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https://www.readbyqxmd.com/read/28734179/computational-analysis-for-the-determination-of-deleterious-nssnps-in-human-mthfd1-gene
#1
Mansi Desai, J B Chauhan
Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol...
July 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28732173/exploring-the-potential-of-gametic-reconstruction-of-parental-genotypes-by-f-sub-1-sub-hybrids-as-a-bridge-for-rapid-introgression
#2
Charles H Cannon, C Lane Scher
Interspecific hybridization and genetic introgression are commonly observed in natural populations of many species, especially trees. Among oaks, gene flow between closely-related species has been well documented. And yet, hybridization does not lead to a 'melting pot', i.e. the homogenization of phenotypic traits. Here, we explore how the combination of several common reproductive traits and genomic biology could create an avenue for interspecific gene flow that partially explains this apparent paradox. During meiosis, F<sub>1</sub> hybrids will produce approximately (½)<sup>n</sup> 'reconstructed' parental gametes, where n equals the number of chromosomes...
July 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28732154/ironing-out-genes-in-the-environment-an-experimental-study-of-the-dna-goethite-interface
#3
Michael P Schmidt, Carmen Enid Martinez
DNA fate in soil plays an important role in the cycling of genetic information in the environment. Adsorption onto mineral surfaces has great impact on this function. This study probes the kinetics, equilibrium behavior and bonding mechanisms associated with adsorption of DNA onto goethite, a common soil mineral. Surface sensitive ATR-FTIR and XPS approaches are applied to directly characterize the DNA-goethite interface. Adsorption kinetics follow a pseudo-first order model, suggesting adsorption rate is surface limited...
July 21, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28731911/expert-and-self-assessment-of-lifetime-symptoms-and-diagnosis-of-major-depressive-disorder-in-large-scale-genetic-studies-in-the-general-population-comparison-of-a-clinical-interview-and-a-self-administered-checklist
#4
Jessica Martin, Fabian Streit, Jens Treutlein, Maren Lang, Josef Frank, Andreas J Forstner, Franziska Degenhardt, Stephanie H Witt, Thomas G Schulze, Sven Cichon, Markus M Nöthen, Marcella Rietschel, Jana Strohmaier
Major depression disorder (MDD) is a complex neuropsychiatric disorder and an increasing number of genetic risk variants are being identified. Investigation of their influence in the general population requires accurate and efficient assessment of depressive symptoms. Here, clinical interviews conducted by clinicians are the gold standard. We investigated whether valid and reliable clinical phenotypes can be obtained efficiently using self-administered instruments. Lifetime depressive symptoms and lifetime MDD diagnosis were assessed in 464 population-based individuals using a clinical interview and a structured, self-administered checklist...
July 20, 2017: Psychiatric Genetics
https://www.readbyqxmd.com/read/28731826/convergently-evolved-toxic-secondary-metabolites-in-plants-drive-the-parallel-molecular-evolution-of-insect-resistance
#5
Georg Petschenka, Vera Wagschal, Michael von Tschirnhaus, Alexander Donath, Susanne Dobler
Natural selection imposed by natural toxins has led to striking levels of convergent evolution at the molecular level. Cardiac glycosides represent a group of plant toxins that block the Na,K-ATPase, a vital membrane protein in animals. Several herbivorous insects have convergently evolved resistant Na,K-ATPases, and in some species, convergent gene duplications have also arisen, likely to cope with pleiotropic costs of resistance. To understand the genetic basis and predictability of these adaptations, we studied five independent lineages of leaf-mining flies (Diptera: Agromyzidae)...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731825/convergent-phenotypic-evolution-despite-contrasting-demographic-histories-in-the-fauna-of-white-sands
#6
Erica Bree Rosenblum, Christine E Parent, Eveline T Diepeveen, Clay Noss, Ke Bi
