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https://www.readbyqxmd.com/read/28651411/-introduction-to-bayesian-variable-selection-methods-in-high-dimensional-omics-data-analysis
#1
X Q Dong, S H Xu, R Tao, T Wang
With the rapid development of genome sequencing technology and bioinformatics in recent years, it has become possible to measure thousands of omics data which might be associated with the progress of diseases, i.e."high-dimensional data" . This type of omics data have a common feature that the number of variable p is usually greater than the observation cases n, and often has high correlation between independent variables. Therefore, it is a great statistical challenge to identify really meaningful variables from omics data...
May 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28650854/recent-developments-in-deuterium-oxide-tracer-approaches-to-measure-rates-of-substrate-turnover-implications-for-protein-lipid-and-nucleic-acid-research
#2
Matthew S Brook, Daniel J Wilkinson, Philip J Atherton, Ken Smith
PURPOSE OF REVIEW: Methods that inform on dynamic metabolism that can be applied to clinical populations to understand disease progression and responses to therapeutic interventions are of great importance. This review perspective will highlight recent advances, development, and applications of the multivalent stable isotope tracer deuterium oxide (D2O) to the study of substrate metabolism with particular reference to protein, lipids, and nucleic acids, and how these methods can be readily applied within clinical and pharmaceutical research...
June 24, 2017: Current Opinion in Clinical Nutrition and Metabolic Care
https://www.readbyqxmd.com/read/28650741/microbial-culturomics-application-for-global-health-noncontiguous-finished-genome-sequence-and-description-of-pseudomonas-massiliensis-strain-cb-1-t-sp-nov-in-brazil
#3
Lucie Bardet, Teresa Cimmino, Clémence Buffet, Caroline Michelle, Jaishriram Rathored, Fatalmoudou Tandina, Jean-Christophe Lagier, Saber Khelaifia, Jônatas Abrahão, Didier Raoult, Jean-Marc Rolain
Culturomics is a new postgenomics field that explores the microbial diversity of the human gut coupled with taxono-genomic strategy. Culturomics, and the microbiome science more generally, are anticipated to transform global health diagnostics and inform the ways in which gut microbial diversity contributes to human health and disease, and by extension, to personalized medicine. Using culturomics, we report in this study the description of strain CB1(T) ( = CSUR P1334 = DSM 29075), a new species isolated from a stool specimen from a 37-year-old Brazilian woman...
June 26, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28649937/the-genetics-of-platelet-count-and-volume-in-humans
#4
John D Eicher, Guillaume Lettre, Andrew D Johnson
The last decade has witnessed an explosion in the depth, variety, and amount of human genetic data that can be generated. This revolution in technical and analytical capacities has enabled the genetic investigation of human traits and disease in thousands to now millions of participants. Investigators have taken advantage of these advancements to gain insight into platelet biology and the platelet's role in human disease. To do so, large human genetics studies have examined the association of genetic variation with two quantitative traits measured in many population and patient based cohorts: platelet count (PLT) and mean platelet volume (MPV)...
June 26, 2017: Platelets
https://www.readbyqxmd.com/read/28649586/data-from-salivary-gland-proteome-analysis-of-female-aedes-aegypti-linn
#5
Rakhi Dhawan, Ajeet Kumar Mohanty, Manish Kumar, Gourav Dey, Jayshree Advani, T S Keshava Prasad, Ashwani Kumar
Salivary gland proteins from female Aedes aegypti mosquito were extracted and analyzed on high-resolution mass spectrometry. Proteomic data was analysed using two search algorithms SEQUEST and Mascot, which results in acquisition of 83,836 spectra which were assigned to 5417 peptides belonging to 1208 proteins.These proteins were then assigned molecular functions and further analysis revealed biological processes they are involved in using Gene Ontology annotations. Several immunity related pathways were found to be enriched in salivary gland...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28649431/meta-analysis-of-host-response-networks-identifies-a-common-core-in-tuberculosis
#6
Awanti Sambarey, Abhinandan Devaprasad, Priyanka Baloni, Madhulika Mishra, Abhilash Mohan, Priyanka Tyagi, Amit Singh, J S Akshata, Razia Sultana, Shashidhar Buggi, Nagasuma Chandra
Tuberculosis remains a major global health challenge worldwide, causing more than a million deaths annually. To determine newer methods for detecting and combating the disease, it is necessary to characterise global host responses to infection. Several high throughput omics studies have provided a rich resource including a list of several genes differentially regulated in tuberculosis. An integrated analysis of these studies is necessary to identify a unified response to the infection. Such data integration is met with several challenges owing to platform dependency, patient heterogeneity, and variability in the extent of infection, resulting in little overlap among different datasets...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649285/introduction-of-the-diagene-study-clinical-characteristics-pathophysiology-and-determinants-of-vascular-complications-of-type-2-diabetes
#7
Thijs T W van Herpt, Roosmarijn F H Lemmers, Mandy van Hoek, Janneke G Langendonk, Ronald J Erdtsieck, Bert Bravenboer, Annelies Lucas, Monique T Mulder, Harm R Haak, Aloysius G Lieverse, Eric J G Sijbrands
BACKGROUND: Type 2 diabetes is a major healthcare problem. Glucose-, lipid-, and blood pressure-lowering strategies decrease the risk of micro- and macrovascular complications. However, a substantial residual risk remains. To unravel the etiology of type 2 diabetes and its complications, large-scale, well-phenotyped studies with prospective follow-up are needed. This is the goal of the DiaGene study. In this manuscript, we describe the design and baseline characteristics of the study...
