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    Genes to predict VO2max trainability: a systematic review.
    BMC Genomics 2017 Nov 14;18(Suppl 8):831. Epub 2017 Nov 14.
    Centre for Research on Exercise, Physical Activity and Health (CRExPAH), School of Human Movement and Nutrition Sciences, The University of Queensland, Brisbane, Queensland, Australia.
    Background: Cardiorespiratory fitness (VO2max) is an excellent predictor of chronic disease morbidity and mortality risk. Guidelines recommend individuals undertake exercise training to improve VO2max for chronic disease reduction. However, there are large inter-individual differences between exercise training responses. Read More

    Validation of whole-blood transcriptome signature during microdose recombinant human erythropoietin (rHuEpo) administration.
    BMC Genomics 2017 Nov 14;18(Suppl 8):817. Epub 2017 Nov 14.
    Centre of Sports Medicine for Anti-Doping Research, University of Brighton, Eastbourne, UK.
    Background: Recombinant human erythropoietin (rHuEpo) can improve human performance and is therefore frequently abused by athletes. As a result, the World Anti-Doping Agency (WADA) introduced the Athlete Biological Passport (ABP) as an indirect method to detect blood doping. Despite this progress, challenges remain to detect blood manipulations such as the use of microdoses of rHuEpo. Read More

    Consent, ethics and genetic biobanks: the case of the Athlome project.
    BMC Genomics 2017 Nov 14;18(Suppl 8):830. Epub 2017 Nov 14.
    A-STEM, College of Engineering, Swansea University, Crymlyn Burrows, Fabian Way, Swansea, SA1 8EN, UK.
    This article provides a critical overview of the ethics and governance of genetic biobank research, using the Athlome Consortium as a large scale instance of collaborative sports genetic biobanking. We present a traditional model of written informed consent for the acquisition, storage, sharing and analysis of genetic data and articulate the challenges to it from new research practices such as genetic biobanking. We then articulate six possible alternative consent models: verbal consent, blanket consent, broad consent, meta consent, dynamic consent and waived consent. Read More

    Physical activity in the prevention of human diseases: role of epigenetic modifications.
    BMC Genomics 2017 Nov 14;18(Suppl 8):802. Epub 2017 Nov 14.
    Department of Movement, Human and Health Sciences, Unit of Biology, Genetics and Biochemistry, University of Rome "Foro Italico", Rome, Italy.
    Epigenetic modification refers to heritable changes in gene function that cannot be explained by alterations in the DNA sequence. The current literature clearly demonstrates that the epigenetic response is highly dynamic and influenced by different biological and environmental factors such as aging, nutrient availability and physical exercise. As such, it is well accepted that physical activity and exercise can modulate gene expression through epigenetic alternations although the type and duration of exercise eliciting specific epigenetic effects that can result in health benefits and prevent chronic diseases remains to be determined. Read More

    Epistasis, physical capacity-related genes and exceptional longevity: FNDC5 gene interactions with candidate genes FOXOA3 and APOE.
    BMC Genomics 2017 Nov 14;18(Suppl 8):803. Epub 2017 Nov 14.
    European University and Research Institute i+12, Madrid, Spain.
    Background: Forkhead box O3A (FOXOA3) and apolipoprotein E (APOE) are arguably the strongest gene candidates to influence human exceptional longevity (EL, i.e., being a centenarian), but inconsistency exists among cohorts. Read More

    Genotypic and phenotypic features of all Spanish patients with McArdle disease: a 2016 update.
    BMC Genomics 2017 Nov 14;18(Suppl 8):819. Epub 2017 Nov 14.
    Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.
    Background: We recently described the genotype/phenotype features of all Spanish patients diagnosed with McArdle disease as of January 2011 (n = 239, prevalence of ~1/167,000) (J Neurol Neurosurg Psychiatry 2012;83:322-8). Several caveats were however identified suggesting that the prevalence of the disease is actually higher.

