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Omics: a Journal of Integrative Biology

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https://read.qxmd.com/read/30707659/not-all-intelligence-is-artificial-data-science-automation-and-ai-meet-hi
#1
Vural Özdemir
No abstract text is available yet for this article.
February 1, 2019: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30614763/kir-and-hla-c-genetic-polymorphisms-influence-plasma-ip-10-concentration-in-antiretroviral-therapy-naive-hiv-infected-adult-zimbabweans
#2
Kudakwashe Mhandire, Lynn Sodai Zijenah, Mqondisi Tshabalala, Louis-Marie Yindom, Tommy Mlambo, Doreen Zvipo Mhandire, Cuthbert Musarurwa, Kerina Duri, Sarah Rowland-Jones, Collet Dandara, Babill Stray-Pedersen
Past studies on the relationship between Killer cell Immunoglobulin-like Receptor (KIR) and Human Leukocyte Antigen (HLA) genetic variation and chronic immune activation (CIA) in HIV infection are not uniformly consistent. Moreover, interferon-γ-induced protein 10 (IP-10) is a soluble biomarker of immune activation, with high plasma concentrations predicting accelerated disease progression in HIV infection. Thus, we investigated the association of KIR and HLA-C genetic polymorphisms with plasma IP-10 concentration in 183 treatment-naive chronically HIV-infected adults of Bantu origin from Zimbabwe...
January 7, 2019: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30589606/culturomics-based-taxonomic-diversity-of-bacterial-communities-in-the-hot-springs-of-saudi-arabia
#3
Muhammad Yasir, Arooj K Qureshi, Imran Khan, Fehmida Bibi, Mohd Rehan, Sher Bahadar Khan, Esam I Azhar
Hot springs are natural habitats for thermophilic microorganisms and provide a significant opportunity for bioprospecting thermostable biomolecules. However, the scientific community has only a fragmented understanding of the microbial diversity and composition in these biotopes. In this study, bacterial diversity in sediment samples from six hot springs of Saudi Arabia was investigated using an improved culture-dependent approach. High-throughput MALDI-TOF MS (matrix assisted laser desorption/ionization mass spectrometry) and 16S rRNA genes sequencing were used for the identification of purified isolates...
December 27, 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30566377/warfarin-dose-and-cyp2c-gene-cluster-an-african-ancestral-specific-variant-is-a-strong-predictor-of-dose-in-black-south-african-patients
#4
Arinao Ndadza, Zinhle Cindi, Edson Makambwa, Emile Chimusa, Ambroise Wonkam, Andre P Kengne, Mpiko Ntsekhe, Collet Dandara
Warfarin is a widely prescribed anticoagulant with a narrow therapeutic index. The rs12777823G>A single-nucleotide polymorphism (SNP) in the CYP2C gene cluster has been shown to influence optimal warfarin doses in African Americans. We report here effects of rs12777823G>A SNP on warfarin dose requirements in two South African population groups, black Africans (BA) and mixed ancestry (MA). A total of 425 participants on warfarin treatment were enrolled in the study. The age group of the studied population ranged between 44 and 66 years, with 69% females enrolled...
December 19, 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30562127/genetics-of-obstructive-sleep-apnea-vitamin-d-receptor-gene-variation-affects-both-vitamin-d-serum-concentration-and-disease-susceptibility
#5
Georgia Ragia, Kostas Archontogeorgis, Maurizio Simmaco, Giovanna Gentile, Marina Borro, Athanasios Zissimopoulos, Marios Froudarakis, Vangelis G Manolopoulos, Paschalis Steiropoulos
Obstructive sleep apnea syndrome (OSAS) is a multifactorial and common disorder affecting 10-17% of men and 3-9% of women. A low vitamin D serum concentration has been reportedly linked to OSAS susceptibility, but the underlying molecular genetic mechanisms are poorly understood thus far. We report here original findings on the ways in which vitamin D receptor (VDR) gene polymorphic variation (FokI, BsmI, ApaI, and TaqI polymorphisms) impacts serum vitamin D concentration and, additionally, susceptibility to OSAS...
