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Journal of Proteome Research

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https://www.readbyqxmd.com/read/28252966/metabolic-in-vivo-labeling-highlights-differences-of-metabolically-active-microbes-from-the-mucosal-gastrointestinal-microbiome-between-high-fat-and-normal-chow-diet
#1
Andreas Oberbach, Sven-Bastiaan Haange, Nadine Schlichting, Marco Heinrich, Stefanie Lehmann, Holger Till, Floor Hugenholtz, Yvonne Kullnick, Hauke Smidt, Karin Frank, Jana Seifert, Nico Jehmlich, Martin von Bergen
The gastrointestinal microbiota in the gut interacts metabolically and immunologically with the host tissue in the contact zone of the mucus layer. For understanding the details of these interactions and especially their dynamics it is crucial to identify the metabolically active subset of the microbiome. This became possible by the development of stable isotope probing techniques, which have only sparsely been applied to microbiome research. We applied the in vivo stable isotope approach using (15)N-labeled diet with subsequent identification of metabolically active bacterial species...
March 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28317380/systems-biology-reveals-ns4b-cyclophilin-a-interaction-a-new-target-to-inhibit-yfv-replication
#2
Alessandra Vidotto, Ana T S Morais, Milene Rocha Ribeiro, Carolina C Pacca, Ana C B Terzian, Laura H V G Gil, Ronaldo Mohana-Borges, Philippe Gallay, Mauricio L Nogueira
Yellow fever virus (YFV) replication is highly dependent upon host cell factors. YFV NS4B is reported to be involved in viral replication and immune evasion. Here, interactions between NS4B and human proteins were determined using a GST pull-down assay and analyzed using 1- DE and LC-MS/MS. We present a total of 207 proteins confirmed using Scaffold 3 Software. Cyclophilin A (CypA), a protein which has been shown to be necessary for the positive regulation of flavivirus replication, was identified as a possible NS4B partner...
March 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28317378/scrambled-internal-standard-sis-method-for-high-throughput-protein-quantification-by-maldi-ms-ms
#3
Toshihiro Yoneyama, Sumio Ohtsuki, Masanori Tachikawa, Yasuo Uchida, Tetsuya Terasaki
Matrix-assisted laser desorption ionization (MALDI) would be advantageous for high-throughput MS acquisition, but suffers from low signal reproducibility. The purpose of this study was to establish a reliable MALDI-tandem mass spectrometry (MS/MS)-based high-throughput quantification of tryptic peptides using our newly developed scrambled internal standard (sIS) method. The standard curves obtained with sIS peptides showed good linearity over a wide concentration range (5-1000 fmol/μL) compared to the IS-free method, and the coefficient of variation (CV) of data points at each concentration (5-1000 fmol/μL) was significantly reduced...
March 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28317375/comparison-of-false-discovery-rate-control-strategies-for-variant-peptide-identifications-in-shotgun-proteogenomics
#4
Mark V Ivanov, Anna A Lobas, Dmitry S Karpov, Sergei A Moshkovskii, Mikhail V Gorshkov
Proteogenomic studies aiming at identification of variant peptides using customized database searches of mass spectrometry data are facing a dilemma of selecting the most efficient database search strategy: a choice has to be made between using combined or sequential searches against reference (wild-type) and mutant protein databases, or directly against the mutant database without the wild-type one. Here, we called these approaches "all-together", "one-by-one" and "direct", respectively. In this note we would like to share the results of comparison of these search strategies obtained for large data sets of publicly available proteogenomic data...
March 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28244758/glycosylation-changes-in-serum-proteins-identify-patients-with-pancreatic-cancer
#5
Anna Drabik, Anna Bodzon-Kulakowska, Piotr Suder, Jerzy Silberring, Jan Kulig, Marek Sierzega
After more than a decade of biomarker discovery using advanced proteomic and genomic approaches, very few biomarkers have been involved in clinical diagnostics. Most candidate biomarkers are focused on the protein component. Targeting post-translational modifications (PTMs) in combination with protein sequences will provide superior diagnostic information with regards to sensitivity and specificity. Glycosylation is one of the most common and functionally important PTMs. It plays a central role in many biological processes, including protein folding, host-pathogen interactions, immune response, and inflammation...
