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https://www.readbyqxmd.com/read/29470489/integration-of-machine-learning-and-meta-analysis-identifies-the-transcriptomic-bio-signature-of-mastitis-disease-in-cattle
#1
Somayeh Sharifi, Abbas Pakdel, Mansour Ebrahimi, James M Reecy, Samaneh Fazeli Farsani, Esmaeil Ebrahimie
Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the main agents that cause severe mastitis disease with clinical signs in dairy cattle. Rapid detection of this disease is so important in order to prevent transmission to other cows and helps to reduce inappropriate use of antibiotics. With the rapid progress in high-throughput technologies, and accumulation of various kinds of '-omics' data in public repositories, there is an opportunity to retrieve, integrate, and reanalyze these resources to improve the diagnosis and treatment of different diseases and to provide mechanistic insights into host resistance in an efficient way...
2018: PloS One
https://www.readbyqxmd.com/read/29470400/ramp-a-comprehensive-relational-database-of-metabolomics-pathways-for-pathway-enrichment-analysis-of-genes-and-metabolites
#2
Bofei Zhang, Senyang Hu, Elizabeth Baskin, Andrew Patt, Jalal K Siddiqui, Ewy A Mathé
The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful...
February 22, 2018: Metabolites
https://www.readbyqxmd.com/read/29468972/investigating-hiv-human-interaction-networks-to-unravel-pathogenic-mechanism-for-drug-discovery-a-systems-biology-approach
#3
Cheng-Wei Li, Bor-Sen Chen
BACKGROUND: Two big issues in the study of pathogens are determining how pathogens infect hosts and how the host defends itself against infection. Therefore, investigating host-pathogen interactions is important for understanding pathogenicity and host defensive mechanisms and treating infections. METHODS: In this study, we used omics data, including time-course data from high throughput sequencing, real-time polymerase chain reaction, and human microRNA (miRNA) and protein-protein interaction to construct an interspecies protein-protein and miRNA interaction (PPMI) network of human CD4+ T cells during HIV-1 infection through system modeling and identification...
February 19, 2018: Current HIV Research
https://www.readbyqxmd.com/read/29467935/a-robust-gene-expression-based-prognostic-risk-score-predicts-overall-survival-of-lung-adenocarcinoma-patients
#4
En-Guo Chen, Pin Wang, Haizhou Lou, Yunshan Wang, Hong Yan, Lei Bi, Liang Liu, Bin Li, Antoine M Snijders, Jian-Hua Mao, Bo Hang
Identification of reliable predictive biomarkers and new therapeutic targets is a critical step for significant improvement in patient outcomes. Here, we developed a multi-step bioinformatics analytic strategy to mine large omics and clinical data to build a prognostic scoring system for predicting the overall survival (OS) of lung adenocarcinoma (LuADC) patients. In latter we first identified 1327 significantly and robustly deregulated genes, 600 of which were significantly associated with the OS of LuADC patients...
January 23, 2018: Oncotarget
https://www.readbyqxmd.com/read/29466699/unveiling-network-based-functional-features-through-integration-of-gene-expression-into-protein-networks
#5
REVIEW
Mahdi Jalili, Tom Gebhardt, Olaf Wolkenhauer, Ali Salehzadeh-Yazdi
Decoding health and disease phenotypes is one of the fundamental objectives in biomedicine. Whereas high-throughput omics approaches are available, it is evident that any single omics approach might not be adequate to capture the complexity of phenotypes. Therefore, integrated multi-omics approaches have been used to unravel genotype-phenotype relationships such as global regulatory mechanisms and complex metabolic networks in different eukaryotic organisms. Some of the progress and challenges associated with integrated omics studies have been reviewed previously in comprehensive studies...
February 18, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29465290/global-integrated-analysis-of-methylomes-and-transcriptomes-from-laser-capture-microdissected-bronchial-and-alveolar-cells-in-human-lung
#6
Xiao Dong, Miao Shi, Moonsook Lee, Rafael Toro, Silvia Gravina, Weiguo Han, Shoya Yasuda, Tao Wang, Zhengdong Zhang, Jan Vijg, Yousin Suh, Simon D Spivack
Gene regulatory analysis of highly diverse human tissues in vivo is essentially constrained by the challenge of performing genome-wide, integrated epigenetic and transcriptomic analysis in small selected groups of specific cell types. Here we performed genome-wide bisulfite sequencing and RNA-seq from the same small groups of bronchial and alveolar cells isolated by laser capture microdissection from flash-frozen lung tissue of 12 donors and their peripheral blood T cells. Methylation and transcriptome patterns differed between alveolar and bronchial cells, while each of these epithelia showed more differences from mesodermally-derived T cells...