2017: Diabetology & Metabolic Syndrome
https://www.readbyqxmd.com/read/28647896/omics-based-hybrid-prediction-in-maize
#8
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/28646205/comparative-nanouplc-ms-e-analysis-between-magainin-i-susceptible-and-resistant-escherichia-coli-strains
#9
Marlon H Cardoso, Keyla C de Almeida, Elizabete de S Cândido, André M Murad, Simoni C Dias, Octávio L Franco
In recent years the antimicrobial peptides (AMPs) have been prospected and designed as new alternatives to conventional antibiotics. Indeed, AMPs have presented great potential toward pathogenic bacterial strains by means of complex mechanisms of action. However, reports have increasingly emerged regarding the mechanisms by which bacteria resist AMP administration. In this context, we performed a comparative proteomic study by using the total bacterial lysate of magainin I-susceptible and -resistant E. coli strains...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646024/metabolic-reprogramming-via-ppar%C3%AE-signaling-in-cardiac-hypertrophy-and-failure-from-metabolomics-to-epigenetics
#10
Junco Shibayama Warren, Shin-Ichi Oka, Daniela Zablocki, Junichi Sadoshima
Studies using -omics-based approaches have advanced our knowledge of metabolic remodeling in cardiac hypertrophy and failure. Metabolomic analysis of the failing heart has revealed global changes in mitochondrial substrate metabolism. Peroxisome proliferator-activated receptor alpha (PPARα) plays a critical role in synergistic regulation of cardiac metabolism through transcriptional control. Metabolic reprogramming via PPARα signaling in heart failure ultimately propagates into myocardial energetics. However, emerging evidence suggests that the expression level of PPARα per se does not always explain the energetic state in the heart...
June 23, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28645581/improvement-of-isopropanol-tolerance-of-escherichia-coli-using-adaptive-laboratory-evolution-and-omics-technologies
#11
Takaaki Horinouchi, Aki Sakai, Hazuki Kotani, Kumi Tanabe, Chikara Furusawa
Isopropanol (IPA) is the secondary alcohol that can be dehydrated to yield propylene. To produce IPA using microorganisms, a significant issue is that the toxicity of IPA causes retardation or inhibition of cell growth, decreasing the yield. One possible strategy to overcome this problem is to improve IPA tolerance of production organisms. For the understanding of tolerance to IPA, we performed parallel adaptive laboratory evolution (ALE) of Escherichia coli under IPA stress. To identify the genotypic change during ALE, we performed genome re-sequencing analyses of obtained tolerant strains...
June 20, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28643936/phenotypic-analysis-of-organoids-by-proteomics
#12
REVIEW
Alexis Gonneaud, Claude Asselin, François Boudreau, François-Michel Boisvert
The development of 3D cell cultures into self-organizing organ-like structures named organoids provides a model that better reflects in vivo organ physiology and their functional properties. Organoids have been established from several organs, such as the intestine, prostate, brain, liver, kidney and pancreas. With recent advances in high-throughput and -omics profiling technologies, it is now possible to study the mechanisms of cellular organisation at the systems level. It is therefore not surprising that these methods are now used to characterize organoids at the transcriptomic, proteomic, chromatin state and transcription factor DNA-binding levels...
