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Genetic variation

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https://www.readbyqxmd.com/read/28441787/codon-usage-optimization-and-construction-of-plasmid-encoding-iranian-human-papillomavirus-type-16-e7-oncogene-for-lactococcus-lactis-subsp-cremoris-mg1363
#1
Amir Hossein Mohseni, Vadood Razavilar, Hossein Keyvani, Mohammad Reza Razavi, Ramazan Ali Khavari Nejad
HPV 16 intratypic sequence variations has been recognized in association with oncogenic potential diverge and geographic distribution. This study aimed to investigate nucleotide modifications and optimization of HPV 16 E7 regions from Iranian infected women. Cervical biopsies from 79/163 HPV 16 positive cancer patients detected in our study were analyzed by PCR in a couple of cloning of a complete ORF of the E7 gene, and sequencing. The most frequently observed variant was C196T in E7 which led to an amino acid change of R66W...
March 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28441456/genome-wide-association-study-of-facial-morphology-reveals-novel-associations-with-frem1-and-park2
#2
Myoung Keun Lee, John R Shaffer, Elizabeth J Leslie, Ekaterina Orlova, Jenna C Carlson, Eleanor Feingold, Mary L Marazita, Seth M Weinberg
Several studies have now shown evidence of association between common genetic variants and quantitative facial traits in humans. The reported associations generally involve simple univariate measures and likely represent only a small fraction of the genetic loci influencing facial morphology. In this study, we applied factor analysis to a set of 276 facial linear distances derived from 3D facial surface images of 2187 unrelated individuals of European ancestry. We retained 23 facial factors, which we then tested for genetic associations using a genome-wide panel of 10,677,593 single nucleotide polymorphisms (SNPs)...
2017: PloS One
https://www.readbyqxmd.com/read/28441395/molecular-phylogeny-of-oncaeidae-copepoda-using-nuclear-ribosomal-internal-transcribed-spacer-its-rdna
#3
Iole Di Capua, Fulvio Maffucci, Raimondo Pannone, Maria Grazia Mazzocchi, Elio Biffali, Alberto Amato
Copepods belonging to the Oncaeidae family are commonly and abundantly found in marine zooplankton. In the Mediterranean Sea, forty-seven oncaeid species occur, of which eleven in the Gulf of Naples. In this Gulf, several Oncaea species were morphologically analysed and described at the end of the XIX century by W. Giesbrecht. In the same area, oncaeids are being investigated over seasonal and inter-annual scales at the long-term coastal station LTER-MC. In the present work, we identified six oncaeid species using the nuclear ribosomal internal transcribed spacers (ITS rDNA) and the mitochondrial cytochrome c oxidase subunit I (mtCOI)...
2017: PloS One
https://www.readbyqxmd.com/read/28441070/the-thr300ala-variant-of-atg16l1-is-associated-with-decreased-risk-of-brain-metastasis-in-patients-with-non-small-cell-lung-cancer
#4
Qian-Xia Li, Xiao Zhou, Ting-Ting Huang, Yang Tang, Bo Liu, Ping Peng, Li Sun, Yi-Hua Wang, Xiang-Lin Yuan
Non-small cell lung cancer (NSCLC) often metastasizes to the brain, but identifying which patients will develop brain metastases (BM) is difficult. Macroautophagy/autophagy is critical for cancer initiation and progression. We hypothesized that genetic variants of autophagy-related genes may affect brain metastases (BM) in NSCLC patients. We genotyped 16 single nucleotide polymorphisms (SNPs) in 7 autophagy-related (ATG) genes (ATG3, ATG5, ATG7, ATG10, ATG12, ATG16L1, and MAP1LC3/LC3) by using DNA from blood samples of 323 NSCLC patients...
