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https://www.readbyqxmd.com/read/28800136/feathermoss-and-epiphytic-nostoc-cooperate-differently-expanding-the-spectrum-of-plant-cyanobacteria-symbiosis
#1
Denis Warshan, Josh L Espinoza, Rhona K Stuart, R Alexander Richter, Sea-Yong Kim, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Kerrie Barry, Vasanth Singan, Erika Lindquist, Charles Ansong, Samuel O Purvine, Heather M Brewer, Philip D Weyman, Christopher L Dupont, Ulla Rasmussen
Dinitrogen (N2)-fixation by cyanobacteria in symbiosis with feathermosses is the primary pathway of biological nitrogen (N) input into boreal forests. Despite its significance, little is known about the cyanobacterial gene repertoire and regulatory rewiring needed for the establishment and maintenance of the symbiosis. To determine gene acquisitions and regulatory changes allowing cyanobacteria to form and maintain this symbiosis, we compared genomically closely related symbiotic-competent and -incompetent Nostoc strains using a proteogenomics approach and an experimental set up allowing for controlled chemical and physical contact between partners...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28765834/proteogenomics-data-for-deciphering-frankia-coriariae-interactions-with-root-exudates-from-three-host-plants
#2
Guylaine Miotello, Amir Ktari, Abdellatif Gueddou, Imen Nouioui, Faten Ghodhbane-Gtari, Jean Armengaud, Maher Gtari
Frankia coriariae BMG5.1 cells were incubated with root exudates derived from compatible (Coriaria myrtifolia), incompatible (Alnus glutinosa) and non-actinorhizal (Cucumis melo) host plants. Bacteria cells and their exoproteomes were analyzed by high-throughput proteomics using a Q-Exactive HF high resolution tandem mass spectrometer incorporating an ultra-high-field orbitrap analyzer. MS/MS spectra were assigned with two protein sequence databases derived from the closely-related genomes from strains BMG5...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28759593/proteogenomic-analysis-of-the-total-and-surface-exposed-proteomes-of-plasmodium-vivax-salivary-gland-sporozoites
#3
Kristian E Swearingen, Scott E Lindner, Erika L Flannery, Ashley M Vaughan, Robert D Morrison, Rapatbhorn Patrapuvich, Cristian Koepfli, Ivo Muller, Aaron Jex, Robert L Moritz, Stefan H I Kappe, Jetsumon Sattabongkot, Sebastian A Mikolajczak
Plasmodium falciparum and Plasmodium vivax cause the majority of human malaria cases. Research efforts predominantly focus on P. falciparum because of the clinical severity of infection and associated mortality rates. However, P. vivax malaria affects more people in a wider global range. Furthermore, unlike P. falciparum, P. vivax can persist in the liver as dormant hypnozoites that can be activated weeks to years after primary infection, causing relapse of symptomatic blood stages. This feature makes P. vivax unique and difficult to eliminate with the standard tools of vector control and treatment of symptomatic blood stage infection with antimalarial drugs...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28750222/assessing-the-relevance-of-a-multiplexed-methodology-for-proteomic-biomarker-measurement-in-the-invertebrate-species-gammarus-fossarum-a-physiological-and-ecotoxicological-study
#4
D Gouveia, A Chaumot, A Charnot, H Queau, J Armengaud, C Almunia, A Salvador, O Geffard
Recently, a protein sequence database was built specifically for the sentinel non-model species Gammarus fossarum using a proteogenomics approach. A quantitative multiplexed targeted proteomics assay (using Selected Reaction Monitoring mass spectrometry) was then developed for a fast and simultaneous quantification of dozens of biomarker peptides specific of this freshwater sentinel crustacean species. In order to assess the relevance of this breakthrough methodology in ecotoxicology, the response patterns of a panel of 26 peptides reporting for 20 proteins from the Gammarus fossarum proteome with putative key functional roles (homeostasis, osmoregulation, nutrition, reproduction, molting,…) were recorded through male and female reproductive cycles and after exposure to environmental concentrations of cadmium and lead in laboratory-controlled conditions...