    Methods: We have now updated main genotype/phenotype data, as well as potential associations within/between them, of all Spanish individuals currently diagnosed with McArdle disease (December 2016). Read More

    Genetic testing for exercise prescription and injury prevention: AIS-Athlome consortium-FIMS joint statement.
    BMC Genomics 2017 Nov 14;18(Suppl 8):818. Epub 2017 Nov 14.
    Institute of Sport, Exercise and Active Living (ISEAL), College of Sport and Exercise Science, Victoria University, PO Box 14428, Melbourne, VIC, 8001, Australia.
    Background: There has been considerable growth in basic knowledge and understanding of how genes are influencing response to exercise training and predisposition to injuries and chronic diseases. On the basis of this knowledge, clinical genetic tests may in the future allow the personalisation and optimisation of physical activity, thus providing an avenue for increased efficiency of exercise prescription for health and disease.

    Results: This review provides an overview of the current status of genetic testing for the purposes of exercise prescription and injury prevention. Read More

    Why nature prevails over nurture in the making of the elite athlete.
    BMC Genomics 2017 Nov 14;18(Suppl 8):835. Epub 2017 Nov 14.
    Centre of Sports Medicine for Anti-Doping Research, University of Brighton, 30 Carlisle Road, Eastbourne, BN20 7SN, UK.
    While the influence of nature (genes) and nurture (environment) on elite sporting performance remains difficult to precisely determine, the dismissal of either as a contributing factor to performance is unwarranted. It is accepted that a complex interaction of a combination of innumerable factors may mold a talented athlete into a champion. The prevailing view today is that understanding elite human performance will require the deciphering of two major sources of individual differences, genes and the environment. Read More

    The gene SMART study: method, study design, and preliminary findings.
    BMC Genomics 2017 Nov 14;18(Suppl 8):821. Epub 2017 Nov 14.
    Institute of Sport, Exercise and Active Living (ISEAL), College of Sport and Exercise Science, Victoria University, PO Box 14428, Melbourne, VIC, 8001, Australia.
    The gene SMART (genes and the Skeletal Muscle Adaptive Response to Training) Study aims to identify genetic variants that predict the response to both a single session of High-Intensity Interval Exercise (HIIE) and to four weeks of High-Intensity Interval Training (HIIT). While the training and testing centre is located at Victoria University, Melbourne, three other centres have been launched at Bond University, Queensland University of Technology, Australia, and the University of Brighton, UK. Currently 39 participants have already completed the study and the overall aim is to recruit 200 moderately-trained, healthy Caucasians participants (all males 18-45 y, BMI < 30). Read More

    COL5A1 gene variants previously associated with reduced soft tissue injury risk are associated with elite athlete status in rugby.
    BMC Genomics 2017 Nov 14;18(Suppl 8):820. Epub 2017 Nov 14.
    MMU Sports Genomics Laboratory, Manchester Metropolitan University, Crewe, Manchester, UK.
    Background: Two common single nucleotide polymorphisms within the COL5A1 gene (SNPs; rs12722 C/T and rs3196378 C/A) have previously been associated with tendon and ligament pathologies. Given the high incidence of tendon and ligament injuries in elite rugby athletes, we hypothesised that both SNPs would be associated with career success.

    Results: In 1105 participants (RugbyGene project), comprising 460 elite rugby union (RU), 88 elite rugby league athletes and 565 non-athlete controls, DNA was collected and genotyped for the COL5A1 rs12722 and rs3196378 variants using real-time PCR. Read More

    Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan.
    BMC Genomics 2017 Nov 15;18(1):878. Epub 2017 Nov 15.
    Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India.
    Background: Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negatively regulate gene expression at the levels of messenger RNAs stability and translation inhibition, on the other hand, long ncRNAs (lncRNAs) are a large and diverse class of transcribed non-protein coding RNA molecules (> 200nt) that play both up-regulatory as well as down-regulatory roles at the transcriptional level. Cajanus cajan, a leguminosae pulse crop grown in tropical and subtropical areas of the world, is a source of high value protein to vegetarians or very poor populations globally. Read More

