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Journal of Proteomics

Gustavo J Cavallero, Mariano Malamud, Adriana C Casabuono, M de Los Ángeles Serradell, Alicia S Couto
In Gram-positive bacteria, such as lactic acid bacteria, general glycosylation systems have not been documented so far. The aim of this work was to characterize in detail the glycosylation of the S-layer protein of Lactobacillus kefiri CIDCA 83111. A reductive β-elimination treatment followed by anion exchange high performance liquid chromatography analysis was useful to characterize the O-glycosidic structures. MALDI-TOF mass spectrometry analysis confirmed the presence of oligosaccharides bearing from 5 to 8 glucose units carrying galacturonic acid...
April 19, 2017: Journal of Proteomics
Sandra I Anjo, Tania Martins-Marques, Paulo Pereira, Henrique Girão, Bruno Manadas
Considering that proteins are usually engaged in complex and dynamic networks of interactions to exert their activity, a way to understand proteins' functions and the molecular mechanisms in which those proteins are involved, is by studying their interactome. In this sense, this tutorial presents a simple pipeline for the analysis of the network of interactions of a protein in order to reach a biological interpretation of the mechanisms modulated by those interactions, and understand how these interactions are affected by the experimental conditions...
April 19, 2017: Journal of Proteomics
Katja Witzel, Anja Buhtz, Rita Grosch
The soil-borne fungus Verticillium dahliae is the causal agent of wilting disease and affects a wide range of plant species worldwide. Here, we report on the time-resolved analysis of the tomato root proteome in response to fungal colonization. Tomato (Solanum lycopersicum cv. Hildares) was inoculated with V. dahliae at the two-leaf stage and roots were harvested at 7, 14 and 21 days post inoculation (dpi). In order to identify proteins related to the fungal spread at the different time points, a subsequent proteome analysis by two-dimensional differential gel electrophoresis (2D-DIGE) was conducted on samples from three independent experiments...
April 17, 2017: Journal of Proteomics
Sajad Majeed Zargar, Preeti Nagar, Rupesh Deshmukh, Muslima Nazir, Aijaz Ahmad Wani, Khalid Zaffar Masoodi, Ganesh Kumar Agrawal, Randeep Rakwal
Aquaporins (AQPs) are primarily involved in maintaining cellular water homeostasis. Their role in diverse physiological processes has fascinated plant scientists for more than a decade, particularly concerning abiotic stresses. Increasing examples of evidence in various crop plants indicate that the AQPs are responsible for precise regulation of water movement and consequently play a crucial role in the drought stress tolerance. Since drought is one of the major abiotic stresses affecting agricultural production worldwide, it has become a critical agenda to focus research on the development of drought tolerant crop plants...
April 13, 2017: Journal of Proteomics
Jianliang Wang, Jing Guo, Shasha Wang, Zhiyong Zeng, Dehong Zheng, Xiaoyan Yao, Haoquan Yu, Lifang Ruan
Xanthomonas oryzae pv. oryzae (Xoo) is a notorious rice pathogen that causes bacterial leaf blight (BLB), a destructive rice disease. Low-oxygen tension in the xylem vessels of rice stresses Xoo during infection. In this study, differentially expressed proteins under normoxic and hypoxic conditions were identified using high-performance liquid chromatography (HPLC) coupled with LC-MS/MS to investigate the global effects of low oxygen environment on Xoo PXO99(A). A statistically validated list of 187 (normoxia) and 140 (hypoxia) proteins with functional assignments was generated, allowing the reconstruction of central metabolic pathways...
April 12, 2017: Journal of Proteomics
Laura Montero-Morales, Daniel Maresch, Alexandra Castilho, Aysegül Turupcu, Kristina Ilieva, Silvia Crescioli, Sophia Karagiannis, Christian Lupinek, Chris Oostenbrink, Friedrich Altmann, Herta Steinkellner
The increasing biotechnological interest in human IgE antibodies demands advanced systems which allow their proper expression. However, this is still a challenge due to the complexity of the molecule, particularly regarding the diverse N-glycosylation pattern. Here, we present the expression of recombinant IgE in wild type and glycan-engineered Nicotiana benthamiana plants and in-depth N-glycosylation analyses. Mass spectrometric profiling revealed that plant IgE has a site occupancy rate that ranges from non-occupied at glycosite 6 (GS6) to 100% occupancy at GS1 and 2...
April 8, 2017: Journal of Proteomics
Pernille S Lassen, Camilla Thygesen, Martin R Larsen, Stefan J Kempf
Phosphorylation and glycosylation are important protein modifications in the mammalian brain acting as drivers of neural development, neurotransmission signalling and neurite elongation as well as synaptic morphology. Despite their important functional roles in the brain, only a few studies have elucidated them in neurodegenerative diseases such as Alzheimer's disease. Here, we comprehensively review Alzheimer's pathology in relation to protein phosphorylation and glycosylation on synaptic plasticity from neuroproteomics data...
