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Genetic variation

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https://www.readbyqxmd.com/read/27926907/mammalian-meiotic-recombination-a-toolbox-for-genome-evolution
#1
Laia Capilla, Montserrat Garcia Caldés, Aurora Ruiz-Herrera
Meiotic recombination is a process that increases genetic diversity and is fundamental for sexual reproduction. Determining by which mechanisms genetic variation is generated and maintained across different phylogenetic groups provides the basis for our understanding of biodiversity and evolution. In this review, we go through different aspects of this essential phenomenon, paying special attention to mammals. We provide a comprehensive view on the organization of meiotic chromosomes and the mechanisms involved in the formation and genomic distribution of recombination hotspots, focusing on the factors influencing the formation and repair of the massive amount of self-induced DNA breaks in early stages of meiosis...
December 8, 2016: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/27925267/genetic-variation-and-gene-conversions-within-the-bovine-nk-lysin-gene-family
#2
J Chen, M O Lee, J E Womack
In contrast to a single copy of the NK-lysin gene in humans and many other mammals, we previously identified a family of four expressed NK-lysin genes arising by tandem duplications on cattle chromosome 11. Here, we report two genetic variants in the bovine NK-lysin complex with potential importance in the bovine innate immune system. The first one is a 9-bp deletion causing a three-amino-acid deletion in the pro-region of the NK1 gene product. The second is a deletion of NK2B in some Holstein cattle, resulting in copy number variation that is in disequilibrium with a SNP from the bovine 770K HD SNP array...
December 7, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27925170/associations-of-microrna-single-nucleotide-polymorphisms-and-disease-risk-and-pathophysiology
#3
REVIEW
Xiaoxiao Liu, Zhijun Han, Chengjian Yang
Single nucleotide polymorphisms (SNPs) are genetic variations that contribute to human phenotypes associated with various diseases. SNPs are involved in the regulation of a broad range of physiological and pathological processes, such as cellular senescence, apoptosis, inflammation, and immune response, by up-regulating the expression of classical inflammation markers. Recent studies have suggested that SNPs located in gene-encoding microRNAs (miRNAs) affect various aspects of diseases by regulating the expression or activity of miRNAs...
December 7, 2016: Clinical Genetics
https://www.readbyqxmd.com/read/27925136/multidimensional-evaluation-of-endogenous-and-health-factors-affecting-food-preferences-taste-and-smell-perception
#4
D Guido, S Perna, M Carrai, R Barale, M Grassi, M Rondanelli
OBJECTIVE: This study, by taking a holistic approach, investigates the relationships between taste, smell sensitivity and food preference with prognostic (endogenous and health) factors including age, gender, genetic taste markers, body mass, cigarette smoking, and number of drugs used. DESIGN: Cross sectional study. SETTING: Northern Italy. PARTICIPANTS: 203 healthy subjects (160 women/43 men; mean age: 58.2±19.8 years) were examined...
2016: Journal of Nutrition, Health & Aging
https://www.readbyqxmd.com/read/27925006/cryopreservation-of-adventitious-roots-of-cleome-rosea-vahl-cleomaceae-using-a-vitrification-technique-and-assessment-of-genetic-stability
#5
L Da Silva Cordeiro, C Simoes-Gurgel, N Albarello
BACKGROUND:  Cleome rosea, a Brazilian native species, has medicinal potential. Previously a cryopreservation protocol for in vitro roots using the vitrification solution PVS2 has been developed. However, the genetic stability of the cryopreserved material is yet to be assessed. OBJECTIVES: To evaluate the effects of loading and vitrification solutions (PVS2 and PVS3) on post-cryopreservation recovery of C. rosea roots, and to assess their genetic stability using Random Amplified Polymorphic DNA (RAPD) markers...
