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Omics: a Journal of Integrative Biology

Khoudia Diop, Awa Diop, Anthony Levasseur, Oleg Mediannikov, Catherine Robert, Nicholas Armstrong, Carine Couderc, Florence Bretelle, Didier Raoult, Pierre-Edouard Fournier, Florence Fenollar
Microbial culturomics is a new subfield of postgenomic medicine and omics biotechnology application that has broadened our awareness on bacterial diversity of the human microbiome, including the human vaginal flora bacterial diversity. Using culturomics, a new obligate anaerobic Gram-stain-negative rod-shaped bacterium designated strain khD1 T was isolated in the vagina of a patient with bacterial vaginosis and characterized using taxonogenomics. The most abundant cellular fatty acids were C 15:0 anteiso (36%), C 16:0 (19%), and C 15:0 iso (10%)...
February 15, 2018: Omics: a Journal of Integrative Biology
Mustafa Bayram, Çağlar Gökırmaklı
Food and engineering sciences have tended to neglect the importance of human nutrition sciences and clinical study of new molecules discovered by food engineering community, and vice versa. Yet, the value of systems thinking and use of omics technologies in food engineering are rapidly emerging. Foodomics is a new concept and practice to bring about "precision nutrition" and integrative bioengineering studies of food composition, quality, and safety, and applications to improve health of humans, animals, and other living organisms on the planet...
February 12, 2018: Omics: a Journal of Integrative Biology
Vural Özdemir, Simon Springer
Diversity is increasingly at stake in early 21st century. Diversity is often conceptualized across ethnicity, gender, socioeconomic status, sexual preference, and professional credentials, among other categories of difference. These are important and relevant considerations and yet, they are incomplete. Diversity also rests in the way we frame questions long before answers are sought. Such diversity in the framing (epistemology) of scientific and societal questions is important for they influence the types of data, results, and impacts produced by research...
February 12, 2018: Omics: a Journal of Integrative Biology
Praseeda Mol, Uday Kannegundla, Gourav Dey, Lathika Gopalakrishnan, Manjunath Dammalli, Manish Kumar, Arun H Patil, Marappa Basavaraju, Akhila Rao, Kerekoppa P Ramesha, Thottethodi Subrahmanya Keshava Prasad
Bovine milk is important for both veterinary medicine and human nutrition. Understanding the bovine milk proteome at different stages of lactation has therefore broad significance for integrative biology and clinical medicine as well. Indeed, different lactation stages have marked influence on the milk yield, milk constituents, and nourishment of the neonates. We performed a comparative proteome analysis of the bovine milk obtained at different stages of lactation from the Indian indigenous cattle Malnad Gidda (Bos indicus), a widely available breed...
February 1, 2018: Omics: a Journal of Integrative Biology
Shannon N Conley
No abstract text is available yet for this article.
January 17, 2018: Omics: a Journal of Integrative Biology
Vural Özdemir, Nezih Hekim
Driverless cars with artificial intelligence (AI) and automated supermarkets run by collaborative robots (cobots) working without human supervision have sparked off new debates: what will be the impacts of extreme automation, turbocharged by the Internet of Things (IoT), AI, and the Industry 4.0, on Big Data and omics implementation science? The IoT builds on (1) broadband wireless internet connectivity, (2) miniaturized sensors embedded in animate and inanimate objects ranging from the house cat to the milk carton in your smart fridge, and (3) AI and cobots making sense of Big Data collected by sensors...
