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https://www.readbyqxmd.com/read/29141959/an-integrative-strategy-to-identify-the-entire-protein-coding-potential-of-prokaryotic-genomes-by-proteogenomics
#1
Ulrich Omasits, Adithi R Varadarajan, Michael Schmid, Sandra Goetze, Damianos Melidis, Marc Bourqui, Olga Nikolayeva, Maxime Québatte, Andrea Patrignani, Christoph Dehio, Juerg E Frey, Mark D Robinson, Bernd Wollscheid, Christian H Ahrens
Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome...
November 15, 2017: Genome Research
https://www.readbyqxmd.com/read/29132314/proteomics-in-non-human-primates-utilizing-rna-seq-data-to-improve-protein-identification-by-mass-spectrometry-in-vervet-monkeys
#2
J Michael Proffitt, Jeremy Glenn, Anthony J Cesnik, Avinash Jadhav, Michael R Shortreed, Lloyd M Smith, Kylie Kavanagh, Laura A Cox, Michael Olivier
BACKGROUND: Shotgun proteomics utilizes a database search strategy to compare detected mass spectra to a library of theoretical spectra derived from reference genome information. As such, the robustness of proteomics results is contingent upon the completeness and accuracy of the gene annotation in the reference genome. For animal models of disease where genomic annotation is incomplete, such as non-human primates, proteogenomic methods can improve the detection of proteins by incorporating transcriptional data from RNA-Seq to improve proteomics search databases used for peptide spectral matching...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29130603/proteogenomic-re-annotation-of-coccidioides-posadasii-strain-silveira
#3
Natalie M Mitchell, Andrew L Sherrard, Surendra Dasari, D Mitchell Magee, Thomas E Grys, Douglas F Lake
The aims of this study were to provide protein-based evidence upon which to re-annotate of the genome of C. posadasii, one of two closely related species of Coccidioides, a dimorphic fungal pathogen that causes coccidioidomycosis, also called Valley Fever. Proteins present in lysates and filtrates of in vitro grown mycelia and parasitic phase spherules from C. posadasii strain Silveira were analyzed using a GeLC-MS/MS method. Acquired spectra were processed with a proteogenomics workflow comprising a Silveira proteome database, a 6-frame translation of the Silveira genome and an ab initio gene prediction tool prior to validation against published ESTs...
November 12, 2017: Proteomics
https://www.readbyqxmd.com/read/29092937/an-accessible-proteogenomics-informatics-resource-for-cancer-researchers
#4
Matthew C Chambers, Pratik D Jagtap, James E Johnson, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Candace R Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, Björn Grüning, Ira R Cooke, Mohammad Heydarian, Karen L Reddy, Timothy J Griffin
Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry-based proteomics data to directly identify expressed, variant protein sequences that may have functional roles in cancer. This approach is computationally intensive, requiring integration of disparate software tools into sophisticated workflows, challenging its adoption by nonexpert, bench scientists. To address this need, we have developed an extensible, Galaxy-based resource aimed at providing more researchers access to, and training in, proteogenomic informatics...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29077059/network-driven-proteogenomics-unveils-an-aging-related-imbalance-in-the-olfactory-i%C3%AE%C2%BAb%C3%AE-nf%C3%AE%C2%BAb-p65-complex-functionality-in-tg2576-alzheimer-s-disease-mouse-model
#5
Maialen Palomino-Alonso, Mercedes Lachén-Montes, Andrea González-Morales, Karina Ausín, Alberto Pérez-Mediavilla, Joaquín Fernández-Irigoyen, Enrique Santamaría
Olfaction is often deregulated in Alzheimer's disease (AD) patients, and is also impaired in transgenic Tg2576 AD mice, which overexpress the Swedish mutated form of human amyloid precursor protein (APP). However, little is known about the molecular mechanisms that accompany the neurodegeneration of olfactory structures in aged Tg2576 mice. For that, we have applied proteome- and transcriptome-wide approaches to probe molecular disturbances in the olfactory bulb (OB) dissected from aged Tg2576 mice (18 months of age) as compared to those of age matched wild-type (WT) littermates...
October 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29068423/comprehensive-analysis-of-cancer-proteogenome-to-identify-biomarkers-for-the-early-diagnosis-and-prognosis-of-cancer
#6
REVIEW
Hem D Shukla
During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it has steered us into therapeutic target discovery, enabling us to mine the genome using cutting edge proteogenomics tools. A number of novel and promising cancer targets have emerged from the genome project for diagnostics, therapeutics, and prognostic markers, which are being used to monitor response to cancer treatment...
October 25, 2017: Proteomes
https://www.readbyqxmd.com/read/29062388/highlights-from-the-win-2017-symposium-26-27-june-2017-paris-france-expediting-global-innovation-in-precision-cancer-medicine
#7
Will Davies
The Worldwide Innovative Networking (WIN) symposium brings together representatives from academic institutions, pharmaceutical partners, technology companies and charitable organisations from across the globe for an annual summit, discussing ongoing research and the latest developments in precision medicine. Now, in its seventh year, the aims of the WIN consortium's annual meeting, to foster communication and collaboration between members and deliver clinical trial results that improve the care and outcomes of patients are presented in open dialogue to encourage debate and discussion...
2017: Ecancermedicalscience
https://www.readbyqxmd.com/read/29059504/intersection-of-proteomics-and-genomics-to-solve-the-unsolved-in-rare-disorders-such-as-neurodegenerative-and-neuromuscular-diseases
#8
Andreas Roos, Rachel Thompson, Rita Horvath, Hanns Lochmüller, Albert Sickmann
Despite recent rapid advances in sequencing technologies, a significant proportion of patients with rare genetic disorders do not receive a genetic diagnosis after exhaustive testing, and even fewer have a potential therapeutic target identified. Taking rare neuromuscular and neurodegenerative disorders as a paradigm that can be extended to other rare Mendelian disorders, this viewpoint explores the opportunities that are brought about by the integration of genomics and proteomics, as well as the limitations and remaining challenges of this newly emerging field of proteogenomics...
