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proteomics analysis tools

Kusum Mehla, Jayashree Ramana
Campylobacter jejuni remains a major cause of human gastroenteritis with estimated annual incidence rate of 450 million infections worldwide. C. jejuni is a major burden to public health in both socioeconomically developing and industrialized nations. Virulence determinants involved in C. jejuni pathogenesis are multifactorial in nature and not yet fully understood. Despite the completion of the first C. jejuni genome project in 2000, there are currently no vaccines in the market against this pathogen. Traditional vaccinology approach is an arduous and time extensive task...
October 24, 2016: Functional & Integrative Genomics
Allan M Showalter, Brian D Keppler, Xiao Liu, Jens Lichtenberg, Lonnie R Welch
BACKGROUND: Hydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development. This superfamily contains three members: the highly glycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). Chimeric and hybrid HRGPs, however, also exist. A bioinformatics approach is employed here to identify and classify AGPs, EXTs, PRPs, chimeric HRGPs, and hybrid HRGPs from the proteins predicted by the completed genome sequence of poplar (Populus trichocarpa)...
October 21, 2016: BMC Plant Biology
Ishfaq Ahmad Ganaie, Samar Husain Naqvi, Swatantra Kumar Jain, Saima Wajid
Breast cancer is a major global health concern, appealing for precise prognostic approaches. Thus, the need is to have studies focusing on the identification and recognition of preliminary events leading to the disease. The present study reports the tracing of precancerous progression and serum proteomic analysis in a breast cancer model developed as a result of 7,12-dimethylbenz[a]anthracene (DMBA) administration. Mammary gland histological changes of prime importance were examined by histopathology, and immunohistochemical analysis with Ki-67 was performed to monitor enhanced cell proliferation, right from the onset of hyperplasia till neoplasia...
October 20, 2016: Protoplasma
Vincenzo Sannino, Arun M Kolinjivadi, Giorgio Baldi, Vincenzo Costanzo
The correct duplication of genetic information is essential to maintain genome stability, which is lost in cancer cells. Replication fork integrity is ensured by a number of DNA metabolism proteins that assist replication of chromatin regions difficult to replicate due to their intrinsic DNA sequence composition, coordinate repair of DNA molecules resulting from aberrant replication events or protect replication forks in the presence of lesions impairing their progression. Some DNA metabolism genes involved in DNA repair are essential in higher eukaryotes even in unchallenged conditions, suggesting the existence of biological processes requiring these specialized functions in organisms with complex genomes...
2016: International Journal of Developmental Biology
Blaz Skrlj, Tanja Kunej
BACKGROUND: Protein-protein interactions (PPI) play an important role in function of all organisms and enable understanding of underlying metabolic processes. Computational predictions of PPIs are an important aspect in proteomics, as experimental methods may result in high degree of false positive results and are more expensive. Although there are many databases collecting predicted PPIs, exploration of genetics information underlying PPI interactions has not been investigated thoroughly...
October 4, 2016: Computers in Biology and Medicine
Sophie Braga-Lagache, Natasha Buchs, Mircea-Ioan Iacovache, Benoit Zuber, Christopher Benjamin Jackson, Manfred Heller
BACKGROUND: Cells of the vascular system release spherical vesicles, called microparticles, in the size range of 0.1-1μm induced by a variety of stress factors resulting in variable concentrations between health and disease. Furthermore, microparticles have intercellular communication/signaling properties and interfere with inflammation and coagulation pathways. Today's most used analytical technology for mecroparticle characterization, flow cytometry, is lacking sensitivity and specificity, which might have led to the publication of contradicting results in the past...
October 12, 2016: Molecular & Cellular Proteomics: MCP
Vishal Kumar, Mehak Baweja, Puneet K Singh, Pratyoosh Shukla
Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant-microbe interactions using gene editing and system biology tools toward the comprehension in improvement of plant traits...
