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1

Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants  

ERIC Educational Resources Information Center

Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…

Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse

2014-01-01

2

Phenotypic Variation in Plants  

NSDL National Science Digital Library

This resource is a detailed manual of protocols and instructional information for carrying out an undergraduate laboratory exercise in ecology and evolutionary biolog. Students examine the causes of phenotypic variation in Brassica rapa. This exercise provides an excellent example of potential factors associated with the causes of phenotypic variation for lower division undergraduates, but could also be expanded upon to allow unique scientific inquiry in labs for upper-division undergrads. It includes student outlines, instructor's notes, and suggested questions for laboratory reports.

Lawrence Blumer (Morehouse College; )

1997-01-01

3

Beyond Punnett squares: Student word association and explanations of phenotypic variation through an integrative quantitative genetics unit investigating anthocyanin inheritance and expression in Brassica rapa Fast plants.  

PubMed

Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory course focused on the inheritance and expression of a quantitative trait in varying environments. We utilized Brassica rapa Fast Plants as a model organism to study variation in the phenotype anthocyanin pigment intensity. As an initial curriculum assessment, we used free word association to examine students' cognitive structures before and after the unit and explanations in students' final research posters with particular focus on variation (Pv = Gv + Ev). Comparison of pre- and postunit word frequency revealed a shift in words and a pattern of co-occurring concepts indicative of change in cognitive structure, with particular focus on "variation" as a proposed threshold concept and primary goal for students' explanations. Given review of 53 posters, we found ?50% of students capable of intermediate to high-level explanations combining both Gv and Ev influence on expression of anthocyanin intensity (Pv). While far from "plug and play," this conceptually rich, inquiry-based unit holds promise for effective integration of quantitative and Mendelian genetics. PMID:25185225

Batzli, Janet M; Smith, Amber R; Williams, Paul H; McGee, Seth A; Dósa, Katalin; Pfammatter, Jesse

2014-01-01

4

Interpreting phenotypic variation in plants  

NSDL National Science Digital Library

This article by Coleman, McConnaughay, and Ackerly discusses how phenotypic variation (variation in observable traits) in plants is influenced by environment, genetics, and developmental stage. The authors stress that understanding the interplay of these factors is important for investigations that involve plant comparisons.

5

Physiological Integration and Phenotypic Variation  

E-print Network

Physiological Integration and Phenotypic Variation in Vertebrates Seminar and Roundtable Guest Event Schedule 4:00 - 5:00 p.m. EID Seminar, Q & A Session Ecology Building Auditorium 2:00 - 3:00 p.m. EID Roundtable Discussion: Evolutionary Ecology Meets Immunology Paul D. Coverdell Center Auditorium

Arnold, Jonathan

6

Geographical variation in neonatal phenotype  

PubMed Central

Background Recent studies have shown associations between size and body proportions at birth and health outcomes throughout the life cycle, but there are few data on how neonatal phenotype varies in different populations around the world. Methods Data from the UK, Finland, India, Sri Lanka, China, DR Congo, Nigeria and Jamaica (N=22 067) were used to characterise geographical differences in phenotype in singleton, liveborn newborns. Measurements included birthweight, placental weight, length, head, chest, abdominal and arm circumferences and skinfolds. Results Neonates in Europe were the largest, followed by Jamaica, East Asia (China), then Africa and South Asia. Birthweight varied widely (mean values 2730g to 3570g), but in contrast, head circumference was similar in all except China (markedly smaller). The main difference in body proportions between populations was the head to length ratio, with small heads relative to length in China and large heads relative to length in South Asia and Africa. Conclusions These marked geographical differences in neonatal phenotype need to be considered when investigating determinants of fetal growth, and optimal phenotype for short-term and long-term outcomes. PMID:16929412

Leary, Sam; Fall, Caroline; Osmond, Clive; Lovel, Hermione; Campbell, Doris; Eriksson, Johan; Forrester, Terrence; Godfrey, Keith; Hill, Jacqui; Jie, Mi; Law, Catherine; Newby, Rachel; Robinson, Sian; Yajnik, Chittaranjan

2009-01-01

7

Quantitative trait loci for thermotolerance phenotypes in Drosophila melanogaster.  

PubMed

For insects, temperature is a major environmental variable that can influence an individual's behavioral activities and fitness. Drosophila melanogaster is a cosmopolitan species that has had great success in adapting to and colonizing diverse thermal niches. This adaptation and colonization has resulted in complex patterns of genetic variation in thermotolerance phenotypes in nature. Although extensive work has been conducted documenting patterns of genetic variation, substantially less is known about the genomic regions or genes that underlie this ecologically and evolutionarily important genetic variation. To begin to understand and identify the genes controlling thermotolerance phenotypes, we have used a mapping population of recombinant inbred (RI) lines to map quantitative trait loci (QTL) that affect variation in both heat- and cold-stress resistance. The mapping population was derived from a cross between two lines of D. melanogaster (Oregon-R and 2b) that were not selected for thermotolerance phenotypes, but exhibit significant genetic divergence for both phenotypes. Using a design in which each RI line was backcrossed to both parental lines, we mapped seven QTL affecting thermotolerance on the second and third chromosomes. Three of the QTL influence cold-stress resistance and four affect heat-stress resistance. Most of the QTL were trait or sex specific, suggesting that overlapping but generally unique genetic architectures underlie resistance to low- and high-temperature extremes. Each QTL explained between 5 and 14% of the genetic variance among lines, and degrees of dominance ranged from completely additive to partial dominance. Potential thermotolerance candidate loci contained within our QTL regions are identified and discussed. PMID:16404413

Morgan, T J; Mackay, T F C

2006-03-01

8

Quantitative phenotypic analysis of multistress response in Zygosaccharomyces rouxii complex.  

PubMed

Zygosaccharomyces rouxii complex comprises three yeasts clusters sourced from sugar- and salt-rich environments: haploid Zygosaccharomyces rouxii, diploid Zygosaccharomyces sapae and allodiploid/aneuploid strains of uncertain taxonomic affiliations. These yeasts have been characterized with respect to gene copy number variation, karyotype variability and change in ploidy, but functional diversity in stress responses has not been explored yet. Here, we quantitatively analysed the stress response variation in seven strains of the Z. rouxii complex by modelling growth variables via model and model-free fitting methods. Based on the spline fit as most reliable modelling method, we resolved different interstrain responses to 15 environmental perturbations. Compared with Z. rouxii CBS 732(T) and Z. sapae strains ABT301(T) and ABT601, allodiploid strain ATCC 42981 and aneuploid strains CBS 4837 and CBS 4838 displayed higher multistress resistance and better performance in glycerol respiration even in the presence of copper. ?-based logarithmic phenotypic index highlighted that ABT601 is a slow-growing strain insensitive to stress, whereas ABT301(T) grows fast on rich medium and is sensitive to suboptimal conditions. Overall, the differences in stress response could imply different adaptation mechanisms to sugar- and salt-rich niches. The obtained phenotypic profiling contributes to provide quantitative insights for elucidating the adaptive mechanisms to stress in halo- and osmo-tolerant Zygosaccharomyces yeasts. PMID:24533625

Solieri, Lisa; Dakal, Tikam C; Bicciato, Silvio

2014-06-01

9

Patterns of quantitative genetic variation in multiple dimensions Mark Kirkpatrick  

E-print Network

modify phenotypes? A naive reading of the quantita- tive genetics literature might leave onePatterns of quantitative genetic variation in multiple dimensions Mark Kirkpatrick Received: 14 is the extent to which genetic cor- relations limit the ability of populations to respond to selection. Here I

Pillow, Jonathan

10

Epigenetic variation in the Egfr gene generates quantitative variation in a complex trait in ants.  

PubMed

Complex quantitative traits, like size and behaviour, are a pervasive feature of natural populations. Quantitative trait variation is the product of both genetic and environmental factors, yet little is known about the mechanisms through which their interaction generates this variation. Epigenetic processes, such as DNA methylation, can mediate gene-by-environment interactions during development to generate discrete phenotypic variation. We therefore investigated the developmental role of DNA methylation in generating continuous size variation of workers in an ant colony, a key trait associated with division of labour. Here we show that, in the carpenter ant Camponotus floridanus, global (genome-wide) DNA methylation indirectly regulates quantitative methylation of the conserved cell-signalling gene Epidermal growth factor receptor to generate continuous size variation of workers. DNA methylation can therefore generate quantitative variation in a complex trait by quantitatively regulating the transcription of a gene. This mechanism, alongside genetic variation, may determine the phenotypic possibilities of loci for generating quantitative trait variation in natural populations. PMID:25758336

Alvarado, Sebastian; Rajakumar, Rajendhran; Abouheif, Ehab; Szyf, Moshe

2015-01-01

11

A protocol for high-throughput phenotyping, suitable for quantitative trait analysis in mice  

Microsoft Academic Search

Whole-genome genetic association studies in outbred mouse populations represent a novel approach to identifying the molecular\\u000a basis of naturally occurring genetic variants, the major source of quantitative variation between inbred strains of mice.\\u000a Measuring multiple phenotypes in parallel on each mouse would make the approach cost effective, but protocols for phenotyping\\u000a on a large enough scale have not been developed.

Leah C. Solberg; William Valdar; Dominique Gauguier; Graciela Nunez; Amy Taylor; Stephanie Burnett; Carmen Arboledas-Hita; Polinka Hernandez-Pliego; Stuart Davidson; Peter Burns; Shoumo Bhattacharya; Tertius Hough; Douglas Higgs; Paul Klenerman; William O. Cookson; Youming Zhang; Robert M. Deacon; J. Nicholas P. Rawlins; Richard Mott; Jonathan Flint

2006-01-01

12

Quantitative Analysis of Escherichia coli Metabolic Phenotypes within the Context of Phenotypic Phase Planes  

Microsoft Academic Search

In silico models of Escherichia coli metabolism have been developed to predict metabolic behavior and propose experimentally testable hypotheses. However, a thorough assessment of the metabolic phenotype requires well-designed experimentation and reproducible experimental techniques. A method for the quantitative analysis of E. coli metabolism in vivo within the framework of in silico phenotypic phase plane analysis is presented. Using this

R. U. Ibarra; P. Fu; B. O. Palsson; J. R. DiTonno; J. S. Edwards

2003-01-01

13

Epigenetic heredity: RNA-mediated modes of phenotypic variation.  

PubMed

In addition to the Mendelian mutations, several instances of heritable phenotypic variation have been reported. We have observed, in mice, a role for sperm RNAs in the induction of such stable phenotypic variation. When experimentally transferred by RNA microinjection into fertilized mouse eggs, the noncoding RNAs homologous in sequence to the target locus are efficient inducers of variation at the transcriptional level. Transmission of the phenotypic variation to progeny is highly efficient and independent of gender. Here, we have summarized these finding and how they relate to other reports of epigenetic variation. PMID:25726734

Rassoulzadegan, Minoo; Cuzin, François

2015-04-01

14

Quantitative trait loci for thermotolerance phenotypes in Drosophila melanogaster  

E-print Network

Quantitative trait loci for thermotolerance phenotypes in Drosophila melanogaster TJ Morgan1 influence an individual's behavioral activities and fitness. Drosophila melanogaster is a cosmopolitan was derived from a cross between two lines of D. melanogaster (Oregon-R and 2b) that were not selected

Mackay, Trudy F.C.

15

Quantitative phenotyping via deep barcode sequencing  

PubMed Central

Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or “Bar-seq,” outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that ?20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene–environment interactions on a genome-wide scale. PMID:19622793

Smith, Andrew M.; Heisler, Lawrence E.; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J.; Chee, Mark; Roth, Frederick P.; Giaever, Guri; Nislow, Corey

2009-01-01

16

Linking Post-Translational Modifications and Variation of Phenotypic Traits*  

PubMed Central

Enzymes can be post-translationally modified, leading to isoforms with different properties. The phenotypic consequences of the quantitative variability of isoforms have never been studied. We used quantitative proteomics to dissect the relationships between the abundances of the enzymes and isoforms of alcoholic fermentation, metabolic traits, and growth-related traits in Saccharomyces cerevisiae. Although the enzymatic pool allocated to the fermentation proteome was constant over the culture media and the strains considered, there was variation in abundance of individual enzymes and sometimes much more of their isoforms, which suggests the existence of selective constraints on total protein abundance and trade-offs between isoforms. Variations in abundance of some isoforms were significantly associated to metabolic traits and growth-related traits. In particular, cell size and maximum population size were highly correlated to the degree of N-terminal acetylation of the alcohol dehydrogenase. The fermentation proteome was found to be shaped by human selection, through the differential targeting of a few isoforms for each food-processing origin of strains. These results highlight the importance of post-translational modifications in the diversity of metabolic and life-history traits. PMID:23271801

Albertin, Warren; Marullo, Philippe; Bely, Marina; Aigle, Michel; Bourgais, Aurélie; Langella, Olivier; Balliau, Thierry; Chevret, Didier; Valot, Benoît; da Silva, Telma; Dillmann, Christine; de Vienne, Dominique; Sicard, Delphine

2013-01-01

17

Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae  

Microsoft Academic Search

Background: The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits. Results: We compared levels of gene expression among

Justin C. Fay; Heather L. McCullough; Paul D. Sniegowski; Michael B. Eisen

2004-01-01

18

Quantitative trait loci for thermotolerance phenotypes in Drosophila melanogaster  

Microsoft Academic Search

For insects, temperature is a major environmental variable that can influence an individual's behavioral activities and fitness. Drosophila melanogaster is a cosmopolitan species that has had great success in adapting to and colonizing diverse thermal niches. This adaptation and colonization has resulted in complex patterns of genetic variation in thermotolerance phenotypes in nature. Although extensive work has been conducted documenting

T J Morgan; T F C Mackay

2006-01-01

19

Mutation Models and Quantitative Genetic Variation  

Microsoft Academic Search

Analyses of evolution and maintenance of quantitative genetic variation depend on the mutation models assumed. Currently two polygenic mutation models have been used in theoretical analyses. One is the random walk mutation model and the other is the house-of-cards mutation model. Although in the short term the two models give similar results for the evolution of neutral genetic variation within

Zhao-Bang Zeng; C. Clark Cockerham

1993-01-01

20

The biology hidden inside residual within-individual phenotypic variation.  

PubMed

Phenotypes vary hierarchically among taxa and populations, among genotypes within populations, among individuals within genotypes, and also within individuals for repeatedly expressed, labile phenotypic traits. This hierarchy produces some fundamental challenges to clearly defining biological phenomena and constructing a consistent explanatory framework. We use a heuristic statistical model to explore two consequences of this hierarchy. First, although the variation existing among individuals within populations has long been of interest to evolutionary biologists, within-individual variation has been much less emphasized. Within-individual variance occurs when labile phenotypes (behaviour, physiology, and sometimes morphology) exhibit phenotypic plasticity or deviate from a norm-of-reaction within the same individual. A statistical partitioning of phenotypic variance leads us to explore an array of ideas about residual within-individual variation. We use this approach to draw attention to additional processes that may influence within-individual phenotypic variance, including interactions among environmental factors, ecological effects on the fitness consequences of plasticity, and various types of adaptive variance. Second, our framework for investigating variation in phenotypic variance reveals that interactions between levels of the hierarchy form the preconditions for the evolution of all types of plasticity, and we extend this idea to the residual level within individuals, where both adaptive plasticity in residuals and canalization-like processes (stability) can evolve. With the statistical tools now available to examine heterogeneous residual variance, an array of novel questions linking phenotype to environment can be usefully addressed. PMID:25080034

Westneat, David F; Wright, Jonathan; Dingemanse, Niels J

2014-07-30

21

Geographical Variation in Selection, from Phenotypes to Molecules  

E-print Network

sequence evolution within genomic regions that harbor QTLs. The QTLs influence a trait experiencing geographical variation in selection, which is common in nature and produces obvious differentiation at the phenotypic level. Counter to expectations...

Kelly, John K.

