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Omics: a Journal of Integrative Biology

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https://www.readbyqxmd.com/read/28873029/cyp450-genotype-phenotype-concordance-in-mexican-amerindian-indigenous-populations-where-to-from-here-for-global-precision-medicine
#1
Fernando de Andrés, Martha Sosa Macías, Blanca Patricia Lazalde Ramos, María-Eugenia G Naranjo, Adrián LLerena
Global precision medicine demands characterization of drug metabolism and phenotype variation in diverse populations, including the indigenous societies. A related question is the extent to which CYP450 drug metabolizing enzyme genotype and phenotype data are concordant and whether they can be used interchangeably. These issues are increasingly debated as precision medicine continues to expand as a popular research topic worldwide. We report here the first study in clinically relevant CYP450 drug metabolism phenotypes and genotypes in Mexican Amerindian indigenous subjects...
September 5, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28873018/tip60-histone-acetyltransferase-in-adipose-tissue-possible-linkages-with-breast-cancer-development
#2
Gaëlle Judes, Lucas Dubois, Khaldoun Rifaï, Marine Daures, Mouhamed Idrissou, Yves-Jean Bignon, Frédérique Penault-Llorca, Dominique Bernard-Gallon
No abstract text is available yet for this article.
September 5, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28873014/impact-of-preanalytical-variations-in-blood-derived-biospecimens-on-omics-studies-toward-precision-biobanking
#3
Jae-Eun Lee, Young-Youl Kim
Research data and outcomes do vary across populations and persons, but this is not always due to experimental or true biological variation. Preanalytical components of experiments, be they biospecimen acquisition, preparation, storage, or transportation to the laboratory, may all contribute to apparent variability in research data, outcomes, and interpretation. The present review article and biobanking innovation analysis offer new insights with a summary of such preanalytical variables, for example, the type of blood collection tube, centrifugation conditions, long-term sample storage temperature, and duration, on output of omics analyses of blood-derived biospecimens: whole blood, serum, plasma, buffy coat, and peripheral blood mononuclear cells...
September 5, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28873011/response-to-blood-meal-in-the-fat-body-of-anopheles-stephensi-using-quantitative-proteomics-toward-new-vector-control-strategies-against-malaria
#4
Manish Kumar, Ajeet Kumar Mohanty, Sreelakshmi K Sreenivasamurthy, Gourav Dey, Jayshree Advani, Sneha M Pinto, Ashwani Kumar, Thottethodi Subrahmanya Keshava Prasad
Malaria remains a grand challenge for disruptive innovation in global health therapeutics and diagnostics. Anopheles stephensi is one of the major vectors of malaria in Asia. Vector and transmission control are key focus areas in the fight against malaria, a field of postgenomics research where proteomics can play a substantive role. Moreover, to identify novel strategies to control the vector population, it is necessary to understand the vector life processes at a global and molecular scale. In this context, fat body is a vital organ required for vitellogenesis, vector immunity, vector physiology, and vector-parasite interaction...
September 5, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28873001/toward-the-drug-factory-microbiome-microbial-community-variations-in-antibiotic-producing-clean-rooms
#5
Amal M Hamdy, Moamen El-Massry, Mona T Kashef, Magdy A Amin, Ramy K Aziz
Microbiome projects are currently booming around the globe, enabled by advances in culture-independent microbial community analysis and high-throughput sequencing. One emerging application of microbiome science involves exploring microbial diversity in built environments, and one unexplored built environment is the pharmaceutical factory, notably factories producing antibiotics, as they could be enriched in antibiotic-resistant microbes. To examine the drug factory microbiome, we launched this interdisciplinary hypothesis-generating study to benchmark culture-independent microbiome analysis in drug manufacturing units producing antibiotics and nonantibiotic drugs, against traditional microbial identification and quantification techniques...
September 5, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28767318/the-gut-microbiome-and-mental-health-implications-for-anxiety-and-trauma-related-disorders
#6
Stefanie Malan-Muller, Mireia Valles-Colomer, Jeroen Raes, Christopher A Lowry, Soraya Seedat, Sian M J Hemmings
Biological psychiatry research has long focused on the brain in elucidating the neurobiological mechanisms of anxiety- and trauma-related disorders. This review challenges this assumption and suggests that the gut microbiome and its interactome also deserve attention to understand brain disorders and develop innovative treatments and diagnostics in the 21st century. The recent, in-depth characterization of the human microbiome spurred a paradigm shift in human health and disease. Animal models strongly suggest a role for the gut microbiome in anxiety- and trauma-related disorders...
