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Proteomics

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https://www.readbyqxmd.com/read/29044975/comparative-proteomic-analysis-of-three-xanthomonas-spp-cultured-in-minimal-and-rich-media
#1
Hey-Jee Park, Nahee Bae, Hanbi Park, Dae-Wi Kim, Sang-Wook Han
Bacteria change their gene expression when exposed to different nutrient conditions. The levels of proteins do not always correlate with those of RNAs, hence proteomic analysis is required for understanding how bacteria adapt to different conditions. Herein, differentially abundant proteins from Xanthomonas oryzae pv. oryzae (Xoo), X. campestris pv. vesicatoria (Xcv), and X. axonopodis pv. glycines (Xag), which were cultured in rich media and in minimal media, were determined using label-free shotgun proteomic analysis and clusters of orthologous groups classification...
October 17, 2017: Proteomics
https://www.readbyqxmd.com/read/29027377/contribution-of-extracellular-matrix-and-signal-mechanotransduction-to-epithelial-cell-damage-in-inflammatory-bowel-disease-patients-a-proteomic-study
#2
Manuela Moriggi, Luca Pastorelli, Enrica Torretta, Gian Eugenio Tontini, Daniele Capitanio, Stefano Ferrero Bogetto, Maurizio Vecchi, Cecilia Gelfi
This study utilized 2D-DIGE, isotope-coded protein labelling (ICPL) and biochemical assays to characterize protein alteration in Ulcerative Colitis (UC) and Crohn's Disease (CD) in human epithelial cell and mucosal biopsies in Inflammatory Bowel Disease (IBD)-affected patients. The aim of this study is to identify the key molecular signatures involved in epithelial cell structure of IBDs. In non-inflamed UC (QUC) keratins, vimentin and FAK increased, whereas vinculin and de-tyrosinated α-tubulin decreased; inflammation (IUC) exacerbated molecular changes, being COL6A1, tenascin-C and vimentin increased...
October 13, 2017: Proteomics
https://www.readbyqxmd.com/read/29027371/differential-proteomic-analysis-of-dimethylnitrosamine-dmn-induced-liver-fibrosis
#3
Xiujie Liu, Rongji Dai, Ming Ke, Imran Suheryani, Weiwei Meng, Yulin Deng
Liver fibrosis is a common pathological feature of many chronic liver diseases. To characterize the entire panorama of proteome changes in DMN-induced liver fibrosis, iTRAQ-based differential proteomic analysis was performed with DMN-induced liver fibrosis rats. A total of 4155 confidently identified proteins were found, with 365 proteins showing significant changes (fold changes of >1.5 or < 0.67, P < 0.05). In metabolic activation, proteins assigned to drug metabolism enzymes (e.g., CYP2D1) changed, suggesting that the liver protection mechanism was activated to relieve DMN toxicity...
October 13, 2017: Proteomics
https://www.readbyqxmd.com/read/29027362/impact-of-extraction-methods-on-the-detectable-protein-complement-of-metaproteomic-analyses-of-marine-sediments
#4
Lars Wöhlbrand, Christoph Feenders, Jessica Nachbaur, Holger Freund, Bert Engelen, Heinz Wilkes, Hans-Jürgen Brumsack, Ralf Rabus
Metaproteomic analysis targets proteins, the catalytic entities in the habitat, thereby providing direct insights into the metabolic activity of the community studied. A major challenge still remaining for metaproteomics is the effective and comprehensive extraction of proteins from environmental samples, due to their high complexity with respect to organismic diversity and abundance range. Moreover, in certain habitats, the inherent matrix may interfere with protein extraction. In recent years, several studies reported different protein extraction methods for soils known for their complex geochemistry, but only two analyzed marine sediments that generally comprise different though similarly complex geochemistry...
October 13, 2017: Proteomics
https://www.readbyqxmd.com/read/28994248/maldi-mass-spectrometry-imaging-a-novel-tool-for-the-identification-and-classification-of-amyloidosis
#5
Martin Winter, Andreas Tholey, Arnt Kristen, Christoph Röcken
Amyloidosis is a group of diseases caused by extracellular accumulation of fibrillar polypeptide aggregates. So far, diagnosis is performed by Congo red staining of tissue sections in combination with polarization microscopy. Subsequent identification of the causative protein by immunohistochemistry harbors some difficulties regarding sensitivity and specificity. Mass spectrometry-based approaches have been demonstrated to constitute a reliable method to supplement typing of amyloidosis, but still depend on Congo red staining...