    Comparative transcriptome analysis of soybean response to bean pyralid larvae.
    BMC Genomics 2017 Nov 13;18(1):871. Epub 2017 Nov 13.
    Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China.
    Background: Soybean is one of most important oilseed crop worldwide, however, its production is often limited by many insect pests. Bean pyralid is one of the major soybean leaf-feeding insects in China. To explore the defense mechanisms of soybean resistance to bean pyralid, the comparative transcriptome sequencing was completed between the leaves infested with bean pyralid larvae and no worm of soybean (Gantai-2-2 and Wan82-178) on the Illumina HiSeq™ 2000 platform. Read More

    Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections.
    BMC Genomics 2017 Nov 13;18(1):864. Epub 2017 Nov 13.
    Swiss Tropical and Public Health Institute, Basel, Switzerland.
    Background: Amplicon deep sequencing permits sensitive detection of minority clones and improves discriminatory power for genotyping multi-clone Plasmodium falciparum infections. New amplicon sequencing and data analysis protocols are needed for genotyping in epidemiological studies and drug efficacy trials of P. falciparum. Read More

    Genome-wide analysis and transcriptomic profiling of the auxin biosynthesis, transport and signaling family genes in moso bamboo (Phyllostachys heterocycla).
    BMC Genomics 2017 Nov 13;18(1):870. Epub 2017 Nov 13.
    Basic Forestry and Proteomics Center (BFPC), Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fujian, 350002, China.
    Background: Auxin is essential for plant growth and development. Although substantial progress has been made in understanding auxin pathways in model plants such as Arabidopsis and rice, little is known in moso bamboo which is famous for its fast growth resulting from the rapid cell elongation and division.

    Results: Here we showed that exogenous auxin has strong effects on crown and primary roots. Read More

    Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles.
    BMC Genomics 2017 Nov 13;18(1):869. Epub 2017 Nov 13.
    State Key Laboratory of Rice Biology, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
    Background: The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism.

    Results: In present study, we identified 26 CNGC genes in B. Read More

    Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys.
    BMC Genomics 2017 Nov 13;18(1):877. Epub 2017 Nov 13.
    Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA.
    Background: Shotgun proteomics utilizes a database search strategy to compare detected mass spectra to a library of theoretical spectra derived from reference genome information. As such, the robustness of proteomics results is contingent upon the completeness and accuracy of the gene annotation in the reference genome. For animal models of disease where genomic annotation is incomplete, such as non-human primates, proteogenomic methods can improve the detection of proteins by incorporating transcriptional data from RNA-Seq to improve proteomics search databases used for peptide spectral matching. Read More

    Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars - susceptible and resistant to fire blight.
    BMC Genomics 2017 Nov 13;18(1):868. Epub 2017 Nov 13.
    Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland.
    Background: Erwinia amylovora is generally considered to be a homogeneous species in terms of phenotypic and genetic features. However, strains show variation in their virulence, particularly on hosts with different susceptibility to fire blight. We applied the RNA-seq technique to elucidate transcriptome-level changes of the lowly virulent E. Read More

    Genomic analysis of endemic clones of toxigenic and non-toxigenic Corynebacterium diphtheriae in Belarus during and after the major epidemic in 1990s.
    BMC Genomics 2017 Nov 13;18(1):873. Epub 2017 Nov 13.
    Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
    Background: Diphtheria remains a major public health concern with multiple recent outbreaks around the world. Moreover, invasive non-toxigenic strains have emerged globally causing severe infections. A diphtheria epidemic in the former Soviet Union in the 1990s resulted in ~5000 deaths. Read More

    Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI.
    BMC Genomics 2017 Nov 13;18(1):872. Epub 2017 Nov 13.
    Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China.
    Background: The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) to identify significant genes and specific modules related to BMI based on gene expression profile data of 7 discordant monozygotic twins.

