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Omics: a Journal of Integrative Biology

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https://www.readbyqxmd.com/read/29161534/omics-and-bioinformatics-time-for-new-data-analysis-approaches
#1
Chenyu Li, Wei Jiang, Yan Xu
No abstract text is available yet for this article.
November 21, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29161520/ezh2-histone-methyltransferase-and-jmjd3-histone-demethylase-implications-in-prostate-cancer
#2
Mouhamed Idrissou, Marine Daures, Amani Ben Jemia, Gaëlle Judes, Khaldoun Rifaï, Frédérique Penault-Llorca, Yves-Jean Bignon, Laurent Guy, Dominique Bernard-Gallon
No abstract text is available yet for this article.
November 21, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29161519/bioinformatics-advances-to-accelerate-omics-innovations-and-applications-in-the-postgenomic-era
#3
Jayshree Advani, Yashwanth Subbannayya, Harsha Gowda, Aditi Chatterjee
No abstract text is available yet for this article.
November 21, 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
#4
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/29140768/public-health-burden-of-hearing-impairment-and-the-promise-of-genomics-and-environmental-research-a-case-study-in-ghana-africa
#5
Samuel Mawuli Adadey, Gordon Awandare, Goffrey Kwabla Amedofu, Ambroise Wonkam
Hearing impairment (HI) is one of the most disabling conditions of major global health burden that contributes adversely to the social and economic development of a country, if not managed properly. A proper assessment of the nationwide burden and etiology of HI is instrumental in the prevention, treatment, and management of the condition. This article sought to perform an expert review of HI in Ghana to determine the present knowledge of its burden and possible causes of the condition. A literature search was conducted in PubMed using the following keywords: "hearing loss" OR "hearing impairment" OR "deafness" AND "Ghana...
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29140767/genomic-medicine-without-borders-which-strategies-should-developing-countries-employ-to-invest-in-precision-medicine-a-new-fast-second-winner-strategy
#6
Konstantinos Mitropoulos, David N Cooper, Christina Mitropoulou, Spiros Agathos, Jürgen K V Reichardt, Fatima Al-Maskari, Wasun Chantratita, Ambroise Wonkam, Collet Dandara, Theodora Katsila, Catalina Lopez-Correa, Bassam R Ali, George P Patrinos
Genomic medicine has greatly matured in terms of its technical capabilities, but the diffusion of genomic innovations worldwide faces significant barriers beyond mere access to technology. New global development strategies are sorely needed for biotechnologies such as genomics and their applications toward precision medicine without borders. Moreover, diffusion of genomic medicine globally cannot adhere to a "one-size-fits-all-countries" development strategy, in the same way that drug treatments should be customized...
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29091011/clinical-proteomics-and-cytokine-profiling-for-dengue-fever-disease-severity-biomarkers
#7
Manali Jadhav, Monalisha Nayak, Swati Kumar, Apoorva Venkatesh, Sandip K Patel, Vipin Kumar, Sarthak Sharma, Biaus Samanta, Satarupa Deb, Avik Karak, Sumit Verma, Arunansu Talukdar, Sanjay K Kochar, Preeti Mansukhani, Mayuri Gandhi, Sanjeeva Srivastava
Dengue fever (DF) is a major global health burden with a pathophysiology that is still incompletely understood. Biomarkers that predict and explain susceptibility to DF and its progression to its more severe hemorrhagic form are much needed. DF is endemic in tropical and subtropical regions of the world, with a rapidly increasing incidence of disease severity. We conducted a clinical biomarker discovery study using both a case-control and longitudinal study design. Plasma proteome alterations in patients with DF (n = 12) and dengue hemorrhagic fever (DHF, n = 24) were analyzed in comparison to healthy controls (HCs, n = 16), using the isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics methodology (false discovery rate of 1%, ≥2 peptides)...
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29083982/stop-the-spam-conference-ethics-and-decoding-the-subtext-in-post-truth-science-what-would-denis-diderot-say
#8
Vural Özdemir, Collet Dandara, Nezih Hekim, Kean Birch, Simon Springer, Tanja Kunej, Laszlo Endrenyi
Science and its practice always had a subtext, subject to influence by scientists', funders', and other innovation actors' values and assumptions. The recent emergence of post-truth, authoritarian and populist penchants, in both developed and developing countries, has further blurred the already fluid boundaries between material scientific facts and their social construction/shaping by scientific subtext, human values, powers, and hegemony. While there are certain checks, balances, and oversight mechanisms for publication ethics, other pillars of science communication, most notably, scientific conferences and their governance, are ill prepared for post-truth science...
