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https://www.readbyqxmd.com/read/29138111/recent-advances-in-melanoma-research-via-omics-platforms
#1
REVIEW
Carmen Rodríguez-Cerdeira, Alberto Molares-Vila, Miguel Carnero-Gregorio, Alberte Corbalán-Rivas
Melanoma has a high mortality rate and metastatic melanoma is highly resistant to conventional therapies. "Omics" fields such as proteomics and microRNA and exosome studies have provided new knowledge to complement the information generated by genomic studies. This work aimed to review the current status of biomarker discovery for melanoma through multi-"omics" platforms. A few sets of novel microRNAs and proteins are described, some of them with important implications in suppressing melanoma at different stages...
November 11, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29136180/bcntb-bioinformatics-the-next-evolutionary-step-in-the-bioinformatics-of-breast-cancer-tissue-banking
#2
Emanuela Gadaleta, Stefano Pirrò, Abu Zafer Dayem Ullah, Jacek Marzec, Claude Chelala
Here, we present an update of Breast Cancer Now Tissue Bank bioinformatics, a rich platform for the sharing, mining, integration and analysis of breast cancer data. Its modalities provide researchers with access to a centralised information gateway from which they can access a network of bioinformatic resources to query findings from publicly available, in-house and experimental data generated using samples supplied from the Breast Cancer Now Tissue Bank. This in silico environment aims to help researchers use breast cancer data to their full potential, irrespective of any bioinformatics barriers...
October 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29126055/estrogen-responsive-gene-networks-in-the-teleost-liver-what-are-the-key-molecular-indicators
#3
April Feswick, Kelly R Munkittrick, Christopher J Martyniuk
An overarching goal of environmental genomics is to leverage sensitive suites of markers that are robust and reliable to assess biological responses in a range of species inhabiting variable environments. The objective of this study was to identify core groups of transcripts and molecular signaling pathways that respond to 17alpha-ethylinestadiol (EE2), a ubiquitous estrogenic contaminant, using transcriptome datasets generated from six independent laboratories. We sought to determine which biomarkers and gene networks were those most robust and reliably detected in multiple laboratories...
October 31, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/29123200/discordancy-partitioning-for-validating-potentially-inconsistent-pharmacogenomic-studies
#4
J Sunil Rao, Hongmei Liu
The Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE) are two major studies that can be used to mine for therapeutic biomarkers for cancers of a large variety. Model validation using the two datasets however has proved challenging. Both predictions and signatures do not consistently validate well for models built on one dataset and tested on the other. While the genomic profiling seems consistent, the drug response data is not. Some efforts at harmonizing experimental designs has helped but not entirely removed model validation difficulties...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29119738/physiological-characterization-transcriptomic-profiling-and-microsatellite-marker-mining-of-lycium-ruthenicum
#5
Jin-Huan Chen, Dong-Zhi Zhang, Chong Zhang, Mei-Long Xu, Wei-Lun Yin
Lycium ruthenicum is a perennial shrub species that has attracted considerable interest in recent years owing to its nutritional value and ability to thrive in a harsh environment. However, only extremely limited transcriptomic and genomic data related to this species can be found in public databases, thereby limiting breeding research and molecular function analysis. In this study, we characterized the physiological and biochemical responses to saline-alkaline mixed stress by measuring photochemical efficiency, chlorophyll content, and protective enzyme activity...