August 2, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28708456/mosquito-borne-diseases-and-omics-tissue-restricted-expression-and-alternative-splicing-revealed-by-transcriptome-profiling-of-anopheles-stephensi
#7
Sreelakshmi K Sreenivasamurthy, Anil K Madugundu, Arun H Patil, Gourav Dey, Ajeet Kumar Mohanty, Manish Kumar, Krishna Patel, Charles Wang, Ashwani Kumar, Akhilesh Pandey, Thottethodi Subrahmanya Keshava Prasad
Malaria is one of the most debilitating mosquito-borne diseases with high global health burdens. While much of the research on malaria and mosquito-borne diseases is focused on Africa, Southeast Asia accounts for a sizable portion of the global burden of malaria. Moreover, about 50% of the Asian malaria incidence and deaths have been from India. A promising development in this context is that the completion of genome sequence of Anopheles stephensi, a major malaria vector in Asia, offers new opportunities for global health innovation, including the progress in deciphering the vectorial ability of this mosquito species at a molecular level...
July 14, 2017: Omics: a Journal of Integrative Biology
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
#8
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/28816646/chronic-cigarette-smoke-mediated-global-changes-in-lung-mucoepidermoid-cells-a-phosphoproteomic-analysis
#9
Hitendra S Solanki, Jayshree Advani, Aafaque Ahmad Khan, Aneesha Radhakrishnan, Nandini A Sahasrabuddhe, Sneha M Pinto, Xiaofei Chang, Thottethodi Subrahmanya Keshava Prasad, Premendu Prakash Mathur, David Sidransky, Harsha Gowda, Aditi Chatterjee
Proteomics analysis of chronic cigarette smoke exposure is a rapidly emerging postgenomics research field. While smoking is a major cause of lung cancer, functional studies using proteomics approaches could enrich our mechanistic understanding of the elusive lung cancer global molecular signaling and cigarette smoke relationship. We report in this study on a stable isotope labeling by amino acids in cell culture-based quantitative phosphoproteomic analysis of a human lung mucoepidermoid carcinoma cell line, H292 cells, chronically exposed to cigarette smoke...
August 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28816645/a-systems-model-of-parkinson-s-disease-using-biochemical-systems-theory
#10
Hemalatha Sasidharakurup, Nidheesh Melethadathil, Bipin Nair, Shyam Diwakar
Parkinson's disease (PD), a neurodegenerative disorder, affects millions of people and has gained attention because of its clinical roles affecting behaviors related to motor and nonmotor symptoms. Although studies on PD from various aspects are becoming popular, few rely on predictive systems modeling approaches. Using Biochemical Systems Theory (BST), this article attempts to model and characterize dopaminergic cell death and understand pathophysiology of progression of PD. PD pathways were modeled using stochastic differential equations incorporating law of mass action, and initial concentrations for the modeled proteins were obtained from literature...
August 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28816644/cyp2b6-haplotype-predicts-efavirenz-plasma-concentration-in-black-south-african-hiv-1-infected-children-a-longitudinal-pediatric-pharmacogenomic-study
#11
Riaan Reay, Collet Dandara, Michelle Viljoen, Malie Rheeders
South Africa has the highest burden of the human immunodeficiency virus (HIV) infection globally. Efavirenz (EFV), a frequently used drug against HIV infection, displays a relationship between drug concentration and pharmacodynamics effects clinically. However, haplotype-based genetic variation in drug metabolism in a pediatric sample has been little considered in a longitudinal long-term context. CYP2B6 plays a key role in variation of EFV plasma concentration through altered drug metabolism. We report here on a prospective clinical pharmacogenomics/pharmacokinetic study of Bantu-speaking children, importantly, over a period of 24 months post-initiation of EFV-based treatment in South Africa...
August 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28816643/pharmacometabolomics-informs-quantitative-radiomics-for-glioblastoma-diagnostic-innovation
#12
Theodora Katsila, Minos-Timotheos Matsoukas, George P Patrinos, Dimitrios Kardamakis
Applications of omics systems biology technologies have enormous promise for radiology and diagnostics in surgical fields. In this context, the emerging fields of radiomics (a systems scale approach to radiology using a host of technologies, including omics) and pharmacometabolomics (use of metabolomics for patient and disease stratification and guiding precision medicine) offer much synergy for diagnostic innovation in surgery, particularly in neurosurgery. This synthesis of omics fields and applications is timely because diagnostic accuracy in central nervous system tumors still challenges decision-making...
August 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28816642/proteomic-analysis-of-the-human-olfactory-bulb
#13
Manjunath Dammalli, Gourav Dey, Anil K Madugundu, Manish Kumar, Benvil Rodrigues, Harsha Gowda, Bychapur Gowrishankar Siddaiah, Anita Mahadevan, Susarla Krishna Shankar, Thottethodi Subrahmanya Keshava Prasad
The importance of olfaction to human health and disease is often underappreciated. Olfactory dysfunction has been reported in association with a host of common complex diseases, including neurological diseases such as Alzheimer's disease and Parkinson's disease. For health, olfaction or the sense of smell is also important for most mammals, for optimal engagement with their environment. Indeed, animals have developed sophisticated olfactory systems to detect and interpret the rich information presented to them to assist in day-to-day activities such as locating food sources, differentiating food from poisons, identifying mates, promoting reproduction, avoiding predators, and averting death...