October 23, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29046389/the-antibody-repertoire-of-colorectal-cancer
#9
Seong Won Cha, Stefano Bonissone, Seungjin Na, Pavel A Pevzner, Vineet Bafna
Immunotherapy is becoming increasingly important in the fight against cancers, utilizing and manipulating the body's immune response to treat tumors. Understanding the immune repertoire - the collection of immunological proteins - of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to missed identifications in a mass spectrometry search...
October 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29039718/current-status-of-proteomics-of-soft-tissue-sarcomas
#10
Tadashi Kondo
Proteomics has been used in soft tissue sarcoma (STS) research in the attempts to improve the understanding of the disease background and develop novel clinical applications. Using various proteomics modalities, aberrant regulations of numerous intriguing proteins were identified in STSs, and the possible utilities of identified proteins as biomarkers or therapeutic targets have been explored. STS is an exceptionally diverse group of malignant diseases with highly complex molecular backgrounds and, therefore, an overview of the achievements and prospects of STS proteomics could enhance our knowledge of the possibilities and limitations of cancer proteomics...
October 17, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29025326/onco-proteogenomics-multi-omics-level-data-integration-for-accurate-phenotype-prediction
#11
Lampros Dimitrakopoulos, Ioannis Prassas, Eleftherios P Diamandis, George S Charames
The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype...
October 12, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29019919/proteogenomics-in-aid-of-host-pathogen-interaction-studies-a-bacterial-perspective
#12
REVIEW
Ursula Fels, Kris Gevaert, Petra Van Damme
By providing useful tools to study host-pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, the depth of quantitative gene expression profiling has proven to be unsatisfactory when focusing on bacterial pathogens, thus preferentially requiring specific strategies or the development of novel methodologies based on complementary omics approaches...
October 11, 2017: Proteomes
https://www.readbyqxmd.com/read/28994197/in-vino-veritas-an-invitation-for-ambitious-collaborative-proteogenomics-campaigns-on-plant-and-animal-models
#13
Jean Armengaud
Vitis vinifera has been an emblematic plant for Humans since the Neolithic period. Human civilization has been shaped by its domestication as both its medicinal and nutritional values were exploited. It is now cultivated on all habitable continents, and more than 5 thousand varieties have been developed. A global passion for the art of wine fuels innovation and a profound desire for knowledge on this plant. The genome sequence of a homozygotic cultivar and several RNA-seq datasets on other varieties have been released paving the way to gaining further insight into its biology and tailoring improvements to varieties...
October 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28990322/proteogenomics-gets-onto-the-regulation-of-mrna-decoding-and-translation-into-protein
#14
Hubert Hondermarck
Proteogenomics, the integrative analysis of the proteome and the genome, increasingly provides protein-level insights about the regulation of gene expression and protein translation. Armengaud et al. (Proteomics 2017. volume, pages) nicely illustrate this trend with the first in depth proteomic analysis of the eukaryotic and unicellular intestinal parasite Blastocystis sp. Not only this work constitutes an important milestone towards the proteogenomics profile of this human pathogen, but also it demonstrates at the protein level the occurrence of a specific mechanism of mRNA decoding...
October 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28960081/a-systematic-proteogenomic-approach-to-exploring-a-novel-function-for-nherf1-in-human-reproductive-disorder-lessons-for-exploring-missing-proteins
#15
Keun Na, Heon Shin, Jin-Young Cho, Sang Hee Jung, Jaeseung Lim, Jong-Sun Lim, Eun Ah Kim, Hye Sun Kim, Ah Reum Kang, Ji Hye Kim, Jeong Min Shin, Seul-Ki Jeong, Chae-Yeon Kim, Jun Young Park, Hyung-Min Chung, Gilbert S Omenn, William S Hancock, Young-Ki Paik
One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to fill the knowledge gaps between human genomic information and the corresponding proteomic information. These gaps are due to "missing" proteins (MPs)-predicted proteins with insufficient evidence from mass spectrometry (MS), biochemical, structural or antibody analyses-that currently account for 2,579 of the 20,159 predicted human proteins (neXtProt, 2017-02). We address some of the lessons learned from the inconsistent annotations of missing proteins in databases (DB) and demonstrate a systematic proteogenomic approach designed to explore a potential new function of a known protein...
September 29, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28933279/zinc-transporter-protein-tzn-1-may-also-play-a-role-in-conidiation-pathway-of-neurospora-crassa-an-insight-using-proteogenomic-approach
#16
Divya Rupa Venkata Pandala, Jogeswar Gadi, Kiranmayi Patnala
Zinc transporter (tzn-1) of Neurospora crassa plays a crucial role in conidiation pathway, as its removal results in aconidiation which was reported in our earlier studies. Present study depicts the role of tzn-1 in conidiation process, by comparing knockout (KO) mutants zinc transporter KO (Δtzn-1) and aconidiating gene KO (Δacon-3) with wild oak ridge (OR) 74 'A' strain by 'Proteo-genomic' approach. Firstly, nine commonly overexpressed protein spots from the two sets (Δtzn-1 to wild and Δacon-3 to wild) were analyzed by combining 2-Dimensional gel electrophoresis (2DE) with Matrix Associated Laser Desorption/Ionization mass spectrometry -Peptide Mass Fingerprint (MALDI-PMF)...
September 19, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28898539/plant-proteogenomics-improvements-to-the-grapevine-genome-annotation
#17
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 toward 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
#18
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 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 subtype T4 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
#19
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
#20
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
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