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https://www.readbyqxmd.com/read/29440596/multi-omics-driven-assembly-and-annotation-of-the-sandalwood-santalum-album-genome
#1
H B Mahesh, Pratigya Subba, Jayshree Advani, Meghana Deepak Shirke, Ramya Malarini Loganathan, S Chandana, S Shilpa, Oishi Chatterjee, Sneha M Pinto, Keshava Prasad, Malali Gowda
Santalum album (Indian sandalwood) is an important tropical evergreen tree, known for its fragrant heartwood-derived essential oil and its valuable carving wood. Here, we applied an integrated genomic, transcriptomic, and proteomic approach to assemble and annotate the Indian sandalwood genome. Our genome sequencing resulted in the establishment of a draft map of the smallest genome for any woody tree species to date (221 Mb). The genome annotation predicted 38,119 protein-coding genes and 27.42% repetitive DNA elements...
February 12, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29438696/the-integrated-genomic-landscape-of-thymic-epithelial-tumors
#2
Milan Radovich, Curtis R Pickering, Ina Felau, Gavin Ha, Hailei Zhang, Heejoon Jo, Katherine A Hoadley, Pavana Anur, Jiexin Zhang, Mike McLellan, Reanne Bowlby, Thomas Matthew, Ludmila Danilova, Apurva M Hegde, Jaegil Kim, Mark D M Leiserson, Geetika Sethi, Charles Lu, Michael Ryan, Xiaoping Su, Andrew D Cherniack, Gordon Robertson, Rehan Akbani, Paul Spellman, John N Weinstein, D Neil Hayes, Ben Raphael, Tara Lichtenberg, Kristen Leraas, Jean Claude Zenklusen, Junya Fujimoto, Cristovam Scapulatempo-Neto, Andre L Moreira, David Hwang, James Huang, Mirella Marino, Robert Korst, Giuseppe Giaccone, Yesim Gokmen-Polar, Sunil Badve, Arun Rajan, Philipp Ströbel, Nicolas Girard, Ming S Tsao, Alexander Marx, Anne S Tsao, Patrick J Loehrer
Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis...
February 12, 2018: Cancer Cell
https://www.readbyqxmd.com/read/29434260/circulating-exosomal-micrornas-reveal-the-mechanism-of-fructus-meliae-toosendan-induced-liver-injury-in-mice
#3
Jie Zheng, Lingqi Yu, Wen Chen, Xiaoyan Lu, Xiaohui Fan
The toxicological mechanisms of liver injury caused by most traditional Chinese medicine (TCM) remain largely unknown. Due to the unique features, exosomal microRNAs (miRNAs) are currently attracting major interests to provide further insights into toxicological mechanisms. Thus, taking Fructus Meliae Toosendan as an example of hepatoxic TCM, this study aimed to elucidate its hepatotoxicity mechanisms through profiling miRNAs in circulating exosomes of Fructus Meliae Toosendan water extract (FMT)-exposed mice...
February 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29432895/a-cross-omics-approach-to-investigate-temporal-gene-expression-regulation-by-5-hydroxymethylcytosine-via-tbh-derived-oxidative-stress-showed-involvement-of-different-regulatory-kinases
#4
Jacob J Briedé, Lize Deferme, Jarno E J Wolters, Sandra M H Claessen, Twan van den Beucken, J Richard Wagner, Simone G van Breda, Jos C S Kleinjans
Regulation of DNA methylation plays a crucial role in biological processes and carcinogenesis. The formation of 5-hydroxymethylcytosine (5hmC) by oxidation of 5-methylcytosine (5mC) has been proposed as an intermediate of active demethylation. However, whether and how active demethylation is regulated by oxidative stress-related processes is not well understood. Here we investigated whether free oxygen radicals are capable of directly forming 5hmC and how this enhanced whole genome gene expression. We applied LC-MS/MS technology for the analysis of 5mC, 5hmC, 5-formylcytosine (5fC) and 5-hydroxymethyluracyl (5hmU) in HepG2 cells exposed to hydroxyl- and methyl radicals, formed by tert-butyl hydroperoxide (TBH) at multiple time points...
