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Journal of Proteomics

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https://www.readbyqxmd.com/read/28713028/the-effect-of-fusarium-culmorum-infection-and-deoxynivalenol-don-application-on-proteome-response-in-barley-cultivars-chevron-and-pedant
#1
Klára Kosová, Jana Chrpová, Jiří Šantrůček, Radovan Hynek, Lenka Štěrbová, Pavel Vítámvás, Jana Bradová, Ilja Tom Prášil
Fusarium head blight (FHB) disease adversely affects grain quality and final yield in small-grain cereals including barley. In the present study, the effect of an artificial infection with Fusarium culmorum and an application of deoxynivalenol (DON) on barley spikes of cultivars Chevron and Pedant during flowering was investigated at grain mid-dough stage (BBCH 73) 10days after pathogen inoculation (10 dai). Proteomic analysis using a two-dimensional differential gel electrophoresis (2D-DIGE) technique coupled with LC-MS/MS investigated 98 protein spots revealing quantitative or qualitative differences between the experimental variants...
July 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28713027/an-on-matrix-digestion-procedure-for-ap-ms-experiments-dissects-the-interplay-between-complex-conserved-and-serotype-specific-reactivities-in-dengue-virus-human-plasma-interactome
#2
Yassel Ramos, Vivian Huerta, Dayron Martín, Sucel Palomares, Alexis Yero, Dianne Pupo, Sebastien Gallien, Alejandro M Martín, Yasset Pérez-Riverol, Mónica Sarría, Osmany Guirola, Glay Chinea, Bruno Domon, Luis Javier González
The interactions between the four Dengue virus (DENV) serotypes and plasma proteins are crucial in the initial steps of viral infection to humans. Affinity purification combined with quantitative mass spectrometry analysis, has become one of the most powerful tools for the investigation on novel protein-protein interactions. Using this approach, we report here that a significant number of bait-interacting proteins do not dissociate under standard elution conditions, i.e. acid pH and chaotropic agents, and that this problem can be circumvented by using the "on-matrix" digestion procedure described here...
July 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28709933/identification-of-novel-biomarker-and-therapeutic-target-candidates-for-diagnosis-and-treatment-of-follicular-carcinoma
#3
Xianyin Lai, Christopher B Umbricht, Kurt Fisher, Justin Bishop, Qiuying Shi, Shaoxiong Chen
Distinguishing follicular carcinoma from follicular adenoma, based on cytomorphological features, has always been challenging to cytopathologists. Identification of biomarkers for improving diagnostic accuracy is important for clinical management. Meanwhile, it is critical to identify therapeutic target candidates for treatment of follicular carcinoma. Currently, no reliable diagnostic protein biomarkers and therapeutic targets are available. To explore novel protein biomarker and therapeutic target candidates, a liquid chromatography-tandem mass spectrometry approach was applied to analyze control, follicular adenoma, and follicular carcinoma using formalin-fixed, paraffin-embedded tissue samples...
July 11, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28705725/assessing-the-impact-of-protein-extraction-methods-for-human-gut-metaproteomics
#4
Xu Zhang, Leyuan Li, Janice Mayne, Zhibin Ning, Alain Stintzi, Daniel Figeys
Metaproteomics is a promising methodology for the functional characterizations of the gut microbiome. However, the performance of metaproteomic analysis is affected by protein extraction protocols in terms of the amount of protein recovered and the relative abundance of different bacteria observed in microbiome. Currently, there is a lack of consistency on protein extraction methods in published metaproteomics studies. Here we evaluated the effects of different protein extraction methods on human fecal metaproteome characterizations...
July 10, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28688915/targeted-proteome-analysis-with-isotope-coded-protein-labels-for-monitoring-the-influence-of-dietary-phytochemicals-on-the-expression-of-cytoprotective-proteins-in-primary-human-colon-cells
#5
Christiane Östreicher, Sven Bartenbacher, Monika Pischetsrieder
Cytoprotective effects by upregulating cellular expression levels of antioxidant proteins are attributed to a significant number of food ingredients. Evaluation of those cytoprotective effects and identification of the most active components requires reliable and comprehensive proteomic strategies. Thus, promising potential bioactive ingredients could be determined for the prevention of various diseases, including colon cancer formation. We established a multiplexed nanoLC-MS/MS targeted proteomic method, operated in scheduled selected reaction monitoring mode (sSRM), to record modulation of the expression levels of six major antioxidant proteins induced by dietary phytochemicals...