June 23, 2017: Proteomics
https://www.readbyqxmd.com/read/28643821/non-invasive-approaches-in-the-diagnosis-of-acute-rejection-in-kidney-transplant-recipients-part-i-in-vivo-imaging-methods
#13
REVIEW
Oriane Hanssen, Pauline Erpicum, Pierre Lovinfosse, Paul Meunier, Laurent Weekers, Luaba Tshibanda, Jean-Marie Krzesinski, Roland Hustinx, François Jouret
Kidney transplantation (KTx) represents the best available treatment for patients with end-stage renal disease. Still, full benefits of KTx are undermined by acute rejection (AR). The diagnosis of AR ultimately relies on transplant needle biopsy. However, such an invasive procedure is associated with a significant risk of complications and is limited by sampling error and interobserver variability. In the present review, we summarize the current literature about non-invasive approaches for the diagnosis of AR in kidney transplant recipients (KTRs), including in vivo imaging, gene expression profiling and omics analyses of blood and urine samples...
February 2017: Clinical Kidney Journal
https://www.readbyqxmd.com/read/28643819/non-invasive-approaches-in-the-diagnosis-of-acute-rejection-in-kidney-transplant-recipients-part-ii-omics-analyses-of-urine-and-blood-samples
#14
REVIEW
Pauline Erpicum, Oriane Hanssen, Laurent Weekers, Pierre Lovinfosse, Paul Meunier, Luaba Tshibanda, Jean-Marie Krzesinski, Roland Hustinx, François Jouret
Kidney transplantation (KTx) represents the best available treatment for patients with end-stage renal disease. Still, the full benefits of KTx are undermined by acute rejection (AR). The diagnosis of AR ultimately relies on transplant needle biopsy. However, such an invasive procedure is associated with a significant risk of complications and is limited by sampling error and interobserver variability. In the present review, we summarize the current literature about non-invasive approaches for the diagnosis of AR in kidney transplant recipients (KTRs), including in vivo imaging, gene-expression profiling and omics analyses of blood and urine samples...
February 2017: Clinical Kidney Journal
https://www.readbyqxmd.com/read/28643332/integrative-eqtl-analysis-of-tumor-and-host-omics-data-in-individuals-with-bladder-cancer
#15
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/28642845/metabolic-adaptations-of-uropathogenic-e-coli-in-the-urinary-tract
#16
REVIEW
Riti Mann, Daniel G Mediati, Iain G Duggin, Elizabeth J Harry, Amy L Bottomley
Escherichia coli ordinarily resides in the lower gastrointestinal tract in humans, but some strains, known as Uropathogenic E. coli (UPEC), are also adapted to the relatively harsh environment of the urinary tract. Infections of the urine, bladder and kidneys by UPEC may lead to potentially fatal bloodstream infections. To survive this range of conditions, UPEC strains must have broad and flexible metabolic capabilities and efficiently utilize scarce essential nutrients. Whole-organism (or "omics") methods have recently provided significant advances in our understanding of the importance of metabolic adaptation in the success of UPECs...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28640810/lassim-a-network-inference-toolbox-for-genome-wide-mechanistic-modeling
#17
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
#18
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/28638442/computational-dynamic-approaches-for-temporal-omics-data-with-applications-to-systems-medicine
#19
REVIEW
Yulan Liang, Arpad Kelemen
Modeling and predicting biological dynamic systems and simultaneously estimating the kinetic structural and functional parameters are extremely important in systems and computational biology. This is key for understanding the complexity of the human health, drug response, disease susceptibility and pathogenesis for systems medicine. Temporal omics data used to measure the dynamic biological systems are essentials to discover complex biological interactions and clinical mechanism and causations. However, the delineation of the possible associations and causalities of genes, proteins, metabolites, cells and other biological entities from high throughput time course omics data is challenging for which conventional experimental techniques are not suited in the big omics era...
2017: BioData Mining
https://www.readbyqxmd.com/read/28638378/corrigendum-long-term-enrichment-of-stress-tolerant-cellulolytic-soil-populations-following-timber-harvesting-evidenced-by-multi-omic-stable-isotope-probing
#20
Roland C Wilhelm, Erick Cardenas, Hilary Leung, András Szeitz, Lionel D Jensen, William W Mohn
[This corrects the article on p. 537 in vol. 8, PMID: 28443069.].
2017: Frontiers in Microbiology
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