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https://www.readbyqxmd.com/read/28449062/calculating-quality-of-public-high-throughput-sequencing-data-to-obtain-suitable-subset-for-reanalysis-from-the-sequence-read-archive
#1
Tazro Ohta, Takeru Nakazato, Hidemasa Bono
Background: : It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis...
April 25, 2017: GigaScience
https://www.readbyqxmd.com/read/28446914/constructing-integrated-networks-for-identifying-new-secondary-metabolic-pathway-regulators-in-grapevine-recent-applications-and-future-opportunities
#2
Darren C J Wong, José Tomás Matus
Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Whereas, some studies have used gene co-expression networks to find common pathways and putative targets for transcription factors related to development and metabolism, others have defined networks of primary and secondary metabolites for characterizing the main metabolic differences between cultivars throughout fruit ripening...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28444347/fluxomics-links-cellular-functional-analyses-to-whole-plant-phenotyping
#3
Christophe Salon, Jean-Christophe Avice, Sophie Colombié, Martine Dieuaide-Noubhani, Karine Gallardo, Christian Jeudy, Alain Ourry, Marion Prudent, Anne-Sophie Voisin, Dominique Rolin
Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping...
April 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28441463/rapidsnps-a-new-computational-pipeline-for-rapidly-identifying-key-genetic-variants-reveals-previously-unidentified-snps-that-are-significantly-associated-with-individual-platelet-responses
#4
Bajuna Rashid Salehe, Chris Ian Jones, Giuseppe Di Fatta, Liam James McGuffin
Advances in omics technologies have led to the discovery of genetic markers, or single nucleotide polymorphisms (SNPs), that are associated with particular diseases or complex traits. Although there have been significant improvements in the approaches used to analyse associations of SNPs with disease, further optimised and rapid techniques are needed to keep up with the rate of SNP discovery, which has exacerbated the 'missing heritability' problem. Here, we have devised a novel, integrated, heuristic-based, hybrid analytical computational pipeline, for rapidly detecting novel or key genetic variants that are associated with diseases or complex traits...
2017: PloS One
https://www.readbyqxmd.com/read/28440800/the-trichodesmium-consortium-conserved-heterotrophic-co-occurrence-and-genomic-signatures-of-potential-interactions
#5
Michael D Lee, Nathan G Walworth, Erin L McParland, Fei-Xue Fu, Tracy J Mincer, Naomi M Levine, David A Hutchins, Eric A Webb
The nitrogen (N)-fixing cyanobacterium Trichodesmium is globally distributed in warm, oligotrophic oceans, where it contributes a substantial proportion of new N and fuels primary production. These photoautotrophs form macroscopic colonies that serve as relatively nutrient-rich substrates that are colonized by many other organisms. The nature of these associations may modulate ocean N and carbon (C) cycling, and can offer insights into marine co-evolutionary mechanisms. Here we integrate multiple omics-based and experimental approaches to investigate Trichodesmium-associated bacterial consortia in both laboratory cultures and natural environmental samples...
April 25, 2017: ISME Journal
https://www.readbyqxmd.com/read/28438675/integrating-cell-biology-and-proteomic-approaches-in-plants
#6
Tomáš Takáč, Olga Šamajová, Jozef Šamaj
Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science...
April 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28436686/sparking-thinking-studying-modern-precision-medicine-will-accelerate-the-progression-of-traditional-chinese-medicine-patterns
#7
Bao-Cheng Liu, Guang Ji
Incorporating "-omics" studies with environmental interactions could help elucidate the biological mechanisms responsible for Traditional Chinese Medicine (TCM) patterns. Based on the authors' own experiences, this review outlines a model of an ideal combination of "-omics" biomarkers, environmental factors, and TCM pattern classifications; provides a narrative review of the relevant genetic and TCM studies; and lists several successful integrative examples. Two integration tools are briefly introduced. The first is the integration of modern devices into objective diagnostic methods of TCM patterning, which would improve current clinical decision-making and practice...
April 24, 2017: Journal of Alternative and Complementary Medicine: Research on Paradigm, Practice, and Policy
https://www.readbyqxmd.com/read/28435767/green-toxicology-a-strategy-for-sustainable-chemical-and-material-development
#8
EDITORIAL
Sarah E Crawford, Thomas Hartung, Henner Hollert, Björn Mathes, Bennard van Ravenzwaay, Thomas Steger-Hartmann, Christoph Studer, Harald F Krug
Green Toxicology refers to the application of predictive toxicology in the sustainable development and production of new less harmful materials and chemicals, subsequently reducing waste and exposure. Built upon the foundation of "Green Chemistry" and "Green Engineering", "Green Toxicology" aims to shape future manufacturing processes and safe synthesis of chemicals in terms of environmental and human health impacts. Being an integral part of Green Chemistry, the principles of Green Toxicology amplify the role of health-related aspects for the benefit of consumers and the environment, in addition to being economical for manufacturing companies...