January 2, 2018: Omics: a Journal of Integrative Biology
Tariq Jamal Khan, Youssri M Ahmed, Mazin A Zamzami, Aisha M Siddiqui, Imran Khan, Othman A S Baothman, Mohamed G Mehanna, Abudukadeer Kuerban, Mohammed Kaleemuddin, Muhammad Yasir
Hypercholesterolemia is one of the most important risk factors for development of cardiovascular diseases. The composition of gut microbiota (total microbes residing in the gut) impacts on cholesterol and lipid metabolism. On the contrary, alterations in gut microbiota in response to hypercholesterolemia or drug treatment with atorvastatin (a cholesterol-lowering agent) are rarely investigated. We performed 16S rDNA amplicon sequencing to evaluate the gut bacterial community of 15 untreated hypercholesterolemic patients (HP) and 27 atorvastatin-treated hypercholesterolemic patients (At-HP) and compared with 19 healthy subjects (HS)...
February 2018: Omics: a Journal of Integrative Biology
Colin Garvey
No abstract text is available yet for this article.
February 2018: Omics: a Journal of Integrative Biology
Vural Özdemir
No abstract text is available yet for this article.
February 2018: Omics: a Journal of Integrative Biology
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...
February 2018: Omics: a Journal of Integrative Biology
Manjunath Dammalli, Gourav Dey, Manish Kumar, Anil K Madugundu, Lathika Gopalakrishnan, Bychapur Siddaiah Gowrishankar, Anita Mahadevan, Susarla Krishna Shankar, Thottethodi Subrahmanya Keshava Prasad
Human olfactory tract plays a fundamental role in health and disease. Proteomic analysis of the olfactory tract therefore bears fundamental importance for integrative biology and clinical medicine. For example, olfactory dysfunction is one of the earliest findings in neurodegenerative disorders. The objective of the present study was to build the proteome data from human olfactory tract using a mass spectrometry-based approach. We performed a shotgun proteomic analysis of the human olfactory tract obtained from three healthy adult male subjects...
January 2018: Omics: a Journal of Integrative Biology
Manousos E Kambouris, Yiannis Manoussopoulos, Maria Kantzanou, Aristea Velegraki, Georgios Gaitanis, Michalis Arabatzis, George P Patrinos
Global Catastrophic Biological Risks (GCBRs) refer to biological events-natural, deliberate, and accidental-of a global and lasting impact. This challenges the life scientists to raise their game on two hitherto neglected innovation frontiers: a veritable "futures" thinking to "think the unthinkable," and "systems thinking" so as to see both the trees and the forest when it comes to GCBRs. This innovation analysis article outlines the promise of Omics systems science biotechnologies, for example, to deploy rapid fire diagnostics for health security crises at GCBR level, possibly involving neopathogens and/or incurring epidemics (e...
January 2018: Omics: a Journal of Integrative Biology
Kevin Dzobo, Dimakatso Alice Senthebane, Nicholas Ekow Thomford, Arielle Rowe, Collet Dandara, M Iqbal Parker
Disruptive innovations in medicine are game-changing in nature and bring about radical shifts in the way we understand human diseases, their treatment, and/or prevention. Yet, disruptive innovations in cancer drug design and development are still limited. Therapies that cure all cancer patients are in short supply or do not exist at all. Chief among the causes of this predicament is drug resistance, a mechanism that is much more dynamic than previously understood. Drug resistance has limited the initial success experienced with biomarker-guided targeted therapies as well...
January 2018: Omics: a Journal of Integrative Biology
Konstantinos Mitropoulos, Theodora Katsila, George P Patrinos, Georgios Pampalakis
Amyotrophic lateral sclerosis (ALS) is a rare but usually fatal neurodegenerative disease characterized by motor neuron degeneration in the brain and the spinal cord. Two forms are recognized, the familial that accounts for 5-10% and the sporadic that accounts for the rest. New studies suggest that ALS is a highly heterogeneous disease, and this diversity is a major reason for the lack of successful therapeutic treatments. Indeed, only two drugs (riluzole and edaravone) have been approved that provide a limited improvement in the quality of life...
