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Omics: a Journal of Integrative Biology

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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
#1
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...
January 11, 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
#2
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
https://www.readbyqxmd.com/read/27930094/cancer-stem-cell-hypothesis-for-therapeutic-innovation-in-clinical-oncology-taking-the-root-out-not-chopping-the-leaf
#3
Kevin Dzobo, Dimakatso Alice Senthebane, Arielle Rowe, Nicholas Ekow Thomford, Lamech M Mwapagha, Nasir Al-Awwad, Collet Dandara, M Iqbal Parker
Clinical oncology is in need of therapeutic innovation. New hypotheses and concepts for translation of basic research to novel diagnostics and therapeutics are called for. In this context, the cancer stem cell (CSC) hypothesis rests on the premise that tumors comprise tumor cells and a subset of tumor-initiating cells, CSCs, in a quiescent state characterized by slow cell cycling and expression of specific stem cell surface markers with the capability to maintain a tumor in vivo. The CSCs have unlimited self-renewal abilities and propagate tumors through division into asymmetric daughter cells...
December 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27930093/kir-gene-content-diversity-in-a-zimbabwean-population-does-kir2dl2-have-a-role-in-protection-against-human-immunodeficiency-virus-infection
#4
Kudakwashe Mhandire, Lynn Sodai Zijenah, Louis-Marie Yindom, Kerina Duri, Tommy Mlambo, Mqondisi Tshabalala, Lovemore Ronald Mazengera, Doreen Zvipo Mhandire, Cuthbert Musarurwa, Collet Dandara, Sarah Rowland-Jones, Hilda Tendisa Matarira, Babill Stray-Pedersen
Killer cell immunoglobulin-like receptors (KIRs) mediate natural killer cell function through interaction with their cognate human leukocyte antigen ligands. Thus, KIR gene variants have been implicated in resistance or susceptibility to viral infections. However, research on the role of these variants remains contradictory and inconclusive. In the present study, we investigated KIR gene content diversity and its association with human immunodeficiency virus (HIV) infection in an adult Black Zimbabwean population...
December 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27930092/inflammatory-bowel-disease-meets-systems-biology-a-multi-omics-challenge-and-frontier
#5
Orazio Palmieri, Tommaso Mazza, Stefano Castellana, Anna Panza, Tiziana Latiano, Giuseppe Corritore, Angelo Andriulli, Anna Latiano
The inflammatory bowel disease (IBD) is a systemic disease that is characterized by the inflammation of the gastrointestinal tract. It includes ulcerative colitis and the Crohn's disease. Presently, IBD is one of the most investigated common complex human disorders, although its causes remain unclear. Multi-omics mechanisms involving genomic, transcriptomic, proteomic, and epigenomic variations, not to forget the miRNome, together with environmental contributions, result in an impairment of the immune system in persons with IBD...
December 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27849442/to-genotype-or-phenotype-for-personalized-medicine-cyp450-drug-metabolizing-enzyme-genotype-phenotype-concordance-and-discordance-in-the-ecuadorian-population
#6
Fernando De Andrés, Santiago Terán, Francisco Hernández, Enrique Terán, Adrián LLerena
Genetic variations within the cytochrome P450 (CYP450) superfamily of drug metabolizing enzymes confer substantial person-to-person and between-population differences in pharmacokinetics, and by extension, highly variable clinical effects of medicines. In this context, "personalized medicine," "precision medicine," and "stratified medicine" are related concepts attributed to what is essentially targeted therapeutics and companion diagnostics, aimed at improving safety and effectiveness of health interventions...
December 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27849439/liver-proteome-in-diabetes-type-1-rat-model-insulin-dependent-and-independent-changes
#7
Camila Pereira Braga, Cory H T Boone, Ryan A Grove, Dana Adamcova, Ana Angélica Henrique Fernandes, Jiri Adamec, Pedro de Magalhães Padilha
Diabetes mellitus type 1 (DM1) is a major public health problem that continues to burden the healthcare systems worldwide, costing exponentially more as the epidemic grows. Innovative strategies and omics system diagnostics for earlier diagnosis or prognostication of DM1 are essential to prevent secondary complications and alleviate the associated economic burden. In a preclinical study design that involved streptozotocin (STZ)-induced DM1, insulin-treated STZ-induced DM1, and control rats, we characterized the insulin-dependent and -independent changes in protein profiles in liver samples...
December 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27828772/toward-a-reference-gene-catalog-of-human-primary-monocytes
#8
Hoda Mirsafian, Adiratna Mat Ripen, Thamilvaani Manaharan, Saharuddin Bin Mohamad, Amir Feisal Merican
Transcriptome analyses based on high-throughput RNA sequencing (RNA-Seq) provide powerful and quantitative characterization of cell types and in-depth understanding of biological systems in health and disease. In this study, we present a comprehensive transcriptome profile of human primary monocytes, a crucial component of the innate immune system. We performed deep RNA-Seq of monocytes from six healthy subjects and integrated our data with 10 other publicly available RNA-Seq datasets of human monocytes. A total of 1...
