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Proteomics

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https://www.readbyqxmd.com/read/30009483/quantitative-proteomic-analysis-of-biological-processes-and-responses-of-the-bacterium-desulfovibrio-desulfuricans-nd132-upon-deletion-of-its-mercury-methylation-genes
#1
Chen Qian, Hongmei Chen, Alexander Johs, Xia Lu, Jing An, Eric M Pierce, Jerry M Parks, Dwayne A Elias, Robert L Hettich, Baohua Gu
Recent studies of microbial mercury (Hg) methylation revealed a key gene pair, hgcAB, which is essential for methylmercury (MeHg) production in the environment. However, many aspects of the mechanism and biological processes underlying Hg methylation, as well as any additional physiological functions of the hgcAB genes, remain unknown. Here we have used quantitative proteomics to identify changes in potential functional processes related to hgcAB gene deletion in the Hg-methylating bacterium Desulfovibrio desulfuricans ND132...
July 15, 2018: Proteomics
https://www.readbyqxmd.com/read/30004632/reviewing-mechanistic-peptidomics-in-body-fluids-focusing-on-proteases
#2
REVIEW
Beatriz Magalhães, Fábio Trindade, António S Barros, Julie Klein, Francisco Amado, Rita Ferreira, Rui Vitorino
The comprehension of how protease networks sculpt proteomes might help to disclose the functional annotation of the peptidome in health and disease. Envisioning to add new insights on the protease networks involved in the regulation of body fluid peptidomes, we applied the Proteasix software to predict the proteases involved in the generation of the naturally occurring peptides present in six of the most studied human body fluids. Peptidome data was collected from the databases and from experimental studies...
July 13, 2018: Proteomics
https://www.readbyqxmd.com/read/29972280/proteomic-profile-of-daphnia-pulex-using-data-independent-acquisition-mass-spectrometry-and-ion-mobility-separation
#3
Aaron Steevensz, Robert Gombar, Roland Vergilino, Melania E Cristescu, Panayiotis O Vacratsis
Daphnia pulex is a keystone species for aquatic habitats and an ecological/evolution model organism. Although significant progress has been made on characterizing its genome, the D. pulex proteome remains largely uncharacterized partially due to abnormally high protein degradation during homogenization and emphasis on genomic analysis. In this study, various sample preparation and mass spectrometry acquisition methods were performed for the purpose of improving D. pulex proteome exploration. We observed benefits for employing both in-gel and in-solution methods of trypsin digestion...
July 4, 2018: Proteomics
https://www.readbyqxmd.com/read/29968278/a-potential-golden-age-to-come-current-tools-recent-use-cases-and-future-avenues-for-de-novo-sequencing-in-proteomics
#4
REVIEW
Thilo Muth, Felix Hartkopf, Marc Vaudel, Bernhard Y Renard
In shotgun proteomics, peptide and protein identification is most commonly conducted using database search engines, the method of choice when reference protein sequences are available. Despite its widespread use the database-driven approach is limited, mainly because of its static search space. In contrast, de novo sequencing derives peptide sequence information in an unbiased manner, using only the fragment ion information from the tandem mass spectra. In recent years, with the improvements in MS instrumentation, various new methods have been proposed for de novo sequencing...
July 2, 2018: Proteomics
https://www.readbyqxmd.com/read/29963755/soy-derived-phytochemical-genistein-modifies-chromatome-topology-to-restrict-cancer-cell-proliferation
#5
Bamaprasad Dutta, Jung Eun Park, Ivan Toh Yi Qing, Oi Lian Kon, Siu Kwan Sze
Epidemiological data indicate that human cancer risk is significantly reduced by consumption of soy-based foods containing the 'phytoestrogen' genistein, which can signal via host cell estrogen receptors. While additional chemoprotective effects of genistein induced by epigenetic factors have also been reported, the key molecules and mechanisms involved are poorly defined. We therefore investigated genistein effects on chromatin-bound proteins in the estrogen receptor-deficient cell line MDA-MB-231 which is insensitive to phytoestrogen signaling...
