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BMC Genomics

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https://www.readbyqxmd.com/read/29157209/transcriptome-sequencing-and-analysis-of-zinc-uptake-related-genes-in-trichophyton-mentagrophytes
#1
Xinke Zhang, Pengxiu Dai, Yongping Gao, Xiaowen Gong, Hao Cui, Yipeng Jin, Yihua Zhang
BACKGROUND: Trichophyton mentagrophytes is an important zoonotic dermatophytic (ringworm) pathogen; causing severe skin infection in humans and other animals worldwide. Fortunately, commonly used fungal skin disease prevention and treatment measures are relatively simple. However, T. mentagrophytes is primarily studied at the epidemiology and drug efficacy research levels, yet current study has been unable to meet the needs of clinical medicine. Zinc is a crucial trace element for the growth and reproduction of fungi and other microorganisms...
November 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29157201/phylogenetic-and-recombination-analysis-of-the-herpesvirus-genus-varicellovirus
#2
Aaron W Kolb, Andrew C Lewin, Ralph Moeller Trane, Gillian J McLellan, Curtis R Brandt
BACKGROUND: The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of several members of the Varicellovirus genus. Here, currently available varicellovirus genomic sequences were used for phylogenetic, recombination, and genetic distance analysis. RESULTS: A phylogenetic network including genomic sequences of individual species, was generated and suggested a potential restriction between the ungulate and non-ungulate viruses...
November 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29157198/independent-impacts-of-aging-on-mitochondrial-dna-quantity-and-quality-in-humans
#3
Ruoyu Zhang, Yiqin Wang, Kaixiong Ye, Martin Picard, Zhenglong Gu
BACKGROUND: The accumulation of mitochondrial DNA (mtDNA) mutations, and the reduction of mtDNA copy number, both disrupt mitochondrial energetics, and may contribute to aging and age-associated phenotypes. However, there are few genetic and epidemiological studies on the spectra of blood mtDNA heteroplasmies, and the distribution of mtDNA copy numbers in different age groups and their impact on age-related phenotypes. In this work, we used whole-genome sequencing data of isolated peripheral blood mononuclear cells (PBMCs) from the UK10K project to investigate in parallel mtDNA heteroplasmy and copy number in 1511 women, between 17 and 85 years old, recruited in the TwinsUK cohorts...
November 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29157197/selection-for-female-traits-of-high-fertility-affects-male-reproductive-performance-and-alters-the-testicular-transcriptional-profile
#4
Marten Michaelis, Alexander Sobczak, Dirk Koczan, Martina Langhammer, Norbert Reinsch, Jennifer Schoen, Joachim M Weitzel
BACKGROUND: Many genes important for reproductive performance are shared by both sexes. However, fecundity indices are primarily based on female parameters such as litter size. We examined a fertility mouse line (FL2), which has a considerably increased number of offspring and a total litter weight of 180% compared to a randomly bred control line (Ctrl) after more than 170 generations of breeding. In the present study, we investigated whether there might be a parallel evolution in males after more than 40 years of breeding in this outbred mouse model...
November 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29149845/early-nutritional-programming-affects-liver-transcriptome-in-diploid-and-triploid-atlantic-salmon-salmo-salar
#5
L M Vera, C Metochis, J F Taylor, M Clarkson, K H Skjærven, H Migaud, D R Tocher
BACKGROUND: To ensure sustainability of aquaculture, plant-based ingredients are being used in feeds to replace marine-derived products. However, plants contain secondary metabolites which can affect food intake and nutrient utilisation of fish. The application of nutritional stimuli during early development can induce long-term changes in animal physiology. Recently, we successfully used this approach to improve the utilisation of plant-based diets in diploid and triploid Atlantic salmon...
November 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145825/assembling-large-genomes-analysis-of-the-stick-insect-clitarchus-hookeri-genome-reveals-a-high-repeat-content-and-sex-biased-genes-associated-with-reproduction
#6
Chen Wu, Victoria G Twort, Ross N Crowhurst, Richard D Newcomb, Thomas R Buckley
BACKGROUND: Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145809/genome-wide-characterization-and-expression-profiling-of-pdi-family-gene-reveals-function-as-abiotic-and-biotic-stress-tolerance-in-chinese-cabbage-brassica-rapa-ssp-pekinensis
#7
Md Abdul Kayum, Jong-In Park, Ujjal Kumar Nath, Gopal Saha, Manosh Kumar Biswas, Hoy-Taek Kim, Ill-Sup Nou
BACKGROUND: Protein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein folding in endoplasmic reticulum and responses during abiotic stresses.Chinese cabbage is widely recognized as an economically important, nutritious vegetable, but its yield is severely hampered by various biotic and abiotic stresses. Because of, it is prime need to identify those genes whose are responsible for biotic and abiotic stress tolerance...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145803/unraveling-the-evolution-and-coevolution-of-small-regulatory-rnas-and-coding-genes-in-listeria
#8
Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Mélodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
BACKGROUND: Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS: We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145801/comparative-genomics-of-coniophora-olivacea-reveals-different-patterns-of-genome-expansion-in-boletales
#9
Raúl Castanera, Gúmer Pérez, Leticia López-Varas, Joëlle Amselem, Kurt LaButti, Vasanth Singan, Anna Lipzen, Sajeet Haridas, Kerrie Barry, Igor V Grigoriev, Antonio G Pisabarro, Lucía Ramírez
BACKGROUND: Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size. RESULTS: In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29141604/genome-wide-identification-of-mirnas-and-lncrnas-in-cajanus-cajan
#10
Chandran Nithin, Amal Thomas, Jolly Basak, Ranjit Prasad Bahadur
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...