July 2016: Cryo Letters
https://www.readbyqxmd.com/read/27924540/targeting-fumonisin-biosynthetic-genes
#6
Robert H Proctor, Martha M Vaughan
The fungus Fusarium is an agricultural problem because it can cause disease on most crop plants and can contaminate crops with mycotoxins. There is considerable variation in the presence/absence and genomic location of gene clusters responsible for synthesis of mycotoxins and other secondary metabolites among species of Fusarium. Here, we describe a quantitative real-time PCR (qPCR) method for distinguishing between and estimating the biomass of two closely related species, F. proliferatum and F. verticillioides, that are pathogens of maize...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924448/milk-protein-polymorphisms-and-casein-haplotypes-in-butana-cattle
#7
A Said Ahmed, S Rahmatalla, R Bortfeldt, D Arends, M Reissmann, G A Brockmann
Butana is a Bos indicus dairy cattle breed that is well adapted to the local environment of Sudan. The breed has been gradually declining in number due to breed substitution. Therefore, conservation and improvement strategies are required to maintain this breed. The aim of the present study was to assess genetic variation that is characteristic for Butana cattle in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB. In a first step, genomic DNA of five unrelated individuals was comparatively sequenced across all exon and flanking sequences...
December 6, 2016: Journal of Applied Genetics
https://www.readbyqxmd.com/read/27924309/engineering-the-dynamic-properties-of-protein-networks-through-sequence-variation
#8
Lawrence J Dooling, David A Tirrell
The dynamic behavior of macromolecular networks dominates the mechanical properties of soft materials and influences biological processes at multiple length scales. In hydrogels prepared from self-assembling artificial proteins, stress relaxation and energy dissipation arise from the transient character of physical network junctions. Here we show that subtle changes in sequence can be used to program the relaxation behavior of end-linked networks of engineered coiled-coil proteins. Single-site substitutions in the coiled-coil domains caused shifts in relaxation time over 5 orders of magnitude as demonstrated by dynamic oscillatory shear rheometry and stress relaxation measurements...
November 23, 2016: ACS Central Science
https://www.readbyqxmd.com/read/27924270/structural-characterization-of-single-nucleotide-variants-at-ligand-binding-sites-and-enzyme-active-sites-of-human-proteins
#9
Kazunori D Yamada, Hafumi Nishi, Junichi Nakata, Kengo Kinoshita
Functional sites on proteins play an important role in various molecular interactions and reactions between proteins and other molecules. Thus, mutations in functional sites can severely affect the overall phenotype. Progress of genome sequencing projects has yielded a wealth of information on single nucleotide variants (SNVs), especially those with less than 1% minor allele frequency (rare variants). To understand the functional influence of genetic variants at a protein level, we investigated the relationship between SNVs and protein functional sites in terms of minor allele frequency and the structural position of variants...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27924152/molecular-characterization-of-a-rare-analphoid-supernumerary-marker-chromosome-derived-from-7q35%C3%A2-%C3%A2-%C3%A2-qter-a-case-report
#10
Bárbara Marques, Cristina Ferreira, Filomena Brito, Sónia Pedro, Cristina Alves, Teresa Lourenço, Marta Amorim, Hildeberto Correia
BACKGROUND: Analphoid supernumerary marker chromosomes (aSMC) constitute one of the smallest groups of SMC, and are characterized by a centromeric constriction but no detectable alpha-satellite DNA. These marker chromosomes cannot be properly identified by conventional banding techniques alone, and molecular cytogenetic methods are necessary for a detailed characterization. Analphoid SMC derived from chromosome 7 are extremely rare, with only five cases reported so far. CASE PRESENTATION: In this work we report an aSMC involving the terminal long arm of chromosome 7 in a 10-year-old boy with multiple dysmorphic features and severe development delay...
2016: Molecular Cytogenetics
https://www.readbyqxmd.com/read/27924064/toward-the-use-of-precision-medicine-for-the-treatment-of-head-and-neck-squamous-cell-carcinoma
#11
REVIEW
Wang Gong, Yandi Xiao, Zihao Wei, Yao Yuan, Min Qiu, Chongkui Sun, Xin Zeng, Xinhua Liang, Mingye Feng, Qianming Chen
Precision medicine is a new strategy that aims at preventing and treating human diseases by focusing on individual variations in people's genes, environment and lifestyle. Precision medicine has been used for cancer diagnosis and treatment and shows evident clinical efficacy. Rapid developments in molecular biology, genetics and sequencing technologies, as well as computational technology, has enabled the establishment of "big data", such as the Human Genome Project, which provides a basis for precision medicine...
