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Omics: a Journal of Integrative Biology

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https://www.readbyqxmd.com/read/28622116/a-general-theory-for-post-systems-biology-iatromics-and-the-environtome
#1
Nezih Hekim, Vural Özdemir
No abstract text is available yet for this article.
June 16, 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
#2
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...
June 15, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28618240/omics-for-precious-rare-biosamples-characterization-of-ancient-human-hair-by-a-proteomic-approach
#3
Margaux Fresnais, Pascale Richardin, Marcela Sepúlveda, Emmanuelle Leize-Wagner, Armelle Charrié-Duhaut
Omics technologies have far-reaching applications beyond clinical medicine. A case in point is the analysis of ancient hair samples. Indeed, hair is an important biological indicator that has become a material of choice in archeometry to study the ancient civilizations and their environment. Current characterization of ancient hair is based on elemental and structural analyses, but only few studies have focused on the molecular aspects of ancient hair proteins-keratins-and their conservation state. In such cases, applied extraction protocols require large amounts of raw hair, from 30 to 100 mg...
June 15, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28618237/effect-of-sweetened-dried-cranberry-consumption-on-urinary-proteome-and-fecal-microbiome-in-healthy-human-subjects
#4
Nell Bekiares, Christian G Krueger, Jennifer J Meudt, Dhanansayan Shanmuganayagam, Jess D Reed
The relationship among diet, human health, and disease is an area of growing interest in biomarker research. Previous studies suggest that the consumption of cranberries (Vaccinium macrocarpon) could beneficially influence urinary and digestive health. The present study sought to determine if daily consumption of sweetened dried cranberries (SDC) changes the urinary proteome and fecal microbiome, as determined in a prospective sample of 10 healthy individuals. Baseline urine and fecal samples were collected from the subjects in the fasted (8-12 h) state...
June 15, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28402209/culturomics-a-new-kid-on-the-block-of-omics-to-enable-personalized-medicine
#5
Manousos E Kambouris, Cristiana Pavlidis, Efthymios Skoufas, Michael Arabatzis, Maria Kantzanou, Aristea Velegraki, George P Patrinos
This innovation analysis highlights the underestimated and versatile potential of the new field of culturomics and examines its relation to other OMICS system sciences such as infectiomics, metabolomics, phenomics, and pharmacomicrobiomics. The advent of molecular biology, followed by the emergence of various disciplines of the genomics, and most importantly metagenomics, brought about the sharp decline of conventional microbiology methods. Emergence of culturomics has a natural synergy with therapeutic and clinical genomic approaches so as to realize personalized medicine...
April 12, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28617663/an-updated-systematic-review-and-meta-analysis-of-association-between-adiponectin-gene-polymorphisms-and-coronary-artery-disease
#6
Haifeng Hou, Siqi Ge, Linlin Zhao, Chenglin Wang, Wei Wang, Xuezhen Zhao, Zheng Sun
Coronary artery disease (CAD) is a significant contributor to global health burden. Adiponectin gene single nucleotide polymorphisms (SNPs) have been associated with CAD susceptibility, but with inconsistent results across the studies. We present, in this study, an updated meta-analysis to discern the genetic susceptibility of adiponectin SNPs in relation to CAD. PubMed and EMBASE databases were used to identify the relevant published articles using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines...
June 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28617662/telomere-length-and-accelerated-biological-aging-in-the-china-suboptimal-health-cohort-a-case-control-study
#7
Mohamed Ali Alzain, Collins Otieno Asweto, Jie Zhang, Honghong Fang, Zhongyao Zhao, Xiuhua Guo, Manshu Song, Yong Zhou, Naibai Chang, Youxin Wang, Wei Wang
Suboptimal health status (SHS) has been linked to cardiovascular risk factors, psychosocial stress, and unhealthy lifestyle. These factors also contribute to the shortening of telomere length (TL). A case-control study was conducted to examine the association between subjective health measures of SHS from the behavior perspective and also objective measures of TL at molecular level. SHS (cases = 294) was matched by age, sex, and body mass index with ideal health (controls = 294) using a propensity score matching method...
June 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28557556/regulating-the-regulators-in-attention-deficit-hyperactivity-disorder-a-genetic-association-study-of-microrna-biogenesis-pathways
#8
Umit Karakas, Ozlem Izci Ay, Mustafa Ertan Ay, Wei Wang, Mehmet Ali Sungur, Kenan Çevik, Gurbet Dogru, Mehmet Emin Erdal
Attention-deficit/hyperactivity disorder (ADHD) is one of the most prevalent complex psychiatric disorders in children as well as adults. ADHD impacts not only the affected individuals but also their families and social and professional networks. The clinical and diagnostic criteria for ADHD remain imprecise, in part, due to lack of robust biomarkers. ADHD comprises multiple subsets of diseases that present a shared set of downstream clinical findings, while displaying extensive molecular heterogeneity. This calls for innovation in diagnostic strategies that can help establish an ADHD diagnosis unequivocally as well as guiding precision medicine in this common mental health disorder...