July 2, 2018: Proteomics
https://www.readbyqxmd.com/read/29952134/proteomic-profiling-of-enteroid-cultures-skewed-towards-development-of-specific-epithelial-lineages
#6
Lisa Luu, Zoe J Matthews, Stuart D Armstrong, Penelope Powell, Tom Wileman, Jonathan M Wastling, Janine L Coombes
Recently, three-dimensional small intestinal organoids (enteroids) have been developed from cultures of intestinal stem cells which differentiate in vitro to generate all the differentiated epithelial cell types associated with the intestine and mimic the structural properties of the intestine observed in vivo. Small-molecule drug treatment can skew organoid epithelial cell differentiation towards particular lineages, and these skewed enteroids may provide useful tools to study specific epithelial cell populations, such as goblet and Paneth cells...
June 28, 2018: Proteomics
https://www.readbyqxmd.com/read/29952130/temporal-analyses-of-barley-malting-stages-using-shot-gun-proteomics
#7
Ramamurthy Mahalingam
Malt derived from barley malting is an essential raw material for beer brewing. In this study, we performed the first dynamic proteome survey during barley malting using a gel-free proteomics approach. This entailed in-solution tryptic digestion of precipitated proteins and analysis of peptides by nano-liquid chromatography coupled with tandem mass spectrometry. A total of 1418 proteins were identified from the five malting stages - Steep, 1, 3, 5 Days After Germination, and end of Kiln. About 900 proteins identified in this analysis were uncharacterized or predicted proteins...
June 28, 2018: Proteomics
https://www.readbyqxmd.com/read/29952121/the-utility-of-nanopore-technology-for-protein-and-peptide-sensing
#8
REVIEW
Joseph W F Robertson, Joseph E Reiner
Resistive-pulse nanopore sensing enables label-free single-molecule analysis of a wide range of analytes. An increasing number of studies have demonstrated the feasibility and usefulness of nanopore sensing for protein and peptide characterization. Nanopores offer the potential to study a variety of protein-related phenomena that includes unfolding kinetics, differences in unfolding pathways, protein structure stability and free energy profiles of DNA-protein and RNA-protein binding. In addition to providing a tool for fundamental protein characterization, nanopores have also been used as highly selective protein detectors in various solution mixtures and conditions...
June 28, 2018: Proteomics
https://www.readbyqxmd.com/read/29952133/proteomics-in-veterinary-medicine-and-animal-science-neglected-scientific-opportunities-with-immediate-impact
#9
Petra Bilić, Josipa Kuleš, Asier Galan, Leticia Gomes de Pontes, Nicolas Guillemin, Anita Horvatić, Amanda Festa Sabes, Vladimir Mrljak, Peter David Eckersall
Animal/veterinary proteomics is an evolving field which holds a great promise not only for fundamental and applied discoveries regarding biology and pathology of domestic species, but can also be implemented in comparative applications of human diseases research. Experimental proteomics in domestic animals have advantages over use of rodents, such as multiple sampling in time series and availability of biological samples in sufficient volume for multiple analyses, such that both experimental and natural disease processes can be investigated...
June 27, 2018: Proteomics
https://www.readbyqxmd.com/read/29938906/colonic-mucosal-proteome-signature-reveals-reduced-energy-metabolism-and-protein-synthesis-but-activated-autophagy-during-anorexia-induced-malnutrition-in-mice
#10
Séverine Nobis, Najate Achamrah, Alexis Goichon, Clément L'Huillier, Aline Morin, Charlène Guérin, Philippe Chan, Jean Luc do Rego, Jean Claude do Rego, David Vaudry, Pierre Déchelotte, Liliana Belmonte, Moïse Coëffier
Anorexia nervosa is an eating disorder often associated with intestinal disorders. To explore the underlying mechanisms of these disorders, we aimed to evaluate the colonic proteome during activity-based anorexia. Female C57Bl/6 mice were randomized into three groups: Control, Limited Food Access (LFA) and Activity-Based Anorexia (ABA). LFA and ABA mice had a progressive limited access to food but only ABA mice had access to an activity wheel. On colonic mucosal protein extracts, a 2-dimensional PAGE-based comparative proteomic analysis was then performed and differentially expressed proteins were identified by LC-ESI-MS/MS...
