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Omics: a Journal of Integrative Biology

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https://www.readbyqxmd.com/read/28282257/human-microbiome-and-learning-healthcare-systems-integrating-research-and-precision-medicine-for-inflammatory-bowel-disease
#1
Kim H Chuong, David R Mack, Alain Stintzi, Kieran C O'Doherty
Healthcare institutions face widespread challenges of delivering high-quality and cost-effective care, while keeping up with rapid advances in biomedical knowledge and technologies. Moreover, there is increased emphasis on developing personalized or precision medicine targeted to individuals or groups of patients who share a certain biomarker signature. Learning healthcare systems (LHS) have been proposed for integration of research and clinical practice to fill major knowledge gaps, improve care, reduce healthcare costs, and provide precision care...
March 10, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253088/association-between-telomere-length-chronic-kidney-disease-and-renal-traits-a-systematic-review
#2
Oluwatoyin I Ameh, Ikechi G Okpechi, Collet Dandara, André-Pascal Kengne
Telomere length (TL) is an important biological variable that can influence a variety of disease-related complex traits as well as host-environment interactions such as drug and nutritional responses. Chronic kidney disease (CKD) is a common global health challenge especially with the currently aging world population. We conducted a PubMed database search according to the preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines for systematic reviews. Studies in adults (18 years and above) in which TL was determined and correlated with CKD, renal traits, and function were included, while animal model studies were excluded...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253087/genome-wide-association-studies-for-idiosyncratic-drug-induced-hepatotoxicity-looking-back-looking-forward-to-next-generation-innovation
#3
Zelalem Petros, Eyasu Makonnen, Eleni Aklillu
Idiosyncratic drug-induced hepatotoxicity is a formidable challenge for rational drug discovery and development, as well as the science of personalized medicine. There is evidence that hereditary factors, in part, contribute to drug toxicity. This expert analysis and review offer the insights gained, and the challenges ahead, for genome-wide association studies (GWASs) of idiosyncratic drug-induced hepatotoxicity. Published articles on genome-wide and subsequent replication studies were systematically searched in the PubMed electronic database...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253086/oocyte-developmental-competence-insights-from-cross-species-differential-gene-expression-and-human-oocyte-specific-functional-gene-networks
#4
Fernando H Biase
Understanding oocyte developmental competence remains a key challenge for reproductive biology and systems sciences. The transcriptome of oocytes in eutherians is highly complex and is associated with the success of embryo development. Due to sample limitations from humans, animal models are used for investigation of the oocyte transcriptome. Nonetheless, little is known about the diversity of the oocyte transcriptome across eutherians. In this report, comprehensive investigation of 7 public data sets in 4 species, human, macaque, mice, and cattle, shows that 16,572 genes are expressed in oocytes...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253085/water-pipe-shisha-hookah-arghile-smoking-and-secondhand-tobacco-smoke-effects-on-cyp1a2-and-cyp2a6-phenotypes-as-measured-by-caffeine-urine-test
#5
Şenay Görücü Yılmaz, Adrián Llerena, Fernando De Andrés, Ümit Karakaş, Hasan Gündoğar, Kamile Erciyas, Sabit Kimyon, Alper Mete, Kıvanç Güngör, Vural Özdemir
Public policies to stop or reduce cigarette smoking and exposure to secondhand smoke and associated diseases have yielded successful results over the past decade. Yet, the growing worldwide popularity of another form of tobacco consumption, water pipe smoking, has received relatively less attention. To the best of our knowledge, no study to date has evaluated the effects of water pipe smoking on cytochrome P450 (CYP450) activities and drug interaction potential in humans, whereas only limited information is available on the impact of secondhand smoke on drug metabolism...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253084/organic-cation-transporter-2-oct2-slc22a2-gene-variation-in-the-south-african-bantu-speaking-population-and-functional-promoter-variants
