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https://www.readbyqxmd.com/read/28637217/experimental-support-that-natural-selection-has-shaped-the-latitudinal-distribution-of-mitochondrial-haplotypes-in-australian-drosophila-melanogaster
#1
M Florencia Camus, Jonci N Wolff, Carla M Sgrò, Damian K Dowling
Cellular metabolism is regulated by enzyme complexes within the mitochondrion, the function of which are sensitive to the prevailing temperature. Such thermal sensitivity, coupled with the observation that population frequencies of mitochondrial haplotypes tend to associate with latitude, altitude or climatic regions across species distributions, led to the hypothesis that thermal selection has played a role in shaping standing variation in the mitochondrial DNA (mtDNA) sequence. This hypothesis, however, remains controversial, and requires evidence that the distribution of haplotypes observed in nature corresponds with the capacity of these haplotypes to confer differences in thermal tolerance...
June 20, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28636816/impacts-of-the-mitochondrial-genome-on-the-relationship-of-long-term-ambient-fine-particle-exposure-with-blood-dna-methylation-age
#2
Jamaji Nwanaji-Enwerem, Elena Colicino, Lingzhen Dai, Akin Cayir, Marco Sanchez-Guerra, Hannah E Laue, Vy T Nguyen, Qian Di, Allan Just, Lifang Hou, Pantel Vokonas, Brent A Coull, Marc Weisskopf, Andrea Baccarelli, Joel Schwartz
The mitochondrial genome has long been implicated in age-related disease, but no studies have examined its role in the relationship of long-term fine particle (PM2.5) exposure and DNA methylation age (DNAm-age) - a novel measure of biological age. In this analysis based on 940 observations between 2000 and 2011 from 552 Normative Aging Study participants, we determined the roles of mitochondrial DNA haplogroup variation and mitochondrial genome abundance in the relationship of PM2.5 with DNAm-age. We used the GEOS-chem transport model to estimate address-specific, one-year PM2...
June 21, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28636804/new-insights-into-global-biogeography-population-structure-and-natural-selection-from-the-genome-of-the-epipelagic-copepod-oithona
#3
Mohammed-Amin Madoui, Julie Poulain, Kevin Sugier, Marc Wessner, Benjamin Noel, Leo Berline, Karine Labadie, Astrid Cornils, Leocadio Blanco-Bercial, Lars Stemmann, Jean-Louis Jamet, Patrick Wincker
In the epipelagic ocean the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about the Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation, and development, including genes coding Lin12-Notch-Repeat (LNR) domain proteins...
June 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28636766/association-of-tnfsf13-polymorphisms-with-iga-nephropathy-in-chinese-han-population
#4
Zhong Zhong, Shao-Zhen Feng, Ri-Cong Xu, Zhi-Jian Li, Feng-Xian Huang, Pei-Ran Yin, Wen-Ting Liu, Meng Wang, Dian-Chun Shi, Qian Zhou, Xue-Qing Yu, Ming Li
BACKGROUND: Our previous genome-wide association study (GWAS) of IgA nephropathy (IgAN) in Chinese Han population suggested that TNFSF13 gene may be a novel susceptibility gene for IgAN. In this study, we aim to further evaluate the associations of single-nucleotide polymorphisms (SNPs) and expression level of TNFSF13 gene with the risk and clinical parameters of IgAN. METHODS: Six candidate SNPs were selected for genotyping by Sequenom MassARRAY iPLEX in 1000 IgAN cases and 1000 controls...
June 21, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28636311/insights-into-integrated-lead-generation-and-target-identification-in-malaria-and-tuberculosis-drug-discovery
#5
John Okombo, Kelly Chibale
New, safe and effective drugs are urgently needed to treat and control malaria and tuberculosis, which affect millions of people annually. However, financial return on investment in the poor settings where these diseases are mostly prevalent is very minimal to support market-driven drug discovery and development. Moreover, the imminent loss of therapeutic lifespan of existing therapies due to evolution and spread of drug resistance further compounds the urgency to identify novel effective drugs. However, the advent of new public-private partnerships focused on tropical diseases and the recent release of large data sets by pharmaceutical companies on antimalarial and antituberculosis compounds derived from phenotypic whole cell high throughput screening have spurred renewed interest and opened new frontiers in malaria and tuberculosis drug discovery...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28635663/assessing-genetic-diversity-and-population-differentiation-of-colored-calla-lily-zantedeschia-hybrid-for-an-efficient-breeding-program
#6
Zunzheng Wei, Huali Zhang, Yi Wang, Youli Li, Min Xiong, Xian Wang, Di Zhou
Plastome-genome incompatibility (PGI) is prevalent in several plants including the Zantedeschia species, a worldwide commercial flower crop native to South Africa. Generally, hybrids suffering from PGI appear less vigorous and more susceptible than normal plants. Previous reports revealed that the PGI level in interspecific hybrids is correlated with the relatedness of the parental species in the genus Zantedeschia. To provide a basis for utilizing and improving resources in breeding programs, a total of 117 accessions of colored calla lily (Zantedeschia hybrid), collected from New Zealand, the Netherlands and the United States, were genotyped using 31 transferable expressed sequence tags-simple sequence repeats (EST-SSR) markers from the white calla lily (Zantedeschia aethiopica)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28635630/development-of-a-high-density-snp-based-linkage-map-and-detection-of-qtl-for-%C3%AE-glucans-protein-content-grain-yield-per-spike-and-heading-time-in-durum-wheat
#7
Ilaria Marcotuli, Agata Gadaleta, Giacomo Mangini, Antonio Massimo Signorile, Silvana Addolorata Zacheo, Antonio Blanco, Rosanna Simeone, Pasqualina Colasuonno
High-density genetic linkage maps of crop species are particularly useful in detecting qualitative and quantitative trait loci for important agronomic traits and in improving the power of classical approaches to identify candidate genes. The aim of this study was to develop a high-density genetic linkage map in a durum wheat recombinant inbred lines population (RIL) derived from two elite wheat cultivars and to identify, characterize and correlate Quantitative Trait Loci (QTL) for β-glucan, protein content, grain yield per spike and heading time...