June 25, 2018: Proteomics
https://www.readbyqxmd.com/read/29932496/resolution-matters-correlating-quantitative-proteomics-and-nanoscale-precision-microscopy-for-reconstructing-synapse-identity2
#11
Andras Gabor Miklosi, Giorgia Del Favero, Doris Marko, Tibor Harkany, Gert Lubec
For more than a century, the precision at which any protein (or RNA) could be localized in living cells depended on the spatial resolution of microscopy. Light microscopy, even recently benchmarked laser-scanning microscopy, is inherently liable to the diffraction limit of visible light. Electron microscopy that had existed as the only alternative for decades is, in turn, of low through-put and sensitive to processing artefacts. Therefore, researchers have looked for alternative technologies particularly with ever-growing interest in resolving structural underpinnings of cellular heterogeneity in the human body...
June 22, 2018: Proteomics
https://www.readbyqxmd.com/read/29932309/platelet-releasate-proteome-profiling-reveals-a-core-set-of-proteins-with-low-variance-between-healthy-adults
#12
Martin E M Parsons, Paulina B Szklanna, Jose A Guererro, Kieran Wynne, Feidhlim Dervin, Karen O'Connell, Seamus Allen, Karl Egan, Cavan Bennett, Christopher McGuigan, Cedric Gheveart, Fionnuala Ní Áinle, Patricia B Maguire
Upon activation, platelets release a powerful cocktail of soluble and vesicular signals, collectively termed the 'platelet releasate' (PR). Although several studies have used qualitative/quantitative proteomic approaches to characterise PR; with debated content and significant inter-individual variability reported, confident and reliable insights have been hindered. Using label-free quantitative (LFQ)-proteomics analysis, we provide a reproducible, quantifiable investigation of the 1U/ml thrombin-induced PR from 32 healthy adults...
June 22, 2018: Proteomics
https://www.readbyqxmd.com/read/29932303/quantitative-crotonylome-analysis-expands-the-roles-of-p300-in-the-regulation-of-lysine-crotonylation-pathway
#13
He Huang, Dan-Li Wang, Yingming Zhao
Lysine crotonylation (Kcr) is a recently identified PTM that is regulated by an acetyltransferase, p300. The p300-catalyzed histone Kcr is able to stimulate transcription to a greater degree than the well-studied histone lysine acetylation (Kac). Despite these progresses, the global Kcr substrates regulated by p300 remain largely unknown, hindering efforts to establish mechanistic links between Kcr and p300-mediated phenotypes. Here, we used quantitative proteomics to characterize the p300-regulated lysine crotonylome in wild type (WT) and p300 knockout (KO) cells...
June 22, 2018: Proteomics
https://www.readbyqxmd.com/read/29923338/proteomic-analysis-of-synaptoneurosomes-highlights-the-relevant-role-of-local-translation-in-the-hippocampus
#14
Itziar Benito, Juan José Casañas, María Luz Montesinos
Several proteomic analyses have been performed on synaptic fractions isolated from cortex or even total brain, resulting in preparations with a high synaptic heterogeneity and complexity. Synaptoneurosomes (SNs) are subcellular membranous elements that contain sealed pre- and post-synaptic components. They are obtained by subcellular fractionation of brain homogenates and serve as a suitable model to study many aspects of the synapse physiology. Here we report the proteomic content of SNs isolated from hippocampus of adult mice, a brain region involved in memory that presents lower synaptic heterogeneity than cortex...
June 19, 2018: Proteomics
https://www.readbyqxmd.com/read/29920934/an-insight-into-powdery-mildew-infected-susceptible-resistant-and-immune-sunflower-genotypes
#15
Prathap Reddy Kallamadi, Kamakshi Dandu, Pulugurtha Bharadwaja Kirti, Chintalagiri Mohan Rao, Suman S Thakur, Sujatha Mulpuri
Powdery mildew (PM, caused by Golovinomyces orontii) is one of the major diseases on sunflower that causes severe yield losses in the tropics. Sources of resistance to PM are reported in an exotic accession and some wild Helianthus species. The present study aims at quantitative proteomic analysis of susceptible, resistant and immune genotypes of sunflower in response to PM infection at 3, 7, 10 days post infection. The majority of differentially expressed proteins in the resistant genotype belonged to oxidative stress (catalase, ATP-sulfurylase and formate dehydrogenase), defense (HSP-70, heat shock transcription factors) and photosynthesis (LHCB3)...