October 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28994205/proteomics-and-network-analyses-reveal-inhibition-of-akt-mtor-signaling-in-cd4-t-cells-by-mycobacterium-tuberculosis-mannose-capped-lipoarabinomannan
#6
Ahmad F Karim, Obondo J Sande, Sara E Tomeckho, Xuedong Ding, Ming Li, Sean Maxwell, Rob M Ewing, Clifford V Harding, Roxana E Rojas, Mark R Chance, W Henry Boom
Mycobacterium tuberculosis (Mtb) cell wall glycolipid Mannose-capped Lipoarabinomannan (ManLAM) inhibits CD4(+) T cell activation by inhibiting proximal T cell receptor (TCR) signaling when activated by anti-CD3. To understand the impact of ManLAM on CD4(+) T cell function when both the TCR-CD3 complex and major co-stimulator CD28 are engaged, we performed label-free quantitative mass spectrometry (MS) and network analysis. Mixed effect model analysis of peptide intensity identified 149 unique peptides representing 131 proteins that were differentially regulated by ManLAM in anti-CD3 and anti-CD28 activated CD4(+) T cells...
October 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28994197/in-vino-veritas-an-invitation-for-ambitious-collaborative-proteogenomics-campaigns-on-plant-and-animal-models
#7
Jean Armengaud
Vitis vinifera has been an emblematic plant for Humans since the Neolithic period. Human civilization has been shaped by its domestication as both its medicinal and nutritional values were exploited. It is now cultivated on all habitable continents, and more than 5 thousand varieties have been developed. A global passion for the art of wine fuels innovation and a profound desire for knowledge on this plant. The genome sequence of a homozygotic cultivar and several RNA-seq datasets on other varieties have been released paving the way to gaining further insight into its biology and tailoring improvements to varieties...
October 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28990322/proteogenomics-gets-onto-the-regulation-of-mrna-decoding-and-translation-into-protein
#8
Hubert Hondermarck
Proteogenomics, the integrative analysis of the proteome and the genome, increasingly provides protein-level insights about the regulation of gene expression and protein translation. Armengaud et al. (Proteomics 2017. volume, pages) nicely illustrate this trend with the first in depth proteomic analysis of the eukaryotic and unicellular intestinal parasite Blastocystis sp. Not only this work constitutes an important milestone towards the proteogenomics profile of this human pathogen, but also it demonstrates at the protein level the occurrence of a specific mechanism of mRNA decoding...
October 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28961394/molecular-dissection-of-extracellular-matrix-proteome-reveals-discrete-mechanism-regulating-verticillium-dahliae-triggered-vascular-wilt-disease-in-potato
#9
Eman Elagamey, Arunima Sinha, Kanika Narula, Magdi A E Abdellatef, Niranjan Chakraborty, Subhra Chakraborty
Plants exposed to patho-stress mostly succumb due to disease by disruption of cellular integrity and changes in the composition of the extracellular matrix (ECM). Vascular wilt, caused by the soil borne hemibiotrophic filamentous fungus Verticillium dahliae, is one of the most significant diseases that adversely affects plant growth and productivity. The virulence of the pathogen associated with the ECM-related susceptibility of the host plant is far from being understood. To better understand ECM-associated disease responses that allow the pathogen to supress plant immunity, a temporal analysis of ECM proteome was carried out in vascular wilt susceptible potato cultivar upon V...
September 29, 2017: Proteomics
https://www.readbyqxmd.com/read/28961369/phosphoproteomics-profiling-of-non-small-cell-lung-cancer-cells-treated-with-a-novel-phosphatase-activator
#10
Danica D Wiredja, Marzieh Ayati, Sahar Mazhar, Jaya Sangodkar, Sean Maxwell, Daniela Schlatzer, Goutham Narla, Mehmet Koyutürk, Mark R Chance
Activation of protein phosphatase 2A (PP2A) is a promising anti-cancer therapeutic strategy, as this tumor suppressor has the ability to coordinately downregulate multiple pathways involved in the regulation of cellular growth and proliferation. In order to understand the systems-level perturbations mediated by PP2A activation, we carried out mass spectrometry-based phosphoproteomic analysis of two KRAS mutated non-small cell lung cancer (NSCLC) cell lines (A549 and H358) treated with a novel Small Molecule Activator of PP2A (SMAP)...
