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https://www.readbyqxmd.com/read/28724449/novel-promoters-and-coding-first-exons-in-dlg2-linked-to-developmental-disorders-and-intellectual-disability
#1
Claudio Reggiani, Sandra Coppens, Tayeb Sekhara, Ivan Dimov, Bruno Pichon, Nicolas Lufin, Marie-Claude Addor, Elga Fabia Belligni, Maria Cristina Digilio, Flavio Faletra, Giovanni Battista Ferrero, Marion Gerard, Bertrand Isidor, Shelagh Joss, Florence Niel-Bütschi, Maria Dolores Perrone, Florence Petit, Alessandra Renieri, Serge Romana, Alexandra Topa, Joris Robert Vermeesch, Tom Lenaerts, Georges Casimir, Marc Abramowicz, Gianluca Bontempi, Catheline Vilain, Nicolas Deconinck, Guillaume Smits
BACKGROUND: Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. METHODS: Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and murine omics datasets, we combined copy number variations, histone modifications, developmental tissue-specific regulation, and protein data to explore the molecular mechanism at play...
July 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28720581/hit-ndrive-patient-specific-multi-driver-gene-prioritization-for-precision-oncology
#2
Raunak Shrestha, Ermin Hodzic, Thomas Sauerwald, Phuong Dao, Kendric Wang, Jake Yeung, Shawn Anderson, Fabio Vandin, Gholamreza Haffari, Colin C Collins, Cenk Sahinalp
Prioritizing molecular alterations that act as drivers of cancer remains a crucial bottleneck in therapeutic development. Here we introduce HIT'nDRIVE, a computational method that integrates genomic and transcriptomic data to identify a set of patient-specific, sequence-altered genes, with sufficient collective influence over dysregulated transcripts. HIT'nDRIVE aims to solve the "random walk facility location" (RWFL) problem in a gene (or protein) interaction network, which differs from the standard facility location problem by its use of an alternative distance measure: "multi-hitting time", the expected length of the shortest random walk from any one of the set of sequence-altered genes to an expression-altered target gene...
July 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28713550/a-community-proposal-to-integrate-proteomics-activities-in-elixir
#3
Juan Antonio Vizcaíno, Mathias Walzer, Rafael C Jiménez, Wout Bittremieux, David Bouyssié, Christine Carapito, Fernando Corrales, Myriam Ferro, Albert J R Heck, Peter Horvatovich, Martin Hubalek, Lydie Lane, Kris Laukens, Fredrik Levander, Frederique Lisacek, Petr Novak, Magnus Palmblad, Damiano Piovesan, Alfred Pühler, Veit Schwämmle, Dirk Valkenborg, Merlijn van Rijswijk, Jiri Vondrasek, Martin Eisenacher, Lennart Martens, Oliver Kohlbacher
Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes...
2017: F1000Research
https://www.readbyqxmd.com/read/28713412/the-emerging-oilseed-crop-sesamum-indicum-enters-the-omics-era
#4
REVIEW
Komivi Dossa, Diaga Diouf, Linhai Wang, Xin Wei, Yanxin Zhang, Mareme Niang, Daniel Fonceka, Jingyin Yu, Marie A Mmadi, Louis W Yehouessi, Boshou Liao, Xiurong Zhang, Ndiaga Cisse
Sesame (Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28712361/plasmodium-knowlesi-a-superb-in-vivo-nonhuman-primate-model-of-antigenic-variation-in-malaria
#5
M R Galinski, S A Lapp, M S Peterson, F Ay, C J Joyner, K G LE Roch, L L Fonseca, E O Voit
Antigenic variation in malaria was discovered in Plasmodium knowlesi studies involving longitudinal infections of rhesus macaques (M. mulatta). The variant proteins, known as the P. knowlesi Schizont Infected Cell Agglutination (SICA) antigens and the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) antigens, expressed by the SICAvar and var multigene families, respectively, have been studied for over 30 years. Expression of the SICA antigens in P. knowlesi requires a splenic component, and specific antibodies are necessary for variant antigen switch events in vivo...
