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https://www.readbyqxmd.com/read/28630644/isometric-gene-tree-reconciliation-revisited
#1
Broňa Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomáš Vinař
BACKGROUND: Isometric gene tree reconciliation is a gene tree/species tree reconciliation problem where both the gene tree and the species tree include branch lengths, and these branch lengths must be respected by the reconciliation. The problem was introduced by Ma et al. in 2008 in the context of reconstructing evolutionary histories of genomes in the infinite sites model. RESULTS: In this paper, we show that the original algorithm by Ma et al. is incorrect, and we propose a modified algorithm that addresses the problems that we discovered...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28628615/flipping-chromosomes-in-deep-sea-archaea
#2
Matteo Cossu, Catherine Badel, Ryan Catchpole, Danièle Gadelle, Evelyne Marguet, Valérie Barbe, Patrick Forterre, Jacques Oberto
One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal inversions occur so frequently that even closely related genomes are difficult to align. Clearly not resulting from the native homologous recombination machinery, the causative agent of these inversions has remained elusive. We present a model in which genomic inversions are catalyzed by the integrase enzyme encoded by a family of mobile genetic elements...
June 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28626905/genome-architecture-enables-local-adaptation-of-atlantic-cod-despite-high-connectivity
#3
Julia M I Barth, Paul R Berg, Per R Jonsson, Sara Bonanomi, Hanna Corell, Jakob Hemmer-Hansen, Kjetill S Jakobsen, Kerstin Johannesson, Per Erik Jorde, Halvor Knutsen, Per-Olav Moksnes, Bastiaan Star, Nils Chr Stenseth, Henrik Svedäng, Sissel Jentoft, Carl André
Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key traits...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28623589/aranet-a-network-biology-server-for-arabidopsis-thaliana-and-other-non-model-plant-species
#4
Tak Lee, Insuk Lee
Functional gene networks link genes based on their functional relatedness, which is inferred from various complementary biological datasets. Gene networks comprising vast amounts of data can be used to predict which genes are associated with complex traits. Decades of studies in plant biology using the model organism Arabidopsis thaliana have generated large amounts of information, enabling the development of a system-level molecular network. AraNet (currently version 2) is a genome-scale functional gene network for Arabidopsis thaliana, constructed by integrating 19 types of genomics data and can be explored through a web-server (http://www...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28622508/saf-a-regulates-interphase-chromosome-structure-through-oligomerization-with-chromatin-associated-rnas
#5
Ryu-Suke Nozawa, Lora Boteva, Dinesh C Soares, Catherine Naughton, Alison R Dun, Adam Buckle, Bernard Ramsahoye, Peter C Bruton, Rebecca S Saleeb, Maria Arnedo, Bill Hill, Rory R Duncan, Sutherland K Maciver, Nick Gilbert
Higher eukaryotic chromosomes are organized into topologically constrained functional domains; however, the molecular mechanisms required to sustain these complex interphase chromatin structures are unknown. A stable matrix underpinning nuclear organization was hypothesized, but the idea was abandoned as more dynamic models of chromatin behavior became prevalent. Here, we report that scaffold attachment factor A (SAF-A), originally identified as a structural nuclear protein, interacts with chromatin-associated RNAs (caRNAs) via its RGG domain to regulate human interphase chromatin structures in a transcription-dependent manner...
June 15, 2017: Cell
https://www.readbyqxmd.com/read/28617955/expression-atlas-and-comparative-coexpression-network-analyses-reveal-important-genes-involved-in-the-formation-of-lignified-cell-wall-in-brachypodium-distachyon
#6
Richard Sibout, Sebastian Proost, Bjoern Oest Hansen, Neha Vaid, Federico M Giorgi, Severine Ho-Yue-Kuang, Frédéric Legée, Laurent Cézart, Oumaya Bouchabké-Coussa, Camille Soulhat, Nicholas Provart, Asher Pasha, Philippe Le Bris, David Roujol, Herman Hofte, Elisabeth Jamet, Catherine Lapierre, Staffan Persson, Marek Mutwil
While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function...
