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https://www.readbyqxmd.com/read/28647896/omics-based-hybrid-prediction-in-maize
#1
Matthias Westhues, Tobias A Schrag, Claas Heuer, Georg Thaller, H Friedrich Utz, Wolfgang Schipprack, Alexander Thiemann, Felix Seifert, Anita Ehret, Armin Schlereth, Mark Stitt, Zoran Nikoloski, Lothar Willmitzer, Chris C Schön, Stefan Scholten, Albrecht E Melchinger
Complementing genomic data with other "omics" predictors can increase the probability of success for predicting the best hybrid combinations using complex agronomic traits. Accurate prediction of traits with complex genetic architecture is crucial for selecting superior candidates in animal and plant breeding and for guiding decisions in personalized medicine. Whole-genome prediction has revolutionized these areas but has inherent limitations in incorporating intricate epistatic interactions. Downstream "omics" data are expected to integrate interactions within and between different biological strata and provide the opportunity to improve trait prediction...
June 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28643332/integrative-eqtl-analysis-of-tumor-and-host-omics-data-in-individuals-with-bladder-cancer
#2
Silvia Pineda, Kristel Van Steen, Núria Malats
Integrative analyses of several omics data are emerging. The data are usually generated from the same source material (i.e., tumor sample) representing one level of regulation. However, integrating different regulatory levels (i.e., blood) with those from tumor may also reveal important knowledge about the human genetic architecture. To model this multilevel structure, an integrative-expression quantitative trait loci (eQTL) analysis applying two-stage regression (2SR) was proposed. This approach first regressed tumor gene expression levels with tumor markers and the adjusted residuals from the previous model were then regressed with the germline genotypes measured in blood...
June 23, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28640810/lassim-a-network-inference-toolbox-for-genome-wide-mechanistic-modeling
#3
Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28638489/harnessing-integrative-omics-to-facilitate-molecular-imaging-of-the-human-epidermal-growth-factor-receptor-family-for-precision-medicine
#4
REVIEW
Martin Pool, H Rudolf de Boer, Marjolijn N Lub-de Hooge, Marcel A T M van Vugt, Elisabeth G E de Vries
Cancer is a growing problem worldwide. The cause of death in cancer patients is often due to treatment-resistant metastatic disease. Many molecularly targeted anticancer drugs have been developed against 'oncogenic driver' pathways. However, these treatments are usually only effective in properly selected patients. Resistance to molecularly targeted drugs through selective pressure on acquired mutations or molecular rewiring can hinder their effectiveness. This review summarizes how molecular imaging techniques can potentially facilitate the optimal implementation of targeted agents...
2017: Theranostics
https://www.readbyqxmd.com/read/28637856/how-to-get-the-most-bang-for-your-buck-the-evolution-and-physiology-of-nutrition-dependent-resource-allocation-strategies
#5
REVIEW
Enoch Ng'oma, Anna M Perinchery, Elizabeth G King
All organisms use resources to grow, survive and reproduce. The supply of these resources varies widely across landscapes and time, imposing ultimate constraints on the maximal trait values for allocation-related traits. In this review, we address three key questions fundamental to our understanding of the evolution of allocation strategies and their underlying mechanisms. First, we ask: how diverse are flexible resource allocation strategies among different organisms? We find there are many, varied, examples of flexible strategies that depend on nutrition...
June 28, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28636311/insights-into-integrated-lead-generation-and-target-identification-in-malaria-and-tuberculosis-drug-discovery
#6
John Okombo, Kelly Chibale
New, safe and effective drugs are urgently needed to treat and control malaria and tuberculosis, which affect millions of people annually. However, financial return on investment in the poor settings where these diseases are mostly prevalent is very minimal to support market-driven drug discovery and development. Moreover, the imminent loss of therapeutic lifespan of existing therapies due to evolution and spread of drug resistance further compounds the urgency to identify novel effective drugs. However, the advent of new public-private partnerships focused on tropical diseases and the recent release of large data sets by pharmaceutical companies on antimalarial and antituberculosis compounds derived from phenotypic whole cell high throughput screening have spurred renewed interest and opened new frontiers in malaria and tuberculosis drug discovery...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28634240/leucine-biosynthesis-is-involved-in-regulating-high-lipid-accumulation-in-yarrowia-lipolytica
#7
Eduard J Kerkhoven, Young-Mo Kim, Siwei Wei, Carrie D Nicora, Thomas L Fillmore, Samuel O Purvine, Bobbie-Jo Webb-Robertson, Richard D Smith, Scott E Baker, Thomas O Metz, Jens Nielsen
The yeast Yarrowia lipolytica is a potent accumulator of lipids, and lipogenesis in this organism can be influenced by a variety of factors, such as genetics and environmental conditions. Using a multifactorial study, we elucidated the effects of both genetic and environmental factors on regulation of lipogenesis in Y. lipolytica and identified how two opposite regulatory states both result in lipid accumulation. This study involved comparison of a strain overexpressing diacylglycerol acyltransferase (DGA1) with a control strain grown under either nitrogen or carbon limitation conditions...