2017: Environmental Sciences Europe
https://www.readbyqxmd.com/read/28435157/the-systemic-nature-of-ckd
#9
REVIEW
Carmine Zoccali, Raymond Vanholder, Ziad A Massy, Alberto Ortiz, Pantelis Sarafidis, Friedo W Dekker, Danilo Fliser, Denis Fouque, Gunnar H Heine, Kitty J Jager, Mehmet Kanbay, Francesca Mallamaci, Gianfranco Parati, Patrick Rossignol, Andrzej Wiecek, Gerard London
The accurate definition and staging of chronic kidney disease (CKD) is one of the major achievements of modern nephrology. Intensive research is now being undertaken to unravel the risk factors and pathophysiologic underpinnings of this disease. In particular, the relationships between the kidney and other organs have been comprehensively investigated in experimental and clinical studies in the last two decades. Owing to technological and analytical limitations, these links have been studied with a reductionist approach focusing on two organs at a time, such as the heart and the kidney or the bone and the kidney...
April 24, 2017: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/28434033/the-gut-microbiome-as-a-target-for-prevention-and-treatment-of-hyperglycaemia-in-type-2-diabetes-from-current-human-evidence-to-future-possibilities
#10
REVIEW
Louise Brunkwall, Marju Orho-Melander
The totality of microbial genomes in the gut exceeds the size of the human genome, having around 500-fold more genes that importantly complement our coding potential. Microbial genes are essential for key metabolic processes, such as the breakdown of indigestible dietary fibres to short-chain fatty acids, biosynthesis of amino acids and vitamins, and production of neurotransmitters and hormones. During the last decade, evidence has accumulated to support a role for gut microbiota (analysed from faecal samples) in glycaemic control and type 2 diabetes...
April 22, 2017: Diabetologia
https://www.readbyqxmd.com/read/28429721/a-mouse-tissue-transcription-factor-atlas
#11
Quan Zhou, Mingwei Liu, Xia Xia, Tongqing Gong, Jinwen Feng, Wanlin Liu, Yang Liu, Bei Zhen, Yi Wang, Chen Ding, Jun Qin
Transcription factors (TFs) drive various biological processes ranging from embryonic development to carcinogenesis. Here, we employ a recently developed concatenated tandem array of consensus TF response elements (catTFRE) approach to profile the activated TFs in 24 adult and 8 fetal mouse tissues on proteome scale. A total of 941 TFs are quantitatively identified, representing over 60% of the TFs in the mouse genome. Using an integrated omics approach, we present a TF network in the major organs of the mouse, allowing data mining and generating knowledge to elucidate the roles of TFs in various biological processes, including tissue type maintenance and determining the general features of a physiological system...
April 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28423769/linked-data-applications-through-ontology-based-data-access-in-clinical-research
#12
Ann-Kristin Kock-Schoppenhauer, Christian Kamann, Hannes Ulrich, Petra Duhm-Harbeck, Josef Ingenerf
Clinical care and research data are widely dispersed in isolated systems based on heterogeneous data models. Biomedicine predominantly makes use of connected datasets based on the Semantic Web paradigm. Initiatives like Bio2RDF created Resource Description Framework (RDF) versions of Omics resources, enabling sophisticated Linked Data applications. In contrast, electronic healthcare records (EHR) data are generated and processed in diverse clinical subsystems within hospital information systems (HIS). Usually, each of them utilizes a relational database system with a different proprietary schema...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28417080/applying-a-systems-approach-to-thyroid-physiology-looking-at-the-whole-with-a-mitochondrial-perspective-instead-of-judging-single-tsh-values-or-why-we-should-know-more-about-mitochondria-to-understand-metabolism
#13
REVIEW
Roy Moncayo, Helga Moncayo
Classical thinking in endocrine physiology squeezes our diagnostic handling into a simple negative feedback mechanism with a controller and a controlled variable. In the case of the thyroid this is reduced to TSH and fT3 and fT4, respectively. The setting of this tight notion has no free space for any additions. In this paper we want to challenge this model of limited application by proposing a construct based on a systems approach departing from two basic considerations. In first place since the majority of cases of thyroid disease develop and appear during life it has to be considered as an acquired condition...
June 2017: BBA Clinical
https://www.readbyqxmd.com/read/28415856/gene-and-variant-annotation-for-mendelian-disorders-in-the-era-of-advanced-sequencing-technologies
#14
Samya Chakravorty, Madhuri Hegde
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations...