2017: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/29117384/eshre-pgd-consortium-data-collection-xiv-xv-cycles-from-january-2011-to-december-2012-with-pregnancy-follow-up-to-october-2013
#6
M De Rycke, V Goossens, G Kokkali, M Meijer-Hoogeveen, E Coonen, C Moutou
STUDY QUESTION: How does the data collection XIV-XV of the European Society of Human Reproduction and Embryology (ESHRE) PGD Consortium compare with the cumulative data for data collections I-XIII? SUMMARY ANSWER: The 14th and 15th retrospective collection represents valuable data on PGD/PGS cycles, pregnancies and children: the main trend observed is the increased application of array technology at the cost of FISH testing in PGS cycles and in PGD cycles for chromosomal abnormalities...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/29113935/predicting-age-by-mining-electronic-medical-records-with-deep-learning-characterizes-differences-between-chronological-and-physiological-age
#7
Zichen Wang, Li Li, Benjamin S Glicksberg, Ariel Israel, Joel T Dudley, Avi Ma'ayan
Determining the discrepancy between chronological and physiological age of patients is central to preventative and personalized care. Electronic medical records (EMR) provide rich information about the patient physiological state, but it is unclear whether such information can be predictive of chronological age. Here we present a deep learning model the uses vital signs and lab tests contained within the EMR of Mount Sinai Health System (MSHS) to predict chronological age. The model is trained on 377,686 EMR from patients of ages 18-85 years old...
November 4, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29112885/commensal-koch-s-postulates-establishing-causation-in-human-microbiota-research
#8
REVIEW
B Anne Neville, Samuel C Forster, Trevor D Lawley
Advances in high-throughput sequencing technologies and the development of sophisticated bioinformatics analysis methods, algorithms, and pipelines to handle the large amounts of data generated have driven the field of human microbiome research forward. This specialist knowledge has been crucial to thoroughly mine the human gut microbiota, particularly in the absence of methods for the routine cultivation of most enteric microorganisms. In recent years, however, significant efforts have been made to address the 'great plate count anomaly' and to overcome the barriers to cultivation of the fastidious and mostly strictly anaerobic bacteria that reside in the human gut...
November 4, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29112783/toblerols-cyclopropanol-containing-modulators-of-methylobacterial-antibiosis-generated-by-an-unusual-polyketide-synthase
#9
Reiko Ueoka, Miriam Bortfeld-Miller, Brandon Isamu Morinaka, Julia Anne Vorholt, Jörn Piel
Trans-AT polyketide synthases (PKSs) are biosynthetically versatile enzymes that generate bioactive polyketides of high structural diversity. In this study, we detected in the genome of several bacteria a cryptic, unusual trans-AT PKS gene cluster that eluded automated PKS prediction. Genomic mining of one of these strains, the model methylotroph Methylobacterium extorquens AM1, revealed epoxide-cyclopropanol-containing polyketides named toblerols. The stereochemistry was determined by NMR, chemical derivatization, and the comparison of CD data with those of a synthesized model compound...
November 7, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29112695/recent-development-of-antismash-and-other-computational-approaches-to-mine-secondary-metabolite-biosynthetic-gene-clusters
#10
Kai Blin, Hyun Uk Kim, Marnix H Medema, Tilmann Weber
Many drugs are derived from small molecules produced by microorganisms and plants, so-called natural products. Natural products have diverse chemical structures, but the biosynthetic pathways producing those compounds are often organized as biosynthetic gene clusters (BGCs) and follow a highly conserved biosynthetic logic. This allows for the identification of core biosynthetic enzymes using genome mining strategies that are based on the sequence similarity of the involved enzymes/genes. However, mining for a variety of BGCs quickly approaches a complexity level where manual analyses are no longer possible and require the use of automated genome mining pipelines, such as the antiSMASH software...
November 3, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29110697/exutr-a-novel-pipeline-for-large-scale-prediction-of-3-utr-sequences-from-ngs-data
#11
Zixia Huang, Emma C Teeling
BACKGROUND: The three prime untranslated region (3'-UTR) is known to play a pivotal role in modulating gene expression by determining the fate of mRNA. Many crucial developmental events, such as mammalian spermatogenesis, tissue patterning, sex determination and neurogenesis, rely heavily on post-transcriptional regulation by the 3'-UTR. However, 3'-UTR biology seems to be a relatively untapped field, with only limited tools and 3'-UTR resources available. To elucidate the regulatory mechanisms of the 3'-UTR on gene expression, firstly the 3'-UTR sequences must be identified...