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29064337/david-bowie-and-the-art-of-slow-innovation-a-fast-second-winner-strategy-for-biotechnology-and-precision-medicine-global-development
#9
Vural Özdemir, George P Patrinos
Original ideas and innovation cannot always be ordered like a courier service and delivered fresh to our desk at 9 am. Yet, most creativity-based organizations, careers, and professions, science and biotechnology innovation included, emphasize the speed as the prevailing ideology. But a narrow focus on speed has several and overlooked shortcomings. For example, it does not offer the opportunity to draw from, and stitch together disparate concepts and practices for truly disruptive innovation. Preventing false starts, learning from others' or our own mistakes, and customizing innovations for local community needs are difficult in a speed-hungry innovation ecosystem...
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29022860/-making-sense-of-genes-by-kostas-kampourakis-cambridge-cambridge-university-press-2017
#10
George P Patrinos
No abstract text is available yet for this article.
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29022835/time-for-multiple-extraction-methods-in-proteomics-a-comparison-of-three-protein-extraction-methods-in-the-eustigmatophyte-alga-microchloropsis-gaditana-ccmp526
#11
Anbarasu Karthikaichamy, Pranali Deore, Vineeta Rai, Dieter Bulach, John Beardall, Santosh Noronha, Sanjeeva Srivastava
Proteomics is a crucial postgenomic biotechnology for functional and systems scale analyses in cell and integrative biology, not to mention clinical and precision medicine research. However, a fundamental requirement for an accurate examination of the protein complement of cells is an efficient method for extracting the proteins. This study reports on the evaluation of three protein extraction methods: trichloroacetic acid (TCA)-acetone, phenol, and TRIzol, in the eustigmatophyte alga Microchloropsis gaditana CCMP526 for proteomic analysis...
November 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
#12
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.
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29049014/transcriptomic-guided-drug-repositioning-supported-by-a-new-bioinformatics-search-tool-genexpharma
#13
Beste Turanli, Gizem Gulfidan, Kazim Yalcin Arga
Drug repositioning is an innovative approach to identify new therapeutic indications for existing drugs. Drug repositioning offers the promise of reducing drug development timeframes and costs, and because it involves drugs that are already in the clinic, it might remedy some of the drug safety challenges traditionally associated with drug candidates that are not yet available in the clinic. The gene-by-drug interactions are an important dimension of optimal drug repositioning and development strategies. While gene-by-drug interactions have been curated and presented in various databases, novel bioinformatics tools and approaches are timely, and required with a specific focus to support drug positioning...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29049013/identification-and-validation-of-fibroblast-growth-factor-12-gene-as-a-novel-potential-biomarker-in-esophageal-cancer-using-cancer-genomic-datasets
#14
Ashish Bhushan, Avninder Singh, Sujala Kapur, Bibhuti B Borthakar, Jagannath Sharma, Avdhesh K Rai, Amal C Kataki, Sunita Saxena
Esophageal squamous cell carcinoma (ESCC) has a complex, multifactorial etiology in which environmental, geographical, and genetic factors play major roles. It is the second most common cancer among men and the fourth most common among women in India, with a particularly high prevalence in Northeast India. In this study, an integrative in silico [DAVID, NCG5.0, Oncomine, Cancer Cell Line Encyclopedia, and The Cancer Genome Atlas (TCGA)] approach was used to identify the potential biomarkers by using the available three genomic datasets on ESCC from Northeast India followed by its in vitro functional validation...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29049012/transcriptome-profiling-uncovers-potential-common-mechanisms-in-fetal-trisomies-18-and-21
#15
Marija Volk, Aleš Maver, Alenka Hodžić, Luca Lovrečić, Borut Peterlin
Human trisomies have recently been investigated using transcriptomics approaches to identify the gene expression (GE) signatures characteristic of each of these specific aneuploidy conditions. We hypothesized that the viability of cells with gross genomic imbalances might be associated with the activation of resilience mechanisms that are common to different trisomies and that are reflected by specific shared GE patterns. We report in this article our microarray GE analyses of amniocytes from fetuses with viable trisomy conditions, trisomy 21 or trisomy 18, to detect such common expression signatures...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29049011/-omics-of-food-borne-gastroenteritis-global-proteomic-and-mutagenic-analysis-of-salmonella-enterica-serovar-enteritidis