#6
Nina C Wilson, Ananyo Choudhury, Nadia Carstens, Demetra Mavri-Damelin
SLC22A2 facilitates the transport of endogenous and exogenous cationic compounds. Many pharmacologically significant compounds are transported by SLC22A2, including the antidiabetic drug metformin, anticancer agent cisplatin, and antiretroviral lamivudine. Genetic polymorphisms in SLC22A2 can modify the pharmacokinetic profiles of such important medicines and could therefore prove useful as precision medicine biomarkers. Since the frequency of SLC22A2 polymorphisms varies among different ethnic populations, we evaluated these in South African Bantu speakers, a majority group in the South African population, who exhibit unique genetic diversity, and we subsequently functionally characterized promoter polymorphisms...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28157411/novel-lipidomic-biomarkers-in-hyperlipidemia-and-cardiovascular-diseases-an-integrative-biology-analysis
#7
Sneha Rai, Sonika Bhatnagar
Lipidomics is a new frontier of omics research and offers much promise for new-generation biomarkers for common complex phenotypes such as hyperlipidemia (HL) and cardiovascular diseases (CVDs). HL is a disorder characterized by increased levels of blood lipids and is a well-established risk factor for CVD. Traditional clinical markers for prognosis of hyperlipidemic individuals are inadequate to forecast or diagnose cardiac events. In this expert review, lipidomic profiles from recent HL and CVD studies were compared with the normolipidemic profile prepared from the Standard Reference Material...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28186866/toward-postgenomics-ophthalmology-a-proteomic-map-of-the-human-choroid-retinal-pigment-epithelium-tissue
#8
Manjunath Dammalli, Krishna R Murthy, Sneha M Pinto, Kalpana Babu Murthy, Raja Sekhar Nirujogi, Anil K Madugundu, Gourav Dey, Bipin Nair, Harsha Gowda, Thottethodi Subrahmanya Keshava Prasad
Ophthalmology and visual health research have received relatively limited attention from the personalized medicine community, but this trend is rapidly changing. Postgenomics technologies such as proteomics are being utilized to establish a baseline biological variation map of the human eye and related tissues. In this context, the choroid is the vascular layer situated between the outer sclera and the inner retina. The choroidal circulation serves the photoreceptors and retinal pigment epithelium (RPE). The RPE is a layer of cuboidal epithelial cells adjacent to the neurosensory retina and maintains the outer limit of the blood-retina barrier...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28186865/preventing-electromagnetic-pulse-irradiation-damage-on-testis-using-selenium-rich-cordyceps-fungi-a-preclinical-study-in-young-male-mice
#9
Xia Miao, Yafeng Wang, Haiyang Lang, Yanyun Lin, Qiyan Guo, Mingjuan Yang, Juan Guo, Yanjun Zhang, Jie Zhang, Junye Liu, Yaning Liu, Lihua Zeng, Guozhen Guo
Networked 21st century society, globalization, and communications technologies are paralleled by the rise of electromagnetic energy intensity in our environments and the growing pressure of the environtome on human biology and health. The latter is the entire complement of environmental factors, including the electromagnetic energy and the technologies that generate them, enacting on the digital citizen in the new century. Electromagnetic pulse (EMP) irradiation might have serious damaging effects not only on electronic equipment but also in the whole organism and reproductive health, through nonthermal effects and oxidative stress...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28186864/within-day-baseline-variation-in-salivary-biomarkers-in-healthy-men
#10
Firman Prathama Idris, Yunxia Wan, Xi Zhang, Chamindie Punyadeera
Saliva is an easily accessible sample and offers practical and noninvasive biomarker solutions as an alternative to blood and urine-based diagnostics. Saliva contains a plethora of biomolecules such as nucleic acids, hormones, proteins, and electrolytes. On the other hand, little is known on the extent to which the biomolecules in saliva vary over time within a given person. This baseline information is crucial for future development of robust saliva-based diagnostics. We have collected unstimulated whole mouth saliva from 20 healthy young men at four times during the day, including before and after a meal...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28118098/performance-ratio-based-resource-allocation-decision-making-in-genomic-medicine
