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Alexander G Thompson, Elizabeth Gray, Imre Mager, Roman Fischer, Marie-Laëtitia Thézénas, Philip D Charles, Kevin Talbot, Samir El Andaloussi, Benedikt M Kessler, Matthew Wood, Martin R Turner
Cerebrospinal fluid (CSF) extracellular vesicles (EVs) show promise as a source of neurological disease biomarkers, though their precise origin is poorly understood. Current extraction techniques produce disappointing yield and purity. This study describes the application of ultrafiltration liquid chromatography (UFLC) to CSF-EVs, compared with ultracentrifugation (UC), and explores CSF-EV origin. EVs were extracted from human CSF by UC and UFLC and characterized using nanoparticle tracking analysis, electron microscopy and immunoblotting...
November 9, 2018: Proteomics
Gaoyuan Song, Libuse Brachova, Basil J Nikolau, Alan M Jones, Justin W Walley
The G-protein complex is a cytoplasmic on-off molecular switch that is set by plasma membrane receptors that activate upon binding of its cognate extracellular agonist. In animals, the default setting is the "off" resting state, while in plants, the default state is constitutively "on" but repressed by a plasma membrane receptor-like protein. De-repression appears to involve specific phosphorylation of key elements of the G-protein complex and possibly target proteins that are positioned downstream of this complex...
November 8, 2018: Proteomics
Franck Limonier, Sander Willems, Geneviève Waeterloos, Myriam Sneyers, Maarten Dhaenens, Dieter Deforce
SWATH-MS provides large-scale protein quantification with high accuracy and selectivity. Nevertheless, reliable quantification of low-abundant signals in complex samples remains challenging, as recently illustrated in a multicenter benchmark study of different label free software tools. Here, we use the SWATH Replicates Analysis 2.0 template from Sciex to highlight that the relationship between the MS2 peak area and the variability can be described by a function. This functional relationship appears to be largely insensitive to variation in samples or acquisition conditions, suggesting a device-intrinsic property...
November 2, 2018: Proteomics
Pierre Sabatier, Amir Ata Saei, Shiyu Wang, Roman A Zubarev
In chemical proteomics, the changes occurring in cellular proteomes upon drug treatment are used to identify the drug targets and the mechanism of action. However, proteomes of cultured cells undergo also natural alteration associated with changes in the media, attaining a degree of confluence as well as due to cell division and cell metabolism. These changes are implicitly assumed to be smaller in magnitude than the drug-induced changes that ultimately lead to cell demise. In this study, we show that growth-related proteome changes in the untreated control group are comparable in magnitude to drug-induced changes over the course of 48 h treatment...
November 1, 2018: Proteomics
Martyn Howard, Brahim Achour, Zubida Al-Majdoub, Amin Rostami-Hodjegan, Jill Barber
Sample preparation is a critical step in the proteomic workflow. Numerous different approaches are used, tailored to the type of sample, the aims of the experiment, analytical method, and to an extent, user preference. This has resulted in large variation in reported protein abundances. In this study we demonstrate the complementarity of two different sample preparation techniques for the study of absorption, distribution, metabolism and excretion (ADME) related proteins from pig liver tissue. Filter-aided sample preparation (FASP) is a well-established and widely used method, whilst gel-aided sample preparation (GASP) is a relatively new method optimised and simplified from previous gel-associated digestion techniques...
October 29, 2018: Proteomics
Carlo Santambrogio, Antonino Natalello, Stefania Brocca, Erika Ponzini, Rita Grandori
Intrinsically disordered proteins (IDPs) are systematically under-represented in structural proteomics studies. Their structural characterization implies description of the dynamic conformational ensembles populated by these polymers in solution, posing major challenges to biophysical methods. "Native" mass spectrometry (native-MS) has emerged as a central tool in this field, conjugating the unique MS analytical power with structurally meaningful descriptors, like solvent-accessible surface area (SASA) and collisional cross section (CCS)...
October 26, 2018: Proteomics
Aroonroong Suttitheptumrong, Nantapon Rawarak, Onrapak Reamtong, Kobporn Boonnak, Sa-Nga Pattanakitsakul
The clinical sign of dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) in humans is increased vascular permeability. Virus-specific factors and host factors, including secreted cytokines and especially TNF-alpha (TNF-α), are suggested as having roles in the pathogenesis of these conditions. Proteomic analysis with mass spectrometry was performed in membrane fraction isolated from human endothelial cells (EA.hy926) upon DENV infection and TNF-α treatment. In the 451 altered proteins that were identified, decreased plectin expression was revealed by Western blot analysis, while immunofluorescence staining (IFA) showed actin stress fiber rearrangement and decreased VE-cadherin in treated EA...
