC-MS/MS identified 260 proteins with 143 bioinformatically predicted to be secreted. Eighty percent of proteins were identified in both media...
February 24, 2017: Journal of Proteomics
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