    Results: In the differential gene expression analysis, it appeared that 32 differentially expressed genes (DEGs) were with a trend of up-regulation in twins with higher BMI when compared to their siblings. Read More

    Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes.
    BMC Genomics 2017 Nov 13;18(1):876. Epub 2017 Nov 13.
    Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
    Background: Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Read More

    Significant differences in terms of codon usage bias between bacteriophage early and late genes: a comparative genomics analysis.
    BMC Genomics 2017 Nov 13;18(1):866. Epub 2017 Nov 13.
    Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv, Israel.
    Background: Viruses undergo extensive evolutionary selection for efficient replication which effects, among others, their codon distribution. In the current study, we aimed at understanding the way evolution shapes the codon distribution in early vs. late viral genes in terms of their expression during different stages in the viral replication cycle. Read More

    Effect of two non-synonymous ecto-5'-nucleotidase variants on the genetic architecture of inosine 5'-monophosphate (IMP) and its degradation products in Japanese Black beef.
    BMC Genomics 2017 Nov 13;18(1):874. Epub 2017 Nov 13.
    National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.
    Background: Umami is a Japanese term for the fifth basic taste and is an important sensory property of beef palatability. Inosine 5'-monophosphate (IMP) contributes to umami taste in beef. Thus, the overall change in concentration of IMP and its degradation products can potentially affect the beef palatability. Read More

    Correction to: Dual transcriptome of the immediate neutrophil and Candida albicans interplay.
    BMC Genomics 2017 11 13;18(1):863. Epub 2017 Nov 13.
    Department of Clinical Microbiology, Umeå Centre for Microbial Research (UCMR) & Laboratory of Molecular Infection Medicine Sweden (MIMS), Umeå University, Umea, Sweden.

    Artificial selection for odor-guided behavior in Drosophila reveals changes in food consumption.
    BMC Genomics 2017 Nov 13;18(1):867. Epub 2017 Nov 13.
    Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221-0006, USA.
    Background: The olfactory system enables organisms to detect chemical cues in the environment and can signal the availability of food or the presence of a predator. Appropriate behavioral responses to these chemical cues are therefore important for organismal survival and can influence traits such as organismal life span and food consumption. However, understanding the genetic mechanisms underlying odor-guided behavior, correlated responses in other traits, and how these constrain or promote their evolution, remain an important challenge. Read More

    Genomic regions associated with host response to porcine reproductive and respiratory syndrome vaccination and co-infection in nursery pigs.
    BMC Genomics 2017 Nov 13;18(1):865. Epub 2017 Nov 13.
    Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
    Background: The WUR1000125 (WUR) single nucleotide polymorphism (SNP) can be used as a genetic marker for host response to porcine reproductive and respiratory syndrome (PRRS), PRRS vaccination, and co-infection with porcine circovirus type 2b (PCV2b). Objectives of this study were to identify genomic regions other than WUR associated with host response to PRRS vaccination and PRRSV/PCV2b co-infection and regions with a different effect on host response to co-infection, depending on previous vaccination for PRRS.

    Methods: Commercial crossbred nursery pigs were pre-selected for WUR genotype (n = 171 AA and 198 AB pigs) where B is the dominant and favorable allele. Read More

    Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis.
    BMC Genomics 2017 Nov 10;18(1):860. Epub 2017 Nov 10.
    Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.
    Background: Monoallelic expression of autosomal genes has been implicated in human psychiatric disorders. However, there is a paucity of allelic expression studies in human brain cells at the single cell and genome wide levels.

