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Targeted Sequence Capture Provides Insight into Genome Structure and Genetics of Male Sterility in a Gynodioecious Diploid Strawberry, Fragaria vesca ssp. bracteata (Rosaceae)

Tennessen, Jacob A.; Govindarajulu, Rajanikanth; Liston, Aaron; Ashman, Tia-Lynn
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em 01/08/2013 EN
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Gynodioecy is a sexual system wherein females coexist with hermaphrodites. It is of interest not only because male-sterile plants are advantageous in plant breeding but also because it can be a crucial step in the evolutionary transition to entirely separate sexes (dioecy) from a hermaphroditic ancestor. The gynodioecious diploid wild strawberry, Fragaria vesca ssp. bracteata (Rosaceae), is a member of a clade with both dioecious and cultivated species, making it an ideal model in which to study the genetics of male sterility. To create a genetic map of F. v. ssp. bracteata, we identified informative polymorphisms from genomic sequencing (3−5x coverage) of two outbred plants from the same population. Using targeted enrichment, we sequenced 200 bp surrounding each of 6575 polymorphisms in 48 F1 offspring, yielding genotypes at 98% of targeted sites with mean coverage >100x, plus more than 600-kb high-coverage nontargeted sequence. With the resulting linkage map of 7802 stringently filtered markers (5417 targeted), we assessed recombination rates and genomic incongruities. Consistent with past work in strawberries, male sterility is dominant, segregates 1:1, and maps to a single location in the female. Further mapping an additional 55 offspring places male sterility in a gene-dense...

Functional Genetics in the Post-Genomics Era: Building a Better Roadmap in Drosophila

Kulathinal, Rob J.
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em /09/2013 EN
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In this commentary, Rob Kulathinal describes two articles from the Perrimon lab, each describing a new online resource that can assist geneticists with the design of their RNA interference (RNAi) experiments. Hu et al.’s “UP-TORR: online tool for accurate and up-to-date annotation of RNAi reagents” and “FlyPrimerBank: An online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents” are published, respectively, in this month’s issues of GENETICS and G3.

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

Eckert, Andrew J.; Wegrzyn, Jill L.; Liechty, John D.; Lee, Jennifer M.; Cumbie, W. Patrick; Davis, John M.; Goldfarb, Barry; Loopstra, Carol A.; Palle, Sreenath R.; Quesada, Tania; Langley, Charles H.; Neale, David B.
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
EN
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A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for >7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the >1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits...

Epigenome-Wide Association Study of Fasting Measures of Glucose, Insulin, and HOMA-IR in the Genetics of Lipid Lowering Drugs and Diet Network Study

Hidalgo, Bertha; Irvin, M. Ryan; Sha, Jin; Zhi, Degui; Aslibekyan, Stella; Absher, Devin; Tiwari, Hemant K.; Kabagambe, Edmond K.; Ordovas, Jose M.; Arnett, Donna K.
Fonte: American Diabetes Association Publicador: American Diabetes Association
Tipo: Artigo de Revista Científica
EN
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Known genetic susceptibility loci for type 2 diabetes (T2D) explain only a small proportion of heritable T2D risk. We hypothesize that DNA methylation patterns may contribute to variation in diabetes-related risk factors, and this epigenetic variation across the genome can contribute to the missing heritability in T2D and related metabolic traits. We conducted an epigenome-wide association study for fasting glucose, insulin, and homeostasis model assessment of insulin resistance (HOMA-IR) among 837 nondiabetic participants in the Genetics of Lipid Lowering Drugs and Diet Network study, divided into discovery (N = 544) and replication (N = 293) stages. Cytosine guanine dinucleotide (CpG) methylation at ∼470,000 CpG sites was assayed in CD4+ T cells using the Illumina Infinium HumanMethylation 450 Beadchip. We fit a mixed model with the methylation status of each CpG as the dependent variable, adjusting for age, sex, study site, and T-cell purity as fixed-effects and family structure as a random-effect. A Bonferroni corrected P value of 1.1 × 10−7 was considered significant in the discovery stage. Significant associations were tested in the replication stage using identical models. Methylation of a CpG site in ABCG1 on chromosome 21 was significantly associated with insulin (P = 1.83 × 10−7) and HOMA-IR (P = 1.60 × 10−9). Another site in the same gene was significant for HOMA-IR and of borderline significance for insulin (P = 1.29 × 10−7 and P = 3.36 × 10−6...