December 18, 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30481125/comparison-of-microbiota-variation-in-korean-healthy-adolescents-with-adults-suggests-notable-maturity-differences
#6
Joo-Wook Kim, Jin Sook Lee, Jung Ho Kim, Joo-Won Jeong, Dae Ho Lee, Seungyoon Nam
Comparative studies of microbiome variation in world populations and different developmental stages of organisms are essential to decipher the linkages among microbiome, health, and disease. Notably, the gut microbiota are believed to mature in early life. In this context, we compared the gut microbiota diversity in Korean adolescent healthy samples (KAHSs) to healthy Korean adults (HKAs) as well as the Human Microbiome Project healthy samples (HMPHSs), the latter being one of the largest adult cohorts, based on organismal composition, alpha- and beta-diversities, function/pathway prediction analysis, and co-occurrence networks...
November 27, 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30767729/toward-candidate-proteomic-biomarkers-in-clinical-monitoring-of-acute-promyelocytic-leukemia-treatment-with-arsenic-trioxide
#7
Fenglin Cao, Xingang Li, Yiju Yang, Honghong Fang, Haixia Qu, Naibai Chang, Qingwei Ma, Weifan Cao, Jin Zhou, Wei Wang
The introduction of arsenic trioxide (ATO) in treatment of acute promyelocytic leukemia (APL) has resulted in high clinical complete remission (CR) rates over 90%. On the contrary, the risk for early death (ED) in APL patients treated with ATO continues to have a negative impact for optimization of APL therapeutics. There is an urgent need for precision medicine and biomarkers in clinical monitoring of ATO toxicity in APL, and ED in particular. This retrospective case series cohort proteomics study was conducted as a hypothesis generation effort and provides here several potential molecular leads on serum peptides expressed at different times after treatment with ATO in patients with APL...
February 2019: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30767728/epigenomics-guided-drug-development-recent-advances-in-solving-the-cancer-treatment-jigsaw-puzzle
#8
Kevin Dzobo
The human epigenome plays a key role in determining cellular identity and eventually function. Drug discovery undertakings have focused mainly on the role of genomics in carcinogenesis, with the focus turning to the epigenome recently. Drugs targeting DNA and histone modifications are under development with some such as 5-azacytidine, decitabine, vorinostat, and panobinostat already approved by the Food and Drug Administration (FDA) and the European Medicines Agency (EMA). This expert review offers a critical analysis of the epigenomics-guided drug discovery and development and the opportunities and challenges for the next decade...
February 2019: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30767727/proteomic-changes-in-oral-keratinocytes-chronically-exposed-to-shisha-water-pipe
#9
Shankargouda Patil, Tejaswini Subbannayya, Sonali V Mohan, Niraj Babu, Jayshree Advani, Gajanan Sathe, Pavithra Rajagopalan, Krishna Patel, Shilpa Bhandi, Hitendra Solanki, David Sidransky, Harsha Gowda, Aditi Chatterjee, Marco Ferrari
Shisha (water pipe) smoking is falsely believed to be a hazard-free habit and has become a major public health concern. Studies have reported shisha smoking to be associated with oral lesions, as well as carcinomas of the lung, esophagus, bladder, and pancreas. A deeper understanding of the underlying molecular mechanisms would contribute to identification of biomarkers for targeted public health screening, therapeutic innovation, and better prognosis of associated diseases. In this study, we have established an in vitro chronic cellular model of shisha-exposed oral keratinocytes to study the effect of shisha on oral cells...
February 2019: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30767726/proteomics-and-visual-health-research-proteome-of-the-human-sclera-using-high-resolution-mass-spectrometry
#10
Varshasnata Mohanty, Yashwanth Subbannayya, Mohammed Altaf Najar, Sneha M Pinto, Sandeep Kasaragod, Hilda Karuppiah, Bhuvaragavan Sreeramulu, Kunal Kumar Singh, Sunita Dalal, Shyamjith Manikkoth, Cynthia Arunachalam, Thottethodi Subrahmanya Keshava Prasad, Krishna R Murthy
Eye disorders and resulting visual loss are major public health problems affecting millions of people worldwide. In this context, the sclera is an opaque, thick outer coat covering more than 80% of the eye, and essential in maintaining the shape of the eye and protecting the intraocular contents against infection and the external environment. Despite efforts undertaken to decipher the scleral proteome, the functional and structural picture of the sclera still remain elusive. Recently, proteomics has arisen as a powerful tool that enables identification of proteins playing a critical role in health and disease...
