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https://www.readbyqxmd.com/read/28092796/global-open-data-management-in-metabolomics
#1
REVIEW
Kenneth Haug, Reza M Salek, Christoph Steinbeck
Chemical Biology employs chemical synthesis, analytical chemistry and other tools to study biological systems. Recent advances in both molecular biology such as next generation sequencing (NGS) have led to unprecedented insights towards the evolution of organisms' biochemical repertoires. Because of the specific data sharing culture in Genomics, genomes from all kingdoms of life become readily available for further analysis by other researchers. While the genome expresses the potential of an organism to adapt to external influences, the Metabolome presents a molecular phenotype that allows us to asses the external influences under which an organism exists and develops in a dynamic way...
January 13, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28092570/identifying-epigenetic-biomarkers-using-maximal-relevance-and-minimal-redundancy-based-feature-selection-for-multi-omics-data
#2
Saurav Mallik, Tapas Bhadra, Ujjwal Maulik
Epigenetic Biomarker discovery is an important task in bioinformatics. In this article, we develop a new framework of identifying statistically significant epigenetic biomarkers using maximal-relevance and minimal-redundancy criterion based feature (gene) selection for multi-omics dataset. Firstly, we determine the genes that have both expression as well as methylation values, and follow normal distribution. Similarly, we identify the genes which consist of both expression and methylation values, but do not follow normal distribution...
January 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28088864/an-integrated-high-throughput-multi-omics-platform-enables-data-driven-construction-of-cellular-responses-and-reveals-global-drug-mechanisms-of-action
#3
Jeremy L Norris, Melissa A Farrow, Danielle B Gutierrez, Lauren D Palmer, Nicole Muszynski, Stacy D Sherrod, James C Pino, Jamie L Allen, Jeffrey M Spraggins, Alex L R Lubbock, Ashley T Jordan, William Burns, James C Poland, Carrie E Romer, M Lisa Manier, Yuan-Wei Nei, Boone M Prentice, Kristie L Rose, Salisha Hill, Raf Van de Plas, Tina Tsui, Nathaniel M Braman, M Ray Keller, Stacey A Rutherford, Nichole A Lobdell, Carlos F Lopez, D Borden Lacy, John A McLean, John Peter Wikswo, Eric P Skaar, Richard M Caprioli
An understanding of how cells respond to perturbation is essential for biological applications; however, most approaches for profiling cellular response are limited in scope to pre-established targets. Global analysis of molecular mechanism will advance our understanding of the complex networks constituting cellular perturbation and lead to advancements in areas, such as infectious disease pathogenesis, developmental biology, pathophysiology, pharmacology, and toxicology. We have developed a high-throughput multi-omics platform for comprehensive, de novo characterization of cellular mechanisms of action...
January 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28087984/challenges-in-detecting-substances-for-equine-anti-doping
#4
REVIEW
A G Fragkaki, N Kioukia-Fougia, P Kiousi, M Kioussi, M Tsivou
The artificial increase of the physical capability of horses using drugs is well-known in racing and in other equine sports. Both illicit and therapeutic substances are regarded as prohibited substances in competition in most countries. Some countries do make distinctions for a few, specific drugs which are, however, allowed for use in other countries. The primary objective in the case of doping control is the detection of any trace of drug exposure, either parent drug or any of its metabolites, using the most powerful analytical methods which generally are based on chromatographic/mass spectrometric techniques...
January 14, 2017: Drug Testing and Analysis
https://www.readbyqxmd.com/read/28087761/proteomics-technologies-and-their-applications
#5
REVIEW
Bilal Aslam, Madiha Basit, Muhammad Atif Nisar, Mohsin Khurshid, Muhammad Hidayat Rasool
Proteomics involves the applications of technologies for the identification and quantification of overall proteins present content of a cell, tissue or an organism. It supplements the other "omics" technologies such as genomic and transcriptomics to expound the identity of proteins of an organism, and to cognize the structure and functions of a particular protein. Proteomics-based technologies are utilized in various capacities for different research settings such as detection of various diagnostic markers, candidates for vaccine production, understanding pathogenicity mechanisms, alteration of expression patterns in response to different signals and interpretation of functional protein pathways in different diseases...