September 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28747380/identification-of-differentially-expressed-splice-variants-by-the-proteogenomic-pipeline-splicify
#5
Malgorzata A Komor, Thang Pham, Annemieke C Hiemstra, Sander R Piersma, Anne S Bolijn, Tim Schelfhorst, Pien M Delis-van Diemen, Marianne Tijssen, Robert P Sebra, Meredith Ashby, Gerrit A Meijer, Connie R Jimenez, Remond J A Fijneman
Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. Splicify is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions...
July 26, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28734897/exploiting-helminth-host-interactomes-through-big-data
#6
REVIEW
Javier Sotillo, Rafael Toledo, Jason Mulvenna, Alex Loukas
Helminths facilitate their parasitic existence through the production and secretion of different molecules, including proteins. Some helminth proteins can manipulate the host's immune system, a phenomenon that is now being exploited with a view to developing therapeutics for inflammatory diseases. In recent years, hundreds of helminth genomes have been sequenced, but as a community we are still taking baby steps when it comes to identifying proteins that govern host-helminth interactions. The information generated from genomic, immunomic, and proteomic studies, as well as from cutting-edge approaches such as proteogenomics, is leading to a substantial volume of big data that can be utilised to shed light on fundamental biology and provide solutions for the development of bioactive-molecule-based therapeutics...
July 19, 2017: Trends in Parasitology
https://www.readbyqxmd.com/read/28733429/proteogenomic-analysis-and-discovery-of-immune-antigens-in-mycobacterium-vaccae
#7
Jianhua Zheng, Lihong Chen, Liguo Liu, Haifeng Li, Bo Liu, Dandan Zheng, Tao Liu, Jie Dong, Lilian Sun, Yafang Zhu, Jian Yang, Xiaobing Zhang, Qi Jin
Tuberculosis (TB) is one of the leading causes of death worldwide, especially in developing countries. Neonatal BCG vaccination occurs in various regions, but the level of protection varies in different populations. Recently, Mycobacterium vaccae is found to be an immunomodulating therapeutic agent that could confer a significant level of protection against TB. It is the only vaccine in a phase III trial from WHO to assess its efficacy and safety in preventing TB disease in people with latent TB infection. However, the mechanism of immunotherapy of M...
July 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28722704/targeted-proteomic-assays-for-quantitation-of-proteins-identified-by-proteogenomic-analysis-of-ovarian-cancer
#8
Ehwang Song, Yuqian Gao, Chaochao Wu, Tujin Shi, Song Nie, Thomas L Fillmore, Athena A Schepmoes, Marina A Gritsenko, Wei-Jun Qian, Richard D Smith, Karin D Rodland, Tao Liu
Mass spectrometry (MS) based targeted proteomic methods such as selected reaction monitoring (SRM) are emerging as a promising tool for verification of candidate proteins in biological and biomedical applications. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute has investigated the standardization and analytical validation of the SRM assays and demonstrated robust analytical performance on different instruments across different laboratories. An Assay Portal has also been established by CPTAC to provide the research community a resource consisting of large sets of targeted MS-based assays, and a depository to share assays publicly...
July 19, 2017: Scientific Data
https://www.readbyqxmd.com/read/28716134/detecting-protein-variants-by-mass-spectrometry-a-comprehensive-study-in-cancer-cell-lines
#9
Javier A Alfaro, Alexandr Ignatchenko, Vladimir Ignatchenko, Ankit Sinha, Paul C Boutros, Thomas Kislinger
BACKGROUND: Onco-proteogenomics aims to understand how changes in a cancer's genome influences its proteome. One challenge in integrating these molecular data is the identification of aberrant protein products from mass-spectrometry (MS) datasets, as traditional proteomic analyses only identify proteins from a reference sequence database. METHODS: We established proteomic workflows to detect peptide variants within MS datasets. We used a combination of publicly available population variants (dbSNP and UniProt) and somatic variations in cancer (COSMIC) along with sample-specific genomic and transcriptomic data to examine proteome variation within and across 59 cancer cell-lines...