July 17, 2017: Parasitology
https://www.readbyqxmd.com/read/28711145/integrative-approaches-to-understanding-the-pathogenic-role-of-genetic-variation-in-rheumatic-diseases
#6
REVIEW
Vincent A Laufer, Jake Y Chen, Carl D Langefeld, S Louis Bridges
The use of high-throughput omics may help to understand the contribution of genetic variants to the pathogenesis of rheumatic diseases. We discuss the concept of missing heritability: that genetic variants do not explain the heritability of rheumatoid arthritis and related rheumatologic conditions. In addition to an overview of how integrative data analysis can lead to novel insights into mechanisms of rheumatic diseases, we describe statistical approaches to prioritizing genetic variants for future functional analyses...
August 2017: Rheumatic Diseases Clinics of North America
https://www.readbyqxmd.com/read/28709434/integrating-multi-omics-analyses-of-nonomuraea-dietziae-to-reveal-the-role-of-soybean-oil-in-4-oh-meleu-4-csa-overproduction
#7
Huanhuan Liu, Di Huang, Lina Jin, Cheng Wang, Shaoxiong Liang, Jianping Wen
BACKGROUND: Nonomuraea dietziae is a promising microorganism to mediate the region-specific monooxygenation reaction of cyclosporine A (CsA). The main product [(4'-OH)MeLeu](4)-CsA possesses high anti-HIV/HCV and hair growth-stimulating activities while avoiding the immunosuppressive effect of CsA. However, the low conversion efficiency restricts the clinical application. In this study, the production of [(4'-OH)MeLeu](4)-CsA was greatly improved by 55.6% from 182.8 to 284.4 mg/L when supplementing soybean oil into the production medium, which represented the highest production of [(4'-OH)MeLeu](4)-CsA so far...
July 14, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28699531/identification-of-antineoplastic-targets-with-systems-approaches-using-resveratrol-as-an-in-depth-case-study
#8
Nivedita Singh, Sherry Freiesleben, Shailendra K Gupta, Yogeshwer Shukla, Olaf Wolkenhauer
The identification and validation of novel drug-target combinations are key steps in the drug discovery processes. Cancer is a complex disease that involves several genetic and environmental factors. High-throughput omics technologies are now widely available, however the integration of multi-omics data to identify viable anticancer drug-target combinations that allow for a better clinical outcome when considering the efficacy-toxicity spectrum, is challenging. In this review, we provide an overview of systems approaches that can help integrate a broad spectrum of technologies and data...
July 10, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28695748/proteomic-profiling-of-the-cancer-cell-secretome-informing-clinical-research
#9
Yung-Chin Hsiao, Lichieh Julie Chu, Jen-Ting Chen, Ta-Sen Yeh, Jau-Song Yu
Cancer represents one of the major causes of human deaths. Identification of proteins as biomarkers for early detection of cancer and therapeutic targets for cancer treatment are important issues in precision medicine. Secretome of cancer cells represents the collection of proteins secreted or shed from cancer cells. Proteomic profiling of the cancer cell secretome has been proven to be a convenient and efficient way to discover cancer biomarker and/or therapeutic targets. Areas covered: There have been numerous reviews describing the history and application of secretome analysis in cancer biomarker/therapeutic target research...
July 11, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28691371/approaches-to-identify-kinase-dependencies-in-cancer-signalling-networks
#10
REVIEW
Maria Dermit, Arran Dokal, Pedro R Cutillas
Cells integrate extracellular signals into appropriate responses through a complex network of biochemical reactions driven by the activity of protein and lipid kinases, among other proteins. In order to understand this complexity, new approaches, both experimental and computational, have recently been developed with the aim to identify regulatory kinases and infer their activation status in the context of their signalling network. Here, we review such approaches with particular focus on those based on phosphoproteomics...
July 10, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28691305/a-comparison-of-methods-for-inferring-causal-relationships-between-genotype-and-phenotype-using-additional-biological-measurements
#11
Holly F Ainsworth, So-Youn Shin, Heather J Cordell
Genome wide association studies (GWAS) have been very successful over the last decade at identifying genetic variants associated with disease phenotypes. However, interpretation of the results obtained can be challenging. Incorporation of further relevant biological measurements (e.g. 'omics' data) measured in the same individuals for whom we have genotype and phenotype data may help us to learn more about the mechanism and pathways through which causal genetic variants affect disease. We review various methods for causal inference that can be used for assessing the relationships between genetic variables, other biological measures, and phenotypic outcome, and present a simulation study assessing the performance of the methods under different conditions...