    Results: In this report, we reanalyzed a previously published single-cell RNA-seq dataset from several postmortem human brains and observed pervasive monoallelic expression in individual cells, largely in a random manner. Read More

    Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa.
    BMC Genomics 2017 Nov 10;18(1):859. Epub 2017 Nov 10.
    Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.
    Background: Pseudomonas putida is a Gram-negative, non-fermenting bacterium frequently encountered in various environmental niches. P. putida rarely causes disease in humans, though serious infections and outbreaks have been reported from time to time. Read More

    Population differentiation in allele frequencies of obesity-associated SNPs.
    BMC Genomics 2017 Nov 10;18(1):861. Epub 2017 Nov 10.
    Department of Biochemistry and Molecular Biology, Howard University College of Medicine, 520 W Street NW, Washington, DC, 20059, USA.
    Background: Obesity is emerging as a global health problem, with more than one-third of the world's adult population being overweight or obese. In this study, we investigated worldwide population differentiation in allele frequencies of obesity-associated SNPs (single nucleotide polymorphisms).

    Results: We collected a total of 225 obesity-associated SNPs from a public database. Read More

    A systematic survey to identify lethal recessive variation in highly managed pig populations.
    BMC Genomics 2017 Nov 9;18(1):858. Epub 2017 Nov 9.
    Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.
    Background: Lethal recessive variation can cause prenatal death of homozygous offspring. Although usually present at low-frequency in populations, the impact on individual fitness can be substantial. Until recently, the presence of recessive embryonic lethal variation could only be measured indirectly through reduced fertility. Read More

    Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology.
    BMC Genomics 2017 Nov 9;18(1):857. Epub 2017 Nov 9.
    Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland.
    Background: Negative energy balance (NEB) is an imbalance between energy intake and energy requirements for lactation and body maintenance affecting high-yielding dairy cows and is of considerable economic importance due to its negative impact on fertility and health in dairy herds. It is anticipated that the cow hypothalamus experiences extensive biochemical changes during the early post partum period in an effort to re-establish metabolic homeostasis. However, there is variation in the tolerance to NEB between individual cows. Read More

    Temporally distinct transcriptional regulation of myocyte dedifferentiation and Myofiber growth during muscle regeneration.
    BMC Genomics 2017 Nov 9;18(1):854. Epub 2017 Nov 9.
    Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, 1000 Wall St, Ann Arbor, MI, 48105, USA.
    Background: Tissue regeneration requires a series of steps, beginning with generation of the necessary cell mass, followed by cell migration into damaged area, and ending with differentiation and integration with surrounding tissues. Temporal regulation of these steps lies at the heart of the regenerative process, yet its basis is not well understood. The ability of zebrafish to dedifferentiate mature "post-mitotic" myocytes into proliferating myoblasts that in turn regenerate lost muscle tissue provides an opportunity to probe the molecular mechanisms of regeneration. Read More

    Transcriptomics, metabolomics and histology indicate that high-carbohydrate diet negatively affects the liver health of blunt snout bream (Megalobrama amblycephala).
    BMC Genomics 2017 Nov 9;18(1):856. Epub 2017 Nov 9.
    College of Fisheries Huazhong Agricultural University, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, People's Republic of China.
    Background: Global trend of the introduction of high levels of relatively cheap carbohydrates to reduce the amount of costly protein in the aquatic animal feed production has affected the aquaculture of an economically important cyprinid fish, blunt snout bream (Megalobrama amblycephala). This dietary shift has resulted in increased prevalence of metabolic disorders, often causing economic losses. High dietary intake of carbohydrates, associated with obesity, is one of the major causes of non-alcoholic fatty liver disease (NAFLD) in humans. Read More

    Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution.
    BMC Genomics 2017 Nov 9;18(1):853. Epub 2017 Nov 9.
    Agriculture Research Division, Agriculture Victoria, Department of Economic Development, Jobs, Transport and Resources, AgriBio, VIC, 3083, Australia.
    Background: Genotyping and whole-genome sequencing data have been generated for hundreds of thousands of cattle. International consortia used these data to compile imputation reference panels that facilitate the imputation of sequence variant genotypes for animals that have been genotyped using dense microarrays. Association studies with imputed sequence variant genotypes allow for the characterization of quantitative trait loci (QTL) at nucleotide resolution particularly when individuals from several breeds are included in the mapping populations. Read More