2006-04-01

22

Global Climate Change and Phenotypic Variation among Red Deer Cohorts  

Microsoft Academic Search

The variability of two fitness-related phenotypic traits (body weight and a mandibular skeletal ratio) was analysed among cohorts and age-classes of red deer in Norway. Phenotypic variation among cohorts was pronounced for calves, yearlings and reproductively mature adults. Fluctuations in cohort-specific mean body weights and skeletal ratios of adults correlated with global climatic variation in winter conditions influenced by the

Eric Post; Nils Chr. Stenseth; Rolf Langvatn; Jean-Marc Fromentin

1997-01-01

23

Hormones, life-history, and phenotypic variation: Opportunities in evolutionary avian endocrinology  

E-print Network

Review Hormones, life-history, and phenotypic variation: Opportunities in evolutionary avian 2011 Keywords: Phenotypic variation Breeding Clutch size Hormonal pleiotropy Hormonal conflict a b. We have only a rudimentary understanding of the physiological and hormonal basis of phenotypic

24

High Phenotypic and Molecular Variation in Downy Brome (Bromus tectorum)  

E-print Network

High Phenotypic and Molecular Variation in Downy Brome (Bromus tectorum) Rebecca H. Kao, Cynthia S. Brown, and Ruth A. Hufbauer* The invasive grass Bromus tectorum (cheatgrass, downy brome) has extensive, especially into new habitats. Nomenclature: Downy brome, Bromus tectorum L. BROTE. Key words: Broad

Hufbauer, Ruth A.

25

Mutation models and quantitative genetic variation.  

PubMed

Analyses of evolution and maintenance of quantitative genetic variation depend on the mutation models assumed. Currently two polygenic mutation models have been used in theoretical analyses. One is the random walk mutation model and the other is the house-of-cards mutation model. Although in the short term the two models give similar results for the evolution of neutral genetic variation within and between populations, the predictions of the changes of the variation are qualitatively different in the long term. In this paper a more general mutation model, called the regression mutation model, is proposed to bridge the gap of the two models. The model regards the regression coefficient, gamma, of the effect of an allele after mutation on the effect of the allele before mutation as a parameter. When gamma = 1 or 0, the model becomes the random walk model or the house-of-cards model, respectively. The additive genetic variances within and between populations are formulated for this mutation model, and some insights are gained by looking at the changes of the genetic variances as gamma changes. The effects of gamma on the statistical test of selection for quantitative characters during macroevolution are also discussed. The results suggest that the random walk mutation model should not be interpreted as a null hypothesis of neutrality for testing against alternative hypotheses of selection during macroevolution because it can potentially allocate too much variation for the change of population means under neutrality. PMID:8454212

Zeng, Z B; Cockerham, C C

1993-03-01

26

Phenotypic Variation in Infants, Not Adults, Reflects Genotypic Variation among Chimpanzees and Bonobos  

PubMed Central

Studies comparing phenotypic variation with neutral genetic variation in modern humans have shown that genetic drift is a main factor of evolutionary diversification among populations. The genetic population history of our closest living relatives, the chimpanzees and bonobos, is now equally well documented, but phenotypic variation among these taxa remains relatively unexplored, and phenotype-genotype correlations are not yet documented. Also, while the adult phenotype is typically used as a reference, it remains to be investigated how phenotype-genotye correlations change during development. Here we address these questions by analyzing phenotypic evolutionary and developmental diversification in the species and subspecies of the genus Pan. Our analyses focus on the morphology of the femoral diaphysis, which represents a functionally constrained element of the locomotor system. Results show that during infancy phenotypic distances between taxa are largely congruent with non-coding (neutral) genotypic distances. Later during ontogeny, however, phenotypic distances deviate from genotypic distances, mainly as an effect of heterochronic shifts between taxon-specific developmental programs. Early phenotypic differences between Pan taxa are thus likely brought about by genetic drift while late differences reflect taxon-specific adaptations. PMID:25013970

Morimoto, Naoki; Ponce de León, Marcia S.; Zollikofer, Christoph P. E.

2014-01-01

27

Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae  

Microsoft Academic Search

Background  The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood.\\u000a Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences\\u000a are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits.\\u000a \\u000a \\u000a \\u000a \\u000a Results  We compared levels of gene expression among nine natural

Justin C Fay; Heather L McCullough; Paul D Sniegowski; Michael B Eisen

2004-01-01

28

Phenotypical variation within 22 families with Pompe disease  

PubMed Central

Background Pompe disease has a broad clinical spectrum, in which the phenotype is partially explained by the genotype. The aim of this study was to describe phenotypical variation among siblings with non-classic Pompe disease. We hypothesized that siblings and families with the same genotype share more similar phenotypes than the total population of non-classic Pompe patients, and that this might reveal genotype-phenotype correlations. Methods We identified all Dutch families in which two or three siblings were diagnosed with Pompe disease and described genotype, acid ?-glucosidase activity, age at symptom onset, presenting symptoms, specific clinical features, mobility and ventilator dependency. Results We identified 22 families comprising two or three siblings. All carried the most common mutation c.-32-13 T?>?G in combination with another pathogenic mutation. The median age at symptom onset was 33 years (range 1–62 years). Within sibships symptom onset was either in childhood or in adulthood. The median variation in symptom onset between siblings was nine years (range 0–31 years). Presenting symptoms were similar across siblings in 14 out of 22 families. Limb girdle weakness was most frequently reported. In some families ptosis or bulbar weakness were present in all siblings. A large variation in disease severity (based on wheelchair/ventilator dependency) was observed in 11 families. This variation did not always result from a difference in duration of the disease since a third of the less affected siblings had a longer course of the disease. Enzyme activity could not explain this variation either. In most families male patients were more severely affected. Finally, symptom onset varied substantially in twelve families despite the same GAA genotype. Conclusion In most families with non-classic Pompe disease siblings share a similar phenotype regarding symptom onset, presenting symptoms and specific clinical features. However, in some families the course and severity of disease varied substantially. This phenotypical variation was also observed in families with identical GAA genotypes. The commonalities and differences indicate that besides genotype, other factors such as epigenetic and environmental effects influence the clinical presentation and disease course. PMID:24245577

2013-01-01

29

The genetic basis of quantitative variation: numbers of sensory bristles of Drosophila melanogaster as a model system  

Microsoft Academic Search

The numbers of sensory hairs of Drosophila melanogaster present an ideal model system to elucidate the genetic basis of morphological quantitative variation. Loci affecting bristle number can be identified and their properties studied by accumulating spontaneous mutations, by P element mutagenesis, by mapping factors causing divergence between selection lines and by the association of phenotypic variation with molecular variation at

Trudy F. C. Mackay

1995-01-01

30

Y genetic variation and phenotypic diversity in health and disease.  

PubMed

Sexually dimorphic traits arise through the combined effects of sex hormones and sex chromosomes on sex-biased gene expression, and experimental mouse models have been instrumental in determining their relative contribution in modulating sex differences. A role for the Y chromosome (ChrY) in mediating sex differences outside of development and reproduction has historically been overlooked due to its unusual genetic composition and the predominant testes-specific expression of ChrY-encoded genes. However, ample evidence now exists supporting ChrY as a mediator of other physiological traits in males, and genetic variation in ChrY has been linked to several diseases, including heart disease, cancer, and autoimmune diseases in experimental animal models, as well as humans. The genetic and molecular mechanisms by which ChrY modulates phenotypic variation in males remain unknown but may be a function of copy number variation between homologous X-Y multicopy genes driving differential gene expression. Here, we review the literature identifying an association between ChrY polymorphism and phenotypic variation and present the current evidence depicting the mammalian ChrY as a member of the regulatory genome in males and as a factor influencing paternal parent-of-origin effects in female offspring. PMID:25866616

Case, Laure K; Teuscher, Cory

2015-01-01

31

Genetic and phenotypic intra-species variation in Candida albicans.  

PubMed

Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number variations, chromosomal inversions, subtelomeric hypervariation, loss of heterozygosity (LOH), and whole or partial chromosome aneuploidies. All 21 strains were diploid, although karyotypic changes were present in eight of the 21 isolates, with multiple strains being trisomic for Chromosome 4 or Chromosome 7. Aneuploid strains exhibited a general fitness defect relative to euploid strains when grown under replete conditions. All strains were also heterozygous, yet multiple, distinct LOH tracts were present in each isolate. Higher overall levels of genome heterozygosity correlated with faster growth rates, consistent with increased overall fitness. Genes with the highest rates of amino acid substitutions included many cell wall proteins, implicating fast evolving changes in cell adhesion and host interactions. One clinical isolate, P94015, presented several striking properties including a novel cellular phenotype, an inability to filament, drug resistance, and decreased virulence. Several of these properties were shown to be due to a homozygous nonsense mutation in the EFG1 gene. Furthermore, loss of EFG1 function resulted in increased fitness of P94015 in a commensal model of infection. Our analysis therefore reveals intra-species genetic and phenotypic differences in C. albicans and delineates a natural mutation that alters the balance between commensalism and pathogenicity. PMID:25504520

Hirakawa, Matthew P; Martinez, Diego A; Sakthikumar, Sharadha; Anderson, Matthew Z; Berlin, Aaron; Gujja, Sharvari; Zeng, Qiandong; Zisson, Ethan; Wang, Joshua M; Greenberg, Joshua M; Berman, Judith; Bennett, Richard J; Cuomo, Christina A

2015-03-01

32

The Evolution of Human Genetic and Phenotypic Variation in Africa  

PubMed Central

Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations. PMID:20178763

Campbell, Michael C.

2010-01-01

33

The genetic basis of quantitative variation: numbers of sensory bristles of Drosophila melanogaster as a model system.  

PubMed

The numbers of sensory hairs of Drosophila melanogaster present an ideal model system to elucidate the genetic basis of morphological quantitative variation. Loci affecting bristle number can be identified and their properties studied by accumulating spontaneous mutations, by P element mutagenesis, by mapping factors causing divergence between selection lines and by the association of phenotype variation with molecular variation at candidate neurogenic loci. The consensus emerging from the application of all approaches is that much of the mutational and segregating variation affecting bristle number is attributable to alleles with large phenotype effects at a small number of candidate loci. PMID:8533161

Mackay, T F

1995-12-01

34

The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population  

PubMed Central

Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ?200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance. PMID:22027895

Hung, H-Y; Browne, C; Guill, K; Coles, N; Eller, M; Garcia, A; Lepak, N; Melia-Hancock, S; Oropeza-Rosas, M; Salvo, S; Upadyayula, N; Buckler, E S; Flint-Garcia, S; McMullen, M D; Rocheford, T R; Holland, J B

2012-01-01

35

Quantitative X-ray microradiography for high-throughput phenotyping of osteoarthritis in mice  

PubMed Central

Summary Objective To investigate and validate digital X-ray microradiography as a novel, high-throughput and cost-effective screening approach to identify abnormal joint phenotypes in mice. Method Digital X-ray microradiography was used to quantify the subchondral bone mineral content (BMC) in the medial tibial plateau. Accuracy and reproducibility of the method were determined in 22 samples from C57BL/6(B6Brd;B6Dnk;B6N-Tyrc-Brd) wild-type mice. The method was then validated in wild-type mice that had undergone surgical destabilisation of medial meniscus (DMM) and in a genetically modified mouse strain with an established increase in trabecular bone mass. Results The measurement of subchondral BMC by digital X-ray microradiography had a coefficient of variation of 3.6%. Digital X-ray microradiography was able to demonstrate significantly increased subchondral BMC in the medial tibial plateau of male mice 4 and 8 weeks after DMM surgery and in female mice 8 weeks after surgery. Furthermore, digital X-ray microradiography also detected the increase in subchondral BMC in a genetically modified mouse strain with high trabecular bone mass. Conclusion Quantitation of subchondral BMC by digital X-ray microradiography is a rapid, sensitive and cost-effective method to identify abnormal joint phenotypes in mice of both genders at several ages. PMID:24792211

Waung, J.A.; Maynard, S.A.; Gopal, S.; Gogakos, A.; Logan, J.G.; Williams, G.R.; Bassett, J.H.D.

2014-01-01

36

Intraspecific phenotypic variation among alewife populations drives parallel phenotypic shifts in bluegill.  

PubMed

Evolutionary diversification within consumer species may generate selection on local ecological communities, affecting prey community structure. However, the extent to which this niche construction can propagate across food webs and shape trait variation in competing species is unknown. Here, we tested whether niche construction by different life-history variants of the planktivorous fish alewife (Alosa pseudoharengus) can drive phenotypic divergence and resource use in the competing species bluegill (Lepomis macrochirus). Using a combination of common garden experiments and a comparative field study, we found that bluegill from landlocked alewife lakes grew relatively better when fed small than large zooplankton, had gill rakers better adapted for feeding on small-bodied prey and selected smaller zooplankton compared with bluegill from lakes with anadromous or no alewife. Observed shifts in bluegill foraging traits in lakes with landlocked alewife parallel those in alewife, suggesting interspecific competition leading to parallel phenotypic changes rather than to divergence (which is commonly predicted). Our findings suggest that species may be locally adapted to prey communities structured by different life-history variants of a competing dominant species. PMID:24920478

Huss, Magnus; Howeth, Jennifer G; Osterman, Julia I; Post, David M

2014-07-22

37

Population Structure in Daphnia Obtusa: Quantitative Genetic and Allozymic Variation  

PubMed Central

Quantitative genetic analyses for body size and for life history characters within and among populations of Daphnia obtusa reveal substantial genetic variance at both hierarchical levels for all traits measured. Simultaneous allozymic analysis on the same population samples indicate a moderate degree of differentiation: G(ST) = 0.28. No associations between electrophoretic genotype and phenotypic characters were found, providing support for the null hypothesis that the allozymic variants are effectively neutral. Therefore, G(ST) can be used as the null hypothesis that neutral phenotypic evolution within populations led to the observed differentiation for the quantitative traits, which I call Q(ST). The results of this study provide evidence that natural selection has promoted diversification for body size among populations, and has impeded diversification for relative fitness. Analyses of population differentiation for clutch size, age at reproduction, and growth rate indicate that neutral phenotypic evolution cannot be excluded as the cause. PMID:8244001

Spitze, K.

1993-01-01

38

Disentangling the Phylogenetic and Ecological Components of Spider Phenotypic Variation  

PubMed Central

An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure. PMID:24651264

Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

2014-01-01

39

Individual variation in growth trajectories: phenotypic and genetic correlations in ontogeny of the house nch  

E-print Network

Individual variation in growth trajectories: phenotypic and genetic correlations in ontogeny of developmental variation and covariation often change during ontogeny (e.g. Zelditch & Carmichael, 1989; Cowley found variable patterns of allometric relationships during ontogeny, and documented relatively weak

Badyaev, Alex

40

Epigenetic Basis of Morphological Variation and Phenotypic Plasticity in Arabidopsis thaliana.  

PubMed

Epigenetics is receiving growing attention in the plant science community. Epigenetic modifications are thought to play a particularly important role in fluctuating environments. It is hypothesized that epigenetics contributes to plant phenotypic plasticity because epigenetic modifications, in contrast to DNA sequence variation, are more likely to be reversible. The population of decrease in DNA methylation 1-2 (ddm1-2)-derived epigenetic recombinant inbred lines (epiRILs) in Arabidopsis thaliana is well suited for studying this hypothesis, as DNA methylation differences are maximized and DNA sequence variation is minimized. Here, we report on the extensive heritable epigenetic variation in plant growth and morphology in neutral and saline conditions detected among the epiRILs. Plant performance, in terms of branching and leaf area, was both reduced and enhanced by different quantitative trait loci (QTLs) in the ddm1-2 inherited epigenotypes. The variation in plasticity associated significantly with certain genomic regions in which the ddm1-2 inherited epigenotypes caused an increased sensitivity to environmental changes, probably due to impaired genetic regulation in the epiRILs. Many of the QTLs for morphology and plasticity overlapped, suggesting major pleiotropic effects. These findings indicate that epigenetics contributes substantially to variation in plant growth, morphology, and plasticity, especially under stress conditions. PMID:25670769

Kooke, Rik; Johannes, Frank; Wardenaar, René; Becker, Frank; Etcheverry, Mathilde; Colot, Vincent; Vreugdenhil, Dick; Keurentjes, Joost J B

2015-02-01

41

Phenotypic variation of erythrocyte linker histone H1.c in a pheasant (Phasianus colchicus L.) population.  