July 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28693350/proteogenomics-approaches-for-studying-cancer-biology-and-their-potential-in-the-identification-of-acute-myeloid-leukemia-biomarkers
#10
Maria Hernandez-Valladares, Marc Vaudel, Frode Selheim, Frode Berven, Øystein Bruserud
Mass spectrometry (MS)-based proteomics has become an indispensable tool for the characterization of the proteome and its post-translational modifications (PTM). In addition to standard protein sequence databases, proteogenomics strategies search the spectral data against the theoretical spectra obtained from customized protein sequence databases. Up to date, there are no published proteogenomics studies on acute myeloid leukemia (AML) samples. Areas covered: Proteogenomics involves the understanding of genomic and proteomic data...
July 27, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28692290/top-down-atmospheric-ionization-mass-spectrometry-microscopy-combined-with-proteogenomics
#11
Cheng-Chih Hsu, Michael W Baker, Terry Gaasterland, Michael J Meehan, Eduardo R Macagno, Pieter C Dorrestein
Mass spectrometry-based protein analysis has become an important methodology for proteogenomic mapping by providing evidence for the existence of proteins predicted at the genomic level. However, screening and identification of proteins directly on tissue samples, where histological information is preserved, remain challenging. Here we demonstrate that the ambient ionization source, nanospray desorption electrospray ionization (nanoDESI), interfaced with light microscopy allows for protein profiling directly on animal tissues at the microscopic scale...
July 24, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28685163/sulfide-generation-by-dominant-halanaerobium-microorganisms-in-hydraulically-fractured-shales
#12
Anne E Booker, Mikayla A Borton, Rebecca A Daly, Susan A Welch, Carrie D Nicora, David W Hoyt, Travis Wilson, Samuel O Purvine, Richard A Wolfe, Shikha Sharma, Paula J Mouser, David R Cole, Mary S Lipton, Kelly C Wrighton, Michael J Wilkins
Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance of Halanaerobium strains within the in situ microbial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis...
July 2017: MSphere
https://www.readbyqxmd.com/read/28681360/intact-protein-analysis-at-21-tesla-and-x-ray-crystallography-define-structural-differences-in-single-amino-acid-variants-of-human-mitochondrial-branched-chain-amino-acid-aminotransferase-2-bcat2
#13
Lissa C Anderson, Maria Håkansson, Björn Walse, Carol L Nilsson
Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments...
July 5, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28665611/comprehensive-myocardial-proteogenomics-profiling-reveals-c-ebp%C3%AE-as-the-key-factor-in-the-lipid-storage-of-arvc
#14
Liang Chen, Fan Yang, Xiao Chen, Man Rao, Ning-Ning Zhang, Kai Chen, HaiTeng Deng, Jiang-Ping Song, Sheng-Shou Hu
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is hereditary cardiomyopathy characterized by the fibro-fatty replacement of the myocardium. A small number of noncomprehensive profiling studies based on human cardiac tissues have been conducted and reported; consequently, ARVC's gene expression pattern characteristics remain largely undocumented. Our study applies large-scaled, quantitative proteomics based on TMT-labeled LC-MS/MS to analyze the left and right ventricular myocardium of four ARVC and four DCM explanted hearts to compare them with normal hearts...
July 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28625833/colorectal-cancer-cell-line-proteomes-are-representative-of-primary-tumors-and-predict-drug-sensitivity
#15
Jing Wang, Dmitri Mouradov, Xiaojing Wang, Robert N Jorissen, Matthew C Chambers, Lisa J Zimmerman, Suhas Vasaikar, Christopher G Love, Shan Li, Kym Lowes, Karl-Johan Leuchowius, Helene Jousset, Janet Weinstock, Christopher Yau, John Mariadason, Zhiao Shi, Yuguan Ban, Xi Chen, Robert J C Coffey, Robbert J C Slebos, Antony W Burgess, Daniel C Liebler, Bing Zhang, Oliver M Sieber
BACKGROUND AND AIMS: Proteomics holds promise for individualizing cancer treatment. We analyzed to what extent the proteomic landscape of human colorectal cancer (CRC) is maintained in established CRC cell lines and the utility of proteomics for predicting therapeutic responses. METHODS: Proteomic and transcriptomic analyses were performed on 44 CRC cell lines, compared against primary CRCs (n=95) and normal tissues (n=60), and integrated with genomic and drug sensitivity data...