July 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28688916/venom-proteome-of-the-yellow-lipped-sea-krait-laticauda-colubrina-from-bali-insights-into-subvenomic-diversity-venom-antigenicity-and-cross-neutralization-by-antivenom
#6
Choo Hock Tan, Kin Ying Wong, Kae Yi Tan, Nget Hong Tan
The venom proteome of Laticauda colubrina (Bali, Indonesia) was elucidated by nano-ESI-LCMS/MS of the venom reverse-phase HPLC fractions. Altogether 31 distinct forms of proteins were identified and clustered into three toxin families: three-finger toxin (3FTX, 66.12% of total venom proteins), phospholipase A2 (PLA2, 33.26%) and cysteine-rich secretory protein (CRiSP, 0.05%). The 3FTX were α-neurotoxins (five long neurotoxins, LNTX, 48.87%; two short neurotoxins, SNTX, 16.70%) and a trace amount of two cytotoxins (CTX, 0...
July 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28687424/identification-by-serological-proteome-analysis-of-paramyosin-as-prominent-allergen-in-dust-mite-allergy
#7
Antonio Conti, Giulia Burastero, Claudia Suli, Srinita Banerjee, Susanne Vrtala, Massimo Alessio, Samuele E Burastero
Component-resolved diagnosis (CRD) of IgE-mediated hypersensitivities is challenged by the possibility that single patients are sensitized to components not commercially available to the clinical lab. Here, we studied a patient with positive extract-based diagnosis of house dust mite (HDM) allergy based on routine in vivo (prick test) and in vitro (serum specific IgE) tests, whose serum scored negative for IgE to the three recombinant allergens routinely used in CRD (group 1 allergens, group 2 allergens and tropomyosin)...
July 4, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28679110/itraq-based-quantitative-proteomic-analysis-reveals-multiple-effects-of-emodin-to-haemophilus-parasuis
#8
Li Li, Ye Tian, Jiankang Yu, Xu Song, Renyong Jia, Qiankun Cui, Wenzhi Tong, Yuanfeng Zou, Lixia Li, Lizi Yin, Xiaoxia Liang, Changliang He, Guizhou Yue, Gang Ye, Ling Zhao, Fei Shi, Cheng Lv, Sanjie Cao, Zhongqiong Yin
Haemophilus parasuis, a symbiotic bacteria of upper respiratory tract of swine, is the etiological agent of Glässer's disease, which is characterized by fibrinous polyserositis. Emodin, exhibits antibacterial activity against H. parasuis, yet the action mode has not been fully understood. In present study, isobaric tag for relative and absolute quantification (iTRAQ) method was applied to analyze the global protein alteration of H. parasuis in response to 16μg/mL Emodin. In total, 338 proteins exhibiting significant differential expressions were identified...
July 2, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28669816/in-depth-proteomic-analysis-of-glycine-max-seeds-during-controlled-deterioration-treatment-reveals-a-shift-in-seed-metabolism
#9
Cheol Woo Min, Seo Hyun Lee, Ye Eun Cheon, Won Young Han, Jong Min Ko, Hang Won Kang, Yong Chul Kim, Ganesh Kumar Agrawal, Randeep Rakwal, Ravi Gupta, Sun Tae Kim
Seed aging is one of the major events, affecting the overall quality of agricultural seeds. To analyze the effect of seed aging, soybean seeds were exposed to controlled deterioration treatment (CDT) for 3 and 7days, followed by their physiological, biochemical, and proteomic analyses. Seed proteins were subjected to protamine sulfate precipitation for the enrichment of low-abundance proteins and utilized for proteome analysis. A total of 14 differential proteins were identified on 2-DE, whereas label-free quantification resulted in the identification of 1626 non-redundant proteins...