October 26, 2018: Proteomics
Etienne Villain, Aleksei A Nikekhin, Andrey V Kajava
The relationship between amino acid sequences of the β-hairpin structures and amyloidogenic β-arcade-forming motifs are of special interest because, similar to amyloid fibrils, most of the β-hairpin repeat (BHR) structures have the so-called cross-β arrangement. Moreover, β-hairpin is considered as a probable intermediate structure in amyloidogenesis. In this work, we performed a bioinformatics sequence analysis of the known BHR structures in search of amylodogenic motifs able to form β-arcade fibrils...
October 25, 2018: Proteomics
Sharon Ben-Hur, Mirit Biton, Neta Regev-Rudzki
Genetic plasticity of prokaryotic microbial communities is largely dependent on the ongoing exchange of genetic determinants by Horizontal Gene Transfer (HGT). HGT events allow beneficial genetic transitions to occur throughout microbial life, thus promoting adaptation to changing environmental conditions. Here, we discuss the significance of secreted vesicles in mediating HGT between microorganisms, while focusing on the benefits gained by vesicle-mediated gene delivery and its occurrence under different environmental cues...
October 24, 2018: Proteomics
Jinhai Yu, Linqiang Zhang, Yunhai Li, Xiaotong Zhu, Shimeng Xu, Xiao-Ming Zhou, Haizhen Wang, Hongchao Zhang, Bin Liang, Pingsheng Liu
Steroid hormones play essential roles for living organisms. It has been long and well established that the endoplasmic reticulum (ER) and mitochondria are essential sites for steroid hormone biosynthesis because several steroidogenic enzymes are located in these organelles. The adrenal gland lipid droplet (LD) proteomes from human, macaque monkey, and rodent were analyzed, revealing that steroidogenic enzymes are also present in abundance on LDs. The enzymes found include 3β-hydroxysteroid dehydrogenase (HSD3B), and estradiol 17β-dehydrogenase 11 (HSD17B11)...
October 24, 2018: Proteomics
Manuela Moriggi, Marta Giussani, Enrica Torretta, Daniele Capitanio, Marco Sandri, Roberta Leone, Sara De Palma, Michele Vasso, Giovanni Vozzi, Elda Tagliabue, Cecilia Gelfi
Tumor extracellular matrix (ECM) plays a pivotal role in outcome of breast cancer (BC) patients. Overespression of 58 genes, encoding 43 structural ECM proteins, has been identified to determine a specific cluster of BC with accelerated metastatic potential only in the undifferentiated (grade III) phenotype. The scope of this study was to characterize protein repertoire able to predict patient outcome in BC according to ECM gene expression pattern and histological grade. The differential proteomic analysis has been based on 2D-DIGE, MALDI-MS, bioinformatics and immunoblotting...
October 24, 2018: Proteomics
Anubhav Srivastava, Darren John Creek
Early detection and diagnosis of cancer can allow timely medical intervention, which greatly improves chances of survival and enhances quality of life. Biomarkers play an important role in assisting clinicians and health care providers in cancer diagnosis and treatment follow-up. In spite of years of research and the discovery of thousands of candidate cancer biomarkers, only a few have transitioned to routine usage in the clinic. This review highlights advances in proteomics technologies which have enabled high rates of discovery of candidate cancer biomarkers and evaluates integration with other omics technologies to improve their progress through to validation and clinical translation...
October 24, 2018: Proteomics
David Handler, Dana Pascovici, Mehdi Mirzaei, Vivek Gupta, Ghasem Hosseini Salekdeh, Paul A Haynes
Western blotting as an orthogonal validation tool for quantitative proteomics data has rapidly become a de facto requirement for publication. In this viewpoint article, we discuss the pros and cons of Western blotting as a validation approach, using examples from our own published work, and outline how to best apply it to improve the quality of data published. Further, we provide suggestions and guidelines for some other experimental approaches which can be used for validation of quantitative proteomics data in addition to, or in place of, Western blotting...