June 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28635103/uncovering-the-dispersion-history-adaptive-evolution-and-selection-of-wheat-in-china
#8
Yong Zhou, Zhongxu Chen, Mengping Cheng, Jian Chen, Tingting Zhu, Rui Wang, Yaxi Liu, Pengfei Qi, Guoyue Chen, Qiantao Jiang, Yuming Wei, Ming-Cheng Luo, Eviatar Nevo, Robin G Allaby, Dengcai Liu, Jirui Wang, Jan Dvorák, Youliang Zheng
Wheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro-ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27,933 DArTseq (for 717 landraces) and 312,831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China. Environmental stresses and independent selection efforts have resulted in considerable genome-wide divergence at the population level in Chinese wheat landraces...
June 21, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28634866/differential-chromosomal-organization-between-saguinus-midas-and-saguinus-bicolor-with-accumulation-of-differences-the-repetitive-sequence-dna
#9
Dayane Martins Barbosa Serfaty, Natália Dayane Moura Carvalho, Maria Claudia Gross, Marcelo Gordo, Carlos Henrique Schneider
Saguinus is the largest and most complex genus of the subfamily Callitrichinae, with 23 species distributed from the south of Central America to the north of South America with Saguinus midas having the largest geographical distribution while Saguinus bicolor has a very restricted one, affected by the population expansion in the state of Amazonas. Considering the phylogenetic proximity of the two species along with evidence on the existence of hybrids between them, as well as cytogenetic studies on Saguinus describing a conserved karyotypic macrostructure, we carried out a physical mapping of DNA repeated sequences in the mitotic chromosome of both species, since these sequences are less susceptible to evolutionary pressure and possibly perform an important function in speciation...
June 20, 2017: Genetica
https://www.readbyqxmd.com/read/28634825/a-rapid-and-cost-effective-approach-for-the-development-of-polymorphic-microsatellites-in-non-model-species-using-paired-end-rad-sequencing
#10
Dong-Xiu Xue, Yu-Long Li, Jin-Xian Liu
As one of the most informative and versatile DNA-based markers, microsatellites have been widely used in population and conservation genetic studies. However, the development of microsatellites has traditionally been laborious, time-consuming, and expensive. In the present study, a rapid and cost-effective "RAD-seq-Assembly-Microsatellite" approach was developed to identify abundant microsatellite markers in non-model species using the roughskin sculpin Trachidermus fasciatus as a representative. Overlapping paired-end Illumina reads generated by restriction-site-associated DNA sequencing (RAD-seq) were clustered based on the similarity of reads containing the restriction enzyme recognition site and then assembled into contigs, which were used for microsatellite discovery and primer design...
June 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28634808/mapping-of-genetic-locus-for-leaf-trichome-in-brassica-oleracea
#11
Jiaqin Mei, Jinhua Wang, Yuehua Li, Shuai Tian, Dayong Wei, Chaoguo Shao, Jun Si, Qing Xiong, Jiana Li, Wei Qian
The genetic locus for leaf trichome was identified via marker-based mapping and SNP microarray assay, and a functional marker was developed to facilitate the breeding for hairiness in Brassica oleracea. Plant trichomes are involved in various functions particularly in protecting plants against some biotic and abiotic damages. In the present study, an F2 segregating population was developed from the cross between a glabrous cultivated B. oleracea (CC, 2n = 18) and a hairy wild relative, B. incana (CC, 2n = 18)...
June 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28634295/population-genomic-inference-of-the-strength-and-timing-of-selection-against-gene-flow
#12
Simon Aeschbacher, Jessica P Selby, John H Willis, Graham Coop
The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28634029/discovery-of-scors-anciently-derived-highly-conserved-gene-associated-repeats-in-stony-corals
#13
Huan Qiu, Ehud Zelzion, Hollie M Putnam, Ruth D Gates, Nicole E Wagner, Diane K Adams, Debashish Bhattacharya
Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata, Acropora digitifera, and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex secondary structures and are located in untranslated regions and introns, but most abundant in intergenic DNA...