June 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28669815/immuno-proteomic-discovery-of-tumor-tissue-autoantigens-identifies-olfactomedin-4-cd11b-and-integrin-alpha-2-as-markers-of-colorectal-cancer-with-liver-metastases
#10
Qian Yang, Prashant Bavi, Julia Y Wang, Michael H Roehrl
Late-stage colorectal cancer with liver metastasis is common and affords poor prognosis, yet there is a dearth of reliable biomarkers. Cancer is often characterized by an increase in serologic autoantibodies. Hence, we embarked on an immuno-proteomic strategy by using autoantibodies to discover antigens in tumor tissue as potential cancer markers. Matched sets of tissues from primary colon cancer, liver metastases, and adjacent benign tissues were obtained from colon cancer patients. Tissue proteins were extracted, and autoantigens were uncovered by immunoblotting with autoantibodies and sequenced by mass spectrometry...
June 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28669814/quick-96fasp-for-high-throughput-quantitative-proteome-analysis
#11
Yanbao Yu, Shiferaw Bekele, Rembert Pieper
Filter aided sample preparation (FASP) is becoming a central method for proteomic sample cleanup and peptide generation prior to LC-MS analysis. We previously adapted this method to a 96-well filter plate, and applied to prepare protein digests from cell lysate and body fluid samples in a high throughput quantitative manner. While the 96FASP approach is scalable and can handle multiple samples simultaneously, two key advantages compared to single FASP, it is also time-consuming. The centrifugation-based liquid transfer on the filter plate takes 3-5 times longer than single filter...
June 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28648685/proteomic-profiling-of-pachyonychia-congenita-plantar-callus
#12
Robert H Rice, Blythe P Durbin-Johnson, Michelle Salemi, Mary E Schwartz, David M Rocke, Brett S Phinney
Callus samples from the ball and the arch of the foot, collected on tape circles, were compared by shotgun proteomic profiling. Pachyonychia congenita subjects were sampled who exhibited a mutation in KRT6A, KRT6B, KRT6C, KRT16 or KRT17, and the proteins were digested and analyzed by tandem mass spectrometry. In comparison with samples from unaffected control subjects, those from subjects with KRT6A or KRT16 mutations displayed the most differences in profile from normal, while those from subjects with KRT6C or KRT17 mutations showed few differences from normal...
June 23, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28647518/increasing-the-accuracy-of-proteomic-typing-by-decellularisation-of-amyloid-tissue-biopsies
#13
P Patrizia Mangione, Giuseppe Mazza, Janet A Gilbertson, Nigel B Rendell, Diana Canetti, Sofia Giorgetti, Luca Frenguelli, Marco Curti, Tamer Rezk, Sara Raimondi, Mark B Pepys, Philip N Hawkins, Julian D Gillmore, Graham W Taylor, Massimo Pinzani, Vittorio Bellotti
Diagnosis and treatment of systemic amyloidosis depend on accurate identification of the specific amyloid fibril protein forming the tissue deposits. Confirmation of monoclonal immunoglobulin light chain amyloidosis (AL), requiring cytotoxic chemotherapy, and avoidance of such treatment in non-AL amyloidosis, are particularly important. Proteomic analysis characterises amyloid proteins directly. It complements immunohistochemical staining of amyloid to identify fibril proteins and gene sequencing to identify mutations in the fibril precursors...
June 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28647517/proteomics-to-study-macrophage-response-to-viral-infection
#14
Tuula A Nyman, Sampsa Matikainen
Viral infections are a major burden to human and animal health. Immune response against viruses consists of innate and adaptive immunity which are both critical for the eradication of the viral infection. The innate immune system is the first line of defense against viral infections. Proper innate immune response is required for the activation of adaptive, humoral and cell-mediated immunity. Macrophages are innate immune cells which have a central role in detecting viral infections including influenza A and human immunodeficiency viruses...
June 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28645570/quantitative-proteomics-analysis-by-itraq-revealed-underlying-changes-in-thermotolerance-of-arthrospira-platensis
#15
Rong Chang, Bingxin Lv, Bosheng Li
Growth temperature is a critical factor that affects cultivation of Arthrospira platensis which is a type of cyanobacterium widely known as Spirulina that has significant commercial value. To investigate the molecular mechanism underlying the thermotolerance of Spirulina, differential protein expression profiling was carried out using iTRAQ-based quantitative proteomic analysis. This study only analyzed changes in thylakoids. Among the 2085 proteins quantified, 43 differentially expressed proteins were selected based on the fold change cutoff scores of ≥2 or ≤0...