Exploiting the Extraordinary Genetic Polymorphism of Ciona for Developmental Genetics with Whole Genome Sequencing

Abdul-Wajid, Sarah; Veeman, Michael T.; Chiba, Shota; Turner, Thomas L.; Smith, William C.
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
36.15%
Studies in tunicates such as Ciona have revealed new insights into the evolutionary origins of chordate development. Ciona populations are characterized by high levels of natural genetic variation, between 1 and 5%. This variation has provided abundant material for forward genetic studies. In the current study, we make use of deep sequencing and homozygosity mapping to map spontaneous mutations in outbred populations. With this method we have mapped two spontaneous developmental mutants. In Ciona intestinalis we mapped a short-tail mutation with strong phenotypic similarity to a previously identified mutant in the related species Ciona savignyi. Our bioinformatic approach mapped the mutation to a narrow interval containing a single mutated gene, α-laminin3,4,5, which is the gene previously implicated in C. savignyi. In addition, we mapped a novel genetic mutation disrupting neural tube closure in C. savignyi to a T-type Ca2+ channel gene. The high efficiency and unprecedented mapping resolution of our study is a powerful advantage for developmental genetics in Ciona, and may find application in other outbred species.

The Genetics of Immunity

Lazzaro, Brian P.; Schneider, David S.
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
36.15%

The Genetics of Sex: Exploring Differences

N. Arbeitman, Michelle; Kopp, Artyom; L. Siegal, Mark; Van Doren, Mark
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
36.15%

Genetics of kidney disease and related cardiometabolic phenotypes in Zuni Indians: the Zuni Kidney Project

Laston, Sandra L.; Voruganti, V. Saroja; Haack, Karin; Shah, Vallabh O.; Bobelu, Arlene; Bobelu, Jeanette; Ghahate, Donica; Harford, Antonia M.; Paine, Susan S.; Tentori, Francesca; Cole, Shelley A.; MacCluer, Jean W.; Comuzzie, Anthony G.; Zager, Philip
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 30/01/2015 EN
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36.15%
The objective of this study is to identify genetic factors associated with chronic kidney disease (CKD) and related cardiometabolic phenotypes among participants of the Genetics of Kidney Disease in Zuni Indians study. The study was conducted as a community-based participatory research project in the Zuni Indians, a small endogamous tribe in rural New Mexico. We recruited 998 members from 28 extended multigenerational families, ascertained through probands with CKD who had at least one sibling with CKD. We used the Illumina Infinium Human1M-Duo version 3.0 BeadChips to type 1.1 million single nucleotide polymorphisms (SNPs). Prevalence estimates for CKD, hyperuricemia, diabetes, and hypertension were 24%, 30%, 17% and 34%, respectively. We found a significant (p < 1.58 × 10-7) association for a SNP in a novel gene for serum creatinine (PTPLAD2). We replicated significant associations for genes with serum uric acid (SLC2A9), triglyceride levels (APOA1, BUD13, ZNF259), and total cholesterol (PVRL2). We found novel suggestive associations (p < 1.58 × 10-6) for SNPs in genes with systolic (OLFML2B), and diastolic blood pressure (NFIA). We identified a series of genes associated with CKD and related cardiometabolic phenotypes among Zuni Indians...

Population Genetics of Anopheles coluzzii Immune Pathways and Genes

Rottschaefer, Susan M.; Crawford, Jacob E.; Riehle, Michelle M.; Guelbeogo, Wamdaogo M.; Gneme, Awa; Sagnon, N’Fale; Vernick, Kenneth D.; Lazzaro, Brian P.
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em 30/12/2014 EN
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Natural selection is expected to drive adaptive evolution in genes involved in host–pathogen interactions. In this study, we use molecular population genetic analyses to understand how natural selection operates on the immune system of Anopheles coluzzii (formerly A. gambiae “M form”). We analyzed patterns of intraspecific and interspecific genetic variation in 20 immune-related genes and 17 nonimmune genes from a wild population of A. coluzzii and asked if patterns of genetic variation in the immune genes are consistent with pathogen-driven selection shaping the evolution of defense. We found evidence of a balanced polymorphism in CTLMA2, which encodes a C-type lectin involved in regulation of the melanization response. The two CTLMA2 haplotypes, which are distinguished by fixed amino acid differences near the predicted peptide cleavage site, are also segregating in the sister species A. gambiae (“S form”) and A. arabiensis. Comparison of the two haplotypes between species indicates that they were not shared among the species through introgression, but rather that they arose before the species divergence and have been adaptively maintained as a balanced polymorphism in all three species. We additionally found that STAT-B...

