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proteomics and visualization

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https://www.readbyqxmd.com/read/28092651/long-lasting-antinociceptive-effects-of-green-light-in-acute-and-chronic-pain-in-rats
#1
Mohab M Ibrahim, Amol Patwardhan, Kerry B Gilbraith, Aubin Moutal, Xiaofang Yang, Lindsey A Chew, Tally Largent-Milnes, T Philip Malan, Todd W Vanderah, Frank Porreca, Rajesh Khanna
Treatments for chronic pain are inadequate, and new options are needed. Nonpharmaceutical approaches are especially attractive with many potential advantages including safety. Light therapy has been suggested to be beneficial in certain medical conditions such as depression, but this approach remains to be explored for modulation of pain. We investigated the effects of light-emitting diodes (LEDs), in the visible spectrum, on acute sensory thresholds in naive rats as well as in experimental neuropathic pain...
February 2017: Pain
https://www.readbyqxmd.com/read/28092030/proteomic-clustering-analysis-of-sh2-domain-datasets
#2
Karl Jablonowski
Proteomic clustering analysis provides a means of identifying relationships and visualizing those relationships in an extremely complex field of study with many interacting parts. With recent high-throughput studies of Src Homology 2 (SH2) domains, many and varied datasets are being amassed. A strategy for analyzing patterns between these large datasets is required to transform the information into knowledge. The methods for creating neighbor-joining phylogenetic trees, pairs scatter plots, and two-dimensional hierarchical clustering heatmaps are just a few of the diverse methods available to a proteomic researcher...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28065881/an-integrated-transcriptomics-guided-genome-wide-promoter-analysis-and-next-generation-proteomics-approach-to-mine-factor-s-regulating-cellular-differentiation
#3
Kamal Mandal, Samuel L Bader, Pankaj Kumar, Dipankar Malakar, David S Campbell, Bhola Shankar Pradhan, Rajesh K Sarkar, Neerja Wadhwa, Souvik Sensharma, Vaibhav Jain, Robert L Moritz, Subeer S Majumdar
Differential next-generation-omics approaches aid in the visualization of biological processes and pave the way for divulging important events and/or interactions leading to a functional output at cellular or systems level. To this end, we undertook an integrated Nextgen transcriptomics and proteomics approach to divulge differential gene expression of infant and pubertal rat Sertoli cells (Sc).Unlike, pubertal Sc, infant Sc are immature and fail to support spermatogenesis. We found exclusive association of 14 and 19 transcription factor binding sites to infantile and pubertal states of Sc, respectively, using differential transcriptomics-guided genome-wide computational analysis of relevant promoters employing 220 Positional Weight Matrices from the TRANSFAC database...
January 8, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28063280/principles-of-protein-structural-ensemble-determination
#4
REVIEW
Massimiliano Bonomi, Gabriella T Heller, Carlo Camilloni, Michele Vendruscolo
The biological functions of protein molecules are intimately dependent on their conformational dynamics. This aspect is particularly evident for disordered proteins, which constitute perhaps one-third of the human proteome. Therefore, structural ensembles often offer more useful representations of proteins than individual conformations. Here, we describe how the well-established principles of protein structure determination should be extended to the case of protein structural ensembles determination. These principles concern primarily how to deal with conformationally heterogeneous states, and with experimental measurements that are averaged over such states and affected by a variety of errors...
January 4, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28043508/proteome-scale-mdr-tb-antibody-responses-for-identification-of-putative-biomarkers-for-the-diagnosis-of-drug-resistant-mycobacterium-tuberculosis
#5
Shamsi Yari, Alireza Hadizadeh Tasbiti, Mostafa Ghanei, Seyed Davar Siadat, Fatemeh Yari, A Bahrmand
OBJECTIVE: Multidrug-resistant tuberculosis (MDR-TB) is caused by Mycobacterium tuberculosis strains that do not respond to isoniazid and rifampicin, the two most effective first-line anti-TB drugs. Here, we designed and produced antibodies based on biomarkers that exist only in MDR-TB. METHODS: Bacilli were cultured for 4weeks at 37°C, and protein extraction was performed by sequential extraction. Bacterial cells were sonicated, centrifuged at 5000rpm for 45min, and the supernatant was collected and subjected to multiple rounds of treatment to prior to protein isolation...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28025338/tbro-visualization-and-management-of-de-novo-transcriptomes
#6
Markus J Ankenbrand, Lorenz Weber, Dirk Becker, Frank Förster, Felix Bemm
RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28011752/visualizing-and-comparing-results-of-different-peptide-identification-methods
#7
Yassene Mohammed, Magnus Palmblad
In mass spectrometry-based proteomics, peptides are typically identified from tandem mass spectra using spectrum comparison. A sequence search engine compares experimentally obtained spectra with those predicted from protein sequences, applying enzyme cleavage and fragmentation rules. To this, there are two main alternatives: spectral libraries and de novo sequencing. The former compares measured spectra with a collection of previously acquired and identified spectra in a library. De novo attempts to sequence peptides from the tandem mass spectra alone...
