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https://www.readbyqxmd.com/read/28217003/reverse-genetics-and-high-throughput-sequencing-methodologies-for-plant-functional-genomics
#1
Anis Ben-Amar, Samia Daldoul, Götz M Reustle, Gabriele Krczal, Ahmed Mliki
In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism. With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes. Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies...
December 2016: Current Genomics
https://www.readbyqxmd.com/read/28211833/an-anthropometric-study-of-serbian-metal-industry-workers
#2
S Omić, V K Spasojevic Brkić, T A Golubović, A Dj Brkić, M M Klarin
BACKGROUND: There are recent studies using new industrial workers' anthropometric data in different countries, but for Serbia such data are not available. OBJECTIVE: This study is the first anthropometric study of Serbian metal industry workers in the country, whose labor force is increasingly employed both on local and international markets. The metal industry is one of Serbia's most important economic sectors. METHODS: To this end, we collected the basic static anthropometric dimensions of 122 industrial workers and used principal components analysis (PCA) to obtain multivariate anthropometric models...
February 17, 2017: Work: a Journal of Prevention, Assessment, and Rehabilitation
https://www.readbyqxmd.com/read/28211524/epigenetic-and-genetic-dissections-of-uv-induced-global-gene-dysregulation-in-skin-cells-through-multi-omics-analyses
#3
Yao Shen, Milda Stanislauskas, Gen Li, Deyou Zheng, Liang Liu
To elucidate the complex molecular mechanisms underlying the adverse effects UV radiation (UVR) on skin homeostasis, we performed multi-omics studies to characterize UV-induced genetic and epigenetic changes. Human keratinocytes from a single donor treated with or without UVR were analyzed by RNA-seq, exome-seq, and H3K27ac ChIP-seq at 4 h and 72 h following UVR. Compared to the relatively moderate mutagenic effects of UVR, acute UV exposure induced substantial epigenomic and transcriptomic alterations, illuminating a previously underappreciated role of epigenomic and transcriptomic instability in skin pathogenesis...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209619/lapatinib-resistance-in-breast-cancer-cells-is-accompanied-by-phosphorylation-mediated-reprogramming-of-glycolysis
#4
Benjamin Ruprecht, Esther A Zaal, Jana Zecha, Wei Wu, Celia R Berkers, Bernhard Kuster, Simone Lemeer
HER2/ERBB2-overexpressing breast cancers targeted effectively by the small molecule kinase inhibitor lapatinib frequently acquire resistance to this drug. In this study, we employed explorative mass spectrometry to profile proteomic, kinomic, and phosphoproteomic changes in an established model of lapatinib resistance to systematically investigate initial inhibitor response and subsequent reprogramming in resistance. The resulting dataset, which collectively contains quantitative data for >7,800 proteins, >300 protein kinases and >15,000 phosphopeptides, enabled deep insight into signaling recovery and molecular reprogramming upon resistance...
February 16, 2017: Cancer Research
https://www.readbyqxmd.com/read/28208746/evidence-of-a-dha-signature-in-the-lipidome-and-metabolome-of-human-hepatocytes
#5
Veronica Ghini, Mattia Di Nunzio, Leonardo Tenori, Veronica Valli, Francesca Danesi, Francesco Capozzi, Claudio Luchinat, Alessandra Bordoni
Cell supplementation with bioactive molecules often causes a perturbation in the whole intracellular environment. Omics techniques can be applied for the assessment of this perturbation. In this study, the overall effect of docosahexaenoic acid (DHA) supplementation on cultured human hepatocyte lipidome and metabolome has been investigated using nuclear magnetic resonance (NMR) in combination with traditional techniques. The effect of two additional bioactives sharing with DHA the lipid-lowering effect-propionic acid (PRO) and protocatechuic acid (PCA)-has also been evaluated in the context of possible synergism...
February 8, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28193460/multi-omics-a-critical-technical-perspective-on-integrative-lipidomics-approaches
#6
Dominik Kopczynski, Cristina Coman, Rene P Zahedi, Kristina Lorenz, Albert Sickmann, Robert Ahrends
During the past decades, high-throughput approaches for analyzing different molecular classes such as nucleic acids, proteins, metabolites, and lipids have grown rapidly. These approaches became powerful tools for getting a fundamental understanding of biological systems. Considering each approach and its results separately, relations and causal connections between these classes have no chance to be revealed, since only separate molecular snapshots are provided. Only a combined approach, not fully established yet, with the integration of the corresponding data, might yield a comprehensive and complete understanding of biological processes, such as crosstalk and interactions in signaling pathways...