Obesity genetics in mouse and human: back and forth, and back again

Yazdi, Fereshteh T.; Clee, Susanne M.; Meyre, David
Fonte: PeerJ Inc. Publicador: PeerJ Inc.
Tipo: Artigo de Revista Científica
Publicado em 24/03/2015 EN
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Obesity is a major public health concern. This condition results from a constant and complex interplay between predisposing genes and environmental stimuli. Current attempts to manage obesity have been moderately effective and a better understanding of the etiology of obesity is required for the development of more successful and personalized prevention and treatment options. To that effect, mouse models have been an essential tool in expanding our understanding of obesity, due to the availability of their complete genome sequence, genetically identified and defined strains, various tools for genetic manipulation and the accessibility of target tissues for obesity that are not easily attainable from humans. Our knowledge of monogenic obesity in humans greatly benefited from the mouse obesity genetics field. Genes underlying highly penetrant forms of monogenic obesity are part of the leptin-melanocortin pathway in the hypothalamus. Recently, hypothesis-generating genome-wide association studies for polygenic obesity traits in humans have led to the identification of 119 common gene variants with modest effect, most of them having an unknown function. These discoveries have led to novel animal models and have illuminated new biologic pathways. Integrated mouse-human genetic approaches have firmly established new obesity candidate genes. Innovative strategies recently developed by scientists are described in this review to accelerate the identification of causal genes and deepen our understanding of obesity etiology. An exhaustive dissection of the molecular roots of obesity may ultimately help to tackle the growing obesity epidemic worldwide.

Comparative Genetics of Seed Size Traits in Divergent Cereal Lineages Represented by Sorghum (Panicoidae) and Rice (Oryzoidae)

Zhang, Dong; Li, Jingping; Compton, Rosana O.; Robertson, Jon; Goff, Valorie H.; Epps, Ethan; Kong, Wenqian; Kim, Changsoo; Paterson, Andrew H.
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em 31/03/2015 EN
Relevância na Pesquisa
36.15%
Seed size is closely related to fitness of wild plants, and its modification has been a key recurring element in domestication of seed/grain crops. In sorghum, a genomic and morphological model for panicoid cereals, a rich history of research into the genetics of seed size is reflected by a total of 13 likelihood intervals determined by conventional QTL (linkage) mapping in 11 nonoverlapping regions of the genome. To complement QTL data and investigate whether the discovery of seed size QTL is approaching “saturation,” we compared QTL data to GWAS for seed mass, seed length, and seed width studied in 354 accessions from a sorghum association panel (SAP) that have been genotyped at 265,487 SNPs. We identified nine independent GWAS-based “hotspots” for seed size associations. Targeted resequencing near four association peaks with the most notable linkage disequilibrium provides further support of the role(s) of these regions in the genetic control of sorghum seed size and identifies two candidate causal variants with nonsynonymous mutations. Of nine GWAS hotspots in sorghum, seven have significant correspondence with rice QTL intervals and known genes for components of seed size on orthologous chromosomes. Identifying intersections between positional and association genetic data are a potentially powerful means to mitigate constraints associated with each approach...

Genetics of Epilepsy in Clinical Practice

Berkovic, Samuel F.
Fonte: American Epilepsy Society Publicador: American Epilepsy Society
Tipo: Artigo de Revista Científica
Publicado em //2015 EN
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Genetics should now be part of everyday clinical epilepsy practice. Good data exist to provide empiric risks based on epilepsy syndrome diagnosis. Investigation of the molecular basis of some epilepsies is now a practical clinical task and is of clear value to the patient and family. In some cases, specific therapeutic decisions can now be made based on genetic findings, and this scenario of precision therapy is likely to increase in the coming years.