December 4, 2016: Oncotarget
https://www.readbyqxmd.com/read/27924043/arapheno-a-public-database-for-arabidopsis-thaliana-phenotypes
#12
Ümit Seren, Dominik Grimm, Joffrey Fitz, Detlef Weigel, Magnus Nordborg, Karsten Borgwardt, Arthur Korte
Natural genetic variation makes it possible to discover evolutionary changes that have been maintained in a population because they are advantageous. To understand genotype-phenotype relationships and to investigate trait architecture, the existence of both high-resolution genotypic and phenotypic data is necessary. Arabidopsis thaliana is a prime model for these purposes. This herb naturally occurs across much of the Eurasian continent and North America. Thus, it is exposed to a wide range of environmental factors and has been subject to natural selection under distinct conditions...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924022/expanded-national-database-collection-and-data-coverage-in-the-findbase-worldwide-database-for-clinically-relevant-genomic-variation-allele-frequencies
#13
Emmanouil Viennas, Angeliki Komianou, Clint Mizzi, Maja Stojiljkovic, Christina Mitropoulou, Juha Muilu, Mauno Vihinen, Panagiota Grypioti, Styliani Papadaki, Cristiana Pavlidis, Branka Zukic, Theodora Katsila, Peter J van der Spek, Sonja Pavlovic, Giannis Tzimas, George P Patrinos
FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923841/biological-and-clinical-relevance-of-associated-genomic-alterations-in-myd88-l265p-and-non-l265p-mutated-diffuse-large-b-cell-lymphoma-analysis-of-361-cases
#14
Sydney Dubois, Pierre-Julien Viailly, Elodie Bohers, Philippe Bertrand, Philippe Ruminy, Vinciane Marchand, Catherine Maingonnat, Sylvain Mareschal, Jean-Michel Picquenot, Dominique Penther, Jean-Philippe Jais, Bruno Tesson, Pauline Peyrouze, Martin Figeac, Fabienne Desmots, Thierry Fest, Corinne Haioun, Thierry Lamy, Christiane Copie-Bergman, Bettina Fabiani, Richard Delarue, Frederic Peyrade, Marc André, Nicolas Ketterer, Karen Leroy, Gilles Salles, Thierry J Molina, Herve Tilly, Fabrice Jardin
PURPOSE: MYD88 mutations, notably the recurrent gain-of-function L265P variant, are a distinguishing feature of Activated B-Cell like (ABC) Diffuse Large B Cell Lymphoma (DLBCL), leading to constitutive NFkB pathway activation. The aim of this study was to examine the distinct genomic profiles of MYD88 mutant DLBCL, notably according to the presence of the L265P or other non-L265P MYD88 variants. EXPERIMENTAL DESIGN: A cohort of 361 DLBCL cases (94 MYD88 mutant and 267 MYD88 wild-type) was submitted to next generation sequencing (NGS) focusing on 34 genes in order to analyze associated mutations and copy number variations, as well as gene expression profiling, and clinical and prognostic analyses...
December 6, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27923735/a-shadow-detector-for-photosynthesis-efficiency
#15
Kang-Ling Liao, Roger D Jones, Patrick McCarter, Meral Tunc-Ozdemir, James A Draper, Timothy C Elston, David Kramer, Alan M Jones
Plants tolerate large variations in the intensity of the light environment by controlling the efficiency of solar to chemical energy conversion. To do this, plants have a mechanism to detect the intensity, duration, and change in light as they experience moving shadows, flickering light, and cloud cover. Sugars are the primary products of CO2 fixation, a metabolic pathway that is rate limited by this solar energy conversion. We propose that sugar is a signal encoding information about the intensity, duration and change in the light environment...