February 21, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29459480/occupational-exposure-to-pesticides-is-associated-with-differential-dna-methylation
#7
Diana A van der Plaat, Kim de Jong, Maaike de Vries, Cleo C van Diemen, Ivana Nedeljković, Najaf Amin, Hans Kromhout, Roel Vermeulen, Dirkje S Postma, Cornelia M van Duijn, H Marike Boezen, Judith M Vonk
OBJECTIVES: Occupational pesticide exposure is associated with a wide range of diseases, including lung diseases, but it is largely unknown how pesticides influence airway disease pathogenesis. A potential mechanism might be through epigenetic mechanisms, like DNA methylation. Therefore, we assessed associations between occupational exposure to pesticides and genome-wide DNA methylation sites. METHODS: 1561 subjects of LifeLines were included with either no (n=1392), low (n=108) or high (n=61) exposure to any type of pesticides (estimated based on current or last held job)...
February 19, 2018: Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/29458203/precision-pharmacology-for-alzheimer-s-disease
#8
REVIEW
Harald Hampel, Andrea Vergallo, Lisi Flores Aguilar, Norbert Benda, Karl Broich, A Claudio Cuello, Jeffrey Cummings, Bruno Dubois, Howard J Federoff, Massimo Fiandaca, Remy Genthon, Marion Haberkamp, Eric Karran, Mark Mapstone, George Perry, Lon S Schneider, Lindsay A Welikovitch, Janet Woodcock, Filippo Baldacci, Simone Lista
The complex multifactorial nature of polygenic Alzheimer's disease (AD) presents significant challenges for drug development. AD pathophysiology is progressing in a non-linear dynamic fashion across multiple systems levels - from molecules to organ systems - and through adaptation, to compensation, and decompensation to systems failure. Adaptation and compensation maintain homeostasis: a dynamic equilibrium resulting from the dynamic non-linear interaction between genome, epigenome, and environment. An individual vulnerability to stressors exists on the basis of individual triggers, drivers, and thresholds accounting for the initiation and failure of adaptive and compensatory responses...
February 16, 2018: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29457974/a-multi-omics-analysis-of-glycine-max-leaves-reveals-alteration-in-flavonoid-and-isoflavonoid-metabolism-upon-ethylene-and-abscisic-acid-treatment
#9
Ravi Gupta, Cheol Woo Min, Katharina Kramer, Ganesh Kumar Agrawal, Randeep Rakwal, Ki-Hun Park, Yiming Wang, Iris Finkemeier, Sun Tae Kim
Phytohormones are central to the plant growth and development. Despite the advancement in our knowledge of hormone signaling, downstream targets and their interactions upon hormones action remain largely fragmented, especially at the protein and metabolite levels. With an aim to get new insight into the effects of two hormones, ethylene (ET) and abscisic acid (ABA), this study utilizes an integrated proteomics and metabolomics approach to investigate their individual and combined (ABA+ET) signaling in soybean leaves...
February 19, 2018: Proteomics
https://www.readbyqxmd.com/read/29456073/an-integrated-understanding-of-the-rapid-metabolic-benefits-of-a-carbohydrate-restricted-diet-on-hepatic-steatosis-in-humans
#10
Adil Mardinoglu, Hao Wu, Elias Bjornson, Cheng Zhang, Antti Hakkarainen, Sari M Räsänen, Sunjae Lee, Rosellina M Mancina, Mattias Bergentall, Kirsi H Pietiläinen, Sanni Söderlund, Niina Matikainen, Marcus Ståhlman, Per-Olof Bergh, Martin Adiels, Brian D Piening, Marit Granér, Nina Lundbom, Kevin J Williams, Stefano Romeo, Jens Nielsen, Michael Snyder, Mathias Uhlén, Göran Bergström, Rosie Perkins, Hanns-Ulrich Marschall, Fredrik Bäckhed, Marja-Riitta Taskinen, Jan Borén
A carbohydrate-restricted diet is a widely recommended intervention for non-alcoholic fatty liver disease (NAFLD), but a systematic perspective on the multiple benefits of this diet is lacking. Here, we performed a short-term intervention with an isocaloric low-carbohydrate diet with increased protein content in obese subjects with NAFLD and characterized the resulting alterations in metabolism and the gut microbiota using a multi-omics approach. We observed rapid and dramatic reductions of liver fat and other cardiometabolic risk factors paralleled by (1) marked decreases in hepatic de novo lipogenesis; (2) large increases in serum β-hydroxybutyrate concentrations, reflecting increased mitochondrial β-oxidation; and (3) rapid increases in folate-producing Streptococcus and serum folate concentrations...