January 2018: Omics: a Journal of Integrative Biology
Sara Redenšek, Vita Dolžan, Tanja Kunej
Molecular mechanisms of Parkinson's disease (PD) have already been investigated in various different omics landscapes. We reviewed the literature about different omics approaches between November 2005 and November 2017 to depict the main pathological pathways for PD development. In total, 107 articles exploring different layers of omics data associated with PD were retrieved. The studies were grouped into 13 omics layers: genomics-DNA level, transcriptomics, epigenomics, proteomics, ncRNomics, interactomics, metabolomics, glycomics, lipidomics, phenomics, environmental omics, pharmacogenomics, and integromics...
January 2018: Omics: a Journal of Integrative Biology
Afua Adjekum, Marcello Ienca, Effy Vayena
Trust is a ubiquitous term used in emerging technology (e.g., Big Data, precision medicine), innovation policy, and governance literatures in particular. But what exactly is trust? Even though trust is considered a critical requirement for the successful deployment of precision medicine initiatives, nonetheless, there is a need for further conceptualization with regard to what qualifies as trust, and what factors might establish and sustain trust in precision medicine, predictive analytics, and large-scale biology...
December 2017: Omics: a Journal of Integrative Biology
Pritam Chattopadhyay, Goutam Banerjee, Nirmalya Banerjee
Increasing the resolution of population studies in plant biology is one of the leading frontiers for omics sciences. One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets such as individual genes [like ribulose bisphosphate carboxylase large chain (rbcL) and maturase K (matK)] and intergenic spacers (IGS) [like nuclear ribosomal internal transcribed spacer 1 (nrITS 1) and 2 (nrITS 2), and chloroplast IGS between transfer RNA for leucine and phenylalanine (cp trnL-trnF IGS)]...
December 2017: Omics: a Journal of Integrative Biology
Rando Porosk, Anton Terasmaa, Riina Mahlapuu, Ursel Soomets, Kalle Kilk
Wolfram syndrome 1 is a rare autosomal recessive neurodegenerative disease characterized by diabetes insipidus, diabetes mellitus, optic atrophy, and deafness. Mutations in the WFS1 gene encoding the wolframin glycoprotein can lead to endoplasmic reticulum stress and unfolded protein responses in cells, but the pathophysiology at whole organism level is poorly understood. In this study, several organs (heart, liver, kidneys, and pancreas) and bodily fluids (trunk blood and urine) of 2- and 6-month old Wfs1 knockout (KO), heterozygote (HZ), and wild-type (WT) mice were analyzed by untargeted and targeted metabolomics using liquid chromatography-mass spectrometry...
December 2017: Omics: a Journal of Integrative Biology
Angeliki Balasopoulou, Foong-Ming Mooy, Darrol J Baker, Christina Mitropoulou, Efthymios Skoufas, Awang Bulgiba, Theodora Katsila, George P Patrinos
Precision medicine, genomic and diagnostic services are no longer limited to developed countries. This broadening in geography of biomarker applications and omics diagnostics also demands empirical study of implementation, diagnostic testing, and counseling practices in the field. For example, the Malaysian population has large ethnic diversity and high prevalence of genetic disorders such as hemoglobinopathies and metabolic disorders. Increased morbidity and mortality from such diseases have a direct impact on society and health system sustainability and for this, decision-making becomes of outmost importance...
December 2017: Omics: a Journal of Integrative Biology
Efstathia Giannakopoulou, Fotios Konstantinou, Georgia Ragia, Anna Tavridou, Makrina Karaglani, Ekaterini Chatzaki, Andreas Papapetropoulos, Dimitrios Mikroulis, Vangelis G Manolopoulos
Coronary artery disease (CAD) is a major global health burden whereby gene-by-environment-by-sex interactions play an important role. Coronary artery bypass graft (CABG) surgery involves patients with well-documented and severe CAD. Hence, the study of CAD in a context of the CABG surgery serves as an advantageous model for disease phenotype ascertainment and genetic association studies. We report here new observations from a case-control genetic association study on promoter methylation of the cystathionine γ-lyase (CTH) gene and its association with CAD...
December 2017: Omics: a Journal of Integrative Biology
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