PubMed

Our goal was to characterize a phenotypic variation of the pheasant erythrocyte linker histone subtype H1.c. By using two-dimensional polyacrylamide gel electrophoresis three histone H1.c phenotypes were identified. The differently migrating allelic variants H1.c1 and H1.c2 formed either two homozygous phenotypes, c1 and c2, or a single heterozygous phenotype, c1c2. In the pheasant population screened, birds with phenotype c2 were the most common (frequency 0.761) while individuals with phenotype c1 were rare (frequency 0.043). PMID:21637419

Kowalski, Andrzej; Pa Yga, Jan; Górnicka-Michalska, Ewa; Bernacki, Zenon; Adamski, Marek

2010-07-01

42

Quantitative phenotypic and pathway profiling guides rational drug combination strategies  

PubMed Central

Advances in target-based drug discovery strategies have enabled drug discovery groups in academia and industry to become very effective at generating molecules that are potent and selective against single targets. However, it has become apparent from disappointing results in recent clinical trials that a major challenge to the development of successful targeted therapies for treating complex multifactorial diseases is overcoming heterogeneity in target mechanism among patients and inherent or acquired drug resistance. Consequently, reductionist target directed drug-discovery approaches are not appropriately tailored toward identifying and optimizing multi-targeted therapeutics or rational drug combinations for complex disease. In this article, we describe the application of emerging high-content phenotypic profiling and analysis tools to support robust evaluation of drug combination performance following dose-ratio matrix screening. We further describe how the incorporation of high-throughput reverse phase protein microarrays with phenotypic screening can provide rational drug combination hypotheses but also confirm the mechanism-of-action of novel drug combinations, to facilitate future preclinical and clinical development strategies. PMID:24904421

Dawson, John C.; Carragher, Neil O.

2014-01-01

43

Quantitative Variation, Selection and Inheritance with Fast Plants  

NSDL National Science Digital Library

This article describes how Fast Plants can be used to help students understand how, through genetic selection associated with phenotypic variation, traits are passed on to future generations. This resource includes information about how to analyze variation in a population and selectively breed to change the frequency of a particular trait in future generations. Advanced Placement teachers who are teaching AP Inquiry Investigation #1, Artificial Selection, will find this article relevant to that inquiry.

The Wisconsin Fast Plants Program

44

Determination of thiopurine S -methyltransferase phenotype using thin-layer chromatography and quantitative scanning  

Microsoft Academic Search

Objective: To develop a non-high-performance liquid chromatography method for the determination of thiopurine-S-methyltransferase (TPMT) phenotype using thin-layer chromatography and quantitative scanning. Methods: TPMT reaction was performed using a radiochemical assay. The reaction product [14C]-6-methylmercaptopurine was separated using thin-layer chromatography and quantified by means of radioactive scanning. Day-to-day variance was determined to validate results. Results: Determination of TPMT phenotype using thin-layer

Marc Dauer; Johannes Schulze; Florian Loher; Stefan Endres; Andreas Eigler

2002-01-01

45

High throughput quantitative phenotyping of plant resistance using chlorophyll fluorescence image analysis  

PubMed Central

Background In order to select for quantitative plant resistance to pathogens, high throughput approaches that can precisely quantify disease severity are needed. Automation and use of calibrated image analysis should provide more accurate, objective and faster analyses than visual assessments. In contrast to conventional visible imaging, chlorophyll fluorescence imaging is not sensitive to environmental light variations and provides single-channel images prone to a segmentation analysis by simple thresholding approaches. Among the various parameters used in chlorophyll fluorescence imaging, the maximum quantum yield of photosystem II photochemistry (Fv/Fm) is well adapted to phenotyping disease severity. Fv/Fm is an indicator of plant stress that displays a robust contrast between infected and healthy tissues. In the present paper, we aimed at the segmentation of Fv/Fm images to quantify disease severity. Results Based on the Fv/Fm values of each pixel of the image, a thresholding approach was developed to delimit diseased areas. A first step consisted in setting up thresholds to reproduce visual observations by trained raters of symptoms caused by Xanthomonas fuscans subsp. fuscans (Xff) CFBP4834-R on Phaseolus vulgaris cv. Flavert. In order to develop a thresholding approach valuable on any cultivars or species, a second step was based on modeling pixel-wise Fv/Fm-distributions as mixtures of Gaussian distributions. Such a modeling may discriminate various stages of the symptom development but over-weights artifacts that can occur on mock-inoculated samples. Therefore, we developed a thresholding approach based on the probability of misclassification of a healthy pixel. Then, a clustering step is performed on the diseased areas to discriminate between various stages of alteration of plant tissues. Notably, the use of chlorophyll fluorescence imaging could detect pre-symptomatic area. The interest of this image analysis procedure for assessing the levels of quantitative resistance is illustrated with the quantitation of disease severity on five commercial varieties of bean inoculated with Xff CFBP4834-R. Conclusions In this paper, we describe an image analysis procedure for quantifying the leaf area impacted by the pathogen. In a perspective of high throughput phenotyping, the procedure was automated with the software R downloadable at http://www.r-project.org/. The R script is available at http://lisa.univ-angers.fr/PHENOTIC/telechargements.html. PMID:23758798

2013-01-01

46

Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis.  

PubMed

A comprehensive and large-scale metabolome quantitative trait loci (mQTL) analysis was performed to investigate the genetic backgrounds associated with metabolic phenotypes in rice grains. The metabolome dataset consisted of 759?metabolite signals obtained from the grains of 85 lines of rice (Oryza sativa, Sasanishiki?×?Habataki back-crossed inbred lines). Metabolome analysis was performed using four mass spectrometry pipelines to enhance detection of different classes of metabolites. This mQTL analysis of a wide range of metabolites highlighted an uneven distribution of 802 mQTLs on the rice genome, as well as different modes of metabolic trait (m-trait) control among various types of metabolites. The levels of most metabolites within rice grains were highly sensitive to environmental factors, but only weakly associated with mQTLs. Coordinated control was observed for several groups of metabolites, such as amino acids linked to the mQTL hotspot on chromosome?3. For flavonoids, m-trait variation among the experimental lines was tightly governed by genetic factors that alter the glycosylation of flavones. Many loci affecting levels of metabolites were detected by QTL analysis, and plausible gene candidates were evaluated by in silico analysis. Several mQTLs profoundly influenced metabolite levels, providing insight into the control of rice metabolism. The genomic region and genes potentially responsible for the biosynthesis of apigenin-6,8-di-C-?-l-arabinoside are presented as an example of a critical mQTL identified by the analysis. PMID:22229385

Matsuda, Fumio; Okazaki, Yozo; Oikawa, Akira; Kusano, Miyako; Nakabayashi, Ryo; Kikuchi, Jun; Yonemaru, Jun-Ichi; Ebana, Kaworu; Yano, Masahiro; Saito, Kazuki

2012-05-01

47

From phenotypic to molecular polymorphisms involved in naturally occurring variation of plant development.  

PubMed

An enormous amount of naturally occurring genetic variation affecting development is found within wild and domesticated plant species. This diversity is presumably involved in plant adaptation to different natural environments or in human preferences. In addition, such intraspecific variation provides the basis for the evolution of plant development at larger evolutionary scales. Natural phenotypic differences are now amenable to genetic dissection up to the identification of causal DNA polymorphisms. Here we describe 30 genes and their functional nucleotide polymorphisms currently found as underlying allelic variation accounting for plant intraspecific developmental diversity. These studies provide molecular and cellular mechanisms that determine natural variation for quantitative and qualitative traits such as: fruit and seed morphology, colour and composition; flowering time; seedling emergence; plant architecture and inflorescence or flower morphology. Besides, analyses of flowering time variation within several distant species allow molecular comparisons between species, which are detecting homologous genes with partly different functions and unrelated genes with analogous functions. Thus, considerable gene function differences are being revealed also among species. Inspection of a catalogue of intraspecific nucleotide functional polymorphisms shows that transcriptional regulators are the main class of genes involved. Furthermore, barely more than half of the polymorphisms described are located in coding regions and affect protein structure, while the rest are regulatory changes altering gene expression. These limited analyses of intraspecific developmental variation support Doebley and Lukens's proposition (1998) that modifications in cis -regulatory regions of transcriptional regulators represent a predominant mode for the evolution of novel forms, but await more detailed studies in wild plant species. PMID:16096977

Alonso-Blanco, Carlos; Mendez-Vigo, Belén; Koornneef, Maarten

2005-01-01

48

Customized molecular phenotyping by quantitative gene expression and pattern recognition analysis  

Microsoft Academic Search

Description of the molecular phenotypes of pathobiological processes in vivo is a pressing need in genomic biology. We have implemented a high-throughput real-time PCR strategy to establish quantitative expression profiles of a customized set of target genes. It enables rapid, reproducible data acquisition from limited quantities of RNA, permitting serial sampling of mouse blood during disease progression. We developed an

Shreeram Akilesh; Daniel J. Shaffer; Derry Roopenian

2003-01-01

49

Genic and nongenic contributions to natural variation of quantitative traits in maize.  

PubMed

The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene-targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%-59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions. PMID:22701078

Li, Xianran; Zhu, Chengsong; Yeh, Cheng-Ting; Wu, Wei; Takacs, Elizabeth M; Petsch, Katherine A; Tian, Feng; Bai, Guihua; Buckler, Edward S; Muehlbauer, Gary J; Timmermans, Marja C P; Scanlon, Michael J; Schnable, Patrick S; Yu, Jianming

2012-12-01

50

Genic and nongenic contributions to natural variation of quantitative traits in maize  

PubMed Central

The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene–targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%–59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions. PMID:22701078

Li, Xianran; Zhu, Chengsong; Yeh, Cheng-Ting; Wu, Wei; Takacs, Elizabeth M.; Petsch, Katherine A.; Tian, Feng; Bai, Guihua; Buckler, Edward S.; Muehlbauer, Gary J.; Timmermans, Marja C.P.; Scanlon, Michael J.; Schnable, Patrick S.; Yu, Jianming

2012-01-01

51

Resource variation and the evolution of phenotypic plasticity in fishes  

E-print Network

Resource variation and species interactions require organisms to respond behaviorally, physiologically, and morphologically within and among generations to compensate for spatial and temporal environmental variation. One successful evolutionary...

Ruehl, Clifton Benjamin

2004-09-30

52

Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using  

E-print Network

Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Abstract The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds

Paris-Sud XI, Université de

53

From Genotype to Phenotype: Systems Biology Meets Natural Variation  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. The promise that came with genome sequencing was that we would soon know what genes do. We now have the full genomic sequence of human, chimpanzee, mouse, chicken, dog, worm, fly, rice, and cress, as well as those for a wide variety of other species, and yet we still have a lot of trouble figuring out what genes do. Mapping genes to their function is called the "genotype-to-phenotype problem," where phenotype is whatever is changed in the organism when a gene's function is altered.

Philip N. Benfey (Duke University; Department of Biology; Institute for Genome Sciences and Policyâ??Center for Systems Biology)

2008-04-25

54

Revue bibliographique : Variations quantitatives et mtabolisme des lipides  

E-print Network

pregnancy and lactation. These profiles are discussed in relation to litter size, food intake and dietRevue bibliographique : Variations quantitatives et métabolisme des lipides dans les tissus adipeux :body composition and lipid metabolism in adipose tissues and liver during pregnancy and lactation. 2

Paris-Sud XI, Université de

55

Revue bibliographique : Variations quantitatives et mtabolisme des lipides  

E-print Network

to litter size, food intake and diet composition ; the interactions between mechanismsRevue bibliographique : Variations quantitatives et métabolisme des lipides dans les tissus adipeux de la Lactation, 1. N. R.A. Theix 63122 Ceyrat, France. Summary. Literature survey : lipid metabolism

Boyer, Edmond

56

Phenotypic Variation and FMRP Levels in Fragile X  

ERIC Educational Resources Information Center

Data on the relationships between cognitive and physical phenotypes, and a deficit of fragile X mental retardation 1 (FMR1) gene-specific protein product, FMRP, are presented and discussed in context with earlier findings. The previously unpublished results obtained, using standard procedures of regression and correlations, showed highly…

Loesch, Danuta Z.; Huggins, Richard M.; Hagerman, Randi J.

2004-01-01

57

Decoupled phenotypic variation between floral and vegetative traits: distinguishing between developmental and environmental correlations  

PubMed Central

Background and Aims In species with specialized pollination, floral traits are expected to be relatively invariant and decoupled from the phenotypic variation affecting vegetative traits. However, inferring the degree of decoupling between morphological characters from patterns of phenotypic correlations is difficult because phenotypic correlations result from the superimposition of several sources of covariance. In this study it is hypothesized that, in some cases, negative environmental correlations generated by non-congruent reaction norms across traits overshadow positive developmental correlations and generate a decoupling of the phenotypic variation between vegetative and floral traits. Methods To test this hypothesis, Campanula rotundifolia were grown from two distinct populations under two temperature treatments, and patterns of correlation were analysed between leaf size and flower size within and among treatments. Key Results Flower size was less sensitive to temperature variation than leaf size. Furthermore, flower size and leaf size showed temperature-induced reaction norms in opposite directions. Flower size decreased with an increasing temperature, while leaf size increased. Consequently, among treatments, correlations between leaf size and flower size were negative or absent, while, within treatments, these correlations were positive or absent in the cold and warm environments, respectively. Conclusions These results confirm that the decoupling of the phenotypic variation between vegetative and floral traits can be dependent on the environment. They also underline the importance of distinguishing sources of phenotypic covariance when testing hypotheses about phenotypic integration. PMID:23471008

Pélabon, Christophe; Osler, Nora C.; Diekmann, Martin; Graae, Bente J.

2013-01-01

58

Conflicting selection from an antagonist and a mutualist enhances phenotypic variation in a plant.  

PubMed

The raw material for evolution is variation. Consequently, identifying the factors that generate, maintain, and erode phenotypic and genetic variation in ecologically important traits within and among populations is important. Although persistent directional or stabilizing selection can deplete variation, spatial variation in conflicting directional selection can enhance variation. Here, we present evidence that phenotypic variation in limber pine (Pinus flexilis) cone structure is enhanced by conflicting selection pressures exerted by its mutualistic seed disperser (Clark's nutcracker Nucifraga columbiana) and an antagonistic seed predator (pine squirrel Tamiasciurus spp.). Phenotypic variation in cone structure was bimodal and about two times greater where both agents of selection co-occurred than where one (the seed predator) was absent. Within the region where both agents of selection co-occurred, bimodality in cone structure was pronounced where there appears to be a mosaic of habitats with some persistent habitats supporting only the seed disperser. These results indicate that conflicting selection stemming from spatial variation in community diversity can enhance phenotypic variation in ecologically important traits. PMID:19817846

Siepielski, Adam M; Benkman, Craig W

2010-04-01

59

Stochastic developmental variation, an epigenetic source of phenotypic diversity with far-reaching biological consequences.  