June 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28625053/annotation-of-the-domestic-pig-genome-by-quantitative-proteogenomics
#16
Harald Marx, Hannes Hahne, Susanne E Ulbrich, Angelika Schnieke, Oswald Rottmann, Dmitrij Frishman, Bernhard Kuster
The pig is one of the earliest domesticated animals in the history of human civilization and represents one of the most important livestock animals. The recent sequencing of the Sus scrofa genome was a major step toward the comprehensive understanding of porcine biology, evolution, and its utility as a promising large animal model for biomedical and xenotransplantation research. However, the functional and structural annotation of the Sus scrofa genome is far from complete. Here, we present mass spectrometry-based quantitative proteomics data of nine juvenile organs and six embryonic stages between 18 and 39 days after gestation...
June 29, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28607076/functional-proteogenomics-reveals-biomarkers-and-therapeutic-targets-in-lymphomas
#17
Delphine C M Rolland, Venkatesha Basrur, Yoon-Kyung Jeon, Carla McNeil-Schwalm, Damian Fermin, Kevin P Conlon, Yeqiao Zhou, Samuel Y Ng, Chih-Chiang Tsou, Noah A Brown, Dafydd G Thomas, Nathanael G Bailey, Gilbert S Omenn, Alexey I Nesvizhskii, David E Root, David M Weinstock, Robert B Faryabi, Megan S Lim, Kojo S J Elenitoba-Johnson
Identification of biomarkers and therapeutic targets is a critical goal of precision medicine. N-glycoproteins are a particularly attractive class of proteins that constitute potential cancer biomarkers and therapeutic targets for small molecules, antibodies, and cellular therapies. Using mass spectrometry (MS), we generated a compendium of 1,091 N-glycoproteins (from 40 human primary lymphomas and cell lines). Hierarchical clustering revealed distinct subtype signatures that included several subtype-specific biomarkers...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28600764/defining-diagnostic-biomarkers-using-shotgun-proteomics-and-maldi-tof-mass-spectrometry
#18
Jean Armengaud
Whole-cell MALDI-TOF has become a robust and widely used tool to quickly identify any pathogen. In addition to being routinely used in hospitals, it is also useful for low cost dereplication in large scale screening procedures of new environmental isolates for environmental biotechnology or taxonomical applications. Here, I describe how specific biomarkers can be defined using shotgun proteomics and whole-cell MALDI-TOF mass spectrometry. Based on MALDI-TOF spectra recorded on a given set of pathogens with internal calibrants, m/z values of interest are extracted...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28582591/a-tool-for-integrating-genetic-and-mass-spectrometry-based-peptide-data-proteogenomics-viewer-pv-a-genome-browser-like-tool-which-includes-ms-data-visualization-and-peptide-identification-parameters
#19
REVIEW
José Eduardo Kroll, Vandeclécio Lira da Silva, Sandro José de Souza, Gustavo Antonio de Souza
In this manuscript we describe Proteogenomics Viewer, a web-based tool that collects MS peptide identification, indexes to genomic sequence and structure, assigns exon usage, reports the identified protein isoforms with genomic alignments and, most importantly, allows the inspection of MS2 information for proper peptide identification. It also provides all performed indexing to facilitate global analysis of the data. The relevance of such tool is that there has been an increase in the number of proteogenomic efforts to improve the annotation of both genomics and proteomics data, culminating with the release of the two human proteome drafts...
June 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28573858/probamconvert-a-conversion-tool-for-probam-probed
#20
Volodimir Olexiouk, Gerben Menschaert
The introduction of new standard formats, proBAM and proBed, improves the integration of genomics and proteomics information, thus aiding proteogenomics applications. These novel formats enable peptide spectrum matches (PSM) to be stored, inspected, and analyzed within the context of the genome. However, an easy-to-use and transparent tool to convert mass spectrometry identification files to these new formats is indispensable. proBAMconvert enables the conversion of common identification file formats (mzIdentML, mzTab, and pepXML) to proBAM/proBed using an intuitive interface...
June 9, 2017: Journal of Proteome Research
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