February 9, 2018: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/29431584/horizon-scanning-how-will-metabolomics-applications-transform-food-science-bioengineering-and-medical-innovation-in-the-current-era-of-foodomics
#5
Mustafa Bayram, Çağlar Gökırmaklı
Food and engineering sciences have tended to neglect the importance of human nutrition sciences and clinical study of new molecules discovered by food engineering community, and vice versa. Yet, the value of systems thinking and use of omics technologies in food engineering are rapidly emerging. Foodomics is a new concept and practice to bring about "precision nutrition" and integrative bioengineering studies of food composition, quality, and safety, and applications to improve health of humans, animals, and other living organisms on the planet...
February 12, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29429018/mobcdb-a-comprehensive-database-integrating-multi-omics-data-on-breast-cancer-for-precision-medicine
#6
Bingbing Xie, Zifeng Yuan, Yadong Yang, Zhidan Sun, Shuigeng Zhou, Xiangdong Fang
BACKGROUND: Breast cancer is one of the most frequently diagnosed cancers among women worldwide, characterized by diverse biological heterogeneity. It is well known that complex and combined gene regulation of multi-omics is involved in the occurrence and development of breast cancer. RESULTS: In this paper, we present the Multi-Omics Breast Cancer Database (MOBCdb), a simple and easily accessible repository that integrates genomic, transcriptomic, epigenomic, clinical, and drug response data of different subtypes of breast cancer...
February 10, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29428571/integrative-expression-quantitative-trait-locus-based-analysis-of-colorectal-cancer-identified-a-functional-polymorphism-regulating-slc22a5-expression
#7
Danyi Zou, Jiao Lou, Juntao Ke, Shufang Mei, Jiaoyuan Li, Yajie Gong, Yang Yang, Ying Zhu, Jianbo Tian, Jiang Chang, Rong Zhong, Jing Gong, Xiaoping Miao
Multiple single nucleotide polymorphisms (SNPs) have been found to be highly correlated with colorectal cancer (CRC) risk. However, the variants identified thus far only explain a small part of the cases, suggesting the existence of many uncharacterised genetic determinants. In this study, using the multilevel 'omics' data provided in The Cancer Genome Atlas, we systematically performed expression quantitative trait locus (eQTL) analysis for CRC and identified nine SNPs with significant effects on mRNA expression (correlation |r| > 0...
February 8, 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29428530/rotenone-exerts-developmental-neurotoxicity-in-a-human-brain-spheroid-model
#8
David Pamies, Katharina Block, Pierre Lau, Laura Gribaldo, Carlos Pardo, Paula Barreras, Lena Smirnova, Daphne Wiersma, Liang Zhao, Georgina Harris, Thomas Hartung, Helena T Hogberg
Growing concern suggests that some chemicals exert (developmental) neurotoxicity (DNT and NT) and are linked to the increase in incidence of autism, attention deficit and hyperactivity disorders. The high cost of routine tests for DNT and neurotoxicity (NT) assessment make it difficult to test the high numbers of existing chemicals. Thus, more cost effective neurodevelopmental models are needed. The use of induced pluripotent stem cells (iPSC) in combination with the emerging human 3D tissue culture platforms, present a novel tool to predicting and study human toxicity...
February 8, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29427518/multi-omics-approach-to-elucidate-the-gut-microbiota-activity-metaproteomics-and-metagenomics-connection
#9
Maria Guirro, Andrea Costa, Andreu Gual-Grau, Jordi Mayneris-Perxachs, Helena Torrell, Pol Herrero, Núria Canela, Lluís Arola
Over the last few years, the application of high-throughput meta-omics methods has provided great progress in improving the knowledge of the gut ecosystem and linking its biodiversity to host health conditions, offering complementary support to classical microbiology. Gut microbiota plays a crucial role in relevant diseases such as obesity or cardiovascular disease, and its regulation be closely influenced by several factors, such as dietary composition. In fact, polyphenol-rich diets are the most palatable treatment to prevent hypertension associated with cardiovascular disease, although the polyphenol-microbiota interactions have not been completely elucidated...