April 7, 2017: Journal of Proteomics
Yuan Liu, Tingyuan Lang, Bingwei Jin, Feng Chen, Yi Zhang, Roger W Beuerman, Lei Zhou, Zhiqi Zhang
The cyclic AMP (cAMP) response element binding protein 1 (CREB1) is a promising target for cancer therapy. Here, we report that luteolin, a natural product, inhibits the expression of CREB1 at the transcriptional level and blocks epithelial-to-mesenchymal transition (EMT) of colorectal cancer cells. Treatment of colorectal cancer cells with luteolin induced mesenchymal-to-epithelial transition, reduced the expressions of mesenchymal markers and inhibited cell mobility in vitro. Through comparison of the proteomic profile of HCT-116 cells with and without luteolin treatment, we identified 366 differentially expressed proteins...
April 5, 2017: Journal of Proteomics
Ludger J E Goeminne, Kris Gevaert, Lieven Clement
Label-free shotgun proteomics is routinely used to assess proteomes. However, extracting relevant information from the massive amounts of generated data remains difficult. This tutorial provides a strong foundation on analysis of quantitative proteomics data. We provide key statistical concepts that help researchers to design proteomics experiments and we showcase how to analyze quantitative proteomics data using our recent free and open-source R package MSqRob, which was developed to implement the peptide-level robust ridge regression method for relative protein quantification described by Goeminne et al...
April 5, 2017: Journal of Proteomics
Sander Willems, David Bouyssié, Matthieu David, Marie Locard-Paulet, Karl Mechtler, Veit Schwämmle, Julian Uszkoreit, Marc Vaudel, Viktoria Dorfer
The 2017 EuBIC Winter School was held from January 10th to January 13th 2017 in Semmering, Austria. This meeting gathered international researchers in the fields of bioinformatics and proteomics to discuss current challenges in data analysis and biological interpretation. This article outlines the scientific program and exchanges that took place on this occasion and presents the current challenges of this ever-growing field. BIOLOGICAL SIGNIFICANCE: The EUPA bioinformatics community (EuBIC) organized its first winter school in January 2017...
April 3, 2017: Journal of Proteomics
Sophie Bromilow, Lee A Gethings, Mike Buckley, Mike Bromley, Peter R Shewry, James I Langridge, E N Clare Mills
The unique physiochemical properties of wheat gluten enable a diverse range of food products to be manufactured. However, gluten triggers coeliac disease, a condition which is treated using a gluten-free diet. Analytical methods are required to confirm if foods are gluten-free, but current immunoassay-based methods can unreliable and proteomic methods offer an alternative. However, proteomic methods require comprehensive and well annotated sequence databases which are lacking for gluten. A manually a curated database (GluPro V1...
April 3, 2017: Journal of Proteomics
Kai Scheffler, Rosa Viner, Eugen Damoc
Top-down mass spectrometry (MS) strategies allow in-depth characterization of proteins by fragmentation of the entire molecule(s) inside a mass spectrometer without requiring prior proteolytic digestion. Importantly, the fragmentation techniques on commercially available mass spectrometers have become more versatile over the past decade, with different characteristics in regards to the type and wealth of fragment ions that can be obtained while preserving labile protein post-translational modifications. Due to these and other improvements, top-down MS has become of broader interest and has started to be applied in more disciplines, such as the quality control of recombinant proteins, analysis and characterization of biopharmaceuticals, and clinical biochemistry to probe protein forms as potential disease biomarkers...
April 3, 2017: Journal of Proteomics
Valérie Labas, Ana-Paula Teixeira-Gomes, Laura Bouguereau, Audrey Gargaros, Lucie Spina, Aurélie Marestaing, Svetlana Uzbekova
Intact cell MALDI-TOF mass spectrometry (ICM-MS) was adapted to bovine follicular cells from individual ovarian follicles to obtain the protein/peptide signatures (<17kDa) of single oocytes, cumulus cells (CC) and granulosa cells (GC), which shared a total of 439 peaks. By comparing the ICM-MS profiles of single oocytes with CC before and after in vitro maturation (IVM), 71 different peaks were characterised, and their relative abundance was found to vary depending on the stage of oocyte meiotic maturation...