2016: Frontiers in Plant Science
Ulises Carrasco-Navarro, Rosario Vera-Estrella, Bronwyn J Barkla, Eduardo Zúñiga-León, Horacio Reyes-Vivas, Francisco J Fernández, Francisco Fierro
BACKGROUND: The heterotrimeric Gα protein Pga1-mediated signaling pathway regulates the entire developmental program in Penicillium chrysogenum, from spore germination to the formation of conidia. In addition it participates in the regulation of penicillin biosynthesis. We aimed to advance the understanding of this key signaling pathway using a proteomics approach, a powerful tool to identify effectors participating in signal transduction pathways. RESULTS: Penicillium chrysogenum mutants with different levels of activity of the Pga1-mediated signaling pathway were used to perform comparative proteomic analyses by 2D-DIGE and LC-MS/MS...
October 6, 2016: Microbial Cell Factories
Long Pei, Min Xu, Zachary Frazier, Frank Alber
BACKGROUND: Cryo-electron tomography is an important tool to study structures of macromolecular complexes in close to native states. A whole cell cryo electron tomogram contains structural information of all its macromolecular complexes. However, extracting this information remains challenging, and relies on sophisticated image processing, in particular for template-free particle extraction, classification and averaging. To develop these methods it is crucial to realistically simulate tomograms of crowded cellular environments, which can then serve as ground truth models for assessing and optimizing methods for detection of complexes in cell tomograms...
October 5, 2016: BMC Bioinformatics
Christopher S Hughes, Melissa K McConechy, Dawn R Cochrane, Tayyebeh Nazeran, Anthony N Karnezis, David G Huntsman, Gregg B Morin
Although re-sequencing of gene panels and mRNA expression profiling are now firmly established in clinical laboratories, in-depth proteome analysis has remained a niche technology, better suited for studying model systems rather than challenging materials such as clinical trial samples. To address this limitation, we have developed a novel and optimized platform called SP3-Clinical Tissue Proteomics (SP3-CTP) for in-depth proteome profiling of practical quantities of tumour tissues, including formalin fixed and paraffin embedded (FFPE)...
October 7, 2016: Scientific Reports
Han Liu, Bosheng Chen, Sirui Hu, Xili Liang, Xingmeng Lu, Yongqi Shao
The microsporidian Nosema bombycis is an obligate intracellular pathogen of the silkworm Bombyx mori, causing the epidemic disease Pebrine and extensive economic losses in sericulture. Although N. bombycis forms spores with rigid spore walls that protect against various environmental pressures, ingested spores germinate immediately under the extremely alkaline host gut condition (Lepidoptera gut pH > 10.5), which is a key developmental turning point from dormant state to infected state. However, to date this process remains poorly understood due to the complexity of the animal digestive tract and the lack of genetic tools for microsporidia...
2016: Frontiers in Microbiology
Pedro Navarro, Jörg Kuharev, Ludovic C Gillet, Oliver M Bernhardt, Brendan MacLean, Hannes L Röst, Stephen A Tate, Chih-Chiang Tsou, Lukas Reiter, Ute Distler, George Rosenberger, Yasset Perez-Riverol, Alexey I Nesvizhskii, Ruedi Aebersold, Stefan Tenzer
Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification...
October 3, 2016: Nature Biotechnology
Kathrin Elisabeth Witzke, Kristin Rosowski, Christian Müller, Maike Ahrens, Martin Eisenacher, Dominik A Megger, Jürgen Knobloch, Andrea R Koch, Thilo Bracht, Barbara Sitek
Quantitative secretome analyses are a high-performance tool for the discovery of physiological and pathophysiological changes in cellular processes. However, serum supplements in cell culture media limit secretome analyses, but serum depletion often leads to cell starvation and consequently biased results. To overcome these limiting factors, we investigated a model of T cell activation (Jurkat cells) and performed an approach for the selective enrichment of secreted proteins from conditioned medium utilizing metabolic marking of newly synthesized glycoproteins...
October 3, 2016: Journal of Proteome Research
Olga Levin-Kravets, Neta Tanner, Noa Shohat, Ilan Attali, Tal Keren-Kaplan, Anna Shusterman, Shay Artzi, Alexander Varvak, Yael Reshef, Xiaojing Shi, Ori Zucker, Tamir Baram, Corine Katina, Inbar Pilzer, Shay Ben-Aroya, Gali Prag
About one-third of the eukaryotic proteome undergoes ubiquitylation, but the enzymatic cascades leading to substrate modification are largely unknown. We present a genetic selection tool that utilizes Escherichia coli, which lack deubiquitylases, to identify interactions along ubiquitylation cascades. Coexpression of split antibiotic resistance protein tethered to ubiquitin and ubiquitylation target together with a functional ubiquitylation apparatus results in a covalent assembly of the resistance protein, giving rise to bacterial growth on selective media...