    Genome-wide identification and analysis of MAPK and MAPKK gene family in Chinese jujube (Ziziphus jujuba Mill.).
    BMC Genomics 2017 Nov 9;18(1):855. Epub 2017 Nov 9.
    Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China.
    Background: Chinese jujube (Ziziphus jujuba Mill.) is one of the most important members in the Rhamnaceae family. The whole genome sequence and more than 30,000 proteins of Chinese jujube have been obtained in 2014. Read More

    Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq.
    BMC Genomics 2017 Nov 7;18(1):851. Epub 2017 Nov 7.
    Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA.
    Background: Switchgrass is a crop with many desirable traits for bioenergy production. Plant genomes have high DNA methylation levels throughout genes and transposable elements and DNA methylation is known to play a role in silencing transposable elements. Here we analyzed methylomes in two switchgrass genotypes AP13 and VS16. Read More

    Transcriptomic responses to wounding: meta-analysis of gene expression microarray data.
    BMC Genomics 2017 Nov 7;18(1):850. Epub 2017 Nov 7.
    Department Molecular Biotechnology and Microbiology, Gdańsk University of Technology, Gdańsk, Poland.
    Background: A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wounding in different organisms and tissues. This meta-analysis is the first study to compare gene expression profiles in response to wounding in as different tissues as heart, liver, skin, bones, and spinal cord, and species, including rat, mouse and human. Read More

    Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil.
    BMC Genomics 2017 Nov 7;18(1):849. Epub 2017 Nov 7.
    Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
    Background: Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work together to provide partial resistance. In this study, a genome-wide association study (GWAS) was performed to dissect the complex genetic architecture of soybean quantitative resistance to SSR and to provide effective molecular markers that could be used in breeding programs. Read More

    XTHs from Fragaria vesca: genomic structure and transcriptomic analysis in ripening fruit and other tissues.
    BMC Genomics 2017 Nov 7;18(1):852. Epub 2017 Nov 7.
    Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.
    Background: Fragaria vesca or 'woodland strawberry' has emerged as an attractive model for the study of ripening of non-climacteric fruit. It has several advantages, such as its small genome and its diploidy. The recent availability of the complete sequence of its genome opens the possibility for further analysis and its use as a reference species. Read More

    Large-scale analysis reveals that the genome features of simple sequence repeats are generally conserved at the family level in insects.
    BMC Genomics 2017 Nov 6;18(1):848. Epub 2017 Nov 6.
    Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
    Background: Simple sequence repeats (SSR), also called microsatellites, have been widely used as genetic markers, and have been extensively studied in some model insects. At present, the genomes of more than 100 insect species are available. However, the features of SSRs in most insect genomes remain largely unknown. Read More

    ExUTR: a novel pipeline for large-scale prediction of 3'-UTR sequences from NGS data.
    BMC Genomics 2017 Nov 6;18(1):847. Epub 2017 Nov 6.
    UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
    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. Read More

    Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology.
    BMC Genomics 2017 Nov 3;18(1):846. Epub 2017 Nov 3.
    Department of Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.
    Background: The plant growth promoting rhizobacterium Paenibacillus riograndensis SBR5 is a promising candidate to serve as crop inoculant. Despite its potential in providing environmental and economic benefits, the species P. riograndensis is poorly characterized. Read More

    Genome-wide identification and expression analysis of calmodulin-like (CML) genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis).
    BMC Genomics 2017 Nov 2;18(1):842. Epub 2017 Nov 2.
    College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
    Background: Calmodulin-like (CML) proteins are a primary family of plant-specific Ca(2+) sensors that specifically bind to Ca(2+) and deliver a Ca(2+) signal. CML proteins have been identified and characterized in many plant species, such as the model plant Arabidopsis and rice. Based on considerable evidence, the roles of CML proteins are crucial in plant growth and development and in the response to various external stimuli. Read More