June 19, 2018: Proteomics
https://www.readbyqxmd.com/read/29911326/improving-quality-control-of-contagious-caprine-pleuropneumonia-vaccine-with-tandem-mass-spectrometry
#16
François Thiaucourt, Olivier Pible, Guylaine Miotello, Nick Nwankpa, Jean Armengaud
Vaccines to protect livestock against contagious caprine pleuropneumonia (CCPP) consist in inactivated, adjuvanted antigens. Quality control of these vaccines is challenging as total protein quantification provides no indication of protein identity or purity, and culture is not an option. Here, a tandem mass spectrometry approach was used to identify the mycoplasma antigen contained in reference samples and in commercial CCPP vaccines. By the same approach, the relative amounts of mycoplasma antigen and residual proteins originating from the production medium were determined...
June 17, 2018: Proteomics
https://www.readbyqxmd.com/read/29905012/quantitative-secretomics-reveals-extrinsic-signals-involved-in-human-pluripotent-stem-cell-cardiomyogenesis
#17
Hanna Wolling, Sarah A Konze, Anne Höfer, Jelena Erdmann, Andreas Pich, Robert Zweigerdt, Falk F R Buettner
Human pluripotent stem cells (hPSCs) can be differentiated in vitro into cardiomyocytes (CMs) but the molecular mechanisms behind this process are still not fully understood. In particular identification of morphogens remained elusive because the mass spectrometry (MS)-based identification of secreted proteins from cell culture supernatants is impeded by high levels of albumin present in common differentiation media. Thus we established an albumin-free cardiomyogenic differentiation medium and performed secretomics at seven different time points during in vitro differentiation...
June 14, 2018: Proteomics
https://www.readbyqxmd.com/read/29901268/integrative-analysis-of-proteome-and-ubiquitylome-reveals-unique-features-of-lysosomal-and-endocytic-pathways-in-gefitinib-resistant-non-small-cell-lung-cancer-cells
#18
Wang Li, Heyong Wang, Yan Yang, Tian Zhao, Zhixiong Zhang, Ye Tian, Zhaomie Shi, Xiaojun Peng, Fei Li, Yonghong Feng, Lei Zhang, Gening Jiang, Fan Zhang
Non-small cell lung cancer (NSCLC) patients carrying EGFR activating mutations treated with gefitinib, a tyrosine kinase inhibitor, will develop drug resistance. Ubiquitylation is one of major posttranslational modifications of proteins affecting the stability or function of proteins. However, the role of protein ubiquitylation in gefitinib resistance is poorly understood. To systematically identify the global change in protein expression and ubiquitylation during gefitinib resistance, we carried out quantitative global proteome and ubiquitylome study in a pair of gefitinib resistant and sensitive NSCLC cells...
June 14, 2018: Proteomics
https://www.readbyqxmd.com/read/29888524/proteomic-study-of-the-exponential-stationary-growth-phase-transition-in-the-haloarchaea-natrialba-magadii-and-haloferax-volcanii
#19
Micaela Cerletti, María Ines Giménez, Christian Tröetschel, Celeste D' Alessandro, Ansgar Poetsch, Rosana Ester De Castro, Roberto A Paggi
The dynamic changes that take place along the phases of microbial growth (lag, exponential, stationary, and death) have been widely studied in bacteria at the molecular and cellular levels, but little is known for archaea. In this study, a high-throughput approach was used to analyze and compare the proteomes of two haloarchaea during exponential and stationary growth: the neutrophilic Haloferax volcanii and the alkaliphilic Natrialba magadii. Almost 2000 proteins were identified in each species (≈50% of the predicted proteome)...
June 10, 2018: Proteomics
https://www.readbyqxmd.com/read/29882266/future-prospects-of-spectral-clustering-approaches-in-proteomics
#20
Yasset Perez-Riverol, Juan Antonio Vizcaíno, Johannes Griss
In this Viewpoint article, we discuss current and future applications of spectral clustering in the context of mass spectrometry-based proteomics approaches. First of all, we are introducing the main algorithms and tools that can currently be used to perform spectral clustering. In addition, we explain its main applications and their use in current computational proteomics workflows, including the generation of spectral libraries and spectral archives. Finally, we discuss possible future directions for spectral clustering, including its potential use to achieve a deeper coverage of the proteome and the discovery of novel post-translational modifications and single amino acid variants...
June 7, 2018: Proteomics
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