September 29, 2017: Proteomics
https://www.readbyqxmd.com/read/28949093/dj-1-regulates-differentiation-of-human-mesenchymal-stem-cells-into-smooth-muscle-like-cells-in-response-to-sphingosylphosphorylcholine
#11
Suji Baek, Kang Pa Lee, Seung Hyo Jung, Long Cui, Kinarm Ko, Bokyung Kim, Kyung Jong Won
Although multiple factors contribute to the differentiation of human mesenchymal stem cells (hMSCs) into various types of cells, the differentiation of hMSCs into smooth muscle cells (SMCs), one of central events in vascular remodeling, remains to be clarified. ROS participate in the differentiation of hMSCs into several cell types and were regulated by redox-sensitive molecules including a multifunctional protein DJ-1. Here, we investigated the correlation between altered proteins, especially those related to ROS, and SMC differentiation in sphingosylphosphorylcholine (SPC)-stimulated hMSCs...
September 26, 2017: Proteomics
https://www.readbyqxmd.com/read/28941238/discovery-of-antimicrobial-peptides-in-cervical-vaginal-fluid-from-healthy-non-pregnant-women-via-an-integrated-proteome-and-peptidome-analysis
#12
Carla M J Muytjens, Yijing Yu, Eleftherios P Diamandis
Cervical-vaginal fluid (CVF) covers the lower part of the female reproductive system and functions in the homeostasis and immunity of the surrounding tissues. In contrast to the CVF proteome of both non-pregnant and pregnant women, the CVF peptidome has not been reported to date. In the current study, we identified 1,087 proteins in CVF, of which 801 proteins were not previously identified in CVF proteomes. The presence of the tissue-specific proteins oviductal glycoprotein-1 (OVGP-1) and tubulin polymerization-promoting protein family member 3 (TPPP3) strongly suggests that the tissues of the upper female reproductive tract contribute to the protein composition of CVF...
September 23, 2017: Proteomics
https://www.readbyqxmd.com/read/28941129/mechanisms-of-drug-resistance-in-cancer-the-role-of-extracellular-vesicles
#13
REVIEW
Priya Samuel, Muller Fabbri, David Raul Francisco Carter
Drug resistance remains a major barrier to the successful treatment of cancer. The mechanisms by which therapeutic resistance arises multifactorial. Recent evidence has shown that extracellular vesicles (EVs) play a role in mediating drug resistance. EVs are small vesicles carrying a variety of macromolecular cargo released by cells into the extracellular space and can be taken up into recipient cells, resulting in transfer of cellular material. EVs can mediate drug resistance by several mechanisms. They can serve as a pathway for sequestration of cytotoxic drugs, reducing the effective concentration at target sites...
September 23, 2017: Proteomics
https://www.readbyqxmd.com/read/28941069/identification-and-functional-analysis-of-chitin-synthase-a-in-oriental-armyworm-mythimna-separata
#14
Yifan Zhai, Xiaobin Fan, Zhenjuan Yin, Xiangzhao Yue, Xingyuan Men, Li Zheng, Wenqing Zhang
Chitin synthases are very important enzymes for chitin synthesis in various species, which makes them a specific target of insecticides. In the present study, we investigated the function of the chitin synthase A (CHSA) gene isolated from Mythimna separata. The majority of dsMysCHSA treated larvae (89.50%) exhibited lethal phenotypes, including three phenotypes with severe cuticle deformations. The dsMysCHSA treatment in adult females affected oogenesis, and significantly reduced the ovary size and the oviposition number compared with controls...
September 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28940701/a-bioinformatic-algorithm-for-analyzing-cell-signaling-using-temporal-proteomic-data
#15
Chunchao Zhang, Yue Chen, Xinfang Mao, Yin Huang, Sung Yun Jung, Antrix Jain, Jun Qin, Yi Wang
Significance analysis of proteomic data generated by LC-MS/MS is challenging owing to great data variability originated from biological, operational and instrumental variations. Protein quantification by LC-MS/MS either in absolute or relative scale is often highly skewed, which put limitations on model-based statistical inference. For this purpose, we have developed an alternative non-parametric statistical algorithm (named IQR algorithm) for significance analysis of temporal proteomic data and have successfully applied our strategy in finding gefitinib-targeted transcription factors and coregulators in EGF (Epidermal Growth Factor)-stimulated HeLa cells...