November 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29109919/the-unexpected-depths-of-genome-skimming-data-a-case-study-examining-goodeniaceae-floral-symmetry-genes
#12
Brent A Berger, Jiahong Han, Emily B Sessa, Andrew G Gardner, Kelly A Shepherd, Vincent A Ricigliano, Rachel S Jabaily, Dianella G Howarth
Premise of the study: The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes...
October 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29107797/establishment-of-a-de-novo-reference-transcriptome-of-histomonas-meleagridis-reveals-basic-insights-about-biological-functions-and-potential-pathogenic-mechanisms-of-the-parasite
#13
Rounik Mazumdar, Lukas Endler, Andreas Monoyios, Michael Hess, Ivana Bilic
The protozoan flagellate Histomonas meleagridis is the causative agent of histomonosis in poultry. In turkeys, high mortality might be noticed whereas in chickens the disease is less severe despite production losses. Discovered over a century ago, molecular data on this parasite are scarce and genetic studies are in its infancy. To expand genomic information, a de novo transcriptome sequencing of H. meleagridis was performed from a virulent and an attenuated strain, cultivated in vitro as monoxenic mono-eukaryotic culture...
October 6, 2017: Protist
https://www.readbyqxmd.com/read/29106666/tadb-2-0-an-updated-database-of-bacterial-type-ii-toxin-antitoxin-loci
#14
Yingzhou Xie, Yiqing Wei, Yue Shen, Xiaobin Li, Hao Zhou, Cui Tai, Zixin Deng, Hong-Yu Ou
TADB2.0 (http://bioinfo-mml.sjtu.edu.cn/TADB2/) is an updated database that provides comprehensive information about bacterial type II toxin-antitoxin (TA) loci. Compared with the previous version, the database refined and the new data schema is employed. With the aid of text mining and manual curation, it recorded 6193 type II TA loci in 870 replicons of bacteria and archaea, including 105 experimentally validated TA loci. In addition, the newly developed tool TAfinder combines the homolog searches and the operon structure detection, allowing the prediction for type II TA pairs in bacterial genome sequences...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29106455/virapipe-scalable-parallel-pipeline-for-viral-metagenome-analysis-from-next-generation-sequencing-reads
#15
Altti Ilari Maarala, Zurab Bzhalava, Joakim Dillner, Keijo Heljanko, Davit Bzhalava
Motivation: Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments...
November 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29104519/metabolite-profiling-of-yam-dioscorea-spp-accessions-for-use-in-crop-improvement-programmes
#16
Elliott J Price, Ranjana Bhattacharjee, Antonio Lopez-Montes, Paul D Fraser
Introduction: Ninety-seven percent of yam (Dioscorea spp.) production takes place in low income food deficit countries (LIFDCs) and the crop provides 200 calories a day to approximately 300 million people. Therefore, yams are vital for food security. Yams have high-yield potential and high market value potential yet current breeding of yam is hindered by a lack of genomic information and genetic resources. New tools are needed to modernise breeding strategies and unlock the potential of yam to improve livelihood in LIFDCs...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/29100083/high-rate-of-recurrent-de-novo-mutations-in-developmental-and-epileptic-encephalopathies
#17