June 17, 2017: Genomics
https://www.readbyqxmd.com/read/28633664/a-review-of-sarcoptes-scabiei-past-present-and-future
#14
REVIEW
Larry G Arlian, Marjorie S Morgan
The disease scabies is one of the earliest diseases of humans for which the cause was known. It is caused by the mite, Sarcoptes scabiei, that burrows in the epidermis of the skin of humans and many other mammals. This mite was previously known as Acarus scabiei DeGeer, 1778 before the genus Sarcoptes was established (Latreille 1802) and it became S. scabiei. Research during the last 40 years has tremendously increased insight into the mite's biology, parasite-host interactions, and the mechanisms it uses to evade the host's defenses...
June 20, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28633473/experimental-evolution-and-the-adjustment-of-metabolic-strategies-in-lactic-acid-bacteria
#15
Herwig Bachmann, Douwe Molenaar, Filipe Branco Dos Santos, Bas Teusink
Experimental evolution of microbes has gained lots of interest in recent years, mainly due to the ease of strain characterisation through next-generation sequencing. While evolutionary and systems biologists use experimental evolution to address fundamental questions in their respective fields, studies with lactic acid bacteria are often more directed by applied questions. Insight into population and genome dynamics are valuable for experimental design and data interpretation, and it is becoming increasingly apparent how different constraints limit and govern the outcome of microbial adaptation to a selective environment...
June 19, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28633446/genetic-indicators-of-drug-resistance-in-the-highly-repetitive-genome-of-trichomonas-vaginalis
#16
Martina Bradic, Sally D Warring, Grace E Tooley, Paul Scheid, William E Secor, Kirkwood M Land, Po-Jung Huang, Ting-Wen Chen, Chi-Ching Lee, Petrus Tang, Steven A Sullivan, Jane M Carlton
Trichomonas vaginalis, the most common non-viral sexually transmitted parasite, causes ∼283 million trichomoniasis infections annually and is associated with pregnancy complications and increased risk of HIV-1 acquisition. The antimicrobial drug metronidazole is used for treatment, but in a fraction of clinical cases, the parasites can become resistant to this drug. We undertook sequencing of multiple clinical isolates and lab derived lines to identify genetic markers and mechanisms of metronidazole resistance...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633403/structured-populations-of-sulfolobus-acidocaldarius-with-susceptibility-to-mobile-genetic-elements
#17
Rika E Anderson, Angela Kouris, Christopher H Seward, Kate M Campbell, Rachel J Whitaker
The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633351/data-compression-can-discriminate-broilers-by-selection-line-detect-haplotypes-and-estimate-genetic-potential-for-complex-phenotypes
#18
N J Hudson, R J Hawken, R Okimoto, R L Sapp, A Reverter
Accurately establishing the relationships among individuals lays the foundation for genetic analyses such as genome-wide association studies and identification of selection signatures. Of particular interest to the poultry industry are estimates of genetic merit based on molecular data. These estimates can be commercially exploited in marker-assisted breeding programs to accelerate genetic improvement. Here, we test the utility of a new method we have recently developed to estimate animal relatedness and applied it to genetic parameter estimation in commercial broilers...
June 15, 2017: Poultry Science
https://www.readbyqxmd.com/read/28633309/tmprss2-erg-gene-fusions-in-prostate-cancer-of-west-african-men-and-a-meta-analysis-of-racial-differences
#19
Cindy Ke Zhou, Denise Young, Edward D Yeboah, Sally B Coburn, Yao Tettey, Richard B Biritwum, Andrew A Adjei, Evelyn Tay, Shelley Niwa, Ann Truelove, Judith Welsh, James E Mensah, Robert N Hoover, Isabell A Sesterhenn, Ann W Hsing, Shiv Srivastava, Michael B Cook
The prevalence of TMPRSS2-ERG fusions in prostate cancer varies by race. However, such somatic aberration and its association with prognostic factors have neither been studied in a West African population nor been systematically reviewed in the context of racial differences. We used immunohistochemistry to assess ERG expression as the established surrogate of ERG fusion genes among 262 prostate cancer biopsies from the Ghana Prostate Study. Poisson regression with robust variance estimation provided prevalence ratios and 95% confidence intervals of ERG expression in relation to patients' characteristics...
June 12, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28633205/advancing-the-science-of-myocardial-recovery-with-mechanical-circulatory-support-a-working-group-of-the-national-heart-lung-and-blood-institute
#20
EDITORIAL
Stavros G Drakos, Francis D Pagani, Martha S Lundberg, Timothy J Baldwin
The medical burden of heart failure (HF) has spurred interest in clinicians and scientists to develop therapies to restore the function of a failing heart. To advance this agenda, the National Heart, Lung, and Blood Institute (NHLBI) convened a Working Group of experts from June 2 to 3, 2016, in Bethesda, Maryland, to develop NHLBI recommendations aimed at advancing the science of cardiac recovery in the setting of mechanical circulatory support (MCS). MCS devices effectively reduce volume and pressure overload that drives the cycle of progressive myocardial dysfunction, thereby triggering structural and functional reverse remodeling...
July 2017: Journal of Thoracic and Cardiovascular Surgery
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