August 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28692419/long-term-cigarette-smoke-exposure-and-changes-in-mirna-expression-and-proteome-in-non-small-cell-lung-cancer
#14
Jayshree Advani, Yashwanth Subbannayya, Krishna Patel, Aafaque Ahmad Khan, Arun H Patil, Ankit P Jain, Hitendra S Solanki, Aneesha Radhakrishnan, Sneha M Pinto, Nandini A Sahasrabuddhe, Joji K Thomas, Premendu P Mathur, Bipin G Nair, Xiaofei Chang, T S Keshava Prasad, David Sidransky, Harsha Gowda, Aditi Chatterjee
Chronic exposure to cigarette smoke markedly increases the risk for lung cancer. Regulation of gene expression at the post-transcriptional level by miRNAs influences a variety of cancer-related interactomes. Yet, relatively little is known on the effects of long-term cigarette smoke exposure on miRNA expression and gene regulation. NCI-H292 (H292) is a cell line sensitive to cigarette smoke with mucoepidermoid characteristics in culture. We report, in this study, original observations on long-term (12 months) cigarette smoke effects in the H292 cell line, using microarray-based miRNA expression profiling, and stable isotopic labeling with amino acids in cell culture-based quantitative proteomic analysis...
July 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28692418/contribution-of-genetic-polymorphisms-and-haplotypes-in-drd2-bdnf-and-opioid-receptors-to-heroin-dependence-and-endophenotypes-among-the-han-chinese
#15
Xuan Gao, Youxin Wang, Minglin Lang, Li Yuan, Albert Stuart Reece, Wei Wang
Heroin and drug dependence are major contributors to global health burden worldwide, but their underlying mechanisms remain elusive and may vary from population to population. Reward- and memory-related candidate genes dopamine D2 receptor (DRD2) and brain-derived neurotrophic factor (BDNF), as well as the opioid receptor genes (OPRM1, OPRD1, and OPRK1), have been implicated in drug dependence, but relatively little is known on their contributions to heroin dependence in populations worldwide. Hence, we evaluated the contributions of the above five candidate genes in heroin dependence and several important related endophenotypes (the onset age of heroin use and subjective response to first heroin use), at single single-nucleotide polymorphism as well as haplotype levels, in a Han Chinese population sample...
July 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28692417/hypothesis-are-there-molecular-signatures-of-yoga-practice-in-peripheral-blood-mononuclear-cells
#16
Dilara Ayyildiz, Kazim Yalcin Arga
No abstract text is available yet for this article.
July 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28692416/immunoglobulin-g-n-glycans-as-potential-postgenomic-biomarkers-for-hypertension-in-the-kazakh-population
#17
Qing Gao, Mamatyusupu Dolikun, Jerko Štambuk, Hao Wang, Feifei Zhao, Nizam Yiliham, Youxin Wang, Irena Trbojević-Akmačić, Jie Zhang, Honghong Fang, Yang Sun, Hongli Peng, Zhongyao Zhao, Di Liu, Jiaonan Liu, Qihuan Li, Qi Sun, Lijuan Wu, Gordan Lauc, Wei Wang, Manshu Song
Next-generation (postgenomic) biomarkers from the nascent field of glycomics now offer fresh vistas for innovation in chronic disease biomarkers and system diagnostics in clinical medicine. Our previous work has shown an association between hypertension and immunoglobulin G (IgG) glycome composition, suggesting that individual variation in N-glycosylation of IgG might contribute to hypertension pathogenesis. The present study examined, for the first time to the best of our knowledge, the IgG N-glycans as potential biomarkers for hypertension in the Kazakh population...
July 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28692415/whole-genome-sequencing-of-mycobacterium-tuberculosis-isolates-from-extrapulmonary-sites
#18
Kusum Sharma, Renu Verma, Jayshree Advani, Oishi Chatterjee, Hitendra S Solanki, Aman Sharma, Subhash Varma, Manish Modi, Pallab Ray, Kanchan K Mukherjee, Megha Sharma, Mandeed Singh Dhillion, Mrutyunjay Suar, Aditi Chatterjee, Akhilesh Pandey, Thottethodi Subrahmanya Keshava Prasad, Harsha Gowda
Tuberculosis (TB) remains one of the leading causes of morbidity and mortality worldwide. Extrapulmonary tuberculosis (EPTB) constitutes around 15-20% of TB cases in immunocompetent individuals. Extrapulmonary sites that are affected by TB include bones, lymph nodes, meningitis, pleura, and genitourinary tract. Whole genome sequencing has emerged as a powerful tool to map genetic diversity among Mycobacterium tuberculosis (MTB) isolates and identify the genomic signatures associated with drug resistance, pathogenesis, and disease transmission...
July 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28622116/a-general-theory-for-post-systems-biology-iatromics-and-the-environtome
#19
Nezih Hekim, Vural Özdemir
No abstract text is available yet for this article.
July 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28618245/multi-omics-integrative-investigation-of-fatty-acid-metabolism-in-obese-and-lean-subcutaneous-tissue
#20
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...
July 2017: Omics: a Journal of Integrative Biology
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