June 15, 2017: New Phytologist
https://www.readbyqxmd.com/read/28612184/autopolyploidy-leads-to-rapid-genomic-changes-in-arabidopsis-thaliana
#7
Shihong Liu, Yan Yang, Fang Wei, Jifa Duan, Janeen Braynen, Baoming Tian, Gangqiang Cao, Gongyao Shi, Jiachen Yuan
Polyploidy is a widespread feature of plant genomes. As a typical model of polyploidy, autopolyploidy has been postulated evolutionary dead ends and received little attention compared with allopolyploidy. For the limited data available so far, the evolutionary outcome of genome diversity in autopolyploids remains controversial in comparison with its diploid ancestors. In the present study, the effects of autopolyploidy on genome diversity were revealed at a genome-wide scale by comparative analyses of polymorphism between Arabidopsis autopolyploids (autotetraploids and autotriploids) and related diploids within the first ten successive inbred generations using amplified fragment length polymorphism...
June 13, 2017: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/28611825/epigenetic-combinatorial-patterns-predict-disease-variants
#8
Yu Zhang
Most genetic variants identified in genome-wide association studies are noncoding and are likely tagging nearby causal variants. It is a challenging task to pinpoint the precise locations of disease-causal variants and understand their functions in disease. A promising approach to improve fine mapping is to integrate the functional data currently available on hundreds of human tissues and cell types. Although there are several methods that use functional data to prioritize disease variants, they mainly use linear models, or equivalent naive likelihood-based models for prediction...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28611810/evolutionary-analysis-of-mikc-c-type-mads-box-genes-in-gymnosperms-and-angiosperms
#9
Fei Chen, Xingtan Zhang, Xing Liu, Liangsheng Zhang
MIKC(c)-type MADS-box genes encode transcription factors that control floral organ morphogenesis and flowering time in flowering plants. Here, in order to determine when the subfamilies of MIKC(c) originated and their early evolutionary trajectory, we sampled and analyzed the genomes and large-scale transcriptomes representing all the orders of gymnosperms and basal angiosperms. Through phylogenetic inference, the MIKC(c)-type MADS-box genes were subdivided into 14 monophyletic clades. Among them, the gymnosperm orthologs of AGL6, SEP, AP1, GMADS, SOC1, AGL32, AP3/PI, SVP, AGL15, ANR1, and AG were identified...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28611042/competition-between-dna-methylation-nucleotide-synthesis-and-anti-oxidation-in-cancer-versus-normal-tissues
#10
Sha Cao, Xiwen Zhu, Chi Zhang, Hong Qian, Heinz-Bernd Schuttler, Jian-Ping Gong, Ying Xu
Global DNA hypomethylation occurs in many cancer types but there is no explanation for its differential occurance or possible impact on cancer cell physiology. Here we address these issues with a computational study of genome-scale DNA methylation in 16 cancer types. Specifically, we identified (1) a possible determinant for global DNA methylation in cancer cells, and (2) a relationship between levels of DNA methylation, nucleotide synthesis and intracellular oxidative stress in cells. We developed a system of kinetic equations to capture the metabolic relations among DNA methylation, nucleotide synthesis, and anti-oxidative stress response, including their competitions for methyl and sulfur groups, based on known information about one-carbon metabolism and trans-sulfuration pathways...
June 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28610458/large-scale-parallel-genome-assembler-over-cloud-computing-environment
#11
Arghya Kusum Das, Praveen Kumar Koppa, Sayan Goswami, Richard Platania, Seung-Jong Park
The size of high throughput DNA sequencing data has already reached the terabyte scale. To manage this huge volume of data, many downstream sequencing applications started using locality-based computing over different cloud infrastructures to take advantage of elastic (pay as you go) resources at a lower cost. However, the locality-based programming model (e.g. MapReduce) is relatively new. Consequently, developing scalable data-intensive bioinformatics applications using this model and understanding the hardware environment that these applications require for good performance, both require further research...