October 23, 2018: Proteomics
Martin Whitham, Mark A Febbraio
Protein signalling between tissues, or tissue cross-talk is becoming recognised as a fundamental biological process that is incompletely understood. Shotgun proteomic analyses of tissues and plasma to explore this concept are regularly challenged by high dynamic range of protein abundance, which limits the identification of lower abundance proteins. In this viewpoint article, we highlight how a focus on proteins contained within extracellular vesicles (EVs) not only partially addresses this issue, it can reveal a underappreciated complexity of the circulating proteome in various physiological and pathological contexts...
October 23, 2018: Proteomics
Anthony Yan-Tang Wu, Koji Ueda, Charles Pin-Kuang Lai
Extracellular vesicles (EVs) including exosomes and microvesicles are lipid bilayer-encapsulated nanoparticles released by cells, ranging from 40 nm to several microns in diameter. Biological cargoes including proteins, RNAs and DNAs can be ferried by EVs to neighboring and distant cells via biofluids, serving as a means of cell-to-cell communication under normal and pathological conditions, especially cancers. On the other hand, EVs have been investigated as a novel "information capsule" for early disease detection and monitoring via liquid biopsy...
October 18, 2018: Proteomics
Vladimir N Uversky
Articles assembled to this Special Issue use the perspective of protein intrinsic disorder to highlight different aspects of the dark proteome (i.e., a part of protein universe that includes proteins, which are not amenable to experimental structure determination by existing means and inaccessible to homology modeling) and some of its components. They illustrate that IDPs/IDPRs do not only serve as important constituents of the biological dark matter, but clearly act as the dark horse of the protein universe, being almost completely unknown or at least very little known in a recent past, but suddenly emerging to prominence...
October 18, 2018: Proteomics
Ronesh Sharma, Alok Sharma, Gaurav Raicar, Tatsuhiko Tsunoda, Ashwini Patil
Intrinsically disordered proteins (IDPs) contain long unstructured regions, which play an important role in their function. These intrinsically disordered regions (IDRs) participate in binding events through regions called molecular recognition features (MoRFs). Computational prediction of MoRFs helps identify the potentially functional regions in IDRs. In this study, OPAL+, a novel MoRF predictor, is presented. OPAL+ uses separate models to predict MoRFs of varying lengths along with incorporating the hidden Markov model (HMM) profiles and physicochemical properties of MoRFs and their flanking regions...
October 15, 2018: Proteomics
Andrea Schafferhans, Seán I O'Donoghue, Michael Heinzinger, Burkhard Rost
Despite substantial and successful projects for structural genomics, many proteins remain for which neither experimental structures nor homology-based models are known for any part of the amino acid sequence. These have been called dark proteins, in contrast to non-dark proteins, in which at least part of the sequence has a known or inferred structure. We hypothesized that non-dark proteins may be more abundantly expressed than dark proteins which are known to have much fewer sequence relatives. Surprisingly, we observed the opposite: human dark and non-dark proteins had quite similar levels of expression, in terms of both mRNA and protein abundance...
October 15, 2018: Proteomics
Julia A Bubis, Lev I Levitsky, Mark V Ivanov, Mikhail V Gorshkov
The efficiency of proteome analysis depends strongly on the configuration parameters of the search engine. One of the murkiest and nontrivial among them is the list of amino acid modifications included for the search. Here, an approach called AA_stat is presented for uncovering the unexpected modifications of amino acid residues in the protein sequences, as well as possible artifacts of data acquisition or processing, in the results of proteome analyses. The approach is based on comparing the amino acid frequencies of different mass shifts observed using the open search method introduced recently...
October 11, 2018: Proteomics
Xiaxiang Zhang, Petra Högy, Xu Na Wu, Iris Schmid, Xiulin Wang, Waltraud X Schulze, Dong Jiang, Andreas Fangmeier
Elevated CO2 promotes leaf photosynthesis and improves crop grain yield. However, as a major anthropogenic greenhouse gas, CO2 contributes to more frequent and severe heat stress, which threatens crop productivity. The combined effects of elevated CO2 and heat stress are complex, and the underlying mechanisms are poorly understood. In the present study, we examined the effects of elevated CO2 and high-temperature on foliar physiological traits and the proteome of spring wheat grown under two CO2 concentrations (380 and 550 μmol mol-1 ) and two temperature conditions (ambient and post-anthesis heat stress)...
October 11, 2018: Proteomics
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