February 2017: Journal of Chromatographic Science
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#6
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28079714/radiomic-phenotyping-in-brain-cancer-to-unravel-hidden-information-in-medical-images
#7
Srishti Abrol, Aikaterini Kotrotsou, Ahmed Salem, Pascal O Zinn, Rivka R Colen
Radiomics is a new area of research in the field of imaging with tremendous potential to unravel the hidden information in digital images. The scope of radiology has grown exponentially over the last two decades; since the advent of radiomics, many quantitative imaging features can now be extracted from medical images through high-throughput computing, and these can be converted into mineable data that can help in linking imaging phenotypes with clinical data, genomics, proteomics, and other "omics" information...
January 11, 2017: Topics in Magnetic Resonance Imaging: TMRI
https://www.readbyqxmd.com/read/28079125/establishment-of-a-integrative-multi-omics-expression-database-ckddb-in-the-context-of-chronic-kidney-disease-ckd
#8
Marco Fernandes, Holger Husi
Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28077967/integrated-omics-analyses-reveal-the-details-of-metabolic-adaptation-of-clostridium-thermocellum-to-lignocellulose-derived-growth-inhibitors-released-during-the-deconstruction-of-switchgrass
#9
Suresh Poudel, Richard J Giannone, Miguel Rodriguez, Babu Raman, Madhavi Z Martin, Nancy L Engle, Jonathan R Mielenz, Intawat Nookaew, Steven D Brown, Timothy J Tschaplinski, David Ussery, Robert L Hettich
BACKGROUND: Clostridium thermocellum is capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe's growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand its metabolism on more complex, lignocellulosic substrates to identify relevant industrial bottlenecks that could undermine efficient biofuel production. To this end, we have examined a time course progression of C...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28077457/systems-biology-derived-biomarkers-to-predict-progression-of-renal-function-decline-in-type-2-diabetes-mellitus
#10
Gert Mayer, Hiddo J L Heerspink, Constantin Aschauer, Andreas Heinzel, Georg Heinze, Alexander Kainz, Judith Sunzenauer, Paul Perco, Dick de Zeeuw, Peter Rossing, Michelle Pena, Rainer Oberbauer
OBJECTIVE: Chronic kidney disease (CKD) in diabetes has a complex molecular and likely multifaceted pathophysiology. We aimed to validate a panel of biomarkers identified using a systems biology approach to predict the individual decline of estimated glomerular filtration rate (eGFR) in a large group of patients with type 2 diabetes mellitus and CKD at various stages. RESEARCH DESIGN AND METHODS: We used publicly available "omics" data to develop a molecular process model of CKD in diabetes and identified a representative parsimonious set of nine molecular biomarkers: chitinase 3-like protein 1, growth hormone 1, hepatocyte growth factor, matrix metalloproteinase (MMP) 2, MMP7, MMP8, MMP13, tyrosine kinase, and tumor necrosis factor receptor-1...
January 11, 2017: Diabetes Care
https://www.readbyqxmd.com/read/28077200/expression-of-heat-shock-protein-70-in-transport-stressed-broiler-pectoralis-major-muscle-and-its-relationship-with-meat-quality
#11
T Xing, M F Wang, M Y Han, X S Zhu, X L Xu, G H Zhou
Omics research has indicated that heat shock protein 70 (HSP70) is a potential biomarker of meat quality. However, the specific changes and the potential role of HSP70 in postmortem meat quality development need to be further defined. In this study, Arbor Acres broiler chickens (n=126) were randomly categorized into three treatment groups of unstressed control (C), 0.5-h transport (T) and subsequent water shower spray following transport (T/W). Each treatment consisted of six replicates with seven birds each...
January 12, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28075450/integrated-analysis-of-differentially-expressed-genes-and-pathways-in-triple%C3%A2-negative-breast-cancer
#12
Cancan Peng, Wenli Ma, Wei Xia, Wenling Zheng
Triple‑negative breast cancer (TNBC) is a heterogeneous disease characterized by an aggressive phenotype and reduced survival. The aim of the present study was to investigate the molecular mechanisms involved in the carcinogenesis of TNBC and to identify novel target molecules for therapy. The differentially expressed genes (DEGs) in TNBC and normal adjacent tissue were assessed by analyzing the GSE41970 microarray data using Qlucore Omics Explorer, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes...
January 4, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28073349/the-mir-34a-5p-promotes-the-multi-chemoresistance-of-osteosarcoma-via-repression-of-the-agtr1-gene
#13
Youguang Pu, Fangfang Zhao, Yinpeng Li, Mingda Cui, Haiyan Wang, Xianghui Meng, Shanbao Cai
BACKGROUND: Chemoresistance hinders the curative cancer chemotherapy. MicroRNAs (miRNAs) are key players in diverse biological processes including the chemoresistance of cancers. METHODS: A RNA-seq-based miR-omic analysis of osteosarcoma (OS) cells was performed to detect the levels of miR-34a-5p. Bioinformatics analysis revealed that AGTR1 is one of the target genes of miR-34a-5p. The mRNA and protein levels of AGTR1 were detected in both the miR-34a-5p-mimic transfected G-292 and miR-34a-5p-antagomiR transfected SJSA-1 cells...