June 20, 2017: MBio
https://www.readbyqxmd.com/read/28627406/multi-omics-facilitated-variable-selection-in-cox-regression-model-for-cancer-prognosis-prediction
#8
Cong Liu, Xujun Wang, Georgi Z Genchev, Hui Lu
Motivation New developments in high-throughput genomic technologies have enabled the measurement of diverse types of omics biomarkers in a cost-efficient and clinically-feasible manner. Developing computational methods and tools for analysis and translation of such genomic data into clinically-relevant information is an ongoing and active area of investigation. For example, several studies have utilized an unsupervised learning framework to cluster patients by integrating omics data. Despite such recent advances, predicting cancer prognosis using integrated omics biomarkers remains a challenge...
June 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28627174/integrative-analysis-of-renal-ischemia-reperfusion-injury-and-remote-ischemic-preconditioning-in-mice
#9
Kumsun Cho, Sang-Il Min, Sanghyun Ahn, Seung-Kee Min, Curie Ahn, Kyung-Sang Yu, In-Jin Jang, Joo-Youn Cho, Jongwon Ha
Remote ischemic preconditioning (RIPC) is a strategy to induce resistance in a target organ against the oxidative stress and injury caused by ischemia and reperfusion (IR). RIPC harnesses the body's endogenous protective capabilities through brief episodes of IR applied in organs remote from the target. Few studies have analyzed this phenomenon in the kidney. Furthermore, the window of protection representing RIPC efficacy has not been fully elucidated. Here, we performed a multi-omics study to specify those associated with protective effects of RIPC against the IR injury...
June 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28624903/early-diagnosis-of-sepsis-is-an-integrated-omics-approach-the-way-forward
#10
REVIEW
Raymond J Langley, Hector R Wong
Sepsis remains one of the leading causes of death in the USA and it is expected to get worse as the population ages. Moreover, the standard of care, which recommends aggressive treatment with appropriate antibiotics, has led to an increase in multiple drug-resistant organisms. There is a dire need for the development of new antibiotics, improved antibiotic stewardship, and therapies that treat the host response. Development of new sepsis therapeutics has been a disappointment as no drugs are currently approved to treat the various complications from sepsis...
June 17, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28622780/-iron-metabolism
#11
S Vaulont
Iron is an essential trace element ensuring many functions in the body. However, excess iron can be toxic with deleterious consequences on function and tissue integrity. The understanding of the molecular and cellular mechanisms allowing iron level to be kept at physiological concentration has greatly progressed in recent years, in particular with the identification of the iron-regulatory hormone, hepcidin and its receptor ferroportin, the sole iron exporter known to date. This discovery has improved our ability to diagnose and manage iron disorders and offered new therapeutic perspectives for an important class of human diseases...
May 2017: Archives de Pédiatrie: Organe Officiel de la Sociéte Française de Pédiatrie
https://www.readbyqxmd.com/read/28621886/review-of-emerging-metabolomic-tools-and-resources-2015-2016
#12
REVIEW
Biswapriya Biswavas Misra, Johannes F Fahrmann, Dmitry Grapov
Data processing and analysis are major bottlenecks in high-throughput metabolomic experiments. Recent advancements in data acquisition platforms are driving trends toward increasing data size (e.g. petabyte scale) and complexity (multiple omic platforms). Improvements in data analysis software and in silico methods are similarly required to effectively utilize these advancements and link the acquired data with biological interpretations. Herein we provide an overview of recently developed and freely-available metabolomic tools, algorithms, databases and data analysis frameworks...