Assessment of Response to Lithium Maintenance Treatment in Bipolar Disorder: A Consortium on Lithium Genetics (ConLiGen) Report

Manchia, Mirko; Adli, Mazda; Akula, Nirmala; Ardau, Raffaella; Aubry, Jean-Michel; Backlund, Lena; Banzato, Claudio EM.; Baune, Bernhard T.; Bellivier, Frank; Bengesser, Susanne; Biernacka, Joanna M.; Brichant-Petitjean, Clara; Bui, Elise; Calkin, Cynthia
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
EN_US
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36.15%
Objective: The assessment of response to lithium maintenance treatment in bipolar disorder (BD) is complicated by variable length of treatment, unpredictable clinical course, and often inconsistent compliance. Prospective and retrospective methods of assessment of lithium response have been proposed in the literature. In this study we report the key phenotypic measures of the “Retrospective Criteria of Long-Term Treatment Response in Research Subjects with Bipolar Disorder” scale currently used in the Consortium on Lithium Genetics (ConLiGen) study. Materials and Methods Twenty-nine ConLiGen sites took part in a two-stage case-vignette rating procedure to examine inter-rater agreement [Kappa (κ)] and reliability [intra-class correlation coefficient (ICC)] of lithium response. Annotated first-round vignettes and rating guidelines were circulated to expert research clinicians for training purposes between the two stages. Further, we analyzed the distributional properties of the treatment response scores available for 1,308 patients using mixture modeling. Results: Substantial and moderate agreement was shown across sites in the first and second sets of vignettes (κ = 0.66 and κ = 0.54, respectively), without significant improvement from training. However...

Is There a Role for Treating Inflammation in Moyamoya Disease?: A Review of Histopathology, Genetics, and Signaling Cascades

Young, Adam M. H.; Karri, Surya K.; Ogilvy, Christopher S.; Zhao, Ninghui
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
EN_US
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Moyamoya disease is a slowly progressing steno-occlusive condition affecting the cerebrovasculature. Affecting the terminal internal carotid arteries (ICA) and there branches, bilaterally, a resulting in a fine vascular network in the base of the brain to allow for compensation of the stenosed vessels. While there is obvious evidence of the involvement of inflammatory proteins in the condition, this has historically not been acknowledged as a causal factor. Here we describe the fundamental histopathology, genetics, and signaling cascades involved in moyamoya and debate whether these factors can be linked as causal factor for the condition or whether they are simply a secondary result of the ischemia described in the condition. A particular focus has been placed on the multitude of signaling cascades linked to the condition as these are viewed as having the greatest therapeutic potential. As such we hope to draw some novel insight into potential diagnostic and therapeutic inflammatory targets in the condition.

Effect of Genetic Variation in a Drosophila Model of Diabetes-Associated Misfolded Human Proinsulin

He, Bin Z.; Ludwig, Michael Z.; Dickerson, Desiree A.; Barse, Levi; Arun, Bharath; Vilhjálmsson, Bjarni J.; Jiang, Pengyao; Park, Soo-Young; Tamarina, Natalia A.; Selleck, Scott B.; Wittkopp, Patricia J.; Bell, Graeme I.; Kreitman, Martin
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
36.15%
The identification and validation of gene–gene interactions is a major challenge in human studies. Here, we explore an approach for studying epistasis in humans using a Drosophila melanogaster model of neonatal diabetes mellitus. Expression of the mutant preproinsulin (hINSC96Y) in the eye imaginal disc mimics the human disease: it activates conserved stress-response pathways and leads to cell death (reduction in eye area). Dominant-acting variants in wild-derived inbred lines from the Drosophila Genetics Reference Panel produce a continuous, highly heritable distribution of eye-degeneration phenotypes in a hINSC96Y background. A genome-wide association study (GWAS) in 154 sequenced lines identified a sharp peak on chromosome 3L, which mapped to a 400-bp linkage block within an intron of the gene sulfateless (sfl). RNAi knockdown of sfl enhanced the eye-degeneration phenotype in a mutant-hINS-dependent manner. RNAi against two additional genes in the heparan sulfate (HS) biosynthetic pathway (ttv and botv), in which sfl acts, also modified the eye phenotype in a hINSC96Y-dependent manner, strongly suggesting a novel link between HS-modified proteins and cellular responses to misfolded proteins. Finally, we evaluated allele-specific expression difference between the two major sfl-intronic haplotypes in heterozygtes. The results showed significant heterogeneity in marker-associated gene expression...