#11
Vasilios Fragoulakis, Christina Mitropoulou, Daphne Katelidou, Ron H van Schaik, Nikolaos Maniadakis, George P Patrinos
In modern healthcare systems, the available resources may influence the morbidity, mortality, and-consequently-the level of healthcare provided in every country. This is of particular interest in developing countries where the resources are limited and must be spent wisely to address social justice and the right for equal access in healthcare services by all the citizens in economically viable terms. In this light, the current allocation is, in practice, inefficient and rests mostly on each country's individual political and historical context and, thus, does not always incorporate decision-making enabled by economic models...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28118095/multiomics-approach-to-novel-therapeutic-targets-for-cancer-and-aging-related-diseases-role-of-sld7-in-yeast-aging-network
#12
Irem E Dayan, Kazim Yalcin Arga, Kutlu O Ulgen
Genome instability has long been implicated as a salient causal factor in aging and age-related diseases such as cancer and neurodegeneration. However, the molecular mechanisms associated with genome instability remain unclear. Recent studies suggest growth signaling in the organism Saccharomyces cerevisiae and in higher eukaryotes might affect oxidative stress and aging/age-related diseases by activating DNA replication stress that causes DNA damage. In this broader integrative biology and clinical context, MDM two binding protein (MTBP) is a binding protein that has a role in activation of the tumor suppressor protein p53...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28075205/a-genomic-and-protein-protein-interaction-analyses-of-nonsyndromic-hearing-impairment-in-cameroon-using-targeted-genomic-enrichment-and-massively-parallel-sequencing
#13
Kamogelo Lebeko, Noluthando Manyisa, Emile R Chimusa, Nicola Mulder, Collet Dandara, Ambroise Wonkam
Hearing impairment (HI) is one of the leading causes of disability in the world, impacting the social, economic, and psychological well-being of the affected individual. This is particularly true in sub-Saharan Africa, which carries one of the highest burdens of this condition. Despite this, there are limited data on the most prevalent genes or mutations that cause HI among sub-Saharan Africans. Next-generation technologies, such as targeted genomic enrichment and massively parallel sequencing, offer new promise in this context...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28271982/hepatic-mir-301a-as-a-liver-transplant-rejection-biomarker-and-its-role-for-interleukin-6-production-in-hepatocytes
#14
Toshiaki Nakano, I-Hsuan Chen, Shigeru Goto, Chia-Yun Lai, Hui-Peng Tseng, Li-Wen Hsu, King-Wah Chiu, Chih-Che Lin, Chih-Chi Wang, Yu-Fan Cheng, Chao-Long Chen
Acute rejection (AR) of liver transplantation remains a formidable challenge for diagnostic medicine and biomarker discovery. We characterized AR-related microRNAs (miRNAs) and the underlying AR mechanisms in liver transplantation. Using a rat model of orthotopic liver transplantation (OLT) as well as microarrays, we compared the miRNA expression profiles between naive and AR livers on day 7 after OLT with short- (<14 days, donor Dark Agouti [DA] liver into Lewis [LEW] recipient) and long-term (>60 days, donor DA liver into Piebald Virol Glaxo [PVG] recipient) survival fates...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28271981/understanding-epstein-barr-virus-life-cycle-with-proteomics-a-temporal-analysis-of-ubiquitination-during-virus-reactivation
#15
Dong-Wen Lv, Jun Zhong, Kun Zhang, Akhilesh Pandey, Renfeng Li
Epstein-Barr virus (EBV) is a human γ-herpesvirus associated with cancer, including Burkitt lymphoma, nasopharyngeal, and gastric carcinoma. EBV reactivation in latently infected B cells is essential for persistent infection whereby B cell receptor (BCR) activation is a physiologically relevant stimulus. Yet, a global view of BCR activation-regulated protein ubiquitination is lacking when EBV is actively replicating. We report here, for the first time, the long-term effects of IgG cross-linking-regulated protein ubiquitination and offer a basis for dissecting the cellular environment during the course of EBV lytic replication...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28271980/mosquito-borne-diseases-and-omics-salivary-gland-proteome-of-the-female-aedes-aegypti-mosquito
