keyword
MENU ▼
Read by QxMD icon Read
search

proteogenomics

keyword
https://www.readbyqxmd.com/read/28898539/plant-proteogenomics-improvements-to-the-grapevine-genome-annotation
#1
Brett Chapman, Matthew Bellgard
Grapevine is an important perennial fruit to the wine industry, and has implications for the health industry with some causative agents proven to reduce heart disease. Since the sequencing and assembly of grapevine cultivar Pinot Noir, several studies have contributed to its genome annotation. This new study further contributes towards genome annotation efforts by conducting a proteogenomics analysis using the latest genome annotation from CRIBI, legacy proteomics dataset from cultivar Cabernet Sauvignon and a large RNA-seq dataset...
September 12, 2017: Proteomics
https://www.readbyqxmd.com/read/28869791/proteogenomic-insights-into-the-intestinal-parasite-blastocystis-sp-subtype-4-isolate-wr1
#2
Jean Armengaud, Olivier Pible, Jean-Charles Gaillard, Amandine Cian, Nausicaa Gantois, Kevin S W Tan, Magali Chabé, Eric Viscogliosi
Blastocystis sp. is known for years as a highly prevalent anaerobic eukaryotic parasite of humans and animals. Several monophyletic clades have been delineated based on molecular data and the occurrence of each subtype (ST) in humans and/or animal hosts has been documented. The genome of several representatives has been sequenced revealing specific traits such as an intriguing 3'-end processing of primary transcripts. Here, a first high-throughput proteomics dataset acquired on this difficult to cultivate parasite is presented for the zoonotic ST4 isolate WR1...
September 4, 2017: Proteomics
https://www.readbyqxmd.com/read/28867676/a-varroa-destructor-protein-atlas-reveals-molecular-underpinnings-of-developmental-transitions-and-sexual-differentiation
#3
Alison McAfee, Queenie Chan, Jay Evans, Leonard J Foster
Varroa destructor is the most economically damaging honey bee pest, weakening colonies by simultaneously parasitizing bees and transmitting harmful viruses. Despite these impacts on honey bee health, surprisingly little is known about its fundamental molecular biology. Here we present a Varroa protein atlas crossing all major developmental stages (egg, protonymph, deutonymph and adult) for both male and female mites as a web-based interactive tool (http://foster.nce.ubc.ca/varroa/index.html). We used intensity-based label-free quantitation to find 1,433 differentially expressed proteins across developmental stages...
September 3, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28830566/the-ninth-enbdc-weggis-meeting-growth-and-in-depth-characterisation-of-normal-and-neoplastic-breast-cells
#4
Katrin E Wiese, Romain J Amante, Maria dM Vivanco, Mohamed Bentires-Alj, Richard D Iggo
Mammary gland biologists gathered for the ninth annual workshop of the European Network for Breast Development and Cancer (ENBDC) at Weggis on the shores of Lake Lucerne in March 2017. The main themes were oestrogen receptor alpha signalling, new techniques for mammary cell culture, CRISPR screening and proteogenomics.
August 22, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28823056/exploiting-non-canonical-translation-to-identify-new-targets-for-t-cell-based-cancer-immunotherapy
#5
REVIEW
Céline M Laumont, Claude Perreault
Cryptic MHC I-associated peptides (MAPs) are produced via two mechanisms: translation of protein-coding genes in non-canonical reading frames and translation of allegedly non-coding sequences. In general, cryptic MAPs are coded by relatively short open reading frames whose translation can be regulated at the level of initiation, elongation or termination. In contrast to conventional MAPs, the processing of cryptic MAPs is frequently proteasome independent. The existence of cryptic MAPs derived from allegedly non-coding regions enlarges the scope of CD8 T cell immunosurveillance from a mere ~2% to as much as ~75% of the human genome...
August 19, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28820946/proteogenomic-investigation-of-strain-variation-in-clinical-mycobacterium-tuberculosis-isolates
#6
Tiaan Heunis, Anzaan Dippenaar, Robin M Warren, Paul D van Helden, Ruben G van der Merwe, Nicolaas C Gey van Pittius, Arnab Pain, Samantha L Sampson, David L Tabb
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M...
August 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28814272/identification-of-new-protein-coding-genes-with-a-potential-role-in-the-virulence-of-the-plant-pathogen-xanthomonas-euvesicatoria
#7
Ulrike Abendroth, Norman Adlung, Andreas Otto, Benjamin Grüneisen, Dörte Becher, Ulla Bonas
BACKGROUND: Bacteria of the genus Xanthomonas are economically important plant pathogens. Pathogenicity of Xanthomonas spp. depends on the type III-secretion system and additional virulence determinants. The number of sequenced Xanthomonas genomes increases rapidly, however, accurate annotation of these genomes is difficult, because it relies on gene prediction programs. In this study, we used a mass-spectrometry (MS)-based approach to identify the proteome of Xanthomonas euvesicatoria (Xe) strain 85-10 also known as X...
August 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28800136/feathermoss-and-epiphytic-nostoc-cooperate-differently-expanding-the-spectrum-of-plant-cyanobacteria-symbiosis
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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...
September 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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
116770
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"