October 3, 2016: Nature Methods
Dhirendra Kumar, Debasis Dash
Proteogenomic strategies aim to refine genome-wide annotations of protein coding features by using actual protein level observations. Most of the currently applied proteogenomic approaches include integrative analysis of multiple types of high-throughput omics data, e.g., genomics, transcriptomics, proteomics, etc. Recent efforts towards creating a human proteome map were primarily targeted to experimentally detect at least one protein product for each gene in the genome and extensively utilized proteogenomic approaches...
2016: Advances in Experimental Medicine and Biology
Bensu Karahalil
Traditional technologies using reductionist approach are relatively insufficient to solve problems in a biological system. Rather than a reductionist approach, system biology uses a holistic and integrative approach to better figure out the whole process. Both qualitatively and quantitatively of biological system provide information about diseases, toxicities, therapies etc. Omics technologies, which system biology bring, are valuable tools for comprehensive analyses. Automated DNA sequencers enabled the sequencing of genomes; microarray and mass spectrometry analysis permit global transcriptional profiling and lead to large-scale proteomic and metabolomics analysis...
September 26, 2016: Current Medicinal Chemistry
Alexia Kakourou, Werner Vach, Simone Nicolardi, Yuri van der Burgt, Bart Mertens
Mass spectrometry based clinical proteomics has emerged as a powerful tool for high-throughput protein profiling and biomarker discovery. Recent improvements in mass spectrometry technology have boosted the potential of proteomic studies in biomedical research. However, the complexity of the proteomic expression introduces new statistical challenges in summarizing and analyzing the acquired data. Statistical methods for optimally processing proteomic data are currently a growing field of research. In this paper we present simple, yet appropriate methods to preprocess, summarize and analyze high-throughput MALDI-FTICR mass spectrometry data, collected in a case-control fashion, while dealing with the statistical challenges that accompany such data...
October 1, 2016: Statistical Applications in Genetics and Molecular Biology
Brent M Kuenzi, Adam L Borne, Jiannong Li, Eric B Haura, Steven A Eschrich, John M Koomen, Uwe Rix, Paul A Stewart
With continuously increasing scale and depth of coverage in affinity proteomics (AP-MS) data, the analysis and visualization is becoming more challenging. A number of tools have been developed to identify high-confidence interactions; however, a cohesive and intuitive pipeline for analysis and visualization is still needed. Here we present Automated Processing of SAINT Templated Layouts (APOSTL), a freely available Galaxy-integrated software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data...
October 21, 2016: Journal of Proteome Research
W Niżański, A Partyka, S Prochowska
Conventional microscopic semen analysis does not provide precise information on the fertilizing potential of a male. The traditional basis for semen evaluation is that male fertility is dependent on production of a "proper" concentration/number of motile, morphologically normal spermatozoa in excess to achieve conception. Many independent studies, especially in human medicine, have demonstrated that the absolute number of spermatozoa does not accurately determine fertility, but their functional competence. Many functional tests of spermatozoa are developed over the last decades...
September 2016: Reproduction in Domestic Animals, Zuchthygiene
Jonathan A Stefely, Nicholas W Kwiecien, Elyse C Freiberger, Alicia L Richards, Adam Jochem, Matthew J P Rush, Arne Ulbrich, Kyle P Robinson, Paul D Hutchins, Mike T Veling, Xiao Guo, Zachary A Kemmerer, Kyle J Connors, Edna A Trujillo, Jacob Sokol, Harald Marx, Michael S Westphall, Alexander S Hebert, David J Pagliarini, Joshua J Coon
Mitochondrial dysfunction is associated with many human diseases, including cancer and neurodegeneration, that are often linked to proteins and pathways that are not well-characterized. To begin defining the functions of such poorly characterized proteins, we used mass spectrometry to map the proteomes, lipidomes, and metabolomes of 174 yeast strains, each lacking a single gene related to mitochondrial biology. 144 of these genes have human homologs, 60 of which are associated with disease and 39 of which are uncharacterized...
September 26, 2016: Nature Biotechnology
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