May 23, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28600895/metabolic-modeling-of-energy-balances-in-mycoplasma-hyopneumoniae-shows-that-pyruvate-addition-increases-growth-rate
#12
Tjerko Kamminga, Simen-Jan Slagman, Jetta J E Bijlsma, Vitor A P Martins Dos Santos, Maria Suarez-Diez, Peter J Schaap
Mycoplasma hyopneumoniae is cultured on large-scale to produce antigen for inactivated whole-cell vaccines against respiratory disease in pigs. However, the fastidious nutrient requirements of this minimal bacterium and the low growth rate make it challenging to reach sufficient biomass yield for antigen production. In this study, we sequenced the genome of M. hyopneumoniae strain 11 and constructed a high quality constraint-based genome-scale metabolic model of 284 chemical reactions and 298 metabolites. We validated the model with time-series data of duplicate fermentation cultures to aim for an integrated model describing the dynamic profiles measured in fermentations...
June 10, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28598965/metabolic-network-segmentation-a-probabilistic-graphical-modeling-approach-to-identify-the-sites-and-sequential-order-of-metabolic-regulation-from-non-targeted-metabolomics-data
#13
Andreas Kuehne, Urs Mayr, Daniel C Sévin, Manfred Claassen, Nicola Zamboni
In recent years, the number of large-scale metabolomics studies on various cellular processes in different organisms has increased drastically. However, it remains a major challenge to perform a systematic identification of mechanistic regulatory events that mediate the observed changes in metabolite levels, due to complex interdependencies within metabolic networks. We present the metabolic network segmentation (MNS) algorithm, a probabilistic graphical modeling approach that enables genome-scale, automated prediction of regulated metabolic reactions from differential or serial metabolomics data...
June 9, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28596713/performances-of-different-fragment-sizes-for-reduced-representation-bisulfite-sequencing-in-pigs
#14
Xiao-Long Yuan, Zhe Zhang, Rong-Yang Pan, Ning Gao, Xi Deng, Bin Li, Hao Zhang, Per Torp Sangild, Jia-Qi Li
BACKGROUND: Reduced representation bisulfite sequencing (RRBS) has been widely used to profile genome-scale DNA methylation in mammalian genomes. However, the applications and technical performances of RRBS with different fragment sizes have not been systematically reported in pigs, which serve as one of the important biomedical models for humans. The aims of this study were to evaluate capacities of RRBS libraries with different fragment sizes to characterize the porcine genome. RESULTS: We found that the MspI-digested segments between 40 and 220 bp harbored a high distribution peak at 74 bp, which were highly overlapped with the repetitive elements and might reduce the unique mapping alignment...
2017: Biological Procedures Online
https://www.readbyqxmd.com/read/28595363/more-on-the-best-evolutionary-rate-for-phylogenetic-analysis
#15
Seraina Klopfstein, Tim Massingham, Nick Goldman
The accumulation of genome-scale molecular datasets for non-model taxa brings us ever closer to resolving the tree of life of all living organisms. However, despite the depth of data available, a number of studies that each used thousands of genes have reported conflicting results. The focus of phylogenomic projects must thus shift to more careful experimental design. Even though we still have a limited understanding of what are the best predictors of the phylogenetic informativeness of a gene, there is wide agreement that one key factor is its evolutionary rate; but there is no consensus as to whether the rates derived as optimal in various analytical, empirical, and simulation approaches have any general applicability...
June 8, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28594821/dynamics-of-dna-methylomes-underlie-oyster-development
#16
Guillaume Riviere, Yan He, Samuele Tecchio, Elizabeth Crowell, Michaël Gras, Pascal Sourdaine, Ximing Guo, Pascal Favrel
DNA methylation is a critical epigenetic regulator of development in mammals and social insects, but its significance in development outside these groups is not understood. Here we investigated the genome-wide dynamics of DNA methylation in a mollusc model, the oyster Crassostrea gigas, from the egg to the completion of organogenesis. Large-scale methylation maps reveal that the oyster genome displays a succession of methylated and non methylated regions, which persist throughout development. Differentially methylated regions (DMRs) are strongly regulated during cleavage and metamorphosis...