April 25, 2017: Autophagy
https://www.readbyqxmd.com/read/28441061/precisely-where-are-we-going-charting-the-new-terrain-of-precision-prevention
#5
Karen M Meagher, Michelle L McGowan, Richard A Settersten, Jennifer R Fishman, Eric T Juengst
In addition to genetic data, precision medicine research gathers information about three factors that modulate gene expression: lifestyles, environments, and communities. The relevant research tools-epidemiology, environmental assessment, and socioeconomic analysis-are those of public health sciences rather than molecular biology. Because these methods are designed to support inferences and interventions addressing population health, the aspirations of this research are expanding from individualized treatment toward precision prevention in public health...
April 24, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28440827/molecular-dynamics-investigations-of-membrane-bound-cyp2c19-polymorphisms-reveal-distinct-mechanisms-for-peripheral-variants-by-long-range-effects-on-the-enzymatic-activity
#6
Ying-Lu Cui, Rong-Ling Wu
Increasing sophistication in methods used to account for human polymorphisms in susceptibility to drug metabolism has been one of the success stories in the prevention of adverse drug reactions. Genetic polymorphisms in drug-metabolizing enzymes can affect enzyme activity and cause differences in treatment response or drug toxicity. CYP2C19 is one of the most highly polymorphic CYP enzymes and acts on 10-15% of drugs in current clinical use. Despite the number of experimental analyses carried out for this system, the detailed structural basis for altered catalytic properties of polymorphic CYP2C19 variants remains unexplained at the atomic level...
April 25, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28440817/effects-of-dopamine-d2-d3-receptor-antagonism-on-human-planning-and-spatial-working-memory
#7
M Naef, U Müller, A Linssen, L Clark, T W Robbins, C Eisenegger
Psychopharmacological studies in humans suggest important roles for dopamine (DA) D2 receptors in human executive functions, such as cognitive planning and spatial working memory (SWM). However, studies that investigate an impairment of such functions using the selective DA D2/3 receptor antagonist sulpiride have yielded inconsistent results, perhaps because relatively low doses were used. We believe we report for the first time, the effects of a higher (800 mg p.o.) single dose of sulpiride as well as of genetic variation in the DA receptor D2 gene (DA receptor D2 Taq1A polymorphism), on planning and working memory...
April 25, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28440562/the-evolvability-of-herkogamy-quantifying-the-evolutionary-potential-of-a-composite-trait
#8
Øystein H Opedal, Geir H Bolstad, Thomas F Hansen, W Scott Armbruster, Christophe Pélabon
Accurate estimates of trait evolvabilities are central to predicting the short-term evolutionary potential of populations, and hence their ability to adapt to changing environments. We quantify and evaluate the evolvability of herkogamy, the spatial separation of male and female structures in flowers, a key floral trait associated with variation in mating systems. We compiled genetic-variance estimates for herkogamy and related floral traits, computed evolvabilities, and compared these among trait groups and among species differing in their mating systems...
April 25, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28440405/copy-number-variation-analysis-in-familial-nonsyndromic-congenital-anomalies-of-the-kidney-and-urinary-tract-evidence-for-the-causative-role-of-a-transposable-element-associated-genomic-rearrangement
#9
Ekaterini Siomou, Artemis G Mitsioni, Vasileios Giapros, Ioanna Bouba, Dimitrios Noutsopoulos, Ioannis Georgiou
Most congenital anomalies of the kidney and urinary tract (CAKUT) are sporadic, but familial occurrence has been described, suggesting a genetic contribution. Copy‑number variations (CNVs) were detected in patients with CAKUT to identify possible novel genomic regions associated with CAKUT. CNVs were investigated in 7 children with CAKUT from three unrelated families using array comparative genomic hybridization: female monozygotic twins with bilateral duplex collecting system/vesicoureteral reflux (VUR)/unilateral renal hypodyspasia (URHD); two male siblings with VUR/URHD; 3 male second cousins, one with bilateral VUR/URHD, one with bilateral VUR and one with ureterovesical junction obstruction (UVJO)...