February 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28188532/pathway-informed-discovery-and-targeted-proteomic-workflows-using-mass-spectrometry
#7
Caroline S Chu, Christine A Miller, Andy Gieschen, Steve M Fischer
Recent advancements in mass spectrometry (MS) and data analysis software have enabled new strategies for biological discovery using proteomics. Proteomics has evolved from routine discovery and identification of proteins to integrated multi-omics projects relating specific proteins to their genes and metabolites. Using additional information, such as that contained in biological pathways, has enabled the use of targeted protein quantitation for monitoring fold changes in expression as well as biomarker discovery...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28187790/retinoic-acid-and-tgf-%C3%AE-signalling-cooperate-to-overcome-mycn-induced-retinoid-resistance
#8
David J Duffy, Aleksandar Krstic, Melinda Halasz, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G Higgins, Walter Kolch
BACKGROUND: Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblastoma, are innately resistant to retinoid therapy. Therefore, we employed a precision medicine approach to globally profile the retinoid signalling response and to determine how an excess of cellular MYCN antagonises these signalling events to prevent differentiation and confer resistance...
February 10, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28187412/omics-fusion-a-platform-for-integrative-analysis-of-omics-data
#9
Benedikt G Brink, Annica Seidel, Nils Kleinbölting, Tim W Nattkemper, Stefan P Albaum
We present Omics Fusion, a new web-based platform for integrative analysis of omics data. Omics Fusion provides a collection of new and established tools and visualization methods to support researchers in exploring omics data, validating results or understanding how to adjust experiments in order to make new discoveries. It is easily extendible and new visualization methods are added continuously. It is available for free under: https://fusion.cebitec.uni-bielefeld.de/.
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187207/a-multi-objective-constraint-based-approach-for-modeling-genome-scale-microbial-ecosystems
#10
Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard
Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients...
2017: PloS One
https://www.readbyqxmd.com/read/28185573/rgmatch-matching-genomic-regions-to-proximal-genes-in-omics-data-integration
#11
Pedro Furió-Tarí, Ana Conesa, Sonia Tarazona
BACKGROUND: The integrative analysis of multiple genomics data often requires that genome coordinates-based signals have to be associated with proximal genes. The relative location of a genomic region with respect to the gene (gene area) is important for functional data interpretation; hence algorithms that match regions to genes should be able to deliver insight into this information. RESULTS: In this work we review the tools that are publicly available for making region-to-gene associations...
November 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28185567/from-comorbidities-of-chronic-obstructive-pulmonary-disease-to-identification-of-shared-molecular-mechanisms-by-data-integration
#12
David Gomez-Cabrero, Jörg Menche, Claudia Vargas, Isaac Cano, Dieter Maier, Albert-László Barabási, Jesper Tegnér, Josep Roca
BACKGROUND: Deep mining of healthcare data has provided maps of comorbidity relationships between diseases. In parallel, integrative multi-omics investigations have generated high-resolution molecular maps of putative relevance for understanding disease initiation and progression. Yet, it is unclear how to advance an observation of comorbidity relations (one disease to others) to a molecular understanding of the driver processes and associated biomarkers. RESULTS: Since Chronic Obstructive Pulmonary disease (COPD) has emerged as a central hub in temporal comorbidity networks, we developed a systematic integrative data-driven framework to identify shared disease-associated genes and pathways, as a proxy for the underlying generative mechanisms inducing comorbidity...