March 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28241730/quantitative-proteomic-and-phosphoproteomic-analysis-of-h37ra-and-h37rv-strains-of-mycobacterium-tuberculosis
#6
Renu Verma, Sneha Maria Pinto, Arun Hanumana Patil, Jayshree Advani, Pratigya Subba, Manish Kumar, Jyoti Sharma, Gourav Dey, Raju Ravikumar, Shashidhar Buggi, Parthasarathy Satishchandra, Kusum Sharma, Mrutyunjay Suar, Srikanth Prasad Tripathy, Devendra Singh Chauhan, Harsha Gowda, Akhilesh Pandey, Sheetal Gandotra, Thottethodi Subrahmanya Keshava Prasad
Mycobacterium tuberculosis, the causative agent of tuberculosis, accounts for 1.5 million human deaths annually worldwide. Despite efforts to eradicate tuberculosis, it still remains a deadly disease. The two best characterized strains of M. tuberculosis, virulent H37Rv and avirulent H37Ra, provide a unique platform to investigate biochemical and signaling pathways associated with pathogenicity. To delineate the biomolecular dynamics that may account for pathogenicity and attenuation of virulence in M. tuberculosis, we compared the proteome and phosphoproteome profiles of H37Rv and H37Ra strains...
March 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28314371/intrauterine-growth-restriction-programs-the-hypothalamus-of-adult-male-rats-integrated-analysis-of-proteomic-and-metabolomic-data
#7
Amanda Paula Pedroso, Adriana Pereira de Souza, Ana Paula Segantine Dornellas, Lila Missae Oyama, Cláudia Maria Oller Nascimento, Gianni Mara Silva Santos, José C Rosa, Ricardo Pimenta Bertolla, Jelena Klawitter, Uwe Christians, Alexandre Keiji Tashima, Eliane Beraldi Ribeiro
Programming of hypothalamic functions regulating energy homeostasis may play a role in intrauterine growth restriction (IUGR)-induced adulthood obesity. The present study investigated the effects of IUGR on the hypothalamus proteome and metabolome of adult rats submitted to 50% protein-energy restriction throughout pregnancy. Proteomic and metabolomic analyzes were performed by data independent acquisition mass spectrometry and multiple reaction monitoring, respectively. At age 4 months, the restricted rats showed elevated adiposity, increased leptin and signs of insulin resistance...
March 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28271897/branched-chain-amino-acids-as-predictors-for-individual-differences-of-cisplatin-nephrotoxicity-in-rats-a-pharmacometabonomics-study
#8
Pei Zhang, Wei Li, Jiaqing Chen, Ruiting Li, Zunjian Zhang, Yin Huang, Fengguo Xu
Nephrotoxicity is the dose-limiting adverse effect of cisplatin with large individual differences. Up to now, little has been done on how to recognize and predict the individual differences in either preclinical or clinical research. In the present study, important postdose indicators were screened out first and integrated into a grouping factor, according to which rats were recognized as lowly or highly sensitive individuals. Then, mass-spectrometry-based untargeted metabolomics approach was performed to dissect the metabolic differences in predose serum of the two groups...
March 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28301166/brachyspira-hyodysenteriae-infection-regulates-mucin-glycosylation-synthesis-inducing-an-increased-expression-of-core-2-o-glycans-in-porcine-colon
#9
Vignesh Venkatakrishnan, Macarena Paz Quintana-Hayashi, Maxime Mahu, Freddy Haesebrouck, Frank Pasmans, Sara K Lindén
Brachyspira hyodysenteriae causes swine dysentery (SD), leading to global financial losses to the pig industry. Infection with this pathogen results in an increase of B. hyodysenteriae binding sites on mucins, along with increased colonic mucin secretion. We here predict that B. hyodysenteriae modifies the glycosylation pattern of the porcine intestinal mucus layer to optimize its host niche. We characterized the swine colonic mucin O-glycome and identified the differences in glycosylation between B. hyodysenteriae infected and non-infected pigs...
March 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28299940/epsilon-q-an-automated-analyzer-interface-for-mass-spectral-library-search-and-label-free-protein-quantification
#10
Jin-Young Cho, Hyoung-Joo Lee, Seul-Ki Jeong, Young-Ki Paik
Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variables and modification options can increase processing time and false-positive errors in large and complicated MS datasets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity...