June 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28634120/highly-reproducible-improved-label-free-quantitative-analysis-of-cellular-phosphoproteome-by-optimization-of-lc-ms-ms-gradient-and-analytical-column-construction
#16
Nagib Ahsan, Judson Belmont, Zhuo Chen, James G Clifton, Arthur R Salomon
Expanding the sequencing depth of the peptides with a statistically significant quantitative change derived from a biological stimulation is critical. Here we demonstrate that optimization of LC gradient and analytical column construction can reveal over 30,000 unique peptides and 23,000 phosphopeptides at high confidence. The quantitative reproducibility of different analytical workflows was evaluated by comparing the phosphoproteome of CD3/4 stimulated and unstimulated T-cells as a model system. A fritless, 50cm-long column packed with 1...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28634119/an-ultrasensitive-stain-for-negative-protein-detection-in-sds-page-via-4-5-dibromofluorescein
#17
Dongdong Yu, Yang Wang, Shaoqing Zhang, Zhiwei Chen, Mei Xue, Ying Wang, Weitao Cong, Litai Jin, Zhongxin Zhu
A highly sensitive method for brief and economical staining of proteins in 1-D and 2-D sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) by 4',5'-Dibromofluorescein (DBF) was developed in this study. Down to 0.025-0.05ng protein could be detected within 10min (only 2 steps) by DBF stain, which is approximately 10-fold more sensitive than those of Eosin Y (EY) and SYPRO Ruby stains, and 20-fold more sensitive than that of imidazole-zinc (IZ) negative stain. In addition, the LC-MS/MS results indicated that the newly developed staining method is compatible with the downstream protein identification...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28634118/identification-of-chickpea-seed-proteins-resistant-to-simulated-in-vitro-human-digestion
#18
I C Ribeiro, C C Leclercq, N Simões, A Toureiro, I Duarte, J B Freire, M M Chaves, J Renaut, C Pinheiro
Proteins and peptides able to resist gastrointestinal digestion and reach the intestinal mucosa have the potential to influence human health. Chickpea (Cicer arietinum L.) seed proteins are able to resist cooking (86.9% total protein) and/or in vitro simulated human digestion (15.9% total protein resists soaking, cooking and digestion with pepsin and pancreatin). To identify and characterize proteins resisting digestion we made use of different MS methodologies. The efficiency of several proteases (trypsin, AspN, chymotrypsin and LysC) was tested, and two technologies were employed (MALDI-TOF-TOF and LC-nESI-MS/MS)...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28629798/proteomic-analysis-of-mesenchymal-to-schwann-cell-transdifferentiation
#19
Anup D Sharma, Jayme Wiederin, Metin Uz, Pawel Ciborowski, Surya K Mallapragada, Howard E Gendelman, Donald S Sakaguchi
While transplantation of Schwann cells facilitates axon regeneration, remyelination and repair after peripheral nerve injury clinical use is limited by cell bioavailability. We posit that such limitation in cell access can be overcome by the use of autologous bone-marrow derived mesenchymal stem cells (MSCs). As MSCs can transdifferentiate to Schwann cell-phenotypes and accelerate nerve regeneration we undertook proteomic evaluation of the cells to uncover the protein contents that affects Schwann cell formulation...
June 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28625740/comparative-proteomic-analysis-of-two-transgenic-low-gliadin-wheat-lines-and-non-transgenic-wheat-control
#20
María Dolores García-Molina, Vera Muccilli, Rosaria Saletti, Salvatore Foti, Stefania Masci, Francisco Barro
Gluten proteins are major determinants of the bread making quality of wheat, but also of important wheat-related disorders, including coeliac disease (CD), and allergies. We carried out a proteomic study using the total grain proteins from two low-gliadin wheat lines, obtained by RNAi, and the untransformed wild type as reference. The impact of silencing on both target and on non-target proteins was evaluated. Because of the great protein complexity, we performed separate analyses of four kernel protein fractions: gliadins and glutenin subunits, and metabolic and CM-like proteins, by using a classical 2D electrophoresis gel based approach followed by RP-HPLC/nESI-MS/MS...
June 15, 2017: Journal of Proteomics
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