November 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28184370/metaproteomics-as-a-complementary-approach-to-gut-microbiota-in-health-and-disease
#13
REVIEW
Bernardo A Petriz, Octávio L Franco
Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28174585/the-understanding-of-the-plant-iron-deficiency-responses-in-strategy-i-plants-and-the-role-of-ethylene-in-this-process-by-omic-approaches
#14
REVIEW
Wenfeng Li, Ping Lan
Iron (Fe) is an essential plant micronutrient but is toxic in excess. Fe deficiency chlorosis is a major constraint for plant growth and causes severe losses of crop yields and quality. Under Fe deficiency conditions, plants have developed sophisticated mechanisms to keep cellular Fe homeostasis via various physiological, morphological, metabolic, and gene expression changes to facilitate the availability of Fe. Ethylene has been found to be involved in the Fe deficiency responses of plants through pharmacological studies or by the use of ethylene mutants...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28168604/the-natural-product-osthole-attenuates-yeast-growth-by-extensively-suppressing-the-gene-expressions-of-mitochondrial-respiration-chain
#15
Zhe Wang, Yan Shen
The fast growing evidences have indicated that the natural product osthole is a promising drug candidate for fighting several serious human diseases, for example, cancer and inflammation. However, the mode-of-action (MoA) of osthole remains largely incomplete. In this study, we investigated the growth inhibition activity of osthole using fission yeast as a model, with the goal of understanding the osthole's mechanism of action, especially from the molecular level. Microarray analysis indicated that osthole has significant impacts on gene transcription levels (In total, 214 genes are up-regulated, and 97 genes are down-regulated)...
February 7, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28167869/bearings-in-hip-arthroplasty-joint-registries-vs-precision-medicine-review-article
#16
REVIEW
Mark J Pearson, Liam M Grover, Janet M Lord, Simon W Jones, Edward T Davis
BACKGROUND: Precision medicine has been adopted in a range of clinical settings where omics data have led to greater characterisation of disease and stratification of patients into subcategories of phenotypes and pathologies. However, in orthopaedics, precision medicine lags behind other disciplines such as cancer. Joint registries have now amassed a huge body of data pertaining to implant performance which can be broken down into performance statistics for different material types in different cohorts of patients...
February 2017: HSS Journal: the Musculoskeletal Journal of Hospital for Special Surgery
https://www.readbyqxmd.com/read/28164855/from-culture-to-high-throughput-sequencing-and-beyond-a-layperson-s-guide-to-the-omics-and-diagnostic-potential-of-the-microbiome
#17
REVIEW
Paul W O'Toole, Burkhardt Flemer
Detailed knowledge of the community of organisms in the gut has become possible in recent years because of the development of culture-independent methods. Largely based on latest DNA sequencing platforms, it is now possible to establish the composition of the microbiota and the repertoire of biochemical functions it encodes. Variations in either or both of these parameters have been linked to intestinal and extraintestinal disease. This article summarizes how these methods are applied, with special reference to gastroenterology, and describes the achievements and future potential of microbiota analysis as a diagnostic tool...
March 2017: Gastroenterology Clinics of North America
https://www.readbyqxmd.com/read/28162022/proteomic-analysis-of-red-blood-cells-and-the-potential-for-the-clinic-what-have-we-learned-so-far
#18
Angelo D'Alessandro, Lello Zolla
Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating "bags of hemoglobin". The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease. Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology...
February 4, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28161522/emouseatlas-an-atlas-based-resource-for-understanding-mammalian-embryogenesis
#19
REVIEW
Chris Armit, Lorna Richardson, Shanmugasundaram Venkataraman, Liz Graham, Nicholas Burton, Bill Hill, Yiya Yang, Richard Baldock
The eMouseAtlas resource is an online database of 3D digital models of mouse development, an ontology of mouse embryo anatomy and a gene-expression database with about 30K spatially mapped gene-expression patterns. It is closely linked with the MGI/GXD database at the Jackson Laboratory and holds links to almost all available image-based gene-expression data for the mouse embryo. In this resource article we describe the novel web-based tools we have developed for 3D visualisation of embryo anatomy and gene expression...
February 1, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28157411/novel-lipidomic-biomarkers-in-hyperlipidemia-and-cardiovascular-diseases-an-integrative-biology-analysis
#20
Sneha Rai, Sonika Bhatnagar
Lipidomics is a new frontier of omics research and offers much promise for new-generation biomarkers for common complex phenotypes such as hyperlipidemia (HL) and cardiovascular diseases (CVDs). HL is a disorder characterized by increased levels of blood lipids and is a well-established risk factor for CVD. Traditional clinical markers for prognosis of hyperlipidemic individuals are inadequate to forecast or diagnose cardiac events. In this expert review, lipidomic profiles from recent HL and CVD studies were compared with the normolipidemic profile prepared from the Standard Reference Material...
February 3, 2017: Omics: a Journal of Integrative Biology
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