June 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28486096/key-pharmacogenomic-considerations-for-sickle-cell-disease-patients
#9
Alexandra Kolliopoulou, Apostolos Stratopoulos, Stavroula Siamoglou, Argyro Sgourou, Bassam R Ali, Adamantia Papachatzopoulou, Theodora Katsila, George P Patrinos
Sickle cell disease (SCD), although a monogenic disease, exhibits a complex clinical phenotype that hampers optimum patient stratification and disease management, especially on hydroxyurea treatment. Moreover, theranostics, the combination of diagnostics to individualize and optimize therapeutic interventions, has not been firmly on the forefront of SCD research and clinical management to date. We suggest that if tailor-made theranostics in SCD is envisaged, pharmacogenomics is anticipated to be the way forward...
June 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28486083/progress-in-mass-spectrometry-based-proteomics-in-hypoxia-related-diseases-and-high-altitude-medicine
#10
Zhiqi Gao, Gang Luo, Bing Ni
Human migration, influenced by social conflict and natural disasters as well as global climate change, has become recognized as a major "planetary force." It has also brought to the forefront, new specialties of integrative biology-such as high-altitude medicine-and the impact of hitherto understudied environmental factors on human pathophysiology in these new geographical settings. For people migrating to or living in high-altitude regions, environmental hypoxia is a primary challenge. Decreased partial pressure of oxygen in environmental air, caused by lower barometric pressure, puts living organisms in a hypoxic state...
June 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481734/hlj1-dnajb4-gene-is-a-novel-biomarker-candidate-in-breast-cancer
#11
Tolga Acun, Natalie Doberstein, Jens K Habermann, Timo Gemoll, Christoph Thorns, Emin Oztas, Thomas Ried
Breast cancer is the most common cancer type and cause of cancer-related mortality among women worldwide. New biomarker discovery is crucial for diagnostic innovation and personalized medicine in breast cancer. Heat shock proteins (HSPs) have been increasingly reported as biomarkers and potential drug targets for cancers. HLJ1 (DNAJB4) belongs to the DNAJ (HSP40) family of HSPs and is regarded as a tumor suppressor gene in lung, colon, and gastric cancers. However, the role of the HLJ1 gene in breast cancer is currently unknown...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481733/tissue-proteome-analysis-of-different-grades-of-human-gliomas-provides-major-cues-for-glioma-pathogenesis
#12
Kishore Gollapalli, Saicharan Ghantasala, Apurva Atak, Srikanth Rapole, Aliasgar Moiyadi, Sridhar Epari, Sanjeeva Srivastava
Gliomas are heterogeneous and most commonly occurring brain tumors. Blood-brain barrier restricts the entry of brain tumor proteins into blood stream thus limiting the usage of serum or plasma for proteomic analysis. Our study aimed at understanding the molecular basis of aggressiveness of various grades of brain tumors using isobaric tagging for relative and absolute quantification (iTRAQ) based mass spectrometry. Tissue proteomic analysis of various grades of gliomas was performed using four-plex iTRAQ. We labeled five sets (each set consists of control, grade-II, III, and IV tumor samples) of individual glioma patients using iTRAQ reagents...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481732/human-cap10-like-protein-46%C3%A2-kda-gene-promotes-malignancy-in-colorectal-cancer
#13
Honghong Fang, Qiaoyun Chu, Jie Zhang, Hao Wang, Xinwei Yu, Siqi Ge, Manshu Song, Lijuan Wu, Minglin Lang, Naibai Chang, Youxin Wang, Wei Wang
Colon cancer patients have major unmet needs in terms of robust diagnostics and molecular biomarkers for personalized therapeutics. We have previously reported that human CAP10-like protein 46 kDa (hCLP46) is overexpressed in human acute myelogenous leukemia, T acute lymphoblastic leukemia, and leukemia cell lines. We extend this line of biomarker and diagnostic discovery research by investigating hCLP46 expression in colorectal cancer (CRC) tissues and examine the possibility of hCLP46 as a candidate biomarker for diagnosis and prognosis of CRC...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481731/posttranslational-modifications-in-spermatozoa-and-effects-on-male-fertility-and-sperm-viability
#14
Rahim Dad Brohi, Li-Jun Huo
Spermatogenesis is a complex and highly regulated process. The ability of spermatozoa to perform its function depends on multiple physiological and genetic factors that are not fully understood. Notably, due to lack of transcriptional and translational activity in spermatozoa, posttranslational modifications (PTMs) play key roles in determining their viability. PTMs not only confer structural changes in the proteome of the spermatozoa cells, but also increase the diversity of the proteome and introduce specific modifications that could be translated into functional changes in the affected spermatozoa...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481730/next-generation-sequencing-reveals-novel-mutations-in-x-linked-intellectual-disability
#15
Babylakshmi Muthusamy, Lakshmi Dhevi N Selvan, Thong T Nguyen, Jesna Manoj, Eric W Stawiski, Bijay S Jaiswal, Weiru Wang, Remya Raja, Vedam Laxmi Ramprasad, Ravi Gupta, Sakthivel Murugan, Jayarama S Kadandale, T S Keshava Prasad, Kavita Reddy, Andrew Peterson, Akhilesh Pandey, Somasekar Seshagiri, Satish Chandra Girimaji, Harsha Gowda