December 3, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27923716/effects-of-cross-fostering-on-play-and-anxiety-in-juvenile-fischer-344-and-lewis-rats
#16
Stephen M Siviy, Samantha R Eck, Lana S McDowell, Jennifer Soroka
A cross-fostering design was used to assess the relative involvement of genetic variability and early postnatal experiences on differential levels of playfulness in juvenile Fischer 344 (F344) and Lewis (LEW) rats and the extent to which strain differences in anxiety may influence play in these two strains. F344 dams were found to lick and groom their pups less than LEW dams and this was not dependent upon the strain of the pups in the litter. As expected, F344 rats were less playful than LEW rats as demonstrated by fewer playful contacts directed to the nape of a Sprague-Dawley (SD) partner and a decreased likelihood of rotating completely to a supine position when their nape was contacted by the SD partner...
December 3, 2016: Physiology & Behavior
https://www.readbyqxmd.com/read/27923068/gene-expression-correlates-with-the-number-of-herpes-viral-genomes-initiating-infection-in-single-cells
#17
Efrat M Cohen, Oren Kobiler
Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants...
December 6, 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27922636/dna-methylation-and-substance-use-risk-a-prospective-genome-wide-study-spanning-gestation-to-adolescence
#18
C A M Cecil, E Walton, R G Smith, E Viding, E J McCrory, C L Relton, M Suderman, J-B Pingault, W McArdle, T R Gaunt, J Mill, E D Barker
Epigenetic processes have been implicated in addiction; yet, it remains unclear whether these represent a risk factor and/or a consequence of substance use. Here, we believe we conducted the first genome-wide, longitudinal study to investigate whether DNA methylation patterns in early life prospectively associate with substance use in adolescence. The sample comprised of 244 youth (51% female) from the Avon Longitudinal Study of Parents and Children (ALSPAC), with repeated assessments of DNA methylation (Illumina 450k array; cord blood at birth, whole blood at age 7) and substance use (tobacco, alcohol and cannabis use; age 14-18)...
December 6, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27922604/common-variants-on-2p16-1-6p22-1-and-10q24-32-are-associated-with-schizophrenia-in-han-chinese-population
#19
H Yu, H Yan, J Li, Z Li, X Zhang, Y Ma, L Mei, C Liu, L Cai, Q Wang, F Zhang, N Iwata, M Ikeda, L Wang, T Lu, M Li, H Xu, X Wu, B Liu, J Yang, K Li, L Lv, X Ma, C Wang, L Li, F Yang, T Jiang, Y Shi, T Li, D Zhang, W Yue
Many schizophrenia susceptibility loci have been identified through genome-wide association studies (GWASs) in European populations. However, until recently, schizophrenia GWASs in non-European populations were limited to small sample sizes and have yielded few loci associated with schizophrenia. To identify genetic risk variations for schizophrenia in the Han Chinese population, we performed a two-stage GWAS of schizophrenia comprising 4384 cases and 5770 controls, followed by independent replications of 13 single-nucleotide polymorphisms in an additional 4339 schizophrenia cases and 7043 controls of Han Chinese ancestry...
December 6, 2016: Molecular Psychiatry
https://www.readbyqxmd.com/read/27922085/diversity-of-major-urinary-proteins-mups-in-wild-house-mice
#20
Michaela Thoß, Viktoria Enk, Hans Yu, Ingrid Miller, Kenneth C Luzynski, Boglarka Balint, Steve Smith, Ebrahim Razzazi-Fazeli, Dustin J Penn
Major urinary proteins (MUPs) are often suggested to be highly polymorphic, and thereby provide unique chemical signatures used for individual and genetic kin recognition; however, studies on MUP variability have been lacking. We surveyed populations of wild house mice (Mus musculus musculus), and examined variation of MUP genes and proteins. We sequenced several Mup genes (9 to 11 loci) and unexpectedly found no inter-individual variation. We also found that microsatellite markers inside the MUP cluster show remarkably low levels of allelic diversity, and significantly lower than the diversity of markers flanking the cluster or other markers in the genome...
December 6, 2016: Scientific Reports
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