April 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28440270/refined-genetic-maps-reveal-sexual-dimorphism-in-human-meiotic-recombination-at-multiple-scales
#10
Claude Bhérer, Christopher L Campbell, Adam Auton
In humans, males have lower recombination rates than females over the majority of the genome, but the opposite is usually true near the telomeres. These broad-scale differences have been known for decades, yet little is known about differences at the fine scale. By combining data sets, we have collected recombination events from over 100,000 meioses and have constructed sex-specific genetic maps at a previously unachievable resolution. Here we show that, although a substantial fraction of the genome shows some degree of sexually dimorphic recombination, the vast majority of hotspots are shared between the sexes, with only a small number of putative sex-specific hotspots...
April 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28440220/rapid-evolution-of-the-human-mutation-spectrum
#11
Kelley Harris, Jonathan K Pritchard
DNA is a remarkably precise medium for copying and storing biological information. This high fidelity results from the action of hundreds of genes involved in replication, proofreading, and damage repair. Evolutionary theory suggests that in such a system, selection has limited ability to remove genetic variants that change mutation rates by small amounts or in specific sequence contexts. Consistent with this, using SNV variation as a proxy for mutational input, we report here that mutational spectra differ substantially among species, human continental groups and even some closely-related populations...
April 25, 2017: ELife
https://www.readbyqxmd.com/read/28439972/mitochondrial-biogenesis-and-pgc-1%C3%AE-gene-expression-in-male-broilers-from-ascites-susceptible-and-resistant-lines
#12
N Khodambashi Emami, A Golian, M Danesh Mesgaran, N B Anthony, D D Rhoads
Ascites is a cardiovascular metabolic disease characterized by accumulation of fluid around the heart and in the abdominal cavity that eventually leads to death. This syndrome is the end-point result of a series of metabolic incidents that are generally caused by impaired oxygen availability. Mitochondria are the major sites of oxygen consumption, therefore major contributors to oxidative stress. Genetic, metabolic and dietary factors can influence variations in mitochondrial biogenesis (mitochondrial size, number and mass) that might have an effect on oxygen consumption and reactive oxygen species production...
April 25, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28439965/identifying-signatures-of-positive-selection-in-pigmentation-genes-in-two-south-asian-populations
#13
Manjari Jonnalagadda, Neeraj Bharti, Yatish Patil, Shantanu Ozarkar, Sunitha Manjari K, Rajendra Joshi, Heather Norton
OBJECTIVES: Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. While numerous pigmentation genes have been identified to be under positive selection among European and East populations, genes contributing to phenotypic variation in skin pigmentation within and among South Asian populations are still poorly understood. The present study uses data from the Phase 3 of the 1000 genomes project focusing on two South Asian populations-GIH (Gujarati Indian from Houston, Texas) and ITU (Indian Telugu from UK), so as to decode the genetic architecture involved in adaptation to ultraviolet radiation in South Asian populations...
April 24, 2017: American Journal of Human Biology: the Official Journal of the Human Biology Council
https://www.readbyqxmd.com/read/28439811/polymorphism-analysis-in-identification-of-genetic-variation-and-relationships-among-stylosanthes-species
#14
Chunqiong Huang, Guodao Liu, Changjun Bai
A total of 148 accessions representing six important species of the genus Stylosanthes, including S. guianensis, S. hamata, S. scabra, S. seabrana, S. macrocephala, and S. capitata, were used to evaluate genetic variation and relationships using sequence-related amplified polymorphism markers. The results showed that the 18 selected primer pairs generated 138 distinct fragments. The fragment sizes ranged from 150 to 2000 bp. Genetic similarity coefficients among the 148 accessions ranged from 0.51 to 0.99, with an average of 0...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28439621/qtl-mapping-of-domestication-and-diversifying-selection-related-traits-in-round-fruited-semi-wild-xishuangbanna-cucumber-cucumis-sativus-l-var-xishuangbannanesis
#15
Yupeng Pan, Shuping Qu, Kailiang Bo, Meiling Gao, Kristin R Haider, Yiqun Weng
QTL analysis revealed 11 QTL underlying flowering time and fruit size variation in the semi-wild Xishuangbanna cucumber, of which, FT6.2 and FS5.2 played the most important roles in determining photoperiod-dependent flowering time and round-fruit shape, respectively. Flowering time and fruit size are two important traits in domestication and diversifying selection in cucumber, but their genetic basis is not well understood. Here we reported QTL mapping results on flowering time and fruit size with F2 and F2:3 segregating populations derived from the cross between WI7200, a small fruited, early flowering primitive cultivated cucumber and WI7167, a round-fruited, later flowering semi-wild Xishuangbanna (XIS) cucumber...