June 16, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28620196/integration-of-dna-methylation-and-gene-transcription-across-nineteen-cell-types-reveals-cell-type-specific-and-genomic-region-dependent-regulatory-patterns
#13
Binhua Tang, Yufan Zhou, Chiou-Miin Wang, Tim H-M Huang, Victor X Jin
Despite numerous studies done on understanding the role of DNA methylation, limited work has focused on systems integration of cell type-specific interplay between DNA methylation and gene transcription. Through a genome-wide analysis of DNA methylation across 19 cell types with T-47D as reference, we identified 106,252 cell type-specific differentially-methylated CpGs categorized into 7,537 differentially (46.6% hyper- and 53.4% hypo-) methylated regions. We found 44% promoter regions and 75% CpG islands were T-47D cell type-specific methylated...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28618245/multi-omics-integrative-investigation-of-fatty-acid-metabolism-in-obese-and-lean-subcutaneous-tissue
#14
Flavia Badoud, Dyanne Brewer, Armen Charchoglyan, Daniel J Cuthbertson, David M Mutch
White adipose tissue (WAT) plays a central role in whole-body energy homeostasis through storage and release of fatty acids. A deeper understanding of the complex and highly integrated pathways regulating WAT fatty acid metabolism, and how they are altered with obesity, is necessary for diagnostic and therapeutic innovations in nutritional disorders. In this multi-omics study, we investigated the influence of obesity on fatty acid metabolism in human subcutaneous adipose tissue (SAT) using an approach that integrated transcriptomic, peptidomic, and fatty acid analyses...
June 15, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28613106/innovative-array-based-assay-for-omics-pattern-in-melanoma
#15
Carmen Dumitru, Carolina Constantin, Cristiana Popp, Mirela Cioplea, Sabina Zurac, Tatiana Vassu, Monica Neagu
Cutaneous melanoma remains a major health issue and still an important challenge for research. Thus omics complex evaluation can provide a more specific molecular classification for this heterogeneous disease. Complex omics analysis based on genomic and proteomic microarrays can identify disease markers that prognosticate disease evolution or can monitor therapies efficacy. Among the technologies that gained momentum in the last years, array based comparative genomic hybridization offered the possibility to analyze chromosomal numerical aberrations within cutaneous melanomas providing important support for molecular classification of melanoma tumors...
June 14, 2017: Journal of Immunoassay & Immunochemistry
https://www.readbyqxmd.com/read/28611656/dissecting-the-molecular-mechanisms-of-neurodegenerative-diseases-through-network-biology
#16
Jose A Santiago, Virginie Bottero, Judith A Potashkin
Neurodegenerative diseases are rarely caused by a mutation in a single gene but rather influenced by a combination of genetic, epigenetic and environmental factors. Emerging high-throughput technologies such as RNA sequencing have been instrumental in deciphering the molecular landscape of neurodegenerative diseases, however, the interpretation of such large amounts of data remains a challenge. Network biology has become a powerful platform to integrate multiple omics data to comprehensively explore the molecular networks in the context of health and disease...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28609292/knowledge-discovery-in-biological-databases-for-revealing-candidate-genes-linked-to-complex-phenotypes
#17
Keywan Hassani-Pak, Christopher Rawlings
Genetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects...
June 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28605519/cancersubtypes-an-r-bioconductor-package-for-molecular-cancer-subtype-identification-validation-and-visualization
#18
Taosheng Xu, Thuc Duy Le, Lin Liu, Ning Su, Rujing Wang, Bingyu Sun, Antonio Colaprico, Gianluca Bontempi, Jiuyong Li
Summary: Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes , an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization...
June 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28605402/sparse-redundancy-analysis-of-high-dimensional-genetic-and-genomic-data
#19
Attila Csala, Frans P J M Voorbraak, Aeilko H Zwinderman, Michel H Hof
Motivation: Recent technological developments have enabled the possibility of genetic and genomic integrated data analysis approaches, where multiple omics data sets from various biological levels are combined and used to describe (disease) phenotypic variations. The main goal is to explain and ultimately predict phenotypic variations by understanding their genetic basis and the interaction of the associated genetic factors. Therefore, understanding the underlying geneticmechanisms of phenotypic variations is an ever increasing research interest in biomedical sciences...
June 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28605387/a-simple-fractionated-extraction-method-for-the-comprehensive-analysis-of-metabolites-lipids-and-proteins-from-a-single-sample
#20
Mohamed Salem, Michal Bernach, Krzysztof Bajdzienko, Patrick Giavalisco
Understanding of complex biological systems requires the measurement, analysis and integration of multiple compound classes of the living cell, usually determined by transcriptomic, proteomic, metabolomics and lipidomic measurements. In this protocol, we introduce a simple method for the reproducible extraction of metabolites, lipids and proteins from biological tissues using a single aliquot per sample. The extraction method is based on a methyl tert-butyl ether: methanol: water system for liquid: liquid partitioning of hydrophobic and polar metabolites into two immiscible phases along with the precipitation of proteins and other macromolecules as a solid pellet...
June 1, 2017: Journal of Visualized Experiments: JoVE
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