July 10, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28690835/dietary-assessment-methods-in-epidemiological-research-current-state-of-the-art-and-future-prospects
#12
REVIEW
Androniki Naska, Areti Lagiou, Pagona Lagiou
Self-reported dietary intake is assessed by methods of real-time recording (food diaries and the duplicate portion method) and methods of recall (dietary histories, food frequency questionnaires, and 24-hour dietary recalls). Being less labor intensive, recall methods are more frequently employed in nutritional epidemiological investigations. However, sources of error, which include the participants' inability to fully and accurately recall their intakes as well as limitations inherent in the food composition databases applied to convert the reported food consumption to energy and nutrient intakes, may limit the validity of the generated information...
2017: F1000Research
https://www.readbyqxmd.com/read/28686852/integrated-meta-omic-analyses-of-the-gastrointestinal-tract-microbiome-in-patients-undergoing-allogeneic-hematopoietic-stem-cell-transplantation
#13
Anne Kaysen, Anna Heintz-Buschart, Emilie E L Muller, Shaman Narayanasamy, Linda Wampach, Cédric C Laczny, Norbert Graf, Arne Simon, Katharina Franke, Jörg Bittenbring, Paul Wilmes, Jochen G Schneider
In patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), treatment-induced changes to the gastrointestinal tract (GIT) microbiome have been linked to adverse outcomes, most notably graft-versus-host disease (GvHD). However, it is presently unknown whether this relationship is causal or consequential. Here, we performed an integrated meta-omic analysis to probe deeper into the GIT microbiome changes, during allo-HSCT, and its accompanying treatments. We used 16S and 18S rRNA gene amplicon sequencing to resolve archaea, bacteria, and eukaryotes within the GIT microbiomes of 16 patients undergoing allo-HSCT for the treatment of hematologic malignancies...
June 20, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28686565/integration-of-ecology-and-environmental-metagenomics-conceptual-and-methodological-frameworks
#14
Diana Marco
Although from its origin metagenomics was concerned with composition of communities of microbial OTUs (Operational Taxonomic Units) living in a given habitat and their diversity and functional heterogeneity (concepts already well rooted in ecology), the new field was more 'environmentally' than 'ecologically' oriented. Probably by circumstantial reasons, metagenomics and ecology followed rather independent trajectories and conceptual and methodological gaps appeared. Recently, calls for the need of integrating the theoretical basis and methodologies coming from metagenomics (and other meta-omics) and ecology have been made...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28684091/visualizing-the-regulatory-role-of-angiopoietin-like-protein-8-angptl8-in-glucose-and-lipid-metabolic-pathways
#15
Amnah Siddiqa, Elisa Cirillo, Samar H K Tareen, Amjad Ali, Martina Kutmon, Lars Eijssen, Jamil Ahmad, Chris T Evelo, Susan L Coort
ANGPTL8 (Angiopoietin-like protein 8) is a newly identified hormone emerging as a novel drug target for treatment of diabetes mellitus and dyslipidemia due to its unique metabolic nature. With increasing number of studies targeting the regulation of ANGPTL8, integration of their findings becomes indispensable. This study has been conducted with the aim to collect, analyze, integrate and visualize the available knowledge in the literature about ANGPTL8 and its regulation. We utilized this knowledge to construct a regulatory pathway of ANGPTL8 which is available at WikiPathways, an open source pathways database...