PubMed

This article reviews the production of different phenotypes from the same genotype in the same environment by stochastic cellular events, nonlinear mechanisms during patterning and morphogenesis, and probabilistic self-reinforcing circuitries in the adult life. These aspects of phenotypic variation are summarized under the term 'stochastic developmental variation' (SDV) in the following. In the past, SDV has been viewed primarily as a nuisance, impairing laboratory experiments, pharmaceutical testing, and true-to-type breeding. This article also emphasizes the positive biological effects of SDV and discusses implications for genotype-to-phenotype mapping, biological individuation, ecology, evolution, and applied biology. There is strong evidence from experiments with genetically identical organisms performed in narrowly standardized laboratory set-ups that SDV is a source of phenotypic variation in its own right aside from genetic variation and environmental variation. It is obviouslymediated bymolecular and higher-order epigeneticmechanisms. Comparison of SDV in animals, plants, fungi, protists, bacteria, archaeans, and viruses suggests that it is a ubiquitous and phylogenetically old phenomenon. In animals, it is usually smallest for morphometric traits and highest for life history traits and behaviour. SDV is thought to contribute to phenotypic diversity in all populations but is particularly relevant for asexually reproducing and genetically impoverished populations, where it generates individuality despite genetic uniformity. In each generation, SDV produces a range of phenotypes around a well-adapted target phenotype, which is interpreted as a bet-hedging strategy to cope with the unpredictability of dynamic environments. At least some manifestations of SDV are heritable, adaptable, selectable, and evolvable, and therefore, SDV may be seen as a hitherto overlooked evolution factor. SDV is also relevant for husbandry, agriculture, and medicine because most pathogens are asexuals that exploit this third source of phenotypic variation tomodify infectivity and resistance to antibiotics. Since SDV affects all types of organisms and almost all aspects of life, it urgently requires more intense research and a better integration into biological thinking. PMID:25740150

Vogt, Gunter

2015-03-01

60

Individual phenotypic variation reduces interaction strengths in a consumer–resource system  

PubMed Central

Natural populations often show variation in traits that can affect the strength of interspecific interactions. Interaction strengths in turn influence the fate of pairwise interacting populations and the stability of food webs. Understanding the mechanisms relating individual phenotypic variation to interaction strengths is thus central to assess how trait variation affects population and community dynamics. We incorporated nonheritable variation in attack rates and handling times into a classical consumer–resource model to investigate how variation may alter interaction strengths, population dynamics, species persistence, and invasiveness. We found that individual variation influences species persistence through its effect on interaction strengths. In many scenarios, interaction strengths decrease with variation, which in turn affects species coexistence and stability. Because environmental change alters the direction and strength of selection acting upon phenotypic traits, our results have implications for species coexistence in a context of habitat fragmentation, climate change, and the arrival of exotic species to native ecosystems. PMID:25478159

Gibert, Jean P; Brassil, Chad E

2014-01-01

61

Gene Expression in Transformed Lymphocytes Reveals Variation in Endomembrane and HLA Pathways Modifying Cystic Fibrosis Pulmonary Phenotypes.  

PubMed

Variation in cystic fibrosis (CF) phenotypes, including lung disease severity, age of onset of persistent Pseudomonas aeruginosa (P. aeruginosa) lung infection, and presence of meconium ileus (MI), has been partially explained by genome-wide association studies (GWASs). It is not expected that GWASs alone are sufficiently powered to uncover all heritable traits associated with CF phenotypic diversity. Therefore, we utilized gene expression association from lymphoblastoid cells lines from 754 p.Phe508del CF-affected homozygous individuals to identify genes and pathways. LPAR6, a G protein coupled receptor, associated with lung disease severity (false discovery rate q value = 0.0006). Additional pathway analyses, utilizing a stringent permutation-based approach, identified unique signals for all three phenotypes. Pathways associated with lung disease severity were annotated in three broad categories: (1) endomembrane function, containing p.Phe508del processing genes, providing evidence of the importance of p.Phe508del processing to explain lung phenotype variation; (2) HLA class I genes, extending previous GWAS findings in the HLA region; and (3) endoplasmic reticulum stress response genes. Expression pathways associated with lung disease were concordant for some endosome and HLA pathways, with pathways identified using GWAS associations from 1,978 CF-affected individuals. Pathways associated with age of onset of persistent P. aeruginosa infection were enriched for HLA class II genes, and those associated with MI were related to oxidative phosphorylation. Formal testing demonstrated that genes showing differential expression associated with lung disease severity were enriched for heritable genetic variation and expression quantitative traits. Gene expression provided a powerful tool to identify unrecognized heritable variation, complementing ongoing GWASs in this rare disease. PMID:25640674

O'Neal, Wanda K; Gallins, Paul; Pace, Rhonda G; Dang, Hong; Wolf, Whitney E; Jones, Lisa C; Guo, XueLiang; Zhou, Yi-Hui; Madar, Vered; Huang, Jinyan; Liang, Liming; Moffatt, Miriam F; Cutting, Garry R; Drumm, Mitchell L; Rommens, Johanna M; Strug, Lisa J; Sun, Wei; Stonebraker, Jaclyn R; Wright, Fred A; Knowles, Michael R

2015-02-01

62

Tissue Culture-Induced Heritable Genomic Variation in Rice, and Their Phenotypic Implications  

PubMed Central

Background Somaclonal variation generally occurs in plants regenerated from tissue culture. However, fundamental issues regarding molecular characteristics, mutation rates and mutation spectra of plant somatic variation as well as their phenotypic relevance have been addressed only recently. Moreover, these studies have reported highly discrepant results in different plant species and even in the same plant genotype. Methodology/principal findings We investigated heritable genomic variation induced by tissue culture in rice by whole genome re-sequencing of an extensively selfed somaclonal line (TC-reg-2008) and its wild type (WT) donor (cv. Hitomebore). We computed the overall mutation rate, single nucleotide polymorphisms (SNPs), small scale insertions/deletions (Indels) and mobilization of transposable elements (TEs). We assessed chromosomal distribution of the various types of genomic variations, tested correlations between SNPs and Indels, and examined concomitancy between TE activity and its cytosine methylation states. We also performed gene ontology (GO) analysis of genes containing nonsynonymous mutations and large-effect mutations, and assayed effects of the genomic variations on phenotypes under both normal growing condition and several abiotic stresses. We found that heritable somaclonal genomic variation occurred extensively in rice. The genomic variations distributed non-randomly across each of the 12 rice chromosomes, and affected a large number of functional genes. The phenotypic penetrance of the genomic variations was condition-dependent. Conclusions/significance Tissue culture is a potent means to generate heritable genetic variations in rice, which bear distinct difference at least in space (chromosomal distribution) from those occurred under natural settings. Our findings have provided new information regarding the mutation rate and spectrum as well as chromosomal distribution pattern of somaclonal variation in rice. Our data also suggest that rice possesses a strong capacity to canalize genetic variations under normal growing conditions to maintain phenotypic robustness, which however can be released by certain abiotic stresses to generate variable phenotypes. PMID:24804838

Gao, Yang; Liu, Ying; Wu, Ying; Bai, Yan; Zhang, Zhibin; Lin, Xiuyun; Dong, Yuzhu; Ou, Xiufang; Xu, Chunming; Liu, Bao

2014-01-01

63

Detection of differential gene flow from patterns of quantitative variation.  

PubMed

A major goal in anthropological genetics is the assessment of the effects of different microevolutionary forces. Harpending and Ward (1982) developed a model that aids in this effort by comparing observed and expected heterozygosity within populations in a local region. The expected heterozygosity within a population is a function of the total heterozygosity of the entire region and the distance of the population from the regional mean centroid of allele frequencies. Greater than average gene flow from an external source will result in a population having greater heterozygosity than expected. Less than average gene flow from an external source will result in a population having less heterozygosity than expected. We extend the Harpending-Ward model to quantitative traits using an equal and additive effects model of inheritance. Here the additive genetic variance within a population is directly proportional to heterozygosity, and its expectation is directly proportional to the genetic distance from the centroid. Under certain assumptions the expectations for phenotypic variances are similar. Observed and expected genetic or phenotypic variance can then be compared to assess the effects of differential external gene flow. When the additive genetic covariance matrix or heritabilities are not known, the phenotypic covariance matrix can be used to provide a conservative application of the model. In addition, we develop new methods for estimation of the genetic relationship matrix (R) from quantitative traits. We apply these models to two data sets: (1) six principal components derived from twenty dermatoglyphic ridge count measures for nine villages in Nepal and (2) ten anthropometric measurements for seven isolated populations in western Ireland. In both cases both the univariate and multivariate analyses provide results that can be directly interpreted in terms of historically known patterns of gene flow. PMID:2323770

Relethford, J H; Blangero, J

1990-02-01

64

Rapid Plant Invasion in Distinct Climates Involves Different Sources of Phenotypic Variation  

PubMed Central

When exotic species spread over novel environments, their phenotype will depend on a combination of different processes, including phenotypic plasticity (PP), local adaptation (LA), environmental maternal effects (EME) and genetic drift (GD). Few attempts have been made to simultaneously address the importance of those processes in plant invasion. The present study uses the well-documented invasion history of Senecio inaequidens (Asteraceae) in southern France, where it was introduced at a single wool-processing site. It gradually invaded the Mediterranean coast and the Pyrenean Mountains, which have noticeably different climates. We used seeds from Pyrenean and Mediterranean populations, as well as populations from the first introduction area, to explore the phenotypic variation related to climatic variation. A reciprocal sowing experiment was performed with gardens under Mediterranean and Pyrenean climates. We analyzed climatic phenotypic variation in germination, growth, reproduction, leaf physiology and survival. Genetic structure in the studied invasion area was characterized using AFLP. We found consistent genetic differentiation in growth traits but no home-site advantage, so weak support for LA to climate. In contrast, genetic differentiation showed a relationship with colonization history. PP in response to climate was observed for most traits, and it played an important role in leaf trait variation. EME mediated by seed mass influenced all but leaf traits in a Pyrenean climate. Heavier, earlier-germinating seeds produced larger individuals that produced more flower heads throughout the growing season. However, in the Mediterranean garden, seed mass only influenced the germination rate. The results show that phenotypic variation in response to climate depends on various ecological and evolutionary processes associated with geographical zone and life history traits. Seeing the relative importance of EME and GD, we argue that a “local adaptation vs. phenotypic plasticity” approach is therefore not sufficient to fully understand what shapes phenotypic variation and genetic architecture of invasive populations. PMID:23383251

Monty, Arnaud; Bizoux, Jean-Philippe; Escarré, José; Mahy, Grégory

2013-01-01

65

Impact of Temporal Variation on Design and Analysis of Mouse Knockout Phenotyping Studies  

PubMed Central

A significant challenge facing high-throughput phenotyping of in-vivo knockout mice is ensuring phenotype calls are robust and reliable. Central to this problem is selecting an appropriate statistical analysis that models both the experimental design (the workflow and the way control mice are selected for comparison with knockout animals) and the sources of variation. Recently we proposed a mixed model suitable for small batch-oriented studies, where controls are not phenotyped concurrently with mutants. Here we evaluate this method both for its sensitivity to detect phenotypic effects and to control false positives, across a range of workflows used at mouse phenotyping centers. We found the sensitivity and control of false positives depend on the workflow. We show that the phenotypes in control mice fluctuate unexpectedly between batches and this can cause the false positive rate of phenotype calls to be inflated when only a small number of batches are tested, when the effect of knockout becomes confounded with temporal fluctuations in control mice. This effect was observed in both behavioural and physiological assays. Based on this analysis, we recommend two approaches (workflow and accompanying control strategy) and associated analyses, which would be robust, for use in high-throughput phenotyping pipelines. Our results show the importance in modelling all sources of variability in high-throughput phenotyping studies. PMID:25343444

Karp, Natasha A.; Speak, Anneliese O.; White, Jacqueline K.; Adams, David J.; Hrabé de Angelis, Martin; Hérault, Yann; Mott, Richard F.

2014-01-01

66

Mechanisms for phenotypic variation in Lesch–Nyhan disease and its variants  

PubMed Central

Lesch–Nyhan disease is a neurogenetic disorder caused by mutation of the HPRT1 gene on the X chromosome. There is significant variation in the clinical phenotype, with more than 300 different known mutations. There are few studies that have addressed whether similar mutations result in similar phenotypes across different patients because hypoxanthine–guanine phosphoribosyltransferase (HGprt) deficiency is rare, and most mutations are unique or limited to individual families. However, recent studies have revealed multiple unrelated patients with similar mutations, providing an opportunity to examine genotype–phenotype correlations. We found significant variation among the clinical features of 10 patients from 8 unrelated families all carrying a mutation replacing guanine with adenine at base position 143 (c.143G>A) in the HPRT1 gene. This mutation results in replacement of arginine by histidine at amino acid position 48 (p.arg48his) in the HGprt enzyme. Biochemically, the enzyme exhibits reduced thermal integrity, a mechanism that may explain clinical variation. The literature reveals similar clinical variation among other patients with similar mutations, although the variation is relatively minor across the whole population of patients. Identifiable sources of clinical variation include known limitations of clinical ascertainment and mechanisms that affect residual enzyme activity and stability. These results are helpful for understanding genotype–phenotype correlations and discordance and likely are applicable to other neurogenetic disorders where similar variation occurs. PMID:20981450

Sampat, Radhika; Fu, Rong; Larovere, Laura E.; Torres, Rosa J.; Ceballos-Picot, Irene; Fischbach, Michel; de Kremer, Raquel; Schretlen, David J.; Puig, Juan Garcia

2011-01-01

67

Phenotypic variation of transitional forager-farmers in the Sonoran Desert.  

PubMed

This study examines phenotypic variation and biological distances estimated using morphological traits from three Early Agricultural period (EAP) (2100 BC-AD 50) site-complexes in the Sonoran Desert of southern Arizona and northern Sonora. The hypothesis tested is that EAP forager-farmers were phenotypically homogenous as suggested by patterns in material culture and works to refine inferences regarding gene flow and biological affinity during subsistence transitions. Seven measurements from 62 EAP male and female crania were collected and used to calculate phenotypic variances, biological distances, and FST values with RMET 5.0 software. Analyses were applied to both pooled site-complex samples and to males and females separately. Results show differential variation between site-complex population samples, multiple significant biological distances, and significant FST values for the EAP regional sample that indicate widespread phenotypic heterogeneity rather than homogeneity. Significantly lower than expected variance in the Cienega Creek male sample is inferred to suggest a small closely related population present during the Cienega phase. Greater than expected male variation is attributed to higher frequencies of gene flow in the La Playa and Santa Cruz River site-complex samples. These EAP males are inferred to be more mobile across the Sonoran Desert landscape and representative of multiple biological affinities compared with females. This study provides evidence supporting the canalization of phenotypic variation when associated with human populations becoming increasingly sedentary due to transitioning subsistence practices. PMID:25229162

Byrd, Rachael M

2014-12-01

68

Optimizing experimental procedures for quantitative evaluation of crop plant performance in high throughput phenotyping systems  

PubMed Central

Detailed and standardized protocols for plant cultivation in environmentally controlled conditions are an essential prerequisite to conduct reproducible experiments with precisely defined treatments. Setting up appropriate and well defined experimental procedures is thus crucial for the generation of solid evidence and indispensable for successful plant research. Non-invasive and high throughput (HT) phenotyping technologies offer the opportunity to monitor and quantify performance dynamics of several hundreds of plants at a time. Compared to small scale plant cultivations, HT systems have much higher demands, from a conceptual and a logistic point of view, on experimental design, as well as the actual plant cultivation conditions, and the image analysis and statistical methods for data evaluation. Furthermore, cultivation conditions need to be designed that elicit plant performance characteristics corresponding to those under natural conditions. This manuscript describes critical steps in the optimization of procedures for HT plant phenotyping systems. Starting with the model plant Arabidopsis, HT-compatible methods were tested, and optimized with regard to growth substrate, soil coverage, watering regime, experimental design (considering environmental inhomogeneities) in automated plant cultivation and imaging systems. As revealed by metabolite profiling, plant movement did not affect the plants' physiological status. Based on these results, procedures for maize HT cultivation and monitoring were established. Variation of maize vegetative growth in the HT phenotyping system did match well with that observed in the field. The presented results outline important issues to be considered in the design of HT phenotyping experiments for model and crop plants. It thereby provides guidelines for the setup of HT experimental procedures, which are required for the generation of reliable and reproducible data of phenotypic variation for a broad range of applications. PMID:25653655

Junker, Astrid; Muraya, Moses M.; Weigelt-Fischer, Kathleen; Arana-Ceballos, Fernando; Klukas, Christian; Melchinger, Albrecht E.; Meyer, Rhonda C.; Riewe, David; Altmann, Thomas

2015-01-01

69

Relevance of phenotypic variation in risk assessment: The scientific viewpoint  

SciTech Connect

A number of examples are presented indicating the types of variation that may be expected in the responses of the human population to deleterious agents of an endogeneous or exogenous nature. If one assumes that the variations in repair in the normal population are reflected in large variations in carcinogenic risk per unit of exposure, then the dose-response curves at low doses cannot be extrapolated from high doeses without knowing the distribution of sensitivities among humans. The probability of determining this range by ecpidemiological studies on a random population by small. On the other hand, the probability of determining the range by careful genetic and molecular studies appears high enough so that such experiments now are being carried out. They cannot be carried out on real populations, using chronic exposures. Hence, the ability to estimate dose-response relations in the low dose region on human populations can only be by making theoretical constructs that, in turn, are dependent on fundamental research. 12 refs., 2 tabs.