March 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28294621/quantification-of-metabolites-by-nmr-spectroscopy-in-the-presence-of-protein
#11
Jens Wallmeier, Claudia Samol, Lisa Ellmann, Helena Ursula Zacharias, Franziska C Vogl, Muriel Garcia, Katja Dettmer, Peter J Oefner, Wolfram Gronwald
The high reliability of NMR spectroscopy makes it an ideal tool for large-scale metabolomic studies. However, the complexity of biofluids and, in particular, the presence of macromolecules poses a significant challenge. Ultrafiltration and protein precipitation are established means of deproteinization and recovery of free or total metabolite content, but neither is ever complete. In addition, aside from cost and labor, all deproteinization methods constitute an additional source of experimental variation. The Carr-Purcell-Meiboom-Gill (CPMG) echo-train acquisition of NMR spectra obviates the need for prior deproteinization by attenuating signals from macromolecules, but concentration values of metabolites measured in blood plasma will not necessarily reflect total or free metabolite content...
March 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28294620/the-effect-of-antibiotics-and-diet-on-enterolactone-concentration-and-metabolome-studied-by-targeted-and-non-targeted-lc-ms-metabolomics
#12
Anne Katrine Bolvig, Natalja P Nørskov, Mette Skou Hedemann, Leslie Foldager, Brendan McCarthy-Sinclair, Maria L Marco, Helle N Lærke, Knud Erik Bach Knudsen
High plant lignan intake is associated with a number of health benefits, possibly induced by the lignan metabolite enterolactone (ENL). The gut microbiota plays a crucial role in converting dietary lignans into ENL, and epidemiological studies have shown that use of antibiotics is associated with lower levels of ENL. Here, we investigate the link between antibiotic use and lignan metabolism in pigs using LC-MS/MS. The effect of lignan intake and antibiotic use on the gut microbial community and the pig metabolome is studied by 16S rRNA sequencing and non-targeted LC-MS...
March 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28290700/metabolic-response-to-everolimus-in-patient-derived-triple-negative-breast-cancer-xenografts
#13
Leslie R Euceda, Deborah K Hill, Endre Stokke, Rana Hatem, Rania El Botty, Ivan Bièche, Elisabetta Marangoni, Tone F Bathen, Siver A Moestue
Patients with triple negative breast cancer (TNBC) are unresponsive to endocrine and anti-HER2 pharmacotherapy, limiting their therapeutic options to chemotherapy. TNBC is frequently associated with abnormalities in the PI3K/AKT/mTOR signaling pathway; drugs targeting this pathway are currently being evaluated in these patients. However, response is variable, partly due to heterogeneity within TNBC, conferring a need to identify biomarkers predicting response and resistance to targeted therapy. In this study, we used a metabolomics approach to assess response to the mTOR inhibitor everolimus in a panel of TNBC patient-derived xenografts (PDX) (n=103 animals)...
March 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28290203/symbiotic-interplay-of-fungi-algae-and-bacteria-within-the-lung-lichen-i-lobaria-pulmonaria-i-l-hoffm-as-assessed-by-i-state-of-the-art-i-metaproteomics
#14
Christine Eymann, Christian Lassek, Uwe Wegner, Jörg Bernhardt, Ole Arno Fritsch, Stephan Fuchs, Andreas Otto, Dirk Albrecht, Ulf Schiefelbein, Tomislav Cernava, Ines Aschenbrenner, Gabriele Berg, Martin Grube, Katharina Riedel
Lichens are recognized by macroscopic structures formed by a heterotrophic fungus, the mycobiont, which hosts internal autotrophic photosynthetic algal and/or cyanobacterial partners, referred to as the photobiont. We analyzed structure and functionality of the entire lung lichen </i>Lobaria pulmonaria</i> L. Hoffm. collected from two different sites by state-of-the-art metaproteomics. In addition to the green algae and the ascomycetous fungus, a lichenicolous fungus, as well as a complex prokaryotic community (different from the cyanobacteria) was found, the latter dominated by methanotrophic Rhizobiales...
March 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28245357/optimization-and-application-of-direct-infusion-nanoelectrospray-hrms-method-for-large-scale-urinary-metabolic-phenotyping-in-molecular-epidemiology
#15
Elena Chekmeneva, Gonçalo Dos Santos Correia, Queenie Chan, Anisha Wijeyesekera, Adrienne Tin, Jeffery Hunter Young, Paul Elliott, Jeremy K Nicholson, Elaine Holmes
Large-scale metabolic profiling requires the development of novel economical high-throughput analytical methods to facilitate characterization of systemic metabolic variation in population phenotypes. We report a fit-for-purpose direct infusion nanoelectrospray high-resolution mass spectrometry (DI-nESI-HRMS) method with time-of-flight detection for rapid targeted parallel analysis of over 40 urinary metabolites. The newly developed 2 min infusion method requires <10 μL of urine sample and generates high-resolution MS profiles in both positive and negative polarities, enabling further data mining and relative quantification of hundreds of metabolites...