November 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27828771/how-does-chronic-cigarette-smoke-exposure-affect-human-skin-a-global-proteomics-study-in-primary-human-keratinocytes
#9
Pavithra Rajagopalan, Vishalakshi Nanjappa, Remya Raja, Ankit P Jain, Kiran K Mangalaparthi, Gajanan J Sathe, Niraj Babu, Krishna Patel, Nükhet Cavusoglu, Jeremie Soeur, Akhilesh Pandey, Nita Roy, Lionel Breton, Aditi Chatterjee, Namita Misra, Harsha Gowda
Cigarette smoking has been associated with multiple negative effects on human skin. Long-term physiological effects of cigarette smoke are through chronic and not acute exposure. Molecular alterations due to chronic exposure to cigarette smoke remain unclear. Primary human skin keratinocytes chronically exposed to cigarette smoke condensate (CSC) showed a decreased wound-healing capacity with an increased expression of NRF2 and MMP9. Using quantitative proteomics, we identified 4728 proteins, of which 105 proteins were overexpressed (≥2-fold) and 41 proteins were downregulated (≤2-fold) in primary skin keratinocytes chronically exposed to CSC...
November 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27828770/responding-to-a-zoonotic-emergency-with-multi-omics-research-pentatrichomonas-hominis-hydrogenosomal-protein-characterization-with-use-of-rna-sequencing-and-proteomics
#10
Yi-Kai Fang, Kun-Yi Chien, Kuo-Yang Huang, Wei-Hung Cheng, Fu-Mann Ku, Rose Lin, Ting-Wen Chen, Po-Jung Huang, Cheng-Hsun Chiu, Petrus Tang
Pentatrichomonas hominis is an anaerobic flagellated protist that colonizes the large intestine of a number of mammals, including cats, dogs, nonhuman primates, and humans. The wide host range of this organism is alarming and suggests a rising zoonotic emergency. However, knowledge on in-depth biology of this protist is still limited. Similar to the human pathogen, Trichomonas vaginalis, P. hominis possesses hydrogenosomes instead of mitochondria. Studies in T. vaginalis indicated that hydrogenosome is essential for cell survival and associated with numerous pivotal biological functions, including drug resistance...
November 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27828769/metabolic-biomarkers-and-neurodegeneration-a-pathway-enrichment-analysis-of-alzheimer-s-disease-parkinson-s-disease-and-amyotrophic-lateral-sclerosis
#11
Medi Kori, Busra Aydın, Semra Unal, Kazim Yalcin Arga, Dilek Kazan
Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) lack robust diagnostics and prognostic biomarkers. Metabolomics is a postgenomics field that offers fresh insights for biomarkers of common complex as well as rare diseases. Using data on metabolite-disease associations published in the previous decade (2006-2016) in PubMed, ScienceDirect, Scopus, and Web of Science, we identified 101 metabolites as putative biomarkers for these three neurodegenerative diseases...
November 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27753544/travelers-diarrhea-associated-enterotoxigenic-escherichia-coli-gyra-mutants-and-quinolone-antibiotic-affinity-a-molecular-dynamics-simulation-and-residue-interaction-network-analysis
#12
Kusum Mehla, Jayashree Ramana
Travelers' diarrhea (TD) is one of the most important global health issues among international travelers, especially those traveling to developing countries. Enterotoxigenic Escherichia coli (ETEC) is the most frequently isolated pathogen causing TD. Although TD is self-limiting, it is also severely incapacitating. Ciprofloxacin is one of the standard quinolone antibiotics used in patients with TD. However, the alarming levels of antibiotic resistance have necessitated the urgent need to identify new drugs...
October 18, 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27732148/cerebrospinal-fluid-metabolomics-after-natural-product-treatment-in-an-experimental-model-of-cerebral-ischemia
#13
Tao Huan, Jia Wen Xian, Wing Nang Leung, Liang Li, Chun Wai Chan
Cerebrospinal fluid (CSF) is an important biofluid for diagnosis of and research on neurological diseases. However, in-depth metabolomic profiling of CSF remains an analytical challenge due to the small volume of samples, particularly in small animal models. In this work, we report the application of a high-performance chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) workflow for CSF metabolomics in Gastrodia elata and Uncaria rhynchophylla water extract (GUW)-treated experimental cerebral ischemia model of rat...
October 12, 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27726641/precision-medicine-2-0-the-next-wave-of-science
#14
Collet Dandara, Vural Özdemir
No abstract text is available yet for this article.