February 10, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29426915/reference-gene-selection-for-rt-qpcr-analysis-in-harmonia-axyridis-a-global-invasive-lady-beetle
#10
Xiaowei Yang, Huipeng Pan, Ling Yuan, Xuguo Zhou
Harmonia axyridis is a voracious predator, a biological control agent, and one of the world most invasive insect species. The advent of next-generation sequencing platforms has propelled entomological research into the genomics and post-genomics era. Real-time quantitative PCR (RT-qPCR), a primary tool for gene expression analysis, is a core technique governs the genomic research. The selection of internal reference genes, however, can significantly impact the interpretation of RT-qPCR results. The overall goal of this study is to identify the reference genes in the highly invasive H...
February 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29424662/small-rna-omics-for-virome-reconstruction-and-antiviral-defense-characterization-in-mixed-infections-of-cultivated-solanum-plants
#11
Silvia Turco, Victor Golyaev, Jonathan Seguin, Céline Gilli, Laurent Farinelli, Thomas Boller, Oliveir Schumpp, Mikhail Pooggin
In plants, RNA silencing-based antiviral defense generates viral small RNAs (sRNAs) faithfully representing the viral genomes. We employed sRNA sequencing and bioinformatics (sRNA-omics) to characterize antiviral defense and to reconstruct the full genomic sequences and their variants in the evolving viral quasispecies in cultivated solanaceous plants carrying mixed infections. In naturally-infected Solanum tuberosum (potato), one case study revealed a virome comprising Potato virus Y (genus Potyvirus) and Potato virus X (genus Potexvirus), which was reconstructed by de novo assembling separate genome-size sRNA contigs...
February 9, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29423275/a-roadmap-towards-personalized-immunology
#12
Sylvie Delhalle, Sebastian F N Bode, Rudi Balling, Markus Ollert, Feng Q He
Big data generation and computational processing will enable medicine to evolve from a "one-size-fits-all" approach to precise patient stratification and treatment. Significant achievements using "Omics" data have been made especially in personalized oncology. However, immune cells relative to tumor cells show a much higher degree of complexity in heterogeneity, dynamics, memory-capability, plasticity and "social" interactions. There is still a long way ahead on translating our capability to identify potentially targetable personalized biomarkers into effective personalized therapy in immune-centralized diseases...
2018: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/29420853/updates-on-resources-software-tools-and-databases-for-plant-proteomics-in-2016-2017
#13
REVIEW
Biswapriya B Misra
Proteomics data processing, annotation, and analysis can often lead to major hurdles in large-scale high throughput bottom-up proteomics experiments. Given the recent rise in protein-based big datasets being generated, efforts in in silico tool development occurrences have had an unprecedented increase; so much so, that it has become increasingly difficult to keep track of all the advances in a particular academic year. However, these tools benefit the proteomics community in circumventing critical issues in data analysis and visualization, as these continually developing one-source and community-developed tools hold potential in future research efforts...
February 8, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29417942/full-genetic-analysis-for-genome-wide-association-study-of-fangji-a-powerful-approach-for-effectively-dissecting-the-molecular-architecture-of-personalized-traditional-chinese-medicine
#14
REVIEW
Gang Chen, Wen-da Xue, Jun Zhu
Elucidation of the systems biology foundation underlying the effect of Fangji, which are multi-herbal traditional Chinese medicine (TCM) formulas, is one of the major aims in the field. The numerous bioactive ingredients of a Fangji deal with the multiple targets of a complex disease, which is influenced by a number of genes and their interactions with the environment. Genome-wide association study (GWAS) is an unbiased approach for dissecting the genetic variants underlying complex diseases and individual response to a given treatment...
February 8, 2018: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/29417741/how-can-omic-science-be-improved
#15
Kai Simons
One of the promises of multiomic analysis was to transform the clinical diagnostics to deliver much more exact phenotyping of disease states. However, despite enormous investments, the transformation of clinical routine has not taken place. There are many reasons for this lack of success but one is the failure to deliver quantitative and reproducible data. This failure is not only impeding progress in clinical phenotyping but also in the application of omic science in systems biology. The focus in this Viewpoint will be on lipidomics but the lessons learned are generally applicable...
February 8, 2018: Proteomics
https://www.readbyqxmd.com/read/29415010/shinygispa-a-web-application-for-characterizing-phenotype-by-gene-sets-using-multiple-omics-data-combinations
#16
Bhakti Dwivedi, Jeanne Kowalski
While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to their similarity in several molecular changes that are driving a disease phenotype. This tool was developed to help facilitate the usability of a previously published method, Gene Integrated Set Profile Analysis (GISPA), among researchers with limited computer-programming skills...