June 8, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28592605/interaction-between-genes-and-macronutrient-intake-on-the-risk-of-developing-type-2-diabetes-systematic-review-and-findings-from-european-prospective-investigation-into-cancer-epic-interact
#17
Sherly X Li, Fumiaki Imamura, Zheng Ye, Matthias B Schulze, Jusheng Zheng, Eva Ardanaz, Larraitz Arriola, Heiner Boeing, Courtney Dow, Guy Fagherazzi, Paul W Franks, Antonio Agudo, Sara Grioni, Rudolf Kaaks, Verena A Katzke, Timothy J Key, Kay Tee Khaw, Francesca R Mancini, Carmen Navarro, Peter M Nilsson, N Charlotte Onland-Moret, Kim Overvad, Domenico Palli, Salvatore Panico, J Ramón Quirós, Olov Rolandsson, Carlotta Sacerdote, María-José Sánchez, Nadia Slimani, Ivonne Sluijs, Annemieke Mw Spijkerman, Anne Tjonneland, Rosario Tumino, Stephen J Sharp, Elio Riboli, Claudia Langenberg, Robert A Scott, Nita G Forouhi, Nicholas J Wareham
Background: Gene-diet interactions have been reported to contribute to the development of type 2 diabetes (T2D). However, to our knowledge, few examples have been consistently replicated to date.Objective: We aimed to identify existing evidence for gene-macronutrient interactions and T2D and to examine the reported interactions in a large-scale study.Design: We systematically reviewed studies reporting gene-macronutrient interactions and T2D. We searched the MEDLINE, Human Genome Epidemiology Network, and WHO International Clinical Trials Registry Platform electronic databases to identify studies published up to October 2015...
June 7, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28592505/genome-diversity-and-evolution-in-the-budding-yeasts-saccharomycotina
#18
Bernard A Dujon, Edward J Louis
Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes...
June 2017: Genetics
https://www.readbyqxmd.com/read/28592500/epistatic-networks-jointly-influence-phenotypes-related-to-metabolic-disease-and-gene-expression-in-diversity-outbred-mice
#19
Anna L Tyler, Bo Ji, Daniel M Gatti, Steven C Munger, Gary A Churchill, Karen L Svenson, Gregory W Carter
Genetic studies of multidimensional phenotypes can potentially link genetic variation, gene expression, and physiological data to create multi-scale models of complex traits. The challenge of reducing these data to specific hypotheses has become increasingly acute with the advent of genome-scale data resources. Multi-parent populations derived from model organisms provide a resource for developing methods to understand this complexity. In this study, we simultaneously modeled body composition, serum biomarkers, and liver transcript abundances from 474 Diversity Outbred mice...
June 2017: Genetics
https://www.readbyqxmd.com/read/28588010/micronuclei-frequency-in-tumors-is-a-predictive-biomarker-for-genetic-instability-and-sensitivity-to-the-dna-repair-inhibitor-asidna
#20
Wael Jdey, Sylvain Thierry, Tatiana Popova, Marc-Henri Stern, Marie Dutreix
Therapeutic strategies targeting DNA repair pathway defects have been widely explored, but often only benefit small numbers of patients. Here we characterized potential predictive biomarkers for treatment with AsiDNA, a novel first-in-class DNA repair inhibitor. We evaluated genetic instability and DNA repair defects by direct and indirect assays in 12 breast cancer cell lines to estimate the spontaneous occurrence of single-strand and double-strand breaks (DSB). For each cell line, we monitored constitutive poly(ADP-ribose) polymerase (PARP) activation, spontaneous DNA damage by alkaline comet assay, basal micronuclei (MN) levels, the number of large-scale chromosomal rearrangements (LST), and the status of several DNA repair pathways by transcriptome and genome analysis...
June 6, 2017: Cancer Research
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