When are evolutionary outcomes predictable? Cases of convergent evolution can shed light on when, why, and how different species exhibit shared evolutionary trajectories. In particular, studying diverse species in a common environment can illuminate how different factors facilitate or constrain adaptive evolution. Here we integrate studies of pattern and process in the fauna at White Sands (New Mexico) to understand the determinants of convergent evolution. Numerous animal species at White Sands exhibit phenotypic convergence in response to a novel-and shared-selective environment: geologically young gypsum dunes...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731798/most-colorful-example-of-genetic-assimilation-exploring-the-evolutionary-destiny-of-recurrent-phenotypic-accommodation
#7
Alexander V Badyaev, Ahva L Potticary, Erin S Morrison
Evolution of adaptation requires both generation of novel phenotypic variation and retention of a locally beneficial subset of this variation. Such retention can be facilitated by genetic assimilation, the accumulation of genetic and molecular mechanisms that stabilize induced phenotypes and assume progressively greater control over their reliable production. A particularly strong inference into genetic assimilation as an evolutionary process requires a system where it is possible to directly evaluate the extent to which an induced phenotype is progressively incorporated into preexisting developmental pathways...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731690/the-metal-drives-the-chemistry-dual-functions-of-acireductone-dioxygenase
#8
Aditi R Deshpande, Thomas C Pochapsky, Dagmar Ringe
Acireductone dioxygenase (ARD) from the methionine salvage pathway (MSP) is a unique enzyme that exhibits dual chemistry determined solely by the identity of the divalent transition-metal ion (Fe(2+) or Ni(2+)) in the active site. The Fe(2+)-containing isozyme catalyzes the on-pathway reaction using substrates 1,2-dihydroxy-3-keto-5-methylthiopent-1-ene (acireductone) and dioxygen to generate formate and the ketoacid precursor of methionine, 2-keto-4-methylthiobutyrate, whereas the Ni(2+)-containing isozyme catalyzes an off-pathway shunt with the same substrates, generating methylthiopropionate, carbon monoxide, and formate...
July 21, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28731468/a-role-for-the-cell-wall-protein-silacidin-in-cell-size-of-the-diatom-thalassiosira-pseudonana
#9
Amy R Kirkham, Patrick Richthammer, Katrin Schmidt, Martin Wustmann, Yoshiaki Maeda, René Hedrich, Eike Brunner, Tsuyoshi Tanaka, Karl-Heinz van Pée, Angela Falciatore, Thomas Mock
Diatoms contribute 20% of global primary production and form the basis of many marine food webs. Although their species diversity correlates with broad diversity in cell size, there is also an intraspecific cell-size plasticity owing to sexual reproduction and varying environmental conditions. However, despite the ecological significance of the diatom cell size for food-web structure and global biogeochemical cycles, our knowledge about genes underpinning the size of diatom cells remains elusive. Here, a combination of reverse genetics, experimental evolution and comparative RNA-sequencing analyses enabled us to identify a previously unknown genetic control of cell size in the diatom Thalassiosira pseudonana...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731210/ecological-guild-and-enzyme-activities-of-rhizosphere-soil-microbial-communities-associated-with-bt-maize-cultivation-under-field-conditions-in-north-west-province-of-south-africa
#10
Deidré A B van Wyk, Rasheed Adeleke, Owen H J Rhode, Carlos C Bezuidenhout, Charlotte Mienie
Insecticidal proteins expressed by genetically modified Bt maize may alter the enzymatic and microbial communities associated with rhizosphere soil. This study investigated the structure and enzymatic activity of rhizosphere soil microbial communities associated with field grown Bt and non-Bt maize. Rhizosphere soil samples were collected from Bt and non-Bt fields under dryland and irrigated conditions. Samples were subjected to chemical tests, enzyme analyses, and next generation sequencing. Results showed that nitrate and phosphorus concentrations were significantly higher in non-Bt maize dryland soils, while organic carbon was significantly higher in non-Bt maize irrigated field soil...