February 7, 2018: Cell Metabolism
https://www.readbyqxmd.com/read/29454798/functional-bowel-disorders-gastroenterology-s-75-th-anniversary
#11
John W Wiley, Lin Chang
Articles appearing in Gastroenterology have played an integral role in the evolution of our understanding of Functional Bowel Disorders (FBD), including Irritable Bowel Syndrome (IBS), beginning with the prescient contributions of Almy and Tulin in 1947 and 1949 that highlighted the role of stress to enhance perception of abdominal pain and promote colon contractions. Subsequent publications have codified diagnostic criteria and stratified subpopulations of FBD (Manning and ROME I-IV), which resulted in improved symptom-based therapeutic interventions...
February 15, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29450674/risk-assessment-of-pesticides-in-estuaries-a-review-addressing-the-persistence-of-an-old-problem-in-complex-environments
#12
Nagore Cuevas, Marta Martins, Pedro M Costa
Estuaries, coastal lagoons and other transition ecosystems tend to become the ultimate reservoirs of pollutants transported by continental runoff, among which pesticides constitute the class of most concern. High amounts of dissolved and particulated organic matter greatly contribute to the accumulation of pesticides that eventually become trapped in sediments or find their way along food chains. Perhaps not so surprisingly, it is common to find elevated levels of pesticides in estuarine sediments decades after their embargo...
February 15, 2018: Ecotoxicology
https://www.readbyqxmd.com/read/29447068/microbial-culturomics-broadens-human-vaginal-flora-diversity-genome-sequence-and-description-of-prevotella-lascolaii-sp-nov-isolated-from-a-patient-with-bacterial-vaginosis
#13
Khoudia Diop, Awa Diop, Anthony Levasseur, Oleg Mediannikov, Catherine Robert, Nicholas Armstrong, Carine Couderc, Florence Bretelle, Didier Raoult, Pierre-Edouard Fournier, Florence Fenollar
Microbial culturomics is a new subfield of postgenomic medicine and omics biotechnology application that has broadened our awareness on bacterial diversity of the human microbiome, including the human vaginal flora bacterial diversity. Using culturomics, a new obligate anaerobic Gram-stain-negative rod-shaped bacterium designated strain khD1 T was isolated in the vagina of a patient with bacterial vaginosis and characterized using taxonogenomics. The most abundant cellular fatty acids were C 15:0 anteiso (36%), C 16:0 (19%), and C 15:0 iso (10%)...
February 15, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29444308/integration-of-multi-omics-techniques-and-physiological-phenotyping-within-a-holistic-phenomics-approach-to-study-senescence-in-model-and-crop-plants
#14
Dominik K Großkinsky, Syahnada Jaya Syaifullah, Thomas Roitsch
The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence...
February 12, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29441565/metabolomics-and-transcriptomics-profiles-reveal-the-dysregulation-of-the-tricarboxylic-acid-cycle-and-related-mechanisms-in-prostate-cancer
#15
Yaping Shao, Guozhu Ye, Shancheng Ren, Hai-Long Piao, Xinjie Zhao, Xin Lu, Fubo Wang, Ma Wang, Jia Li, Peiyuan Yin, Tian Xia, Chuanliang Xu, Jane J Yu, Yinghao Sun, Guowang Xu
Genetic alterations drive metabolic reprogramming to meet increased biosynthetic precursor and energy demands for cancer cell proliferation and survival in unfavorable environments. A systematic study of gene-metabolite regulatory networks and metabolic dysregulation should reveal the molecular mechanisms underlying prostate cancer (PCa) pathogenesis. Herein, we performed gas chromatography-mass spectrometry (GC-MS)-based metabolomics and RNA-seq analyses in prostate tumors and matched adjacent normal tissues (ANTs) to elucidate the molecular alterations and potential underlying regulatory mechanisms in PCa...
February 14, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29440596/multi-omics-driven-assembly-and-annotation-of-the-sandalwood-santalum-album-genome
#16
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
#17
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
#18
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/29433995/precision-nutrition-for-prevention-and-management-of-type-2-diabetes
#19
REVIEW
Dong D Wang, Frank B Hu
Precision nutrition aims to prevent and manage chronic diseases by tailoring dietary interventions or recommendations to one or a combination of an individual's genetic background, metabolic profile, and environmental exposures. Recent advances in genomics, metabolomics, and gut microbiome technologies have offered opportunities as well as challenges in the use of precision nutrition to prevent and manage type 2 diabetes. Nutrigenomics studies have identified genetic variants that influence intake and metabolism of specific nutrients and predict individuals' variability in response to dietary interventions...
February 9, 2018: Lancet Diabetes & Endocrinology
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
#20
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
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