Fadi F Hamdan, Candace T Myers, Patrick Cossette, Philippe Lemay, Dan Spiegelman, Alexandre Dionne Laporte, Christina Nassif, Ousmane Diallo, Jean Monlong, Maxime Cadieux-Dion, Sylvia Dobrzeniecka, Caroline Meloche, Kyle Retterer, Megan T Cho, Jill A Rosenfeld, Weimin Bi, Christine Massicotte, Marguerite Miguet, Ledia Brunga, Brigid M Regan, Kelly Mo, Cory Tam, Amy Schneider, Georgie Hollingsworth, David R FitzPatrick, Alan Donaldson, Natalie Canham, Edward Blair, Bronwyn Kerr, Andrew E Fry, Rhys H Thomas, Joss Shelagh, Jane A Hurst, Helen Brittain, Moira Blyth, Robert Roger Lebel, Erica H Gerkes, Laura Davis-Keppen, Quinn Stein, Wendy K Chung, Sara J Dorison, Paul J Benke, Emily Fassi, Nicole Corsten-Janssen, Erik-Jan Kamsteeg, Frederic T Mau-Them, Ange-Line Bruel, Alain Verloes, Katrin Õunap, Monica H Wojcik, Dara V F Albert, Sunita Venkateswaran, Tyson Ware, Dean Jones, Yu-Chi Liu, Shekeeb S Mohammad, Peyman Bizargity, Carlos A Bacino, Vincenzo Leuzzi, Simone Martinelli, Bruno Dallapiccola, Marco Tartaglia, Lubov Blumkin, Klaas J Wierenga, Gabriela Purcarin, James J O'Byrne, Sylvia Stockler, Anna Lehman, Boris Keren, Marie-Christine Nougues, Cyril Mignot, Stéphane Auvin, Caroline Nava, Susan M Hiatt, Martina Bebin, Yunru Shao, Fernando Scaglia, Seema R Lalani, Richard E Frye, Imad T Jarjour, Stéphanie Jacques, Renee-Myriam Boucher, Emilie Riou, Myriam Srour, Lionel Carmant, Anne Lortie, Philippe Major, Paola Diadori, François Dubeau, Guy D'Anjou, Guillaume Bourque, Samuel F Berkovic, Lynette G Sadleir, Philippe M Campeau, Zoha Kibar, Ronald G Lafrenière, Simon L Girard, Saadet Mercimek-Mahmutoglu, Cyrus Boelman, Guy A Rouleau, Ingrid E Scheffer, Heather C Mefford, Danielle M Andrade, Elsa Rossignol, Berge A Minassian, Jacques L Michaud
Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants...
November 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29097759/sequencing-genomes-from-mixed-dna-samples-evaluating-the-metagenome-skimming-approach-in-lichenized-fungi
#18
Anjuli Meiser, Jürgen Otte, Imke Schmitt, Francesco Dal Grande
The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi...
November 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29095138/mitsuaria-noduli-sp-nov-isolated-from-the-root-nodules-of-robinia-pseudoacacia-in-a-lead-zinc-mine
#19
Miao-Chun Fan, Li-Jun Nan, Ya-Min Zhu, Wei-Min Chen, Ge-Hong Wei, Yan-Bing Lin
A novel endophytic bacterium, designated strain HZ7(T), was isolated from the root nodules of Robinia pseudoacacia growing in a lead-zinc mine in Mianxian County, Shaanxi Province, China. Cells were Gram-reaction-negative, aerobic, motile, rod-shaped, methyl-red-negative, catalase-positive, positive for chitosan-degrading activity and did not produce H2S. Strain HZ7(T) grew at 4-45 °C (optimum 25-30 °C), at pH 5-9 (optimum pH 7-8) and with 0-1 % (w/v) NaCl. The quinone type was ubiquinone 8 (UQ-8). The major fatty acids were identified as C16 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c)...
November 2, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29094062/metabolomics-for-the-masses-the-future-of-metabolomics-in-a-personalized-world
#20
REVIEW
Drupad K Trivedi, Katherine A Hollywood, Royston Goodacre
Current clinical practices focus on a small number of biochemical directly related to the pathophysiology with patients and thus only describe a very limited metabolome of a patient and fail to consider the interations of these small molecules. This lack of extended information may prevent clinicians from making the best possible therapeutic interventions in sufficient time to improve patient care. Various post-genomics '('omic)' approaches have been used for therapeutic interventions previously. Metabolomics now a well-established'omics approach, has been widely adopted as a novel approach for biomarker discovery and in tandem with genomics (especially SNPs and GWAS) has the potential for providing systemic understanding of the underlying causes of pathology...
March 2017: New Horizons in Translational Medicine
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