July 21, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28730743/inulin-type-fructans-and-whey-protein-both-modulate-appetite-but-only-fructans-alter-gut-microbiota-in-adults-with-overweight-obesity-a-randomized-controlled-trial
#11
Raylene A Reimer, Holly J Willis, Jasmine M Tunnicliffe, Heekuk Park, Karen L Madsen, Adriana Soto-Vaca
SCOPE: Independently, prebiotics and dietary protein have been shown to improve weight loss and/or alter appetite. Our objective was to determine the effect of combined prebiotic and whey protein on appetite, body composition and gut microbiota in adults with overweight/obesity. METHODS AND RESULTS: In a 12 week, placebo-controlled, double-blind study, 125 adults with overweight/obesity were randomly assigned to receive isocaloric snack bars of: 1) Control; 2) Inulin-type fructans (ITF); 3) Whey protein; 4) ITF + Whey protein...
July 21, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28730723/do-assortative-mating-and-immigrant-inviability-help-maintain-population-genetic-structuring-of-an-herbivore-on-a-crop-and-a-wild-relative
#12
Ricardo Ramirez-Romero, Delia Garibay-Benítez, Ofelia Vargas-Ponce, Andrea Joyce, Julio S Bernal
Population genetic structuring is common among herbivorous insects and frequently is associated with divergent host plants, such as crops and their wild relatives. Previous studies showed population genetic structuring in corn leafhopper Dalbulus maidis in Mexico, such that the species consists of two sympatric, host plant-associated populations: an abundant and widespread "pestiferous" population on maize (Zea mays mays), and a small and localized "wild" population on perennial teosinte (Zea diploperennis), a maize wild relative with a limited distribution...
July 21, 2017: Insect Science
https://www.readbyqxmd.com/read/28730641/basal-ganglia-and-autism-a-translational-perspective
#13
REVIEW
Krishna Subramanian, Cheryl Brandenburg, Fernanda Orsati, Jean-Jacques Soghomonian, John P Hussman, Gene J Blatt
The basal ganglia are a collection of nuclei below the cortical surface that are involved in both motor and non-motor functions, including higher order cognition, social interactions, speech, and repetitive behaviors. Motor development milestones that are delayed in autism such as gross motor, fine motor and walking can aid in early diagnosis of autism. Neuropathology and neuroimaging findings in autism cases revealed volumetric changes and altered cell density in select basal ganglia nuclei. Interestingly, in autism, both the basal ganglia and the cerebellum are impacted both in their motor and non-motor domains and recently, found to be connected via the pons through a short disynaptic pathway...
July 21, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28730343/age-at-maturation-has-sex-and-temperature-specific-effects-on-telomere-length-in-a-fish
#14
Kristina Noreikiene, Anna Kuparinen, Juha Merilä
Telomeres are highly conserved nucleoprotein structures which protect genome integrity. The length of telomeres is influenced by both genetic and environmental factors, but relatively little is known about how different hereditary and environmental factors interact in determining telomere length. We manipulated growth rates and timing of maturation by exposing full-sib nine-spined sticklebacks (Pungitius pungitius) to two different temperature treatments and quantified the effects of temperature treatments, sex, timing of maturation, growth rate and family (genetic influences) on telomere length...
July 20, 2017: Oecologia
https://www.readbyqxmd.com/read/28729950/alder-and-the-golden-fleece-high-diversity-of-frankia-and-ectomycorrhizal-fungi-revealed-from-alnus-glutinosa-subsp-barbata-roots-close-to-a-tertiary-and-glacial-refugium
#15
Melanie Roy, Adrien C Pozzi, Raphaëlle Gareil, Melissande Nagati, Sophie Manzi, Imen Nouioui, Nino Sharikadze, Patricia Jargeat, Hervé Gryta, Pierre-Arthur Moreau, Maria P Fernandez, Monique Gardes
BACKGROUND: Recent climatic history has strongly impacted plant populations, but little is known about its effect on microbes. Alders, which host few and specific symbionts, have high genetic diversity in glacial refugia. Here, we tested the prediction that communities of root symbionts survived in refugia with their host populations. We expected to detect endemic symbionts and a higher species richness in refugia as compared to recolonized areas. METHODS: We sampled ectomycorrhizal (EM) root tips and the nitrogen-fixing actinomycete Frankia communities in eight sites colonized by Alnus glutinosa subsp...