Setlow, R.B.

1986-01-01

70

Sources of Variation in Quantitative Computed Tomography of the Lung  

PubMed Central

Summary The goal of quantitative analysis of computed tomography (CT) scans is to understand the anatomic structure that is responsible for the physiological function of the lung. While the gold standard for structural analysis requires the examination of tissue this is not practical in most studies. Quantitative CT allows a method to obtain valuable information on lung structure without having to remove tissue from the body thereby allowing longitudinal studies of chronic lung diseases. This review briefly discusses CT analysis of the lung and some of the sources of variation that can cause differences in the CT metrics used for analysis of lung disease. While there are many sources of variation the purpose of this review will show that if the study is properly designed to take into account these variations and the CT scanner is properly calibrated valuable information can be obtained from CT scans that should allow us to study the pathogenesis of lung disease and the effect of treatment. PMID:23934141

Coxson, Harvey O

2013-01-01

71

Localised intraspecific variation in the swimming phenotype of a coral reef fish across different wave exposures.  

PubMed

Wave-driven water flow is a major force structuring marine communities. Species distributions are partly determined by the ability to cope with variation in water flow, such as differences in the assemblage of fish species found in a given water flow environment being linked to swimming ability (based on fin shape and mode of locomotion). It remains unclear, however, whether similar assembly rules apply within a species. Here we show phenotypic variation among sites in traits functionally linked to swimming ability in the damselfish Acanthochromis polyacanthus. These sites differ in wave energy and the observed patterns of phenotypic differences within A. polyacanthus closely mirrored those seen at the interspecific level. Fish from high-exposure sites had more tapered fins and higher maximum metabolic rates than conspecifics from sheltered sites. This translates to a 36% larger aerobic scope and 33% faster critical swimming speed for fish from exposed sites. Our results suggest that functional relationships among swimming phenotypes and water flow not only structure species assemblages, but can also shape patterns of phenotypic divergence within species. Close links between locomotor phenotype and local water flow conditions appear to be important for species distributions as well as phenotypic divergence across environmental gradients. PMID:24132502

Binning, Sandra A; Roche, Dominique G; Fulton, Christopher J

2014-03-01

72

Molecular and quantitative trait variation within and among small fragmented populations of the endangered plant species Psilopeganum sinense  

PubMed Central

Background and Aims Natural selection and genetic drift are important evolutionary forces in determining genetic and phenotypic differentiation in plant populations. The extent to which these two distinct evolutionary forces affect locally adaptive quantitative traits has been well studied in common plant and animal species. However, we know less about how quantitative traits respond to selection pressures and drift in endangered species that have small population sizes and fragmented distributions. To address this question, this study assessed the relative strengths of selection and genetic drift in shaping population differentiation of phenotypic traits in Psilopeganum sinense, a naturally rare and recently endangered plant species. Methods Population differentiation at five quantitative traits (QST) obtained from a common garden experiment was compared with differentiation at putatively neutral microsatellite markers (FST) in seven populations of P. sinense. QST estimates were derived using a Bayesian hierarchical variance component method. Key Results Trait-specific QST values were equal to or lower than FST. Neutral genetic diversity was not correlated with quantitative genetic variation within the populations of P. sinense. Conclusions Despite the prevalent empirical evidence for QST > FST, the results instead suggest a definitive role of stabilizing selection and drift leading to phenotypic differentiation among small populations. Three traits exhibited a significantly lower QST relative to FST, suggesting that populations of P. sinense might have experienced stabilizing selection for the same optimal phenotypes despite large geographical distances between populations and habitat fragmentation. For the other two traits, QST estimates were of the same magnitude as FST, indicating that divergence in these traits could have been achieved by genetic drift alone. The lack of correlation between molecular marker and quantitative genetic variation suggests that sophisticated considerations are required for the inference of conservation measures of P. sinense from neutral genetic markers. PMID:24265350

Ye, Qigang; Tang, Feiyan; Wei, Na; Yao, Xiaohong

2014-01-01

73

Exploiting induced variation to dissect quantitative traits in barley.  

PubMed

The identification of genes underlying complex quantitative traits such as grain yield by means of conventional genetic analysis (positional cloning) requires the development of several large mapping populations. However, it is possible that phenotypically related, but more extreme, allelic variants generated by mutational studies could provide a means for more efficient cloning of QTLs (quantitative trait loci). In barley (Hordeum vulgare), with the development of high-throughput genome analysis tools, efficient genome-wide identification of genetic loci harbouring mutant alleles has recently become possible. Genotypic data from NILs (near-isogenic lines) that carry induced or natural variants of genes that control aspects of plant development can be compared with the location of QTLs to potentially identify candidate genes for development--related traits such as grain yield. As yield itself can be divided into a number of allometric component traits such as tillers per plant, kernels per spike and kernel size, mutant alleles that both affect these traits and are located within the confidence intervals for major yield QTLs may represent extreme variants of the underlying genes. In addition, the development of detailed comparative genomic models based on the alignment of a high-density barley gene map with the rice and sorghum physical maps, has enabled an informed prioritization of 'known function' genes as candidates for both QTLs and induced mutant genes. PMID:20298243

Druka, Arnis; Franckowiak, Jerome; Lundqvist, Udda; Bonar, Nicola; Alexander, Jill; Guzy-Wrobelska, Justyna; Ramsay, Luke; Druka, Ilze; Grant, Iain; Macaulay, Malcolm; Vendramin, Vera; Shahinnia, Fahimeh; Radovic, Slobodanka; Houston, Kelly; Harrap, David; Cardle, Linda; Marshall, David; Morgante, Michele; Stein, Nils; Waugh, Robbie

2010-04-01

74

Phenotypic plasticity in response to fine-grained environmental variation in predation  

Microsoft Academic Search

Summary 1. In nature, organisms experience environmental variability at coarse-grained (inter-generational) and fine-grained (intra-generational) scales and a common response to environmental variation is phenotypic plasticity. The emphasis of most empirical work on plasticity has been on examining coarse-grained variation with the goal of understanding the costs and benefits of plastic responses in response to a particular environment. 2. In this

Nancy M. Schoeppner; Rick A. Relyea

2009-01-01

75

GenotypePhenotypeMapping and Neutral Variation ---A case study in Genetic  

E-print Network

Introduction Historically, there is a long dispute among evolutionary biologists as to the main engineGenotype­Phenotype­Mapping and Neutral Variation --- A case study in Genetic Programming Wolfgang are therefore frequent and play an important role in maintaining genetic diversity. As a specific example, we

Fernandez, Thomas

76

Genomic Plasticity Enables Phenotypic Variation of Pseudomonas syringae pv. tomato DC3000  

E-print Network

Genomic Plasticity Enables Phenotypic Variation of Pseudomonas syringae pv. tomato DC3000 Zhongmeng of a genomic anomaly in the region of 4.7 to 4.9 Mb of the Pseudomonas syringae pv. tomato (Pst) DC3000 genome pathogenic growth in host tomato plants. These types of chromosomal structures are predicted to be unstable

Myers, Chris

77

Temporal Variation in Phenotypic and Genotypic Traits in Two Sockeye Salmon Populations, Tustumena Lake, Alaska  

Microsoft Academic Search

Sockeye salmon Oncorhynchus nerka in two tributary streams (about 20 km apart) of the same lake were compared for temporal variation in phenotypic (length, depth adjusted for length) and genotypic (six microsatellite loci) traits. Peak run time (July 16 versus 11 August) and run duration (43 versus 26 d) differed between streams. Populations were sampled twice, including an overlapping point

Carol Ann Woody; Jeff Olsen; Joel Reynolds; Paul Bentzen

2000-01-01

78

Estimation Of The Proportion Of Variation Accounted For By DNA Tests. II: Phenotypic Variance  

Technology Transfer Automated Retrieval System (TEKTRAN)

The proportion of phenotypic variation accounted for (Rp2) is an important characteristic of a DNA test. Therefore, several estimators of this quantity were evaluated by simulation of 500 replicates of a population of 1000 progeny of 100 sires (3 levels of narrow sense heritability and 4 levels of ...

79

Phenotypic variation in the mating preferences of female field crickets, Gryllus integer  

Microsoft Academic Search

Phenotypic variation in the mating preferences of female field crickets was examined. Males of this species produce a trilled calling song which varies in the number of pulses per trill, the inter-trill interval and the proportion of missing pulses within a trill. As a population, females preferred male calling songs with more pulses per trill and shorter inter-trill intervals in

ANNE-MARIE MURRAY; WILLIAM H. CADE

1995-01-01

80

Natural Variation in MAM Within and Between Populations of Arabidopsis lyrata Determines Glucosinolate Phenotype  

Microsoft Academic Search

The genetic variation that underlies the glucosinolate phenotype of Arabidopsis lyrata ssp. petraea was investigated between and within populations. A candidate glucosinolate biosynthetic locus (MAM, con- taining methylthioalkylmalate synthase genes) was mapped in A. lyrata to a location on linkage group 6 corresponding to the homologous location for MAM in A. thaliana .I nA. thaliana MAM is responsible for side

Andrew J. Heidel; Maria J. Clauss; Juergen Kroymann; Outi Savolainen; Thomas Mitchell-Olds

2006-01-01

81

Integrating environmental variation, predation pressure, phenotypic plasticity and locomotor performance.  

PubMed

The Wujiang River, a tributary of the Three Gorges Reservoir, has many dams along its length. These dams alter the river's natural habitat and produce various flow regimes and degrees of predator stress. To test whether the swimming performance and external body shape of pale chub (Zacco platypus) have changed as a result of alterations in the flow regime and predator conditions, we measured the steady (U(crit)) and unsteady (fast-start) swimming performances and morphological characteristics of fish collected from different sites along the Wujiang River. We also calculated the maximum respiratory capacity and cost of transport (COT). We demonstrated significant differences in swimming performance and morphological traits among the sampling sites. Steady swimming performance was positively correlated with water velocity and negatively correlated with the abundance of predators, whereas unsteady swimming performance was negatively correlated with water velocity. The body shape was significantly correlated with both swimming performance and ecological parameters. These findings suggested that selection pressure on swimming performance results in a higher U(crit) and a more streamlined body shape in fast-flow and (or) in habitats with low predator stress and subsequently results in a lower COT. These characteristics were accompanied by a poorer fast-start performance than that of the fish from the slow-flow and (or) high-predator habitats. The divergence in U(crit) may also be due in part to variation in respiratory capacity. PMID:23463244

Fu, Shi-Jian; Cao, Zhen-Dong; Yan, Guan-Jie; Fu, Cheng; Pang, Xu

2013-10-01

82

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness.  

PubMed

The relationship between genotype mutations and phenotype variations determines health in the short term and evolution over the long term, and it hinges on the action of mutations on fitness. A fundamental difficulty in determining this action, however, is that it depends on the unique context of each mutation, which is complex and often cryptic. As a result, the effect of most genome variations on molecular function and overall fitness remains unknown and stands apart from population genetics theories linking fitness effect to polymorphism frequency. Here, we hypothesize that evolution is a continuous and differentiable physical process coupling genotype to phenotype. This leads to a formal equation for the action of coding mutations on fitness that can be interpreted as a product of the evolutionary importance of the mutated site with the difference in amino acid similarity. Approximations for these terms are readily computable from phylogenetic sequence analysis, and we show mutational, clinical, and population genetic evidence that this action equation predicts the effect of point mutations in vivo and in vitro in diverse proteins, correlates disease-causing gene mutations with morbidity, and determines the frequency of human coding polymorphisms, respectively. Thus, elementary calculus and phylogenetics can be integrated into a perturbation analysis of the evolutionary relationship between genotype and phenotype that quantitatively links point mutations to function and fitness and that opens a new analytic framework for equations of biology. In practice, this work explicitly bridges molecular evolution with population genetics with applications from protein redesign to the clinical assessment of human genetic variations. PMID:25217195

Katsonis, Panagiotis; Lichtarge, Olivier

2014-12-01

83

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness  

PubMed Central

The relationship between genotype mutations and phenotype variations determines health in the short term and evolution over the long term, and it hinges on the action of mutations on fitness. A fundamental difficulty in determining this action, however, is that it depends on the unique context of each mutation, which is complex and often cryptic. As a result, the effect of most genome variations on molecular function and overall fitness remains unknown and stands apart from population genetics theories linking fitness effect to polymorphism frequency. Here, we hypothesize that evolution is a continuous and differentiable physical process coupling genotype to phenotype. This leads to a formal equation for the action of coding mutations on fitness that can be interpreted as a product of the evolutionary importance of the mutated site with the difference in amino acid similarity. Approximations for these terms are readily computable from phylogenetic sequence analysis, and we show mutational, clinical, and population genetic evidence that this action equation predicts the effect of point mutations in vivo and in vitro in diverse proteins, correlates disease-causing gene mutations with morbidity, and determines the frequency of human coding polymorphisms, respectively. Thus, elementary calculus and phylogenetics can be integrated into a perturbation analysis of the evolutionary relationship between genotype and phenotype that quantitatively links point mutations to function and fitness and that opens a new analytic framework for equations of biology. In practice, this work explicitly bridges molecular evolution with population genetics with applications from protein redesign to the clinical assessment of human genetic variations. PMID:25217195

Katsonis, Panagiotis

2014-01-01

84

Exploration of methods to identify polymorphisms associated with variation in DNA repair capacity phenotypes  

SciTech Connect

Elucidating the relationship between polymorphic sequences and risk of common disease is a challenge. For example, although it is clear that variation in DNA repair genes is associated with familial cancer, aging and neurological disease, progress toward identifying polymorphisms associated with elevated risk of sporadic disease has been slow. This is partly due to the complexity of the genetic variation, the existence of large numbers of mostly low frequency variants and the contribution of many genes to variation in susceptibility. There has been limited development of methods to find associations between genotypes having many polymorphisms and pathway function or health outcome. We have explored several statistical methods for identifying polymorphisms associated with variation in DNA repair phenotypes. The model system used was 80 cell lines that had been resequenced to identify variation; 191 single nucleotide substitution polymorphisms (SNPs) are included, of which 172 are in 31 base excision repair pathway genes, 19 in 5 anti-oxidation genes, and DNA repair phenotypes based on single strand breaks measured by the alkaline Comet assay. Univariate analyses were of limited value in identifying SNPs associated with phenotype variation. Of the multivariable model selection methods tested: the easiest that provided reduced error of prediction of phenotype was simple counting of the variant alleles predicted to encode proteins with reduced activity, which led to a genotype including 52 SNPs; the best and most parsimonious model was achieved using a two-step analysis without regard to potential functional relevance: first SNPs were ranked by importance determined by Random Forests Regression (RFR), followed by cross-validation in a second round of RFR modeling that included ever more SNPs in declining order of importance. With this approach 6 SNPs were found to minimize prediction error. The results should encourage research into utilization of multivariate analytical methods for epidemiological studies of the association of genetic variation in complex genotypes with risk of common diseases.

Jones, I M; Thomas, C B; Xi, T; Mohrenweiser, H W; Nelson, D O

2006-07-03

85

Environmental Heterogeneity and Phenotypic Divergence: Can Heritable Epigenetic Variation Aid Speciation?  

PubMed Central

The dualism of genetic predisposition and environmental influences, their interactions, and respective roles in shaping the phenotype have been a hot topic in biological sciences for more than two centuries. Heritable epigenetic variation mediates between relatively slowly accumulating mutations in the DNA sequence and ephemeral adaptive responses to stress, thereby providing mechanisms for achieving stable, but potentially rapidly evolving phenotypic diversity as a response to environmental stimuli. This suggests that heritable epigenetic signals can play an important role in evolutionary processes, but so far this hypothesis has not been rigorously tested. A promising new area of research focuses on the interaction between the different molecular levels that produce phenotypic variation in wild, closely-related taxa that lack genome-wide genetic differentiation. By pinpointing specific adaptive traits and investigating the mechanisms responsible for phenotypic differentiation, such study systems could allow profound insights into the role of epigenetics in the evolution and stabilization of phenotypic discontinuities, and could add to our understanding of adaptive strategies to diverse environmental conditions and their dynamics. PMID:22567398

Flatscher, Ruth; Frajman, Božo; Schönswetter, Peter; Paun, Ovidiu

2012-01-01

86

Symbiont-mediated phenotypic variation without co-evolution in an insect-fungus association.  