February 2019: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30629480/notch1-gene-microrna-target-variation-and-ventricular-septal-defect-risk
#11
Long Ji, Haifeng Hou, Kai Zhu, Xuezhen Liu, Yizhi Liu, Qian Wang, Jindong Li, Huamin Liu, Qianqian Zhang, Jian Lv, Rachel Alexander, Wei Wang, Dong Li
Birth defects, the ventricular septal defect (VSD) in particular, have major public health significance. There is evidence that genetic factors play a role in VSD risk. We report here our findings on the relationship between VSD and microRNA (miRNA)-3691-3p target sequence single-nucleotide polymorphisms (SNPs) in the 3' untranslated region of the NOTCH1 gene. Functional SNPs in NOTCH1 target sequence were screened from the SNP database. A case-control study in a large Chinese Han population sample of 350 children with VSD and 430 healthy controls examined the association between rs6563 SNPs and VSD...
January 2019: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30629479/male-fertility-potential-molecular-mechanisms-revealed-by-itraq-based-quantitative-proteomic-analysis-of-the-epididymis-from-wip1-mice
#12
Pengxia Niu, Yinghui Wei, Qian Gao, Xue Zhang, Yanqing Hu, Yiqing Qiu, Yulian Mu, Kui Li
Proteomics and postgenomic technologies have found growing recent applications in reproductive biology and fertility research. Mice deficient in the wild-type p53-induced phosphatase 1 (WIP1) exhibit defects in reproductive organs. In this study, we aimed to understand how Wip1 deficiency affects spermatogenesis and sperm maturation using the Wip1-/- mouse model and gel-free isobaric tags for relative and absolute quantitation liquid chromatography-tandem mass spectrometry quantitative proteomic analysis of the whole epididymis, including somatic tissue and sperm...
January 2019: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30571611/genetic-determinants-of-dyslipidemia-in-african-based-populations-a-systematic-review
#13
Jean Jacques Noubiap, Edith Pascale M Mato, Magellan Guewo-Fokeng, Arnaud D Kaze, Houssam Boulenouar, Ambroise Wonkam
Identification of genetic/genomic factors contributing to dyslipidemia is of great interest to prevention and reduction of the onset and burden of cardiovascular diseases in Africa. This systematic review summarizes available data on genetic variants associated with dyslipidemia in populations within Africa. A PubMed and EMBASE database search was conducted to identify all studies published until June 2018 on genetic susceptibility to dyslipidemia in African-based populations, excluding familial hypercholesterolemia...
December 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30571610/proteomic-analysis-of-the-human-anterior-pituitary-gland
#14
Soujanya D Yelamanchi, Ankur Tyagi, Varshasnata Mohanty, Pinaki Dutta, Márta Korbonits, Sandip Chavan, Jayshree Advani, Anil K Madugundu, Gourav Dey, Keshava K Datta, M Rajyalakshmi, Nandini A Sahasrabuddhe, Abhishek Chaturvedi, Amit Kumar, Apabrita Ayan Das, Dhiman Ghosh, Gajendra M Jogdand, Haritha H Nair, Keshav Saini, Manoj Panchal, Mansi Ashwinsinh Sarvaiya, Soundappan S Mohanraj, Nabonita Sengupta, Priti Saxena, Pradeep Annamalai Subramani, Pradeep Kumar, Rakhil Akkali, Saraswatipura Vishwabrahmachar Reshma, Ramachandran Sarojini Santhosh, Sangita Rastogi, Sudarshan Kumar, Susanta Kumar Ghosh, Vamshi Krishna Irlapati, Anand Srinivasan, Bishan Das Radotra, Premendu P Mathur, G William Wong, Parthasarathy Satishchandra, Aditi Chatterjee, Harsha Gowda, Anil Bhansali, Akhilesh Pandey, Susarla K Shankar, Anita Mahadevan, T S Keshava Prasad
The pituitary function is regulated by a complex system involving the hypothalamus and biological networks within the pituitary. Although the hormones secreted from the pituitary have been well studied, comprehensive analyses of the pituitary proteome are limited. Pituitary proteomics is a field of postgenomic research that is crucial to understand human health and pituitary diseases. In this context, we report here a systematic proteomic profiling of human anterior pituitary gland (adenohypophysis) using high-resolution Fourier transform mass spectrometry...