November 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143670/genes-to-predict-vo2max-trainability-a-systematic-review
#11
REVIEW
Camilla J Williams, Mark G Williams, Nir Eynon, Kevin J Ashton, Jonathan P Little, Ulrik Wisloff, Jeff S Coombes
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. This systematic review is aimed at identifying genetic variants that are associated with VO2max trainability. METHODS: Peer-reviewed research papers published up until October 2016 from four databases were examined...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143667/validation-of-whole-blood-transcriptome-signature-during-microdose-recombinant-human-erythropoietin-rhuepo-administration
#12
Guan Wang, Jérôme Durussel, Jonathan Shurlock, Martin Mooses, Noriyuki Fuku, Georgie Bruinvels, Charles Pedlar, Richard Burden, Andrew Murray, Brendan Yee, Anne Keenan, John D McClure, Pierre-Edouard Sottas, Yannis P Pitsiladis
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. METHODS: Forty-five whole-blood transcriptional markers of rHuEpo previously derived from a high-dose rHuEpo administration trial were used to assess whether microdoses of rHuEpo could be detected in 14 trained subjects and whether these markers may be confounded by exercise (n = 14 trained subjects) and altitude training (n = 21 elite runners and n = 4 elite rowers, respectively)...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143655/consent-ethics-and-genetic-biobanks-the-case-of-the-athlome-project
#13
REVIEW
Rachel Thompson, Michael J McNamee
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...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143608/physical-activity-in-the-prevention-of-human-diseases-role-of-epigenetic-modifications
#14
REVIEW
Elisa Grazioli, Ivan Dimauro, Neri Mercatelli, Guan Wang, Yannis Pitsiladis, Luigi Di Luigi, Daniela Caporossi
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...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143599/epistasis-physical-capacity-related-genes-and-exceptional-longevity-fndc5-gene-interactions-with-candidate-genes-foxoa3-and-apoe
#15
Noriyuki Fuku, Roberto Díaz-Peña, Yasumichi Arai, Yukiko Abe, Hirofumi Zempo, Hisashi Naito, Haruka Murakami, Motohiko Miyachi, Carlos Spuch, José A Serra-Rexach, Enzo Emanuele, Nobuyoshi Hirose, Alejandro Lucia
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. Epistasis, defined as the effect of one locus being dependent on the presence of 'modifier genes', may contribute to explain the missing heritability of complex phenotypes such as EL. We assessed the potential association of epistasis among candidate polymorphisms related to physical capacity, as well as antioxidant defense and cardiometabolic traits, and EL in the Japanese population...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143597/genotypic-and-phenotypic-features-of-all-spanish-patients-with-mcardle-disease-a-2016-update
#16
Alfredo Santalla, Gisela Nogales-Gadea, Alberto Blázquez Encinar, Irene Vieitez, Adrian González-Quintana, Pablo Serrano-Lorenzo, Inés García Consuegra, Sara Asensio, Alfonsina Ballester-Lopez, Guillem Pintos-Morell, Jaume Coll-Cantí, Helios Pareja-Galeano, Jorge Díez-Bermejo, Margarita Pérez, Antoni L Andreu, Tomàs Pinós, Joaquín Arenas, Miguel A Martín, Alejandro Lucia
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)...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143596/genetic-testing-for-exercise-prescription-and-injury-prevention-ais-athlome-consortium-fims-joint-statement
#17
REVIEW
Nicole Vlahovich, David C Hughes, Lyn R Griffiths, Guan Wang, Yannis P Pitsiladis, Fabio Pigozzi, Nobert Bachl, Nir Eynon
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...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143595/why-nature-prevails-over-nurture-in-the-making-of-the-elite-athlete
#18
Evelina Georgiades, Vassilis Klissouras, Jamie Baulch, Guan Wang, Yannis Pitsiladis
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...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143594/the-gene-smart-study-method-study-design-and-preliminary-findings
#19
REVIEW
Xu Yan, Nir Eynon, Ioannis D Papadimitriou, Jujiao Kuang, Fiona Munson, Oren Tirosh, Lannie O'Keefe, Lyn R Griffiths, Kevin J Ashton, Nuala Byrne, Yannis P Pitsiladis, David J Bishop
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)...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143593/preface-genomics-and-biology-of-exercise-is-undergoing-a-paradigm-shift
#20
EDITORIAL
Nir Eynon, Sarah Voisin, Alejandro Lucia, Guan Wang, Yannis Pitsiladis
No abstract text is available yet for this article.
November 14, 2017: BMC Genomics
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