PubMed

Recent studies have shown that symbionts can be a source of adaptive phenotypic variation for their hosts. It is assumed that co-evolution between hosts and symbionts underlies these ecologically significant phenotypic traits. We tested this assumption in the ectosymbiotic fungal associate of the gall midge Asteromyia carbonifera. Phylogenetic analysis placed the fungal symbiont within a monophyletic clade formed by Botryosphaeria dothidea, a typically free-living (i.e. not associated with an insect host) plant pathogen. Symbiont isolates from four divergent midge lineages demonstrated none of the patterns common to heritable microbial symbioses, including parallel diversification with their hosts, substitution rate acceleration, or A+T nucleotide bias. Amplified fragment length polymorphism genotyping of the symbiont revealed that within-lineage genetic diversity was not clustered along host population lines. Culture-based experiments demonstrated that the symbiont-mediated variation in gall phenotype is not borne out in the absence of the midge. This study shows that symbionts can be important players in phenotypic variation for their hosts, even in the absence of a co-evolutionary association. PMID:20840311

Janson, E M; Peeden, E R; Stireman, J O; Abbot, P

2010-10-01

87

[The floral meristem undetermination mutation in Papaver somniferum L.: spontaneous phenotypic variation in ontogeny].  

PubMed

A new morphogenetic mutation of the shoot, floral meristem undetermination, was found in Papaver somniferum L. with monocarpic shoot. The expression of the DFM (determination of floral meristem) gene, which limits the proliferative activity of stem cells in the floral meristem, was affected. The mutation displayed spontaneous phenotypic instability in ontogeny, variation in the mutant character expression on different flowers of the same plant in the same genotypic environment. The mutation phenotype varied from no expression or formation of individual phyllomes in the center of the primary ovary to formation of a new flower and a new capsule with viable seeds. PMID:18669291

Beliaeva, R G

2008-01-01

88

Intraspecific phenotypic variation in a fish predator affects multitrophic lake metacommunity structure  

PubMed Central

Contemporary insights from evolutionary ecology suggest that population divergence in ecologically important traits within predators can generate diversifying ecological selection on local community structure. Many studies acknowledging these effects of intraspecific variation assume that local populations are situated in communities that are unconnected to similar communities within a shared region. Recent work from metacommunity ecology suggests that species dispersal among communities can also influence species diversity and composition but can depend upon the relative importance of the local environment. Here, we study the relative effects of intraspecific phenotypic variation in a fish predator and spatial processes related to plankton species dispersal on multitrophic lake plankton metacommunity structure. Intraspecific diversification in foraging traits and residence time of the planktivorous fish alewife (Alosa pseudoharengus) among coastal lakes yields lake metacommunities supporting three lake types which differ in the phenotype and incidence of alewife: lakes with anadromous, landlocked, or no alewives. In coastal lakes, plankton community composition was attributed to dispersal versus local environmental predictors, including intraspecific variation in alewives. Local and beta diversity of zooplankton and phytoplankton was additionally measured in response to intraspecific variation in alewives. Zooplankton communities were structured by species sorting, with a strong influence of intraspecific variation in A. pseudoharengus. Intraspecific variation altered zooplankton species richness and beta diversity, where lake communities with landlocked alewives exhibited intermediate richness between lakes with anadromous alewives and without alewives, and greater community similarity. Phytoplankton diversity, in contrast, was highest in lakes with landlocked alewives. The results indicate that plankton dispersal in the region supplied a migrant pool that was strongly structured by intraspecific variation in alewives. This is one of the first studies to demonstrate that intraspecific phenotypic variation in a predator can maintain contrasting patterns of multitrophic diversity in metacommunities. PMID:24455134

Howeth, Jennifer G; Weis, Jerome J; Brodersen, Jakob; Hatton, Elizabeth C; Post, David M

2013-01-01

89

Cone and Seed Trait Variation in Whitebark Pine (Pinus Albicaulis; Pinaceae) and the Potential for Phenotypic Selection  

Microsoft Academic Search

Phenotypic variation among, individuals is necessary for natural selection to operate and is therefore essential for adaptive evolution. However, extensive variation within individuals can mask variation among individuals and weaken the potential for selection. Here we quantify variation among within individuals in female cone and seed traits of whitebark pine (Pinus albicaulis). In many plants the production of numerous reproductive

R. Garcia; A. M. Siepielski; Craig Benkman

2009-01-01

90

Genetic variation in flowering time induces phenological assortative mating: quantitative genetic methods applied to Brassica rapa  

Microsoft Academic Search

It has been argued from first principles that plants mate assortatively by flowering time. However, there have been very few studies of phenological assortative mating, perhaps because current methods to infer paternal phenotype are difficult to apply to natural populations. Two methods are presented to estimate the phenotypic correlation between mates—the quantitative genetic metric for assortative mating—for phenological traits. The

ARTHUR E. WEIS; TANYA M. KOSSLER

2004-01-01

91

MSH1-Induced Non-Genetic Variation Provides a Source of Phenotypic Diversity in Sorghum bicolor  

PubMed Central

MutS Homolog 1 (MSH1) encodes a plant-specific protein that functions in mitochondria and chloroplasts. We showed previously that disruption or suppression of the MSH1 gene results in a process of developmental reprogramming that is heritable and non-genetic in subsequent generations. In Arabidopsis, this developmental reprogramming process is accompanied by striking changes in gene expression of organellar and stress response genes. This developmentally reprogrammed state, when used in crossing, results in a range of variation for plant growth potential. Here we investigate the implications of MSH1 modulation in a crop species. We found that MSH1-mediated phenotypic variation in Sorghum bicolor is heritable and potentially valuable for crop breeding. We observed phenotypic variation for grain yield, plant height, flowering time, panicle architecture, and above-ground biomass. Focusing on grain yield and plant height, we found some lines that appeared to respond to selection. Based on amenability of this system to implementation in a range of crops, and the scope of phenotypic variation that is derived, our results suggest that MSH1 suppression provides a novel approach for breeding in crops. PMID:25347794

Wang, Guomei; Nino-Liu, David O.; Kundariya, Hardik; Wamboldt, Yashitola; Dweikat, Ismail; Mackenzie, Sally A.

2014-01-01

92

Quantitative phenotyping of leaf margins in three dimensions, demonstrated on KNOTTED and TCP trangenics in Arabidopsis  

PubMed Central

The geometry of leaf margins is an important shape characteristic that distinguishes among different leaf phenotypes. Current definitions of leaf shape are qualitative and do not allow quantification of differences in shape between phenotypes. This is especially true for leaves with some non-trivial three-dimensional (3D) configurations. Here we present a novel geometrical method novel geometrical methods to define, measure, and quantify waviness and lobiness of leaves. The method is based on obtaining the curve of the leaf rim from a 3D surface measurement and decomposing its local curvature vector into the normal and geodesic components. We suggest that leaf waviness is associated with oscillating normal curvature along the margins, while lobiness is associated with oscillating geodesic curvature. We provide a way to integrate these local measures into global waviness and lobiness quantities. Using these novel definitions, we analysed the changes in leaf shape of two Arabidopsis genotypes, either as a function of gene mis-expression induction level or as a function of time. These definitions and experimental methods open the way for a more quantitative study of the shape of leaves and other growing slender organs. PMID:24706720

Sharon, Eran

2014-01-01

93

Quantitative phenotyping of leaf margins in three dimensions, demonstrated on KNOTTED and TCP trangenics in Arabidopsis.  

PubMed

The geometry of leaf margins is an important shape characteristic that distinguishes among different leaf phenotypes. Current definitions of leaf shape are qualitative and do not allow quantification of differences in shape between phenotypes. This is especially true for leaves with some non-trivial three-dimensional (3D) configurations. Here we present a novel geometrical method novel geometrical methods to define, measure, and quantify waviness and lobiness of leaves. The method is based on obtaining the curve of the leaf rim from a 3D surface measurement and decomposing its local curvature vector into the normal and geodesic components. We suggest that leaf waviness is associated with oscillating normal curvature along the margins, while lobiness is associated with oscillating geodesic curvature. We provide a way to integrate these local measures into global waviness and lobiness quantities. Using these novel definitions, we analysed the changes in leaf shape of two Arabidopsis genotypes, either as a function of gene mis-expression induction level or as a function of time. These definitions and experimental methods open the way for a more quantitative study of the shape of leaves and other growing slender organs. PMID:24706720

Armon, Shahaf; Yanai, Osnat; Ori, Naomi; Sharon, Eran

2014-05-01

94

Phenotypic Variation and Fitness in a Metapopulation of Tubeworms (Ridgeia piscesae Jones) at Hydrothermal Vents  

PubMed Central

We examine the nature of variation in a hot vent tubeworm, Ridgeia piscesae, to determine how phenotypes are maintained and how reproductive potential is dictated by habitat. This foundation species at northeast Pacific hydrothermal sites occupies a wide habitat range in a highly heterogeneous environment. Where fluids supply high levels of dissolved sulphide for symbionts, the worm grows rapidly in a “short-fat” phenotype characterized by lush gill plumes; when plumes are healthy, sperm package capture is higher. This form can mature within months and has a high fecundity with continuous gamete output and a lifespan of about three years in unstable conditions. Other phenotypes occupy low fluid flux habitats that are more stable and individuals grow very slowly; however, they have low reproductive readiness that is hampered further by small, predator cropped branchiae, thus reducing fertilization and metabolite uptake. Although only the largest worms were measured, only 17% of low flux worms were reproductively competent compared to 91% of high flux worms. A model of reproductive readiness illustrates that tube diameter is a good predictor of reproductive output and that few low flux worms reached critical reproductive size. We postulate that most of the propagules for the vent fields originate from the larger tubeworms that live in small, unstable habitat patches. The large expanses of worms in more stable low flux habitat sustain a small, but long-term, reproductive output. Phenotypic variation is an adaptation that fosters both morphological and physiological responses to differences in chemical milieu and predator pressure. This foundation species forms a metapopulation with variable growth characteristics in a heterogeneous environment where a strategy of phenotypic variation bestows an advantage over specialization. PMID:25337895

Tunnicliffe, Verena; St. Germain, Candice; Hilário, Ana

2014-01-01

95

Phenotypic variation and fitness in a metapopulation of tubeworms (Ridgeia piscesae Jones) at hydrothermal vents.  

PubMed

We examine the nature of variation in a hot vent tubeworm, Ridgeia piscesae, to determine how phenotypes are maintained and how reproductive potential is dictated by habitat. This foundation species at northeast Pacific hydrothermal sites occupies a wide habitat range in a highly heterogeneous environment. Where fluids supply high levels of dissolved sulphide for symbionts, the worm grows rapidly in a "short-fat" phenotype characterized by lush gill plumes; when plumes are healthy, sperm package capture is higher. This form can mature within months and has a high fecundity with continuous gamete output and a lifespan of about three years in unstable conditions. Other phenotypes occupy low fluid flux habitats that are more stable and individuals grow very slowly; however, they have low reproductive readiness that is hampered further by small, predator cropped branchiae, thus reducing fertilization and metabolite uptake. Although only the largest worms were measured, only 17% of low flux worms were reproductively competent compared to 91% of high flux worms. A model of reproductive readiness illustrates that tube diameter is a good predictor of reproductive output and that few low flux worms reached critical reproductive size. We postulate that most of the propagules for the vent fields originate from the larger tubeworms that live in small, unstable habitat patches. The large expanses of worms in more stable low flux habitat sustain a small, but long-term, reproductive output. Phenotypic variation is an adaptation that fosters both morphological and physiological responses to differences in chemical milieu and predator pressure. This foundation species forms a metapopulation with variable growth characteristics in a heterogeneous environment where a strategy of phenotypic variation bestows an advantage over specialization. PMID:25337895

Tunnicliffe, Verena; St Germain, Candice; Hilário, Ana

2014-01-01

96

Ploidy-Regulated Variation in Biofilm-Related Phenotypes in Natural Isolates of Saccharomyces cerevisiae  

PubMed Central

The ability of yeast to form biofilms contributes to better survival under stressful conditions. We see the impact of yeast biofilms and “flocs” (clumps) in human health and industry, where forming clumps enables yeast to act as a natural filter in brewing and forming biofilms enables yeast to remain virulent in cases of fungal infection. Despite the importance of biofilms in yeast natural isolates, the majority of our knowledge about yeast biofilm genetics comes from work with a few tractable laboratory strains. A new collection of sequenced natural isolates from the Saccharomyces Genome Resequencing Project enabled us to examine the breadth of biofilm-related phenotypes in geographically, ecologically, and genetically diverse strains of Saccharomyces cerevisiae. We present a panel of 31 haploid and 24 diploid strains for which we have characterized six biofilm-related phenotypes: complex colony morphology, complex mat formation, flocculation, agar invasion, polystyrene adhesion, and psuedohyphal growth. Our results show that there is extensive phenotypic variation between and within strains, and that these six phenotypes are primarily uncorrelated or weakly correlated, with the notable exception of complex colony and complex mat formation. We also show that the phenotypic strength of these strains varies significantly depending on ploidy, and the diploid strains demonstrate both decreased and increased phenotypic strength with respect to their haploid counterparts. This is a more complex view of the impact of ploidy on biofilm-related phenotypes than previous work with laboratory strains has suggested, demonstrating the importance and enormous potential of working with natural isolates of yeast. PMID:25060625

Hope, Elyse A.; Dunham, Maitreya J.

2014-01-01

97

Snake venom dipeptidyl peptidase IV: taxonomic distribution and quantitative variation.  

PubMed

The present study examined the taxonomic distribution of dipeptidyl peptidase IV (DPP IV) activity in venoms of 59 ophidian taxa, representing seven subfamilies of the Families Elapidae and Viperidae. DPP IV activity is extremely variable at all taxonomic levels. It ranged from essentially none in laticaudine, hydrophiine, and some bungarine and elapine venoms, to 10.72 mumol 4-methoxy-beta-naphthylamine liberated per min per 200 mug venom, for Ophiophagus hannah. Intra- and interpopulational variation were examined among eight populations of prairie rattlesnakes (Crotalus viridis viridis), Great Basin rattlesnakes (Crotalus viridis lutosus) and southern Pacific rattlesnakes (Crotalus viridis helleri). Among these populations, the mean weighted range of variation was 4.9-fold, and even among litter mates of C. v. lutosus, DPP IV activity varied as much as 5.6-fold. The two most salient findings, the near ubiquity of DPP IV in snake venoms and its great quantitative variability, even among full siblings, are paradoxical. The widespread distribution of the enzyme suggests an important role in envenomation, while the variable activity levels suggest that DPP IV and by extension, other individual enzymatic constituents, may not be under much individual selective pressure. PMID:18440846

Aird, Steven D

2008-06-01

98

Earlier Migration Timing, Decreasing Phenotypic Variation, and Biocomplexity in Multiple Salmonid Species  

PubMed Central

Climate-induced phenological shifts can influence population, evolutionary, and ecological dynamics, but our understanding of these phenomena is hampered by a lack of long-term demographic data. We use a multi-decade census of 5 salmonid species representing 14 life histories in a warming Alaskan stream to address the following key questions about climate change and phenology: How consistent are temporal patterns and drivers of phenology for similar species and alternative life histories? Are shifts in phenology associated with changes in phenotypic variation? How do phenological changes influence the availability of resource subsidies? For most salmonid species, life stages, and life histories, freshwater temperature influences migration timing – migration events are occurring earlier in time (mean?=?1.7 days earlier per decade over the 3–5 decades), and the number of days over which migration events occur is decreasing (mean?=?1.5 days per decade). Temporal trends in migration timing were not correlated with changes in intra-annual phenotypic variation, suggesting that these components of the phenotypic distribution have responded to environmental change independently. Despite commonalities across species and life histories, there was important biocomplexity in the form of disparate shifts in migration timing and variation in the environmental factors influencing migration timing for alternative life history strategies in the same population. Overall, adult populations have been stable during these phenotypic and environmental changes (? ?1.0), but the temporal availability of salmon as a resource in freshwater has decreased by nearly 30 days since 1971 due to changes in the median date of migration timing and decreases in intra-annual variation in migration timing. These novel observations advance our understanding of phenological change in response to climate warming, and indicate that climate change has influenced the ecology of salmon populations, which will have important consequences for the numerous species that depend on this resource. PMID:23326513

Kovach, Ryan P.; Joyce, John E.; Echave, Jesse D.; Lindberg, Mark S.; Tallmon, David A.