April 17, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28410475/exploring-the-potential-of-saccharomyces-cerevisiae-for-biopharmaceutical-protein-production
#15
REVIEW
Guokun Wang, Mingtao Huang, Jens Nielsen
Production of recombinant proteins by yeast plays a vital role in the biopharmaceutical industry. It is therefore desirable to develop yeast platform strains for over-production of various biopharmaceutical proteins, but this requires fundamental knowledge of the cellular machinery, especially the protein secretory pathway. Integrated analyses of multi-omics datasets can provide comprehensive understanding of cellular function, and can enable systems biology-driven and mathematical model-guided strain engineering...
April 11, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28410125/multi-omics-and-male-infertility-status-integration-and-future-prospects
#16
Ashima Sinha, Virendra Singh, Savita Yadav
Within the cell, gene expression analysis is the key to gain information about  different cellular and physiological events. The multifaceted route of fertilization is a combination of different processes, which include production, maturation and ejaculation of the sperm, its travel through the female genital tract, followed by the ultimate fusion of the fertile sperm with the egg. Early embryogenesis and gametogenesis as well as gene expression at tissue level and global gene silencing are under different levels of stringent epigenetic checks...
June 1, 2017: Frontiers in Bioscience (Scholar Edition)
https://www.readbyqxmd.com/read/28404986/ecology-of-cold-environments-new-insights-of-bacterial-metabolic-adaptation-through-an-integrated-genomic-phenomic-approach
#17
Stefano Mocali, Carolina Chiellini, Arturo Fabiani, Silvia Decuzzi, Donatella de Pascale, Ermenegilda Parrilli, Maria Luisa Tutino, Elena Perrin, Emanuele Bosi, Marco Fondi, Angelina Lo Giudice, Renato Fani
Cold environments dominate Earth's biosphere, hosting complex microbial communities with the ability to thrive at low temperatures. However, the underlying molecular mechanisms and the metabolic pathways involved in bacterial cold-adaptation mechanisms are still not fully understood. Herein, we assessed the metabolic features of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125), a model organism for cold-adaptation, at both 4 °C and 15 °C, by integrating genomic and phenomic (high-throughput phenotyping) data and comparing the obtained results to the taxonomically related Antarctic bacterium Pseudoalteromonas sp...
April 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28402545/orio-online-resource-for-integrative-omics-a-web-based-platform-for-rapid-integration-of-next-generation-sequencing-data
#18
Christopher A Lavender, Andrew J Shapiro, Adam B Burkholder, Brian D Bennett, Karen Adelman, David C Fargo
Established and emerging next generation sequencing (NGS)-based technologies allow for genome-wide interrogation of diverse biological processes. However, accessibility of NGS data remains a problem, and few user-friendly resources exist for integrative analysis of NGS data from different sources and experimental techniques. Here, we present Online Resource for Integrative Omics (ORIO; https://orio.niehs.nih.gov/), a web-based resource with an intuitive user interface for rapid analysis and integration of NGS data...
April 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28401970/integrating-multiple-omics-data-for-the-discovery-of-potential-beclin-1-interactions-in-breast-cancer
#19
Yi Chen, Xuan Wang, Guan Wang, Zhaozhi Li, Jinjin Wang, Lingyu Huang, Ziyi Qin, Xiang Yuan, Zhong Cheng, Shu Zhang, Yiqiong Yin, Jun He
Breast cancer has been reported as one of the most frequently diagnosed malignant diseases and the leading cause of cancer death in women all around the world. Furthermore, this complicated cancer is divided into multiple subtypes which present different clinical symptoms and need correspondingly directed therapy. We took BECN1, a core gene in autophagy performing a tumor inhibitory effect, as a starting point. The study in this paper aims to identify genes related to breast cancer and its multiple subtypes by integrating multiple omics data using the least absolute shrinkage and selection operator (LASSO), which is a statistical method that can integrate more than two types of omics data...
April 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28397398/proteomic-profile-of-mabuya-sp-squamata-scincidae-ovary-and-placenta-during-gestation
#20
Nathaly Hernández-Díaz, Rodrigo Torres, Martha Patricia Ramírez-Pinilla
Reptiles are one of the most diverse groups of vertebrates, providing an integrated system for comparative studies on metabolic, animal physiology, and developmental biology. However, the molecular data available are limited and only recently have started to call attention in the "omics" sciences. Mabuya sp. is a viviparous placentrotrophic skink with particular reproductive features, including microlecithal eggs, early luteolysis, prolonged gestation, and development of a highly specialized placenta. This placenta is responsible for respiratory exchange and the transference of all nutrients necessary for embryonic development...
April 11, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
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