October 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27726640/harnessing-knowledge-on-very-important-pharmacogenes-cyp2c9-and-cyp2c19-variation-for-precision-medicine-in-resource-limited-global-conflict-zones
#15
İbrahim Ömer Barlas, Orhan Sezgin, Collet Dandara, Gözde Türköz, Emre Yengel, Zinhle Cindi, Handan Ankaralı, Semra Şardaş
Pharmacogenomics harnesses the utility of a patient's genome (n = 1) in decisions on which therapeutic drugs and in what amounts should be administered. Often, patients with shared ancestry present with comparable genetic profiles that predict drug response. However, populations are not static, thus, often, population mobility through migration, especially enmasse as is seen for refugees, changes the pharmacogenetic profiles of resultant populations and therefore observed responses to commonly used therapeutic drugs...
October 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27726639/genetics-of-sickle-cell-associated-cardiovascular-disease-an-expert-review-with-lessons-learned-in-africa
#16
Amy Geard, Gift D Pule, David Chelo, Valentina Josiane Ngo Bitoungui, Ambroise Wonkam
Sickle cell disease (SCD) vastly impacts the African continent and is associated with cardiovascular diseases. Stroke, kidney disease, and pulmonary hypertension are considered as proxies of severity in SCD with several genomic loci implicated in their heritability. The present expert review examined the current data on epidemiology and genetic risk factors of stroke, pulmonary hypertension, and kidney disease associated with SCD, as indexed in PubMed(®) and Google Scholar(®). Studies collectively show that stroke and kidney disease each affect ∼10% of SCD patients, with pulmonary hypertension displaying a higher prevalence of 30% among adults with SCD...
October 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27643672/pharmacogenomics-and-global-precision-medicine-in-the-context-of-adverse-drug-reactions-top-10-opportunities-and-challenges-for-the-next-decade
#17
Marco Alessandrini, Mamoonah Chaudhry, Tyren M Dodgen, Michael S Pepper
In a move indicative of the enthusiastic support of precision medicine, the U.S. President Barack Obama announced the Precision Medicine Initiative in January 2015. The global precision medicine ecosystem is, thus, receiving generous support from the United States ($215 million), and numerous other governments have followed suit. In the context of precision medicine, drug treatment and prediction of its outcomes have been important for nearly six decades in the field of pharmacogenomics. The field offers an elegant solution for minimizing the effects and occurrence of adverse drug reactions (ADRs)...
October 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27636225/an-expert-review-of-pharmacogenomics-of-sickle-cell-disease-therapeutics-not-yet-ready-for-global-precision-medicine
#18
Khuthala Mnika, Gift D Pule, Collet Dandara, Ambroise Wonkam
Sickle cell disease (SCD) is a blood disease caused by a single nucleotide substitution (T > A) in the beta globin gene on chromosome 11. The single point mutation (Glu6Val) promotes polymerization of hemoglobin S (HbS) and causes sickling of erythrocytes. Vaso-occlusive painful crises are associated with recurrent and long-term use of analgesics/opioids and hydroxyurea (HU) by people living with SCD. The present analysis offers a state-of-the-art expert review of the effectiveness of pharmacogenomics/genetics of pain management in SCD, with specific focus on HU and opioids...
October 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27636104/toward-a-global-roadmap-for-precision-medicine-in-psychiatry-challenges-and-opportunities
#19
Shareefa Dalvie, Nastassja Koen, Nathaniel McGregor, Kevin O'Connell, Louise Warnich, Raj Ramesar, Caroline M Nievergelt, Dan J Stein
Mental disorders represent a major public health burden worldwide. This is likely to rise in the next decade, with the highest increases predicted to occur in low- and middle-income countries. Current psychotropic medication treatment guidelines focus on uniform approaches to the treatment of heterogeneous disorders and achieve only partial therapeutic success. Developing a global precision medicine approach in psychiatry appears attractive, given the value of this approach in other fields of medicine, such as oncology and infectious diseases...
October 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27627692/rolling-out-efavirenz-for-hiv-precision-medicine-in-africa-are-we-ready-for-pharmacovigilance-and-tackling-neuropsychiatric-adverse-effects
#20
Collen Masimirembwa, Collet Dandara, Peter Derek Christian Leutscher
The introduction of antiretroviral therapy (ART) led to huge reductions in human immunodeficiency virus (HIV)-related deaths, turning HIV-infection into a chronic condition. Attention is now turning to quality of life for patients on lifelong ART treatment, reflecting on the safety of antiretroviral drugs. In sub-Saharan Africa, efavirenz (EFV) forms the preferred first-line ART but adverse drug events have also been reported. We express our concern on EFV-based regimens being part of mass rollout programs without full attention to toxicities...
October 2016: Omics: a Journal of Integrative Biology
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