2013-01-01

99

Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes.  

PubMed

The characterization of the metabolome has rapidly evolved over two decades, from early developments in analytical chemistry to systems biology. Metabolites and small molecules are not independent; they are organized in biochemical pathways and in a wider metabolic network, which is itself dependent on various genetic and signaling networks for its regulation. Recent advances in genomics, transcriptomics, proteomics and metabolomics have been matched by the development of publicly available repositories, which have helped shaping a new generation of integrative studies using metabolite measurements in molecular epidemiology and genetic studies. Although the environment influences metabolism, the identification of the genetic determinants of metabolic phenotypes (metabotypes) was made possible by the development of metabotype quantitative trait locus (mQTL) mapping and metabolomic genome-wide association studies (mGWAS) in a rigorous statistical genetics framework, deriving associations between metabolite concentrations and genetic polymorphisms. However, given the complexity of the biomolecular events involved in the regulation of metabolic patterns, alternative network biology approaches have also been recently introduced, such as integrated metabolome and interactome mapping (iMIM). This unprecedented convergence of metabolic biochemistry, quantitative genetics and network biology already has had a strong impact on the role of the metabolome in biomedical sciences, and this review gives a foretaste of its anticipated successes in eventually delivering personalized medicine. PMID:22868675

Dumas, Marc-Emmanuel

2012-10-01

100

Sources of phenotypic variation in floral traits in wild radish, Raphanus raphanistrum (Brassicaceae).  

PubMed

Pollinator-mediated natural selection has been shown to act on phenotypic variation in floral morphology, and this variation has often been demonstrated to be heritable, but few details are available concerning the sources of floral variation. We examined phenotypic variation in seven floral traits in wild radish (Raphanus raphanistrum) at six levels: between two populations grown in a common garden, among plants within populations, among flowers measured on different weeks, between flowers on two flowering stalks measured on the same day, between adjacent flowers on a flowering stalk, and within individual flowers. There were no significant differences between plants derived from the two source populations, which were ?800 km apart. Most of the variance was within individual plants; repeatabilities were all <0.35. There were highly significant differences between flowers measured in different weeks and also highly significant plant by week interactions, indicating that the among-plant variation was not consistent over time. There was substantial variance among adjacent flowers on the same stalk, particularly in the gynoecium. This high within-plant variance is partly responsible for the low heritability of floral traits in the field and the weak selection on floral traits found in previous studies of wild radish. PMID:21669690

Williams, J L; Conner, J K

2001-09-01

101

Geographical variation in relationships between parental body size and offspring phenotype at birth  

PubMed Central

Background Size and body proportions at birth are partly determined by maternal body composition, but most studies of mother-baby relationships have only considered the effects of maternal height and weight on offspring birthweight, and few have examined the size of effects. Paternal size and body composition also play a role, primarily through the fetal genome, although few studies have investigated relationships with neonatal phenotype. Methods Data from the UK, Finland, India, Sri Lanka, China, DR Congo, Nigeria and Jamaica were used to investigate the effects of maternal measures including estimates of muscle and fat (derived at 30-weeks gestation, N=16 418), and also paternal size (N=3 733) on neonatal phenotype, for singleton, liveborn, term births. Results After accounting for variation in maternal size and shape across populations, differences in neonatal phenotype were markedly reduced. Mother-baby relationships were similar across populations, although some were stronger in developing countries. Maternal height was generally the strongest predictor of neonatal length, maternal head circumference of neonatal head circumference, and maternal skinfold thickness of neonatal skinfolds. Relationships with maternal arm muscle area were generally weak. Data from fathers were limited to height and body mass index, but when compared with maternal height and body mass index, paternal effects were weaker in most studies. Conclusions Differences in maternal body composition account for a large part of the geographical variation in neonatal phenotype. The size of the effects of all maternal measures on neonatal phenotype suggests that nutrition at every stage of the mother's life cycle may influence fetal growth. Further research is needed into father-baby relationships and the genetic mechanisms which influence fetal growth. PMID:16929411

Leary, Sam; Fall, Caroline; Osmond, Clive; Lovel, Hermione; Campbell, Doris; Eriksson, Johan; Forrester, Terrence; Godfrey, Keith; Hill, Jacqui; Jie, Mi; Law, Catherine; Newby, Rachel; Robinson, Sian; Yajnik, Chittaranjan

2009-01-01

102

Genetic and phenotypic variation across a hybrid zone between ecologically divergent tree squirrels (Tamiasciurus).  

PubMed

A hybrid zone along an environmental gradient should contain a clinal pattern of genetic and phenotypic variation. This occurs because divergent selection in the two parental habitats is typically strong enough to overcome the homogenizing effects of gene flow across the environmental transition. We studied hybridization between two parapatric tree squirrels (Tamiasciurus spp.) across a forest gradient over which the two species vary in coloration, cranial morphology and body size. We sampled 397 individuals at 29 locations across a 600-km transect to seek genetic evidence for hybridization; upon confirming hybridization, we examined levels of genetic admixture in relation to maintenance of phenotypic divergence despite potentially homogenizing gene flow. Applying population assignment analyses to microsatellite data, we found that Tamiasciurus douglasii and T. hudsonicus form two distinct genetic clusters but also hybridize, mostly within transitional forest habitat. Overall, based on this nuclear analysis, 48% of the specimens were characterized as T. douglasii, 9% as hybrids and 43% as T. hudsonicus. Hybrids appeared to be reproductively viable, as evidenced by the presence of later-generation hybrid genotypes. Observed clines in ecologically important phenotypic traits-fur coloration and cranial morphology-were sharper than the cline of putatively neutral mtDNA, which suggests that divergent selection may maintain phenotypic distinctiveness. The relatively recent divergence of these two species (probably late Pleistocene), apparent lack of prezygotic isolating mechanisms and geographic coincidence of cline centres for both genetic and phenotypic variation suggest that environmental factors play a large role in maintaining the distinctiveness of these two species across the hybrid zone. PMID:21771139

Chavez, Andreas S; Saltzberg, Carl J; Kenagy, G J

2011-08-01

103

Quantitative analysis of ruminal methanogenic microbial populations in beef cattle divergent in phenotypic residual feed intake (RFI) offered contrasting diets  

PubMed Central

Background Methane (CH4) emissions in cattle are an undesirable end product of rumen methanogenic fermentative activity as they are associated not only with negative environmental impacts but also with reduced host feed efficiency. The aim of this study was to quantify total and specific rumen microbial methanogenic populations in beef cattle divergently selected for residual feed intake (RFI) while offered (i) a low energy high forage (HF) diet followed by (ii) a high energy low forage (LF) diet. Ruminal fluid was collected from 14 high (H) and 14 low (L) RFI animals across both dietary periods. Quantitative real time PCR (qRT-PCR) analysis was conducted to quantify the abundance of total and specific rumen methanogenic microbes. Spearman correlation analysis was used to investigate the association between the relative abundance of methanogens and animal performance, rumen fermentation variables and diet digestibility. Results Abundance of methanogens, did not differ between RFI phenotypes. However, relative abundance of total and specific methanogen species was affected (P?variation in CH4 emissions between efficient and inefficient animals, however dietary manipulation can influence the abundance of total and specific methanogen species. PMID:25276350

2014-01-01

104

A pleiotropic nonadditive model of variation in quantitative traits  

SciTech Connect

A model of mutation-selection-drift balance incorporating pleiotropic and dominance effects of new mutations on quantitative traits and fitness is investigated and used to predict the amount and nature of genetic variation maintained in segregating populations. The model is based on recent information on the joint distribution of mutant effects on bristle traits and fitness in Drosophila melanogaster from experiments on the accumulation of spontaneous and P element-induced mutations. Mutants of large effect tend to be partially recessive while those with smaller effect are on average additive, but apparently with very variable gene action. The model is parameterized with two different sets of information derived from P element insertion and spontaneous mutation data, though the latter are not fully known. They differ in the number of mutations per generation which is assumed to affect the trait. Predictions of the variance maintained for bristle number assuming parameters derived from effects of P element insertions fit reasonably well with experimental observations. The equilibrium genetic variance is nearly independent of the degree of dominance of new mutations. Heritabilities of between 0.4 and 0.6 are predicted with population sizes from 10{sup 4} to 10{sup 6}, and most of the variance for the metric trait in segregating populations is due to a small proportion of mutations with neutral or nearly neutral effects on fitness and intermediate effects on the trait. Much of the genetic variance is contributed by recessive or partially recessive mutants, but only a small proportion of the genetic variance is dominance variance. If a model is assumed in which all mutation events have an effect on the quantitative trait, the majority of the genetic variance is contributed by deleterious mutations with tiny effects on the trait. If such a model is assumed for variability, the heritability is about 0.1, independent of the population size. 83 refs., 8 figs., 8 tabs.

Caballero, A.; Keightley, P.D. [Univ. of Edinburgh, Scotland (United Kingdom)

1994-11-01

105

Quantitative and evolutionary biology of alternative splicing: how changing the mix of alternative transcripts affects phenotypic plasticity and reaction norms  

Microsoft Academic Search

Alternative splicing (AS) of pre-messenger RNA is a common phenomenon that creates different transcripts from a single gene, and these alternative transcripts affect phenotypes. The majority of AS research has examined tissue and developmental specificity of expression of particular AS transcripts, how this specificity affects cell function, and how aberrant AS is related to disease. Few studies have examined quantitative

J H Marden

2008-01-01

106

Quantitative DNA methylation analysis improves epigenotype-phenotype correlations in Beckwith-Wiedemann syndrome  

PubMed Central

Beckwith-Wiedemann syndrome (BWS) is a rare disorder characterized by overgrowth and predisposition to embryonal tumors. BWS is caused by various epigenetic and/or genetic alterations that dysregulate the imprinted genes on chromosome region 11p15.5. Molecular analysis is required to reinforce the clinical diagnosis of BWS and to identify BWS patients with cancer susceptibility. This is particularly crucial prenatally because most signs of BWS cannot be recognized in utero. We established a reliable molecular assay by pyrosequencing to quantitatively evaluate the methylation profiles of ICR1 and ICR2. We explored epigenotype-phenotype correlations in 19 patients that fulfilled the clinical diagnostic criteria for BWS, 22 patients with suspected BWS, and three fetuses with omphalocele. Abnormal methylation was observed in one prenatal case and 19 postnatal cases, including seven suspected BWS. Seven cases showed ICR1 hypermethylation, five cases showed ICR2 hypomethylation, and eight cases showed abnormal methylation of ICR1 and ICR2 indicating paternal uniparental disomy (UPD). More cases of ICR1 alterations and UPD were found than expected. This is likely due to the sensitivity of this approach, which can detect slight deviations in methylation from normal levels. There was a significant correlation (p < 0.001) between the percentage of ICR1 methylation and BWS features: severe hypermethylation (range: 75–86%) was associated with macroglossia, macrosomia, and visceromegaly, whereas mild hypermethylation (range: 55–59%) was associated with umbilical hernia and diastasis recti. Evaluation of ICR1 and ICR2 methylation by pyrosequencing in BWS can improve epigenotype-phenotype correlations, detection of methylation alterations in suspected cases, and identification of UPD. PMID:23917791

Calvello, Mariarosaria; Tabano, Silvia; Colapietro, Patrizia; Maitz, Silvia; Pansa, Alessandra; Augello, Claudia; Lalatta, Faustina; Gentilin, Barbara; Spreafico, Filippo; Calzari, Luciano; Perotti, Daniela; Larizza, Lidia; Russo, Silvia; Selicorni, Angelo; Sirchia, Silvia M; Miozzo, Monica

2013-01-01

107

The relationship between mimetic imperfection and phenotypic variation in insect colour patterns.  

PubMed Central

Many hoverflies (Syrphidae) mimic wasps or bees through colour or behavioural adaptations. The relationship between phenotypic variation in colour pattern and mimetic perfection (as determined by pigeons) was investigated in three species of Müllerian mimics (Vespula spp.) and 10 Batesian hoverfly mimics, plus two non-mimetic species of flies. Four predictions were tested: (i) Batesian mimics might be imperfect because they are in the process of evolving towards perfection, hence there should be a positive relationship between variation and imperfection; (ii) some Batesian mimics are imperfect because they do not have the appropriate genetic variation to improve and have evolved to be as good as possible, hence there should be no differences between species, all displaying a low level of variation; (iii) very common hoverflies should show the highest levels of variation because they outnumber their models, resulting in high predation and a breakdown in the mimetic relationship; and (iv) social wasps (Vespula) have such a powerful defence that anything resembling a wasp, both Müllerian and perfect Batesian mimics, would be avoided, resulting in relaxed selection and high variance. Poor mimics may still evolve to resemble wasps as well as possible and display lower levels of variation. The data only provided support for the fourth prediction. The Müllerian mimics, one of the most perfect Batesian mimics, and the non-mimetic flies displayed much higher levels of variation than the other species of Batesian mimics. PMID:11886630

Holloway, Graham; Gilbert, Francis; Brandt, Amoret

2002-01-01

108

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease  

PubMed Central

The Rat Genome Database (RGD, http://rgd.mcw.edu) provides the most comprehensive data repository and informatics platform related to the laboratory rat, one of the most important model organisms for disease studies. RGD maintains and updates datasets for genomic elements such as genes, transcripts and increasingly in recent years, sequence variations, as well as map positions for multiple assemblies and sequence information. Functional annotations for genomic elements are curated from published literature, submitted by researchers and integrated from other public resources. Complementing the genomic data catalogs are those associated with phenotypes and disease, including strains, QTL and experimental phenotype measurements across hundreds of strains. Data are submitted by researchers, acquired through bulk data pipelines or curated from published literature. Innovative software tools provide users with an integrated platform to query, mine, display and analyze valuable genomic and phenomic datasets for discovery and enhancement of their own research. This update highlights recent developments that reflect an increasing focus on: (i) genomic variation, (ii) phenotypes and diseases, (iii) data related to the environment and experimental conditions and (iv) datasets and software tools that allow the user to explore and analyze the interactions among these and their impact on disease. PMID:25355511

Shimoyama, Mary; De Pons, Jeff; Hayman, G. Thomas; Laulederkind, Stanley J.F.; Liu, Weisong; Nigam, Rajni; Petri, Victoria; Smith, Jennifer R.; Tutaj, Marek; Wang, Shur-Jen; Worthey, Elizabeth; Dwinell, Melinda; Jacob, Howard

2015-01-01

109

Effects of genotypic and phenotypic variation on establishment are important for conservation, invasion, and infection biology  

PubMed Central

There is abundant evidence that the probability of successful establishment in novel environments increases with number of individuals in founder groups and with number of repeated introductions. Theory posits that the genotypic and phenotypic variation among individuals should also be important, but few studies have examined whether founder diversity influences establishment independent of propagule pressure, nor whether the effect is model or context dependent. I summarize the results of 18 experimental studies and report on a metaanalysis that provides strong evidence that higher levels of genotypic and phenotypic diversity in founder groups increase establishment success in plants and animals. The effect of diversity is stronger in experiments carried out under natural conditions in the wild than under seminatural or standardized laboratory conditions. The realization that genetic and phenotypic variation is key to successful establishment may improve the outcome of reintroduction and translocation programs used to vitalize or restore declining and extinct populations. Founder diversity may also improve the ability of invasive species to establish and subsequently spread in environments outside of their native community, and enhance the ability of pathogens and parasites to colonize and invade the environment constituted by their hosts. It is argued that exchange of ideas, methodological approaches, and insights of the role of diversity for establishment in different contexts may further our knowledge, vitalize future research, and improve management plans in different disciplines. PMID:24367109

Forsman, Anders

2014-01-01

110

Propagule Limitation, Disparate Habitat Quality, and Variation in Phenotypic Selection at a Local Species Range Boundary  

PubMed Central

Adaptation to novel conditions beyond current range boundaries requires the presence of suitable sites within dispersal range, but may be impeded when emigrants encounter poor habitat and sharply different selection pressures. We investigated fine-scale spatial heterogeneity in ecological dynamics and selection at a local population boundary of the annual plant Gilia tricolor. In two years, we planted G. tricolor seeds in core habitat, margin habitat at the edge of the local range, and exterior habitat in order to measure spatial and temporal variation in habitat quality, opportunity for selection, and selection on phenotypic traits. We found a striking decline in average habitat quality with distance from the population core, yet some migrant seeds were successful in suitable, unoccupied microsites at and beyond the range boundary. Total and direct selection on four out of five measured phenotypic traits varied across habitat zones, as well as between years. Moreover, the margin habitat often exerted unique selection pressures that were not intermediate between core and exterior habitats. This study reveals that a combination of ecological and evolutionary forces, including propagule limitation, variation in habitat quality and spatial heterogeneity in phenotypic selection may reduce opportunities for adaptive range expansion, even across a very local population boundary. PMID:24717472

Moore, Kara A.; Stanton, Maureen L.