#16
Aryashree Arunima, Soujanya D Yelamanchi, Chandrashekhar Padhi, Sangeeta Jaiswal, Daniel Ryan, Bhawna Gupta, Gajanan Sathe, Jayshree Advani, Harsha Gowda, T S Keshava Prasad, Mrutyunjay Suar
Salmonella Enteritidis causes food-borne gastroenteritis by the two type three secretion systems (TTSS). TTSS-1 mediates invasion through intestinal lining, and TTSS-2 facilitates phagocytic survival. The pathogens' ability to infect effectively under TTSS-1-deficient background in host's phagocytes is poorly understood. Therefore, pathobiological understanding of TTSS-1-defective nontyphoidal Salmonellosis is highly important. We performed a comparative global proteomic analysis of the isogenic TTSS-1 mutant of Salmonella Enteritidis (M1511) and its wild-type isolate P125109...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29049010/biofilm-related-diseases-and-omics-global-transcriptional-profiling-of-enterococcus-faecium-reveals-different-gene-expression-patterns-in-the-biofilm-and-planktonic-cells
#17
Shu Yong Lim, Cindy Shuan Ju Teh, Kwai Lin Thong
Enterococcus faecium is an opportunistic pathogen with a remarkable ability to acquire resistance toward multiple antibiotics, including those of last-resort drugs such as vancomycin and daptomycin. The occurrence of vancomycin-resistant E. faecium is on the rise and there is a need to understand the virulence of this organism. One of the factors that contributes to the virulence is the ability to form biofilms. Since bacteria in biofilm state are more resistant to antibiotics and host immune response, understanding the molecular mechanism of biofilm development is important to control biofilm-related diseases...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28937943/multiomics-analysis-of-tumor-microenvironment-reveals-gata2-and-mirna-124-3p-as-potential-novel-biomarkers-in-ovarian-cancer
#18
Esra Gov, Medi Kori, Kazim Yalcin Arga
Ovarian cancer is a common and, yet, one of the most deadly human cancers due to its insidious onset and the current lack of robust early diagnostic tests. Tumors are complex tissues comprised of not only malignant cells but also genetically stable stromal cells. Understanding the molecular mechanisms behind epithelial-stromal crosstalk in ovarian cancer is a great challenge in particular. In the present study, we performed comparative analyses of transcriptome data from laser microdissected epithelial, stromal, and ovarian tumor tissues, and identified common and tissue-specific reporter biomolecules-genes, receptors, membrane proteins, transcription factors (TFs), microRNAs (miRNAs), and metabolites-by integration of transcriptome data with genome-scale biomolecular networks...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28934030/metabolomic-analysis-of-n-acetylcysteine-protection-of-injury-from-gadolinium-dtpa-contrast-agent-in-rats-with-chronic-renal-failure
#19
Chuanling Wan, Rong Xue, Youyang Zhan, Yijie Wu, Xiaojing Li, Fengkui Pei
Gadolinium-based contrast agents (GBCAs) are frequently used to enhance the diagnostic efficacy of magnetic resonance imaging. On the other hand, the association between GBCA administration in patients with advanced renal disease and nephrogenic systemic fibrosis (NSF) was also noted. NSF is a systemic disorder characterized by widespread tissue fibrosis that may lead to death. N-acetylcysteine (NAC) protects rats from injury induced by gadolinium-based contrast agents, but the underlying mechanisms remain unclear...
September 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28934029/comparative-proteomics-of-streptococcus-pneumoniae-response-to-vancomycin-treatment
#20
Xiao-Yan Yang, Jing-Yu Xu, Qiu-Xia Wei, Xuesong Sun, Qing-Yu He
Streptococcus pneumoniae is a gram-positive pathogen that causes otitis media, pneumonia, meningitis, and other serious diseases. Vancomycin is one of the most important drugs currently used for the treatment of gram-positive bacterial infections, representing, importantly, the last line of defense against bacteria that have developed resistance to other antibiotics. While primary efforts of most investigations focused on the antibacterial mechanism of vancomycin, few studies have been performed to assess the tolerance mechanism of bacteria to vancomycin...
September 2017: Omics: a Journal of Integrative Biology
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