April 3, 2017: Journal of Proteomics
Akiko Hashiguchi, Keisuke Hitachi, Wei Zhu, Jingkui Tian, Kunihiro Tsuchida, Setsuko Komatsu
The immunomodulatory effect of mung bean is mainly attributed to antioxidant properties of flavonoids; however, the precise machinery for biological effect on animal cells remains uncertain. To understand the physiological change produced by mung bean consumption, proteomic and metabolomic techniques were used. In vitro assay confirmed the importance of synergistic interaction among multiple flavonoids by IL-6 expression. Proteomic analysis detected that the abundance of 190 proteins was changed in lipopolysaccharide-stimulated RAW264...
March 31, 2017: Journal of Proteomics
Letizia Bernardo, Caterina Morcia, Paolo Carletti, Roberta Ghizzoni, Franz W Badeck, Fulvia Rizza, Luigi Lucini, Valeria Terzi
Arbuscular mycorrhizal fungi (AMF) are plant growth promoters that ameliorate plant-water relations and the nutrient uptake of wheat. In this work, two cultivars of Triticum spp., a bread and a durum wheat, grown under drought stress and inoculated or not by AMF, are evaluated through a shotgun proteomic approach. The AMF association had beneficial effects as compared to non-mycorrhizal roots, in both bread and durum wheat. The beneficial symbiosis was confirmed by measuring morphological and physiological traits...
March 30, 2017: Journal of Proteomics
Ana M Ferreira, Jonas Grossmann, Claudia Fortes, Tanya Kilminster, Tim Scanlon, John Milton, Johan Greeff, Chris Oldham, Paolo Nanni, André M Almeida
Seasonal Weight Loss (SWL) is one of the most pressing issues in animal production in the tropics and Mediterranean. This work aims to characterize muscle proteome changes as a consequence of SWL in meat producing sheep, using a label-free proteomics approach. We compare three breeds: the Australian Merino (SWL susceptible), the Damara (SWL tolerant) and the Dorper (SWL intermediate tolerance). We identified 668 proteins of the sheep proteome, 95 with differential regulation. Also we observe that the more vulnerable to SWL a breed is, the more differential abundance proteins we find...
March 30, 2017: Journal of Proteomics
Sandra I Anjo, Francisco Figueiredo, Rui Fernandes, Bruno Manadas, Manuela Oliveira
The airborne fungus Aspergillus fumigatus is one of the most common agents of human fungal infections with a remarkable impact on public health. However, A. fumigatus conidia atmospheric resistance and longevity mechanisms are still unknown. Therefore, in this work, the processes underlying conidial adaptation were studied by a time course evaluation of the proteomics and ultrastructural changes of A. fumigatus' conidia at three time-points selected according to relevant changes previously established in conidial survival rates...
March 29, 2017: Journal of Proteomics
Laura A Dindia, Sarah L Alderman, Todd E Gillis
The changes in the cardiac proteome of rainbow trout (Oncorhynchus mykiss) were quantified during the early phases (4, 7, and 14d) of a typical exercise-training regime to provide a comprehensive overview of the cellular changes responsible for developing a trained heart phenotype. Enhanced somatic growth during the 14d experiment was paralleled by cardiac growth to maintain relative ventricular mass. This was reflected in the cardiac proteome by the increased abundance of contractile proteins and cellular integrity proteins as early as Day 4, including a pronounced and sustained increase in blood vessel epicardial substance - an intercellular adhesion protein expressed in the vertebrate heart...
March 29, 2017: Journal of Proteomics
Shuo Gu, Kai Chen, Minzhi Yin, Zhixiang Wu, Yeming Wu
Medulloblastoma is the most common malignant brain tumor in children. Around 30% of medulloblastoma patients are diagnosed with metastasis, which often results in a poor prognosis. Unfortunately, molecular mechanisms of medulloblastoma metastasis remain largely unknown. In this study, we employed the recently developed deep proteome analysis approach to quantitatively profile the expression of >10,000 proteins from CHLA-01-MED and CHLA-01R-MED isogenic cell lines derived from the primary and metastatic tumor of the same patient diagnosed with a group IV medulloblastoma...
March 28, 2017: Journal of Proteomics
Lang Pan, Jian Zhang, Junzhi Wang, Qin Yu, Lianyang Bai, Liyao Dong
American sloughgrass (Beckmannia syzigachne Steud.) is a weed widely distributed in wheat fields of China. In recent years, the evolution of herbicide (fenoxaprop-P-ethyl)-resistant populations has decreased the susceptibility of B. syzigachne. This study compared 4 B. syzigachne populations (3 resistant and 1 susceptible) using iTRAQ to characterize fenoxaprop-P-ethyl resistance in B. syzigachne at the proteomic level. Through searching the UniProt database, 3104 protein species were identified from 13,335 unique peptides...
March 24, 2017: Journal of Proteomics
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