    Genomic preselection with genotyping-by-sequencing increases performance of commercial oil palm hybrid crosses.
    BMC Genomics 2017 Nov 2;18(1):839. Epub 2017 Nov 2.
    PalmElit SAS, 34980, Montferrier sur Lez, France.
    Background: There is great potential for the genetic improvement of oil palm yield. Traditional progeny tests allow accurate selection but limit the number of individuals evaluated. Genomic selection (GS) could overcome this constraint. Read More

    Identification and expression profiling of microRNAs involved in the stigma exsertion under high-temperature stress in tomato.
    BMC Genomics 2017 Nov 2;18(1):843. Epub 2017 Nov 2.
    Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China.
    Background: Autogamy in cultivated tomato varieties is a derived trait from wild type tomato plants, which are mostly allogamous. However, environmental stresses can cause morphological defects in tomato flowers and hinder autogamy. Under elevated temperatures, tomato plants usually exhibit the phenotype of stigma exsertion, with severely hindered self-pollination and fruit setting, whereas the inherent mechanism of stigma exsertion have been hitherto unknown. Read More

    Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants.
    BMC Genomics 2017 Nov 2;18(1):841. Epub 2017 Nov 2.
    The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, UK.
    Background: Infants born prematurely, particularly extremely low birth weight infants (ELBW) have altered gut microbial communities. Factors such as maternal health, gut immaturity, delivery mode, and antibiotic treatments are associated with microbiota disturbances, and are linked to an increased risk of certain diseases such as necrotising enterocolitis. Therefore, there is a requirement to optimally characterise microbial profiles in this at-risk cohort, via standardisation of methods, particularly for studying the influence of microbiota therapies (e. Read More

    The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class.
    BMC Genomics 2017 Nov 2;18(1):840. Epub 2017 Nov 2.
    Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.
    Background: Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes. Read More

    Transcriptional analysis of sweet orange trees co-infected with 'Candidatus Liberibacter asiaticus' and mild or severe strains of Citrus tristeza virus.
    BMC Genomics 2017 Oct 31;18(1):837. Epub 2017 Oct 31.
    United States Department of Agriculture-Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD, USA.
    Background: Citrus worldwide is threatened by huanglongbing (HLB) and tristeza diseases caused by 'Candidatus Liberibacter asiaticus' (CaLas) and Citrus tristeza virus (CTV). Although the pathogens are members of the α-proteobacteria and Closteroviridae, respectively, both are restricted to phloem cells in infected citrus and are transmitted by insect vectors. The response of sweet orange to single infection by either of these two pathogens has been characterized previously by global gene expression analysis. Read More

    Genetic basis of the very short life cycle of 'Apogee' wheat.
    BMC Genomics 2017 Oct 31;18(1):838. Epub 2017 Oct 31.
    Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK74078, USA.
    Background: 'Apogee' has a very short life cycle among wheat cultivars (flowering 25 days after planting under a long day and without vernalization), and it is a unique genetic material that can be used to accelerate cycling breeding lines. However, little is known about the genetic basis of the super-short life of Apogee wheat.

    Results: In this study, Apogee was crossed with a strong winter wheat cultivar 'Overland', and 858 F2 plants were generated and tested in a greenhouse under constant warm temperature and long days. Read More

    Transcriptomic study of Salmonella enterica subspecies enterica serovar Typhi biofilm.
    BMC Genomics 2017 Oct 31;18(1):836. Epub 2017 Oct 31.
    Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, USM, Malaysia.
    Background: Typhoid fever is an acute systemic infection of humans caused by Salmonella enterica subspecies enterica serovar Typhi (S. Typhi). In chronic carriers, the bacteria survive the harsh environment of the gallbladder by producing biofilm. Read More

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