#16
Rakhi Dhawan, Manish Kumar, Ajeet Kumar Mohanty, Gourav Dey, Jayshree Advani, T S Keshava Prasad, Ashwani Kumar
The female Aedes aegypti mosquito is an important vector for several tropical and subtropical diseases such as dengue, chikungunya, and Zika and yellow fever. The disease viruses infect the mosquito and subsequently spread to the salivary glands after which the viruses can be transmitted to humans with probing or feeding by the mosquito. Omics systems sciences offer the opportunity to characterize vectors and can inform disease surveillance, vector control and development of innovative diagnostics, personalized medicines, vaccines, and insecticide targets...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28271979/toward-a-taxonomy-for-multi-omics-science-terminology-development-for-whole-genome-study-approaches-by-omics-technology-and-hierarchy
#17
Nina Pirih, Tanja Kunej
Omics is a form of high-throughput systems science. However, taxonomies for omics studies are limited, inviting us to rethink new ways in which we classify, prioritize, and rank various omics systems science studies. In this overarching context, the genome-wide study approaches have proliferated in number and popularity over the past decade. However, their hierarchy is not well organized and the development of attendant terminology is not controlled. In the present study, we searched the literature in PubMed and the Web of Science databases published from March 1999 to September 2016 using the keywords, including genome-wide, association, whole genome, transcriptome-wide, metabolome, epigenome, and phenome...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28271978/lessons-from-cuba-for-global-precision-medicine-cyp2d6-genotype-is-not-a-robust-predictor-of-cyp2d6-ultrarapid-metabolism
#18
Pedro Dorado, Idilio González, María Eugenia G Naranjo, Fernando de Andrés, Eva María Peñas-Lledó, Luis Ramón Calzadilla, Adrián LLerena
A long-standing question and dilemma in precision medicine is whether and to what extent genotyping or phenotyping drug metabolizing enzymes such as CYP2D6 can be used in real-life global clinical and societal settings. Although in an ideal world using both genotype and phenotype biomarkers are desirable, this is not always feasible for economic and practical reasons. Moreover, an additional barrier for clinical implementation of precision medicine is the lack of correlation between genotype and phenotype, considering that most of the current methods include only genotyping...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28206814/biomarkers-in-tumor-microenvironment-upregulation-of-fibroblast-activation-protein-%C3%AE-correlates-with-gastric-cancer-progression-and-poor-prognosis
#19
Mengmou Hu, Chengjia Qian, Ziwei Hu, Bojian Fei, Haibo Zhou
Gastric cancer is the third leading cause of cancer-related mortality worldwide. Recent evidence points to importance of cross talk between cancer cells and the surrounding stroma on gastric cancer progression. Tumor microenvironment biomarkers thus represent a new opportunity for diagnostics innovation. Reactive stromal fibroblasts selectively express the fibroblast activation protein alpha (FAP-α), a homodimeric integral membrane gelatinase that belongs to the serine protease family. We report here that FAP-α expression is significantly elevated in gastric cancer samples by more than fivefold (p < 0...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27930095/multi-omics-data-integration-and-mapping-of-altered-kinases-to-pathways-reveal-gonadotropin-hormone-signaling-in-glioblastoma
#20
Savita Jayaram, Manoj Kumar Gupta, Rajesh Raju, Poonam Gautam, Ravi Sirdeshmukh
Glioblastoma multiforme (GBM) is one of the most lethal brain tumors with an inadequately understood pathophysiology. Biomarkers that guide accurate diagnosis and treatment decisions would greatly support precision medicine for GBM. Previous studies of GBM have focused on signaling pathways such as epidermal growth factor receptor (EGFR), platelet-derived growth factor receptors (PDGFRs), notch, wnt, and others, identified with single omics technology platforms (genomics, transcriptomics, or proteomics), but not with their integrated use...
December 2016: Omics: a Journal of Integrative Biology
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