December 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30571609/three-dimensional-organoids-in-cancer-research-the-search-for-the-holy-grail-of-preclinical-cancer-modeling
#15
Kevin Dzobo, Arielle Rowe, Dimakatso A Senthebane, Mousa A M AlMazyadi, Victoria Patten, M Iqbal Parker
Most solid tumors become therapy resistant and will relapse, with no durable treatment option available. One major impediment to our understanding of cancer biology and finding innovative approaches to cancer treatment stems from the lack of better preclinical tumor models that address and explain tumor heterogeneity and person-to-person differences in therapeutic and toxic responses. Past cancer research has been driven by inadequate in vitro assays utilizing two-dimensional monolayers of cancer cells and animal models...
December 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30571608/toxicomicrobiomics-narrowing-the-gap-between-environmental-and-medicinal-toxicogenomics
#16
Ramy K Aziz
No abstract text is available yet for this article.
December 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30457927/comparison-of-three-methods-for-cell-surface-proteome-extraction-of-listeria-monocytogenes-biofilms
#17
Julia Esbelin, Tiago Santos, Céline Ribière, Mickaël Desvaux, Didier Viala, Christophe Chambon, Michel Hébraud
The cell surface proteome of the foodborne pathogen Listeria monocytogenes, the etiological agent of listeriosis, is critical for understanding the physiological processes associated with stress resistance and persistence in the environment. In this context, the most widespread mode of growth for bacterial cells in natural and industrial environments is in biofilms. Cell surface proteins are, however, challenging to characterize because of their low abundance and poor solubility. Moreover, cell surface protein extracts are usually contaminated with cytoplasmic proteins that constitute the main signal in proteomic analysis...
November 20, 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30457469/microrna-target-interactions-reloaded-identification-of-potentially-functional-sequence-variants-within-validated-microrna-target-interactions
#18
Klara Piletic, Tanja Kunej
MicroRNAs (miRNAs) serve as critical regulators of gene expression. However, their binding to target genes can be influenced by genetic variability within the miRNA-target interaction (MTI) sites. We performed an in silico sequence reanalysis to identify novel sequence variants within MTIs with potential functional impacts. A literature search of the PubMed and the Web of Science spanning the years 2008 to April 2018 identified 240 articles reporting MTIs in humans. Sequence reanalysis of reported MTI regions was performed using the Ensembl browser...
November 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30457468/what-are-the-multi-omics-mechanisms-for-adaptation-by-microorganisms-to-high-alkalinity-a-transcriptomic-and-proteomic-study-of-a-bacillus-strain-with-industrial-potential
#19
Fatma Ece Altinisik Kaya, Fatma Gizem Avci, Nihat Alpagu Sayar, Dilek Kazan, Ahmet Alp Sayar, Berna Sariyar Akbulut
Alkaliphilic organisms are among an industrially important class of extremophile microorganisms with the ability to thrive at pH 10-11.5. Microorganisms that exhibit alkaliphilic characteristics are sources of alkali-tolerant enzymes such as proteases, starch degrading enzymes, cellulases, and metabolites such as antibiotics, enzyme inhibitors, siderophores, organic acids, and cholic acid derivatives, which have found various applications in industry for human and environmental health. Yet, multi-omics mechanisms governing adaptation to high alkalinity have been poorly studied...
November 2018: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/30457467/imass-time-the-future-in-future
#20
Qingwei Ma, Eric Adua, Mary C Boyce, Xingang Li, Guang Ji, Wei Wang
Joseph John Thomson discovered and proved the existence of electrons through a series of experiments. His work earned him a Nobel Prize in 1906 and initiated the era of mass spectrometry (MS). In the intervening time, other researchers have also been awarded the Nobel Prize for significant advances in MS technology. The development of soft ionization techniques was central to the application of MS to large biological molecules and led to an unprecedented interest in the study of biomolecules such as proteins (proteomics), metabolites (metabolomics), carbohydrates (glycomics), and lipids (lipidomics), allowing a better understanding of the molecular underpinnings of health and disease...
November 2018: Omics: a Journal of Integrative Biology
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