Robust diagnostics for many human genetic disorders are much needed in the pursuit of global personalized medicine. Next-generation sequencing now offers new promise for biomarker and diagnostic discovery, in developed as well as resource-limited countries. In this broader global health context, X-linked intellectual disability (XLID) is an inherited genetic disorder that is associated with a range of phenotypes impacting societies in both developed and developing countries. Although intellectual disability arises due to diverse causes, a substantial proportion is caused by genomic alterations...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28375712/ovarian-cancer-differential-interactome-and-network-entropy-analysis-reveal-new-candidate-biomarkers
#16
Dilara Ayyildiz, Esra Gov, Raghu Sinha, Kazim Yalcin Arga
Ovarian cancer is one of the most common cancers and has a high mortality rate due to insidious symptoms and lack of robust diagnostics. A hitherto understudied concept in cancer pathogenesis may offer new avenues for innovation in ovarian cancer biomarker development. Cancer cells are characterized by an increase in network entropy, and several studies have exploited this concept to identify disease-associated gene and protein modules. We report in this study the changes in protein-protein interactions (PPIs) in ovarian cancer within a differential network (interactome) analysis framework utilizing the entropy concept and gene expression data...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388302/genome-wide-association-and-replication-study-of-hepatotoxicity-induced-by-antiretrovirals-alone-or-with-concomitant-anti-tuberculosis-drugs
#17
Zelalem Petros, Ming Ta Michael Lee, Atsushi Takahashi, Yanfei Zhang, Getnet Yimer, Abiy Habtewold, Ina Schuppe-Koistinen, Taisei Mushiroda, Eyasu Makonnen, Michiaki Kubo, Eleni Aklillu
Drug-induced hepatotoxicity (DIH) is a common adverse event that is associated with both antiretroviral (ARV) and anti-tuberculosis drugs (ATD). Moreover, the genetic variations predisposing ARV- and ARV-ATD-induced liver toxicity in African populations are not well investigated, despite the two diseases being the major global health problems in sub-Saharan Africa. We performed a genome-wide association study (GWAS) and replication study to identify the genetic variants linked to the risk of developing DIH due to ARV drugs alone, and ARV-ATD co-treatment in Ethiopian HIV-positive patients...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388301/procalcitonin-biomarker-algorithm-reduces-antibiotic-prescriptions-duration-of-therapy-and-costs-in-chronic-obstructive-pulmonary-disease-a-comparison-in-the-netherlands-germany-and-the-united-kingdom
#18
Marloes E van der Maas, Gertjan Mantjes, Lotte M G Steuten
Antibiotics are often recommended as treatment for patients with chronic obstructive pulmonary disease (COPD) exacerbations. However, not all COPD exacerbations are caused by bacterial infections and there is consequently considerable misuse and overuse of antibiotics among patients with COPD. This poses a severe burden on healthcare resources such as increased risk of developing antibiotic resistance. The biomarker procalcitonin (PCT) displays specificity to distinguish bacterial inflammations from nonbacterial inflammations and may therefore help to rationalize antibiotic prescriptions...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388300/minimal-standards-for-reporting-microrna-target-interactions
#19
Klara Piletič, Tanja Kunej
Epigenomics is one of the leading frontiers of postgenomics medicine. The challenges and prospects ahead in epigenomics are related not merely to technology innovation and clinical implementation but also to science communication. In this context, microRNAs (miRNAs) are an important part of the epigenomic regulatory machinery. As the number of publications reporting miRNA-target interactions (MTIs) is growing rapidly, there is an urgent need to standardize reporting. This study reports (1) an analysis of the published literature and databases reporting validated MTIs, and for the first time to the best of our knowledge (2) suggests a solution as a way forward, the minimum information required for MTI standard reporting...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388299/innovation-analysis-on-postgenomic-biomarkers-glycomics-for-chronic-diseases
#20
Eric Adua, Alyce Russell, Peter Roberts, Youxin Wang, Manshu Song, Wei Wang
Despite decades of investment in biomarker research, we still do not have robust and field-tested biomarkers for many chronic diseases so as to anticipate clinical outcomes and thus move toward personalized medicine. Biomarker innovations have tended to focus on genomics, but next-generation biomarkers from the nascent field of glycomics now offer fresh vistas for innovation in chronic disease biomarkers and systems diagnostics. Glycosylation, regarded as a complex enzymatic process where sugars (glycans) bind to proteins and lipids, affects many human biological functions, including cell signaling, adhesion, and motility...
April 2017: Omics: a Journal of Integrative Biology
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