Landscape genetics of Phaedranassa herb. (Amaryllidaceae) in Ecuador

Oleas Gallo, Nora Helena
Fonte: FIU Digital Commons Publicador: FIU Digital Commons
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
36.15%
Speciation can be understood as a continuum occurring at different levels, from population to species. The recent molecular revolution in population genetics has opened a pathway towards understanding species evolution. At the same time, speciation patterns can be better explained by incorporating a geographic context, through the use of geographic information systems (GIS). Phaedranassa (Amaryllidaceae) is a genus restricted to one of the world’s most biodiverse hotspots, the Northern Andes. I studied seven Phaedranassa species from Ecuador. Six of these species are endemic to the country. The topographic complexity of the Andes, which creates local microhabitats ranging from moist slopes to dry valleys, might explain the patterns of Phaedranassa species differentiation. With a Bayesian individual assignment approach, I assessed the genetic structure of the genus throughout Ecuador using twelve microsatellite loci. I also used bioclimatic variables and species geographic coordinates under a Maximum Entropy algorithm to generate distribution models of the species. My results show that Phaedranassa species are genetically well-differentiated. Furthermore, with the exception of two species, all Phaedranassa showed non-overlapping distributions. Phaedranassa viridiflora and P. glauciflora were the only species in which the model predicted a broad species distribution...

Landscape Genetics of Phaedranassa Herb. (Amaryllidaceae) in Ecuador

Oleas, Nora
Fonte: FIU Digital Commons Publicador: FIU Digital Commons
Tipo: Artigo de Revista Científica Formato: application/pdf
Relevância na Pesquisa
36.15%
Speciation can be understood as a continuum occurring at different levels, from population to species. The recent molecular revolution in population genetics has opened a pathway towards understanding species evolution. At the same time, speciation patterns can be better explained by incorporating a geographic context, through the use of geographic information systems (GIS). Phaedranassa (Amaryllidaceae) is a genus restricted to one of the world’s most biodiverse hotspots, the Northern Andes. I studied seven Phaedranassa species from Ecuador. Six of these species are endemic to the country. The topographic complexity of the Andes, which creates local microhabitats ranging from moist slopes to dry valleys, might explain the patterns of Phaedranassa species differentiation. With a Bayesian individual assignment approach, I assessed the genetic structure of the genus throughout Ecuador using twelve microsatellite loci. I also used bioclimatic variables and species geographic coordinates under a Maximum Entropy algorithm to generate distribution models of the species. My results show that Phaedranassa species are genetically well-differentiated. Furthermore, with the exception of two species, all Phaedranassa showed non-overlapping distributions. Phaedranassa viridiflora and P. glauciflora were the only species in which the model predicted a broad species distribution...

Theoretical population genetics of spatially structured populations / Ian J. Lundy.

Lundy, Ian J.
Fonte: Universidade de Adelaide Publicador: Universidade de Adelaide
Tipo: Tese de Doutorado Formato: 248714 bytes; application/pdf
Publicado em //1997 EN
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36.15%
This thesis considers the question of fixation probabilities and mean absorption times for alleles when a population is divided into a number of subpopulations with asymmetric migration between the subpopulations. The emphasis of the thesis is on small populations and conservation genetics. Results have important implications for management of remnant subpopulations in order to maintain genetic diversity when migration between the remnant subpopulations is not symmetric.; Thesis (Ph.D.)--University of Adelaide, Dept. of Applied Mathematics, 1999?; Errata is pasted onto front end-paper.; Bibliography: leaves 166-171.; ix, 171 leaves : ill. ; 30 cm.; Title page, contents and abstract only. The complete thesis in print form is available from the University Library.

Mitochondrial genetics of yeast / by David F. Callen

Callen, David Frederick
Fonte: Adelaide, Publicador: Adelaide,
Tipo: Tese de Doutorado Formato: 365157 bytes; application/pdf
Publicado em //1975 EN
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Thesis (Ph.D.1976) from the Dept. of Genetics, University of Adelaide; v, 100 leaves : ill., graphs, tables ; 30 cm.; Title page, contents and abstract only. The complete thesis in print form is available from the University Library.

Genetics of pathogenicity in flax rust / by Gregory J. Lawrence

Lawrence, Gregory James
Fonte: Universidade de Adelaide Publicador: Universidade de Adelaide
Tipo: Tese de Doutorado Formato: 65779 bytes; application/pdf
Publicado em //1977 EN
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36.15%
Thesis (Ph.D.)--University of Adelaide, Dept. of Genetics, 1978; Typescript (photocopy); iv, 123 leaves, [3] leaves of plates : ill. (part col.) ; 30 cm.; Title page, contents and abstract only. The complete thesis in print form is available from the University Library.