December 22, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27975292/network-tools-for-the-analysis-of-proteomic-data
#8
David Chisanga, Shivakumar Keerthikumar, Suresh Mathivanan, Naveen Chilamkurti
Recent advancements in high-throughput technologies such as mass spectrometry have led to an increase in the rate at which data is generated and accumulated. As a result, standard statistical methods no longer suffice as a way of analyzing such gigantic amounts of data. Network analysis, the evaluation of how nodes relate to one another, has over the years become an integral tool for analyzing high throughput proteomic data as they provide a structure that helps reduce the complexity of the underlying data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27975220/visualization-inspection-and-interpretation-of-shotgun-proteomics-identification-results
#9
Ragnhild R Lereim, Eystein Oveland, Frode S Berven, Marc Vaudel, Harald Barsnes
Shotgun proteomics is a high throughput technique for protein identification able to identify up to several thousand proteins from a single sample. In order to make sense of this large amount of data, proteomics analysis software is needed, aimed at making the data intuitively accessible to beginners as well as experienced scientists. This chapter provides insight on where to start when analyzing shotgun proteomics data, with a focus on explaining the most common pitfalls in protein identification analysis and how to avoid them...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27943495/the-mitochondrial-complexome-of-arabidopsis-thaliana
#10
Jennifer Senkler, Michael Senkler, Holger Eubel, Tatjana Hildebrandt, Christian Lengwenus, Peter Schertl, Markus Schwarzländer, Stephan Wagner, Ilka Wittig, Hans-Peter Braun
Mitochondria are central to cellular metabolism and energy conversion. In plants they also enable photosynthesis through additional components and functional flexibility. A majority of those processes rely on the assembly of individual proteins to larger protein complexes, some of which operate as large molecular machines. There has been a strong interest in the makeup and function of mitochondrial protein complexes and protein-protein interactions in plants, but the experimental approaches used typically suffer from selectivity or bias...
December 10, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27940385/proteomic-analysis-reveals-contrasting-stress-response-to-uranium-in-two-nitrogen-fixing-anabaena-strains-differentially-tolerant-to-uranium
#11
COMPARATIVE STUDY
Bandita Panda, Bhakti Basu, Celin Acharya, Hema Rajaram, Shree Kumar Apte
: Two strains of the nitrogen-fixing cyanobacterium Anabaena, native to Indian paddy fields, displayed differential sensitivity to exposure to uranyl carbonate at neutral pH. Anabaena sp. strain PCC 7120 and Anabaena sp. strain L-31 displayed 50% reduction in survival (LD50 dose), following 3h exposure to 75μM and 200μM uranyl carbonate, respectively. Uranium responsive proteome alterations were visualized by 2D gel electrophoresis, followed by protein identification by MALDI-ToF mass spectrometry...
January 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/27935040/network-based-characterization-of-the-synaptic-proteome-reveals-that-removal-of-epigenetic-regulator-prmt8-restricts-proteins-associated-with-synaptic-maturation
#12
Patrick Kia Ming Lee, Wilson Wen Bin Goh, Judy Chia Ghee Sng
The brain adapts to dynamic environmental conditions by altering its epigenetic state, thereby influencing neuronal transcriptional programs. An example of an epigenetic modification is protein methylation, catalyzed by protein arginine methyltransferases (PRMT). One member, Prmt8, is selectively expressed in the central nervous system during a crucial phase of early development, but little else is known regarding its function. We hypothesize Prmt8 plays a role in synaptic maturation during development. To evaluate this, we used a proteome-wide approach to characterize the synaptic proteome of Prmt8 knockout versus wildtype mice...
December 9, 2016: Journal of Neurochemistry
https://www.readbyqxmd.com/read/27924301/data-on-the-identity-of-non-canonical-complexes-formed-from-proteasome-subunits-in-vivo
#13
Lindsay J Hammack, Andrew R Kusmierczyk
The dataset presented here represents analysis supplied by the local proteomics core facility on samples submitted to it in support of the article "Assembly of proteasome subunits into non-canonical complexes in vivo" Hammack and Kusmierczyk (2016) [1]. This article provides the detailed protein contents of gel slices, cut from non-denaturing polyacrylamide gels, containing distinct protein complexes visualized following gel staining. The identification of the protein contents of these complexes was carried out by liquid chromatography tandem mass-spectrometry (LC-MS/MS)...