2018: PloS One
https://www.readbyqxmd.com/read/29412690/platelet-procoagulant-phenotype-is-modulated-by-a-p38-mk2-axis-regulating-rtn4-nogo-proximal-to-the-endoplasmic-reticulum-utility-of-pathway-analysis
#17
Özgün Babur, Anh T P Ngo, Rachel A Rigg, Jiaqing Pang, Zhoe T Rub, Ariana E Buchanan, Annachiara Mitrugno, Larry L David, Owen J T McCarty, Emek Demir, Joseph E Aslan
Upon encountering physiological cues associated with damaged or inflamed endothelium, blood platelets set forth intracellular responses to ultimately support hemostatic plug formation and vascular repair. To gain insights into the molecular events underlying platelet function, we used a combination of interactome, pathway analysis and other systems biology tools to analyze associations amongst proteins functionally modified by reversible phosphorylation upon platelet activation. While an interaction analysis mapped out a relative organization of intracellular mediators in platelet signaling, pathway analysis revealed directional signaling relations around protein kinase C (PKC) isoforms and mitogen activated protein kinases (MAPKs) associated with platelet cytoskeletal dynamics, inflammatory responses and hemostatic function...
February 7, 2018: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/29404426/omics-based-insights-into-flavor-development-and-microbial-succession-within-surface-ripened-cheese
#18
A S Bertuzzi, A M Walsh, J J Sheehan, P D Cotter, F Crispie, P L H McSweeney, K N Kilcawley, M C Rea
In this study, a young Cheddar curd was used to produce two types of surface-ripened cheese, using two commercial smear-culture mixes of yeasts and bacteria. Whole-metagenome shotgun sequencing was used to screen the microbial population within the smear-culture mixes and on the cheese surface, with comparisons of microorganisms at both the species and the strain level. The use of two smear mixes resulted in the development of distinct microbiotas on the surfaces of the two test cheeses. In one case, most of the species inoculated on the cheese established themselves successfully on the surface during ripening, while in the other, some of the species inoculated were not detected during ripening and the most dominant bacterial species, Glutamicibacter arilaitensis, was not a constituent of the culture mix...
January 2018: MSystems
https://www.readbyqxmd.com/read/29401451/broad-views-of-non-alcoholic-fatty-liver-disease
#19
Adil Mardinoglu, Mathias Uhlen, Jan Borén
Multi-omics multi-tissue data are used to interpret genome-wide association study results from mice to identify key driver genes of non-alcoholic fatty liver disease. Non-alcoholic fatty liver disease (NAFLD) is the accumulation of fat (steatosis) in the liver due to causes other than excessive alcohol consumption. The disease may progress to more severe forms of liver diseases, including non-alcoholic steatohepatitis, cirrhosis, and hepatocellular carcinoma. In this issue of Cell Systems, Krishnan et al. (2018) reveal mechanisms underlying NAFLD by generating multi-omics data using liver and adipose tissues obtained from the Hybrid Mouse Diversity Panel, consisting of 113 mouse strains with various degrees of NAFLD...
January 24, 2018: Cell Systems
https://www.readbyqxmd.com/read/29399631/dna-methylation-as-a-mediator-of-the-association-between-prenatal-adversity-and-risk-factors-for-metabolic-disease-in-adulthood
#20
Elmar W Tobi, Roderick C Slieker, René Luijk, Koen F Dekkers, Aryeh D Stein, Kate M Xu, P Eline Slagboom, Erik W van Zwet, L H Lumey, Bastiaan T Heijmans
Although it is assumed that epigenetic mechanisms, such as changes in DNA methylation (DNAm), underlie the relationship between adverse intrauterine conditions and adult metabolic health, evidence from human studies remains scarce. Therefore, we evaluated whether DNAm in whole blood mediated the association between prenatal famine exposure and metabolic health in 422 individuals exposed to famine in utero and 463 (sibling) controls. We implemented a two-step analysis, namely, a genome-wide exploration across 342,596 cytosine-phosphate-guanine dinucleotides (CpGs) for potential mediators of the association between prenatal famine exposure and adult body mass index (BMI), serum triglycerides (TG), or glucose concentrations, which was followed by formal mediation analysis...
January 2018: Science Advances
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