January 10, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28071925/gene-editing-and-genetic-engineering-approaches-for-advanced-probiotics-a-review
#14
Ruby Yadav, Vishal Kumar, Mehak Baweja, Pratyoosh Shukla
The applications of probiotics are significant and thus resulted in need of genome analysis of probiotic strains. Various omics methods and systems biology approaches enables us to understand and optimize the metabolic processes. These techniques have increased the researcher's attention towards gut microbiome and provided a new source for the revelation of uncharacterized biosynthetic pathways which enables novel metabolic engineering approaches. In recent years, the broad and quantitative analysis of modified strains relies on systems biology tools such as in silico design which are commonly used methods for improving strain performance...
January 10, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28065937/dynomics-to-identify-delays-and-co-expression-patterns-across-time-course-experiments
#15
Jasmin Straube, Bevan Emma Huang, Kim-Anh Lê Cao
Dynamic changes in biological systems can be captured by measuring molecular expression from different levels (e.g., genes and proteins) across time. Integration of such data aims to identify molecules that show similar expression changes over time; such molecules may be co-regulated and thus involved in similar biological processes. Combining data sources presents a systematic approach to study molecular behaviour. It can compensate for missing data in one source, and can reduce false positives when multiple sources highlight the same pathways...
January 9, 2017: Scientific Reports
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
#16
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/28062517/firebrowser-an-r-client-to-the-broad-institute-s-firehose-pipeline
#17
Mario Deng, Johannes Brägelmann, Ivan Kryukov, Nuno Saraiva-Agostinho, Sven Perner
With its Firebrowse service (http://firebrowse.org/) the Broad Institute is making large-scale multi-platform omics data analysis results publicly available through a Representational State Transfer (REST) Application Programmable Interface (API). Querying this database through an API client from an arbitrary programming environment is an essential task, allowing other developers and researchers to focus on their analysis and avoid data wrangling. Hence, as a first result, we developed a workflow to automatically generate, test and deploy such clients for rapid response to API changes...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28061817/the-rumen-microbial-metaproteome-as-revealed-by-sds-page
#18
Timothy J Snelling, R John Wallace
BACKGROUND: Ruminal digestion is carried out by large numbers of bacteria, archaea, protozoa and fungi. Understanding the microbiota is important because ruminal fermentation dictates the efficiency of feed utilisation by the animal and is also responsible for major emissions of the greenhouse gas, methane. Recent metagenomic and metatranscriptomic studies have helped to elucidate many features of the composition and activity of the microbiota. The metaproteome provides complementary information to these other -omics technologies...
January 7, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28054015/data-on-master-regulators-and-transcription-factor-binding-sites-found-by-upstream-analysis-of-multi-omics-data-on-methotrexate-resistance-of-colon-cancer
#19
AlexanderE Kel
Computational analysis of master regulators through the search for transcription factor binding sites followed by analysis of signal transduction networks of a cell is a new approach of causal analysis of multi-omics data. This paper contains results on analysis of multi-omics data that include transcriptomics, proteomics and epigenomics data of methotrexate (MTX) resistant colon cancer cell line. The data were used for analysis of mechanisms of resistance and for prediction of potential drug targets and promising compounds for reverting the MTX resistance of these cancer cells...
February 2017: Data in Brief
https://www.readbyqxmd.com/read/28049741/integrating-omics-and-alternative-splicing-reveals-insights-into-grape-response-to-high-temperature
#20
Jianfu Jiang, Xinna Liu, Guotian Liu, Chonghuai Liu, Shaohua Li, Lijun Wang
Heat stress is one of the primary abiotic stresses that limit crop production. Grape is a cultivated fruit with high economic value throughout the world, with its growth and development often influenced by high temperature. Alternative splicing (AS) is a widespread phenomenon increasing transcriptome and proteome diversity. We conducted high temperature treatments (35oC, 40oC and 45oC) on grapevines (Vitis vinifera), and assessed transcriptomic (especially AS) and proteomic changes in leaves. We found that nearly 70% of the genes were alternatively spliced under high temperature...
January 3, 2017: Plant Physiology
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