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27924013/the-proteomexchange-consortium-in-2017-supporting-the-cultural-change-in-proteomics-public-data-deposition
#14
Eric W Deutsch, Attila Csordas, Zhi Sun, Andrew Jarnuczak, Yasset Perez-Riverol, Tobias Ternent, David S Campbell, Manuel Bernal-Llinares, Shujiro Okuda, Shin Kawano, Robert L Moritz, Jeremy J Carver, Mingxun Wang, Yasushi Ishihama, Nuno Bandeira, Henning Hermjakob, Juan Antonio Vizcaíno
The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide. We give an overview of the current consortium activities and describe the advances of the past few years. Augmenting the PX founding members (PRIDE and PeptideAtlas, including the PASSEL resource), two new members have joined the consortium: MassIVE and jPOST. ProteomeCentral remains as the common data access portal, providing the ability to search for data sets in all participating PX resources, now with enhanced data visualization components...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27922118/mining-visualizing-and-comparing-multidimensional-biomolecular-data-using-the-genomics-data-miner-gmine-web-server
#15
Carla Proietti, Martha Zakrzewski, Thomas S Watkins, Bernard Berger, Shihab Hasan, Champa N Ratnatunga, Marie-Jo Brion, Peter D Crompton, John J Miles, Denise L Doolan, Lutz Krause
Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922054/first-insight-into-the-proteome-landscape-of-the-porcine-short-posterior-ciliary-arteries-key-signalling-pathways-maintaining-physiologic-functions
#16
Caroline Manicam, Natarajan Perumal, Norbert Pfeiffer, Franz H Grus, Adrian Gericke
Short posterior ciliary arteries (sPCA) provide the major blood supply to the optic nerve head. Emerging evidence has linked structural and functional anomalies of sPCA to the pathogenesis of several ocular disorders that cause varying degrees of visual loss, particularly anterior ischaemic optic neuropathy and glaucoma. Although the functional relevance of this vascular bed is well-recognized, the proteome of sPCA remains uncharacterized. Since the porcine ocular system closely resembles that of the human's and is increasingly employed in translational ophthalmic research, this study characterized the proteome of porcine sPCA employing the mass spectrometry-based proteomics strategy...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27903906/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#17
Cristina Aurrecoechea, Ana Barreto, Evelina Y Basenko, John Brestelli, Brian P Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C Kissinger, Cris Lawrence, Wei Li, Deborah F Pinney, Jane A Pulman, David S Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J Stoeckert, Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899614/suba4-the-interactive-data-analysis-centre-for-arabidopsis-subcellular-protein-locations
#18
Cornelia M Hooper, Ian R Castleden, Sandra K Tanz, Nader Aryamanesh, A Harvey Millar
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The experimental PPI data has been expanded to 26 327 PPI pairs including 856 PPI localizations from experimental fluorescent visualizations...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27890865/csf-pr-2-0-an-interactive-literature-guide-to-quantitative-cerebrospinal-fluid-mass-spectrometry-data-from-neurodegenerative-disorders
#19
Astrid Guldbrandsen, Yehia Farag, Ann C Kroksveen, Eystein Oveland, Ragnhild R Lereim, Jill A Opsahl, Kjell-Morten Myhr, Frode S Berven, Harald Barsnes
The rapidly growing number of biomedical studies supported by mass spectrometry based quantitative proteomics data has made it increasingly difficult to obtain an overview of the current status of the research field. A better way of organizing the biomedical proteomics information from these studies and making it available to the research community is therefore called for. In the presented work, we have investigated scientific publications describing the analysis of the cerebrospinal fluid proteome in relation to multiple sclerosis, Parkinsons disease and Alzheimers disease...
November 27, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27877091/conserved-chemosensory-proteins-in-the-proboscis-and-eyes-of-lepidoptera
#20
Jiao Zhu, Immacolata Iovinella, Francesca Romana Dani, Yu-Ling Liu, Ling-Qiao Huang, Yang Liu, Chen-Zhu Wang, Paolo Pelosi, Guirong Wang
Odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) are endowed with several different functions besides being carriers for pheromones and odorants. Based on a previous report of a CSP acting as surfactant in the proboscis of the moth Helicoverpa armigera, we revealed the presence of orthologue proteins in two other moths Plutella xylostella and Chilo suppressalis, as well as two butterflies Papilio machaon and Pieris rapae, using immunodetection and proteomic analysis. The unusual conservation of these proteins across large phylogenetic distances indicated a common specific function for these CSPs...
2016: International Journal of Biological Sciences
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