2017: PeerJ
https://www.readbyqxmd.com/read/28729877/genetic-diversity-population-structure-and-linkage-disequilibrium-of-an-association-mapping-panel-revealed-by-genome-wide-snp-markers-in-sesame
#16
Chengqi Cui, Hongxian Mei, Yanyang Liu, Haiyang Zhang, Yongzhan Zheng
The characterization of genetic diversity and population structure can be used in tandem to detect reliable phenotype-genotype associations. In the present study, we genotyped a set of 366 sesame germplasm accessions by using 89,924 single-nucleotide polymorphisms (SNPs). The number of SNPs on each chromosome was consistent with the physical length of the respective chromosome, and the average marker density was approximately 2.67 kb/SNP. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28729848/the-functional-genetics-of-handedness-and-language-lateralization-insights-from-gene-ontology-pathway-and-disease-association-analyses
#17
Judith Schmitz, Stephanie Lor, Rena Klose, Onur Güntürkün, Sebastian Ocklenburg
Handedness and language lateralization are partially determined by genetic influences. It has been estimated that at least 40 (and potentially more) possibly interacting genes may influence the ontogenesis of hemispheric asymmetries. Recently, it has been suggested that analyzing the genetics of hemispheric asymmetries on the level of gene ontology sets, rather than at the level of individual genes, might be more informative for understanding the underlying functional cascades. Here, we performed gene ontology, pathway and disease association analyses on genes that have previously been associated with handedness and language lateralization...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28729708/new-mycobacterium-tuberculosis-beijing-clonal-complexes-in-china-revealed-by-phylogenetic-and-bayesian-population-structure-analyses-of-24-loci-miru-vntrs
#18
Chao Zheng, Yann Reynaud, Changsong Zhao, Thierry Zozio, Song Li, Dongxia Luo, Qun Sun, Nalin Rastogi
Beijing lineage of Mycobacterium tuberculosis constitutes the most predominant lineage in East Asia. Beijing epidemiology, evolutionary history, genetics are studied in details for years revealing probable origin from China followed by worldwide expansion, partially linked to higher mutation rate, hypervirulence, drug-resistance, and association with cases of mixed infections. Considering huge amount of data available for 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats, we performed detailed phylogenetic and Bayesian population structure analyses of Beijing lineage strains in mainland China and Taiwan using available 24-loci MIRU-VNTR data extracted from publications or the SITVIT2 database (n = 1490)...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729648/a-haplotype-in-cfh-family-genes-confers-high-risk-of-rare-glomerular-nephropathies
#19
Yin Ding, Weiwei Zhao, Tao Zhang, Hao Qiang, Jianping Lu, Xin Su, Shuzhen Wen, Feng Xu, Mingchao Zhang, Haitao Zhang, Caihong Zeng, Zhihong Liu, Huimei Chen
Despite distinct renal lesions, a series of rare glomerular nephropathies are reportedly mediated by complement overactivation. Genetic variations in complement genes contribute to disease risk, but the relationship of genotype to phenotype has not been straightforward. Here, we screened 11 complement genes from 91 patients with atypical hemolytic uremic syndrome (aHUS), C3 glomerulopathy (C3G) and membranoproliferative glomerulonephritis type I (MPGN I), and identified the concomitant presence of three missense variations located within the human complement Factor H (CFH) gene cluster...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729554/comparison-of-traditional-and-new-generation-dna-markers-declares-high-genetic-diversity-and-differentiated-population-structure-of-wild-almond-species
#20
Karim Sorkheh, Mehrana Koohi Dehkordi, Sezai Ercisli, Attila Hegedus, Júlia Halász
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome...
July 20, 2017: Scientific Reports
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