April 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28439469/migratory-orientation-in-a-narrow-avian-hybrid-zone
#16
David P L Toews, Kira E Delmore, Matthew M Osmond, Philip D Taylor, Darren E Irwin
BACKGROUND: Zones of contact between closely related taxa with divergent migratory routes, termed migratory divides, have been suggested as areas where hybrid offspring may have intermediate and inferior migratory routes, resulting in low fitness of hybrids and thereby promoting speciation. In the Rocky Mountains of Canada there is a narrow hybrid zone between Audubon's and myrtle warblers that is likely maintained by selection against hybrids. Band recoveries and isotopic studies indicate that this hybrid zone broadly corresponds to the location of a possible migratory divide, with Audubon's warblers migrating south-southwest and myrtle warblers migrating southeast...
2017: PeerJ
https://www.readbyqxmd.com/read/28439467/floral-pathway-integrator-gene-expression-mediates-gradual-transmission-of-environmental-and-endogenous-cues-to-flowering-time
#17
Aalt D J van Dijk, Jaap Molenaar
The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral pathway integrator genes. At a quantitative level, it is currently unclear how the impact of genetic variation in signaling pathways on flowering time is mediated by floral pathway integrator genes. Here, using datasets available from literature, we connect Arabidopsis thaliana flowering time in genetic backgrounds varying in upstream signalling components with the expression levels of floral pathway integrator genes in these genetic backgrounds...
2017: PeerJ
https://www.readbyqxmd.com/read/28439286/snp-discovery-and-genetic-variation-of-candidate-genes-relevant-to-heat-tolerance-and-agronomic-traits-in-natural-populations-of-sand-rice-agriophyllum-squarrosum
#18
Pengshan Zhao, Jiwei Zhang, Chaoju Qian, Qin Zhou, Xin Zhao, Guoxiong Chen, Xiao-Fei Ma
The extreme stress tolerance and high nutritional value of sand rice (Agriophyllum squarrosum) make it attractive for use as an alternative crop in response to concerns about ongoing climate change and future food security. However, a lack of genetic information hinders understanding of the mechanisms underpinning the morphological and physiological adaptations of sand rice. In the present study, we sequenced and analyzed the transcriptomes of two individuals representing semi-arid [Naiman (NM)] and arid [Shapotou (SPT)] sand rice genotypes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28439068/limited-genomic-consequences-of-hybridization-between-two-african-clawed-frogs-xenopus-gilli-and-x-laevis-anura-pipidae
#19
Benjamin L S Furman, Caroline M S Cauret, Graham A Colby, G John Measey, Ben J Evans
The Cape platanna, Xenopus gilli, an endangered frog, hybridizes with the African clawed frog, X. laevis, in South Africa. Estimates of the extent of gene flow between these species range from pervasive to rare. Efforts have been made in the last 30 years to minimize hybridization between these two species in the west population of X. gilli, but not the east populations. To further explore the impact of hybridization and the efforts to minimize it, we examined molecular variation in one mitochondrial and 13 nuclear genes in genetic samples collected recently (2013) and also over two decades ago (1994)...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28439034/teleosts-as-model-organisms-to-understand-host-microbe-interactions
#20
Emily A Lescak, Kathryn C Milligan-Myhre
Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns whether observations in artificial conditions are actually reflective of what occurs in the wild...
April 24, 2017: Journal of Bacteriology
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