March 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28245130/-1-h-nmr-to-evaluate-the-metabolome-of-bronchoalveolar-lavage-fluid-balf-in-bronchiolitis-obliterans-syndrome-bos-toward-the-development-of-a-new-approach-for-biomarker-identification
#16
Carlotta Ciaramelli, Marco Fumagalli, Simona Viglio, Anna Maria Bardoni, Davide Piloni, Federica Meloni, Paolo Iadarola, Cristina Airoldi
This report describes the application of NMR spectroscopy to the profiling of metabolites in bronchoalveolar lavage fluid (BALf) of lung transplant recipients without bronchiolitis obliterans syndrome (BOS) (stable, S, n = 10), and with BOS at different degrees of severity (BOS 0p, n = 10; BOS I, n = 10). Through the fine-tuning of a number of parameters concerning both sample preparation/processing and variations of spectra acquisition modes, an efficient and reproducible protocol was designed for the screening of metabolites in a pulmonary fluid that should reflect the status of airway inflammation/injury...
March 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28244322/impact-of-the-pd2spermine-chelate-on-osteosarcoma-metabolism-an-nmr-metabolomics-study
#17
Inês Lamego, M Paula M Marques, Iola F Duarte, Ana S Martins, Helena Oliveira, Ana M Gil
A metabolomics study of Pd2Spermine(Spm) on osteosarcoma MG-63 and osteoblastic HOb cells is presented to assess the impact of the potential palladium drug on cell metabolism compared with cisplatin (cDDP). Despite its higher cytotoxicity, Pd2Spm induced lower (and reversible) metabolic impact on MG-63 cells and the absence of apoptosis; conversely, it induced significant deviations in osteoblastic amino acid metabolism. However, when in combination with doxorubicin and methotrexate, Pd2Spm induced strong metabolic deviations on lipids, choline compounds, amino acids, nucleotides, and compounds related to antioxidative mechanisms (e...
March 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28287739/the-application-of-metabolic-profiling-to-abdominal-aortic-aneurysm-research
#18
Mahim Irfan Qureshi, Michele Greco, Panagiotis Andrea Vorkas, Elaine Holmes, Alun H Davies
Rationale Abdominal aortic aneurysm (AAA) is a complex disease posing diagnostic and therapeutic challenges. Metabonomics may aid in the diagnosis of AAA, determination of individualised risk, discovery of therapeutic targets, and improve understanding of pathogenesis. Objective To review the diversity and outcomes of existing AAA metabonomic research. Methods and Results A systematic review has been performed. Original research studies applying metabonomics to human aneurysmal disease were included. Seven relevant articles were identified: four studies were based on plasma/serum metabolite profiling, and three studies examined aneurysmal tissue...
March 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28287737/large-scale-srm-screen-of-urothelial-bladder-cancer-candidate-biomarkers-in-urine
#19
Elodie Duriez, Christophe D Masselon, Cédric Mesmin, Magali Court, Kevin Demeure, Yves Allory, Nuria Malats, Mariette Matondo, François Radvanyi, Jérôme Garin, Bruno Domon
Urothelial bladder cancer is a condition associated with high recurrence and substantial morbidity and mortality. Non-invasive urinary tests that would detect bladder cancer and tumor recurrence are required to significantly improve patient care. Over the last decade, numerous bladder cancer candidate biomarkers have been identified in the context of extensive proteomics or transcriptomics studies. To translate these findings in clinically useful biomarkers, the systematic evaluation of these candidates remains the bottleneck...
March 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28287268/nmr-based-lipid-profiling-of-high-density-lipoprotein-particles-in-healthy-subjects-with-low-normal-and-elevated-hdl-cholesterol
#20
Christina E Kostara, Vasilis Tsimihodimos, Moses S Elisaf, Eleni T Bairaktari
Recent studies suggest that the cholesterol content of HDL (High Density Lipoproteins) lipoproteins may provide limited information on their antiatherogenic properties and that the composition and particles' structure provide more information on their functionality. We used NMR-based (Nuclear Magnetic Resonance-based) lipidomics to study the relationships of serum HDL-C (HDL-Cholesterol) levels with the lipid composition of HDL particles in three groups of subjects selected on the basis of their HDL-C levels...
March 13, 2017: Journal of Proteome Research
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