July 3, 2017: Genomics
https://www.readbyqxmd.com/read/28683746/multi-omics-of-34-colorectal-cancer-cell-lines-a-resource-for-biomedical-studies
#16
Kaja C G Berg, Peter W Eide, Ina A Eilertsen, Bjarne Johannessen, Jarle Bruun, Stine A Danielsen, Merete Bjørnslett, Leonardo A Meza-Zepeda, Mette Eknæs, Guro E Lind, Ola Myklebost, Rolf I Skotheim, Anita Sveen, Ragnhild A Lothe
BACKGROUND: Colorectal cancer (CRC) cell lines are widely used pre-clinical model systems. Comprehensive insights into their molecular characteristics may improve model selection for biomedical studies. METHODS: We have performed DNA, RNA and protein profiling of 34 cell lines, including (i) targeted deep sequencing (n = 612 genes) to detect single nucleotide variants and insertions/deletions; (ii) high resolution DNA copy number profiling; (iii) gene expression profiling at exon resolution; (iv) small RNA expression profiling by deep sequencing; and (v) protein expression analysis (n = 297 proteins) by reverse phase protein microarrays...
July 6, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28683736/security-controls-in-an-integrated-biobank-to-protect-privacy-in-data-sharing-rationale-and-study-design
#17
Takako Takai-Igarashi, Kengo Kinoshita, Masao Nagasaki, Soichi Ogishima, Naoki Nakamura, Sachiko Nagase, Satoshi Nagaie, Tomo Saito, Fuji Nagami, Naoko Minegishi, Yoichi Suzuki, Kichiya Suzuki, Hiroaki Hashizume, Shinichi Kuriyama, Atsushi Hozawa, Nobuo Yaegashi, Shigeo Kure, Gen Tamiya, Yoshio Kawaguchi, Hiroshi Tanaka, Masayuki Yamamoto
BACKGROUND: With the goal of realizing genome-based personalized healthcare, we have developed a biobank that integrates personal health, genome, and omics data along with biospecimens donated by volunteers of 150,000. Such a large-scale of data integration involves obvious risks of privacy violation. The research use of personal genome and health information is a topic of global discussion with regard to the protection of privacy while promoting scientific advancement. The present paper reports on our plans, current attempts, and accomplishments in addressing security problems involved in data sharing to ensure donor privacy while promoting scientific advancement...
July 6, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28682479/metabolomic-studies-of-indonesian-jamu-medicines-prediction-of-jamu-efficacy-and-identification-of-important-metabolites
#18
Sony Hartono Wijaya, Irmanida Batubara, Takaaki Nishioka, Md Altaf-Ul-Amin, Shigehiko Kanaya
In order to obtain a better understanding why some Jamu formulas can be used to treat a specific disease, we performed metabolomic studies of Jamu by taking into consideration the biologically active compounds existing in plants used as Jamu ingredients. A thorough integration of information from omics is expected to provide solid evidence-based scientific rationales for the development of modern phytomedicines. This study focused on prediction of Jamu efficacy based on its component metabolites and also identification of important metabolites related to each efficacy group...
July 6, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28679163/network-approaches-to-systems-biology-analysis-of-complex-disease-integrative-methods-for-multi-omics-data
#19
Jingwen Yan, Shannon L Risacher, Li Shen, Andrew J Saykin
In the past decade, significant progress has been made in complex disease research across multiple omics layers from genome, transcriptome and proteome to metabolome. There is an increasing awareness of the importance of biological interconnections, and much success has been achieved using systems biology approaches. However, because of the typical focus on one single omics layer at a time, existing systems biology findings explain only a modest portion of complex disease. Recent advances in multi-omics data collection and sharing present us new opportunities for studying complex diseases in a more comprehensive fashion, and yet simultaneously create new challenges considering the unprecedented data dimensionality and diversity...
June 30, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28676813/a-concise-review-on-multi-omics-data-integration-for-terroir-analysis-in-vitis-vinifera
#20
REVIEW
Pastor Jullian Fabres, Cassandra Collins, Timothy R Cavagnaro, Carlos M Rodríguez López
Vitis vinifera (grapevine) is one of the most important fruit crops, both for fresh consumption and wine and spirit production. The term terroir is frequently used in viticulture and the wine industry to relate wine sensory attributes to its geographic origin. Although, it can be cultivated in a wide range of environments, differences in growing conditions have a significant impact on fruit traits that ultimately affect wine quality. Understanding how fruit quality and yield are controlled at a molecular level in grapevine in response to environmental cues has been a major driver of research...
2017: Frontiers in Plant Science
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