September 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28941183/tubulin-or-not-tubulin-heading-towards-total-protein-staining-as-loading-control-in-western-blots
#16
REVIEW
Christian P Moritz
Western blotting is an analytical method widely used for detecting and (semi-)quantifying specific proteins in given samples. Western blots are continuously applied and developed by the protein community. This review article focuses on a significant, but not yet well-established, improvement concerning the internal loading control as a prerequisite to accurately quantifying Western blots. Currently, housekeeping proteins (HKPs) like actin, tubulin, or GAPDH are often used to check for equal loading or to compensate potential loading differences...
September 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28940772/enhancing-proteomic-throughput-in-capillary-electrophoresis-mass-spectrometry-by-sequential-sample-injection
#17
Klaus Faserl, Bettina Sarg, Laura Sola, Herbert H Lindner
In this study we demonstrate the potential of sequential injection of samples in capillary electrophoresis-mass spectrometry (CE-MS) for rapid and sensitive proteome characterization of human lymphoblastic T-cells (line CCRF-CEM). Proteins were extracted, enzymatically digested, and the resulting peptides fractionated by RP-HPLC. Twenty fractions were thereafter analyzed by CE-MS within a single MS analysis. The CE-MS method was designed that every 10 minutes a new fraction was injected into the CE system. Without any rinsing or equilibration steps we were able to generate a continuous stream of peptides feeding the mass analyzer...
September 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28929627/strategies-and-challenges-in-identifying-function-for-thousands-of-sorf-encoded-peptides-in-meiosis
#18
Ina Hollerer, Andrea Higdon, Gloria A Brar
Recent genomic analyses have revealed pervasive translation from formerly unrecognized short Open Reading Frames (sORFs) during yeast meiosis. Despite their short length, which has caused these regions to be systematically overlooked by traditional gene annotation approaches, meiotic sORFs share many features with classical genes, implying the potential for similar types of cellular functions. We found that sORF expression accounts for ∼10-20% of the cellular translation capacity in yeast during meiotic differentiation and occurs within well-defined time windows, suggesting the production of relatively abundant peptides with stage-specific meiotic roles from these regions...
September 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28922568/spectral-libraries-for-swath-ms-assays-for-drosophila-melanogaster-and-solanum-lycopersicum
#19
Bertrand Fabre, Dagmara Korona, Clara I Mata-Martinez, Harriet T Parsons, Michael J Deery, Maarten L A T M Hertog, Bart M Nicolaï, Steven Russell, Kathryn S Lilley
Quantitative proteomics methods have emerged as powerful tools for measuring protein expression changes at the proteome level. Using mass-spectrometry (MS) based approaches, it is now possible to routinely quantify thousands of proteins. However, pre-fractionation of the samples at the protein or peptide level is usually necessary to go deep into the proteome, increasing both MS analysis time and technical variability. Recently, a new MS acquisition method named SWATH was introduced with the potential to provide good coverage of the proteome as well as a good measurement precision without prior sample fractionation...
September 18, 2017: Proteomics
https://www.readbyqxmd.com/read/28921918/proteomic-response-of-human-umbilical-vein-endothelial-cells-to-histamine-stimulation
#20
Pelin Esma Emirbayer, Ankit Sinha, Vladimir Ignatchenko, Stefanie Hoyer, Jan Dörrie, Niels Schaft, Monika Pischetsrieder, Thomas Kislinger
The histamine receptors (HRs) represent a subclass of G protein-coupled receptors (GPCRs) and comprise four subtypes. Due to their numerous physiological and pathological effects, HRs are popular drug targets for the treatment of allergic reactions or the regulation of gastric acid secretion. Hence, an understanding of the functional selectivity of HR ligands has gained importance. These ligands can bind to specific GPCRs and selectively activate defined pathways. Supporting the activation of a therapeutically necessary pathway without the activation of other signaling cascades can result in drugs with more specific activity and fewer side effects...
September 18, 2017: Proteomics
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