2014-01-01

111

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease.  

PubMed

The Rat Genome Database (RGD, http://rgd.mcw.edu) provides the most comprehensive data repository and informatics platform related to the laboratory rat, one of the most important model organisms for disease studies. RGD maintains and updates datasets for genomic elements such as genes, transcripts and increasingly in recent years, sequence variations, as well as map positions for multiple assemblies and sequence information. Functional annotations for genomic elements are curated from published literature, submitted by researchers and integrated from other public resources. Complementing the genomic data catalogs are those associated with phenotypes and disease, including strains, QTL and experimental phenotype measurements across hundreds of strains. Data are submitted by researchers, acquired through bulk data pipelines or curated from published literature. Innovative software tools provide users with an integrated platform to query, mine, display and analyze valuable genomic and phenomic datasets for discovery and enhancement of their own research. This update highlights recent developments that reflect an increasing focus on: (i) genomic variation, (ii) phenotypes and diseases, (iii) data related to the environment and experimental conditions and (iv) datasets and software tools that allow the user to explore and analyze the interactions among these and their impact on disease. PMID:25355511

Shimoyama, Mary; De Pons, Jeff; Hayman, G Thomas; Laulederkind, Stanley J F; Liu, Weisong; Nigam, Rajni; Petri, Victoria; Smith, Jennifer R; Tutaj, Marek; Wang, Shur-Jen; Worthey, Elizabeth; Dwinell, Melinda; Jacob, Howard

2015-01-01

112

Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping  

PubMed Central

The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease. PMID:22022279

Derrien, Thomas; Axelsson, Erik; Rosengren Pielberg, Gerli; Sigurdsson, Snaevar; Fall, Tove; Seppälä, Eija H.; Hansen, Mark S. T.; Lawley, Cindy T.; Karlsson, Elinor K.; Bannasch, Danika; Vilà, Carles; Lohi, Hannes; Galibert, Francis; Fredholm, Merete; Häggström, Jens; Hedhammar, Åke; André, Catherine; Lindblad-Toh, Kerstin; Hitte, Christophe; Webster, Matthew T.

2011-01-01

113

Genetic and phenotypically flexible components of seasonal variation in immune function.  

PubMed

Animals cope with seasonal variation in environmental factors by adjustments of physiology and life history. When seasonal variation is partly predictable, such adjustments can be based on a genetic component or be phenotypically flexible. Animals have to allocate limited resources over different demands, including immune function. Accordingly, immune traits could change seasonally, and such changes could have a genetic component that differs between environments. We tested this hypothesis in genotypically distinct groups of a widespread songbird, the stonechat (Saxicola torquata). We compared variation in immunity during 1 year in long-distance migrants, short-distance migrants, tropical residents and hybrids in a common garden environment. Additionally, we investigated phenotypically flexible responses to temperature by applying different temperature regimes to one group. We assessed constitutive immunity by measuring hemagglutination, hemolysis, haptoglobin and bactericidal ability against Escherichia coli and Staphylococcus aureus. Genotypic groups differed in patterns of variation of all measured immune indices except haptoglobin. Hybrids differed from, but were rarely intermediate to, parental subspecies. Temperature treatment only influenced patterns of hemolysis and bactericidal ability against E. coli. We conclude that seasonal variation in constitutive immunity has a genetic component, that heredity does not follow simple Mendelian rules, and that some immune measures are relatively rigid while others are more flexible. Furthermore, our results support the idea that seasonal variability in constitutive immunity is associated with variability in environment and annual-cycle demands. This study stresses the importance of considering seasonal variation in immune function in relation to the ecology and life history of the organism of interest. PMID:24436383

Versteegh, M A; Helm, B; Kleynhans, E J; Gwinner, E; Tieleman, B I

2014-05-01

114

Phenotypic variation of the Mexican duck (Anas platyrhynchos diazi) in Mexico  

USGS Publications Warehouse

A collection of 98 breeding Mexican Ducks (Anas platyrhynchos diazi) was made in Mexico from six areas between the United States border with Chihuahua and Lake Chapala, Jalisco, in order to study geographic variation. Plumage indices showed a relatively smooth clinal change from north to south; northern populations were most influenced by the Northern Mallard (A. platyrhynchos) phenotype. Measurements of total, wing, and culmen lengths and bill width were usually significantly larger in males at any one site, but showed no regular geographic trends. Hybridization between platyrhynchos and diazi phenotypes may or may not be increasing in the middle Rio Grande and Rio Conchos valleys; available data are insufficient to decide. A spring 1978 aerial census yielded an estimate of 55,500 diazi -like birds in Mexico. Populations of diazi appear to be as large as the available habitat allows; management should be directed towards increasing and stabilizing the nesting habitat; and the stability of the zone of intergradation should be investigated.

Scott, N.J., Jr.; Reynolds, R.P.

1984-01-01

115

Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle  

NASA Astrophysics Data System (ADS)

Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from minimal mass-balance assumptions upon prescribing in- and outtake fluxes. Here we consider the problem of inferring intracellular flux patterns from extracellular metabolite levels. Resorting to a thermodynamic out of equilibrium variational principle to describe the network at steady state, we show that the switch from fermentative to oxidative phenotypes in cells can be characterized in terms of the glucose, lactate, oxygen and carbon dioxide concentrations. Results obtained for an exactly solvable toy model are fully recovered for a large scale reconstruction of human catabolism. Finally we argue that, in spite of the many approximations involved in the theory, available data for several human cell types are well described by the predicted phenotypic map of the problem.

De Martino, Daniele; Capuani, Fabrizio; De Martino, Andrea

2014-11-01

116

Quantitative mouse brain phenotyping based on single and multispectral MR protocols  

PubMed Central

Sophisticated image analysis methods have been developed for the human brain, but such tools still need to be adapted and optimized for quantitative small animal imaging. We propose a framework for quantitative anatomical phenotyping in mouse models of neurological and psychiatric conditions. The framework encompasses an atlas space, image acquisition protocols, and software tools to register images into this space. We show that a suite of segmentation tools (Avants, Epstein et al., 2008) designed for human neuroimaging can be incorporated into a pipeline for segmenting mouse brain images acquired with multispectral magnetic resonance imaging (MR) protocols. We present a flexible approach for segmenting such hyperimages, optimizing registration, and identifying optimal combinations of image channels for particular structures. Brain imaging with T1, T2* and T2 contrasts yielded accuracy in the range of 83% for hippocampus and caudate putamen (Hc and CPu), but only 54% in white matter tracts, and 44% for the ventricles. The addition of diffusion tensor parameter images improved accuracy for large gray matter structures (by >5%), white matter (10%), and ventricles (15%). The use of Markov random field segmentation further improved overall accuracy in the C57BL/6 strain by 6%; so Dice coefficients for Hc and CPu reached 93%, for white matter 79%, for ventricles 68%, and for substantia nigra 80%. We demonstrate the segmentation pipeline for the widely used C57BL/6 strain, and two test strains (BXD29, APP/TTA). This approach appears promising for characterizing temporal changes in mouse models of human neurological and psychiatric conditions, and may provide anatomical constraints for other preclinical imaging, e.g. fMRI and molecular imaging. This is the first demonstration that multiple MR imaging modalities combined with multivariate segmentation methods lead to significant improvements in anatomical segmentation in the mouse brain. PMID:22836174

Badea, Alexandra; Gewalt, Sally; Avants, Brian B.; Cook, James J.; Johnson, G. Allan

2013-01-01

117

Functional Coding Variation in Recombinant Inbred Mouse Lines Reveals Novel Serotonin Transporter-Associated Phenotypes  

SciTech Connect

The human serotonin (5-hydroxytryptamine, 5-HT) transporter (hSERT, SLC6A4) figures prominently in the etiology or treatment of many prevalent neurobehavioral disorders including anxiety, alcoholism, depression, autism and obsessive-compulsive disorder (OCD). Here we utilize naturally occurring polymorphisms in recombinant inbred (RI) lines to identify novel phenotypes associated with altered SERT function. The widely used mouse strain C57BL/6J, harbors a SERT haplotype defined by two nonsynonymous coding variants (Gly39 and Lys152 (GK)). At these positions, many other mouse lines, including DBA/2J, encode Glu39 and Arg152 (ER haplotype), assignments found also in hSERT. Synaptosomal 5-HT transport studies revealed reduced uptake associated with the GK variant. Heterologous expression studies confirmed a reduced SERT turnover rate for the GK variant. Experimental and in silico approaches using RI lines (C57Bl/6J X DBA/2J=BXD) identifies multiple anatomical, biochemical and behavioral phenotypes specifically impacted by GK/ER variation. Among our findings are multiple traits associated with anxiety and alcohol consumption, as well as of the control of dopamine (DA) signaling. Further bioinformatic analysis of BXD phenotypes, combined with biochemical evaluation of SERT knockout mice, nominates SERT-dependent 5-HT signaling as a major determinant of midbrain iron homeostasis that, in turn, dictates ironregulated DA phenotypes. Our studies provide a novel example of the power of coordinated in vitro, in vivo and in silico approaches using murine RI lines to elucidate and quantify the system-level impact of gene variation.

Carneiro, Ana [Vanderbilt University; Airey, David [University of Tennessee Health Science Center, Memphis; Thompson, Brent [Vanderbilt University; Zhu, C [Vanderbilt University; Rinchik, Eugene M [ORNL; Lu, Lu [University of Tennessee Health Science Center, Memphis; Chesler, Elissa J [ORNL; Erikson, Keith [University of North Carolina; Blakely, Randy [Vanderbilt University

2009-01-01

118

Quantitative Phenotyping of Duchenne Muscular Dystrophy Dogs by Comprehensive Gait Analysis and Overnight Activity Monitoring  

PubMed Central

The dystrophin-deficient dog is excellent large animal model for testing novel therapeutic modalities for Duchenne muscular dystrophy (DMD). Despite well-documented descriptions of dystrophic symptoms in these dogs, very few quantitative studies have been performed. Here, we developed a comprehensive set of non-invasive assays to quantify dog gait (stride length and speed), joint angle and limb mobility (for both forelimb and hind limb), and spontaneous activity at night. To validate these assays, we examined three 8-m-old mix-breed dystrophic dogs. We also included three age-matched siblings as the normal control. High-resolution video recorders were used to digitize dog walking and spontaneous movement at night. Stride speed and length were significantly decreased in affected dogs. The mobility of the limb segments (forearm, front foot, lower thigh, rear foot) and the carpus and hock joints was significantly reduced in dystrophic dogs. There was also a significant reduction of the movement in affected dogs during overnight monitoring. In summary, we have established a comprehensive set of outcome measures for clinical phenotyping of DMD dogs. These non-invasive end points would be valuable in monitoring disease progression and therapeutic efficacy in translational studies in the DMD dog model. PMID:23544107

Shin, Jin-Hong; Greer, Brian; Hakim, Chady H.; Zhou, Zhongna; Chung, Yu-chia; Duan, Ye; He, Zhihai; Duan, Dongsheng

2013-01-01

119

Quantitative genetics: a promising approach for the assessment of genetic variation in endangered species  

Microsoft Academic Search

The measurement of genetic variation is often an important component of endangered species management programs. Each of several tools available to measure genetic diversity has positive and negative attributes. Quantitative genetic techniques have not received much attention in the conservation field, yet they are likely to reveal variation that is most closely associated with components of fitness. In addition, quantitative

Andrew Storfer

1996-01-01

120

Multivariate analysis of allozymic and quantitative trait variation in Alnus rubra  

E-print Network

Multivariate analysis of allozymic and quantitative trait variation in Alnus rubra: geographic (Alnus rubra Bong.). Principal components analysis showed that variation in quantitative traits can ont étudié la différenciation géographique parmi 65 provenances d'aulne rouge (Alnus rubra Bong.) de

Hamann, Andreas

121

Quantitative Social Dialectology: Explaining Linguistic Variation Geographically and Socially  

PubMed Central

In this study we examine linguistic variation and its dependence on both social and geographic factors. We follow dialectometry in applying a quantitative methodology and focusing on dialect distances, and social dialectology in the choice of factors we examine in building a model to predict word pronunciation distances from the standard Dutch language to 424 Dutch dialects. We combine linear mixed-effects regression modeling with generalized additive modeling to predict the pronunciation distance of 559 words. Although geographical position is the dominant predictor, several other factors emerged as significant. The model predicts a greater distance from the standard for smaller communities, for communities with a higher average age, for nouns (as contrasted with verbs and adjectives), for more frequent words, and for words with relatively many vowels. The impact of the demographic variables, however, varied from word to word. For a majority of words, larger, richer and younger communities are moving towards the standard. For a smaller minority of words, larger, richer and younger communities emerge as driving a change away from the standard. Similarly, the strength of the effects of word frequency and word category varied geographically. The peripheral areas of the Netherlands showed a greater distance from the standard for nouns (as opposed to verbs and adjectives) as well as for high-frequency words, compared to the more central areas. Our findings indicate that changes in pronunciation have been spreading (in particular for low-frequency words) from the Hollandic center of economic power to the peripheral areas of the country, meeting resistance that is stronger wherever, for well-documented historical reasons, the political influence of Holland was reduced. Our results are also consistent with the theory of lexical diffusion, in that distances from the Hollandic norm vary systematically and predictably on a word by word basis. PMID:21912639

Wieling, Martijn; Nerbonne, John; Baayen, R. Harald

2011-01-01

122

Phenotypic evolution through variation in splicing of the noncoding RNA COOLAIR.  

PubMed

The extent to which natural polymorphisms in noncoding sequences have functional consequences is still unknown. A large proportion of the natural variation in flowering in Arabidopsis thaliana accessions is due to noncoding cis polymorphisms that define distinct haplotypes of FLOWERING LOCUS C (FLC). Here, we show that a single natural intronic polymorphism in one haplotype affects FLC expression and thus flowering by specifically changing splicing of the FLC antisense transcript COOLAIR. Altered antisense splicing increases FLC expression via a cotranscriptional mechanism involving capping of the FLC nascent transcript. Single noncoding polymorphisms can therefore be a major contributor to phenotypic evolution through modulation of noncoding transcripts. PMID:25805848

Li, Peijin; Tao, Zhen; Dean, Caroline

2015-04-01

123

Phenotypic evolution through variation in splicing of the noncoding RNA COOLAIR  

PubMed Central

The extent to which natural polymorphisms in noncoding sequences have functional consequences is still unknown. A large proportion of the natural variation in flowering in Arabidopsis thaliana accessions is due to noncoding cis polymorphisms that define distinct haplotypes of FLOWERING LOCUS C (FLC). Here, we show that a single natural intronic polymorphism in one haplotype affects FLC expression and thus flowering by specifically changing splicing of the FLC antisense transcript COOLAIR. Altered antisense splicing increases FLC expression via a cotranscriptional mechanism involving capping of the FLC nascent transcript. Single noncoding polymorphisms can therefore be a major contributor to phenotypic evolution through modulation of noncoding transcripts. PMID:25805848

Li, Peijin; Tao, Zhen

2015-01-01

124

Variation and inter-relationships of quantitative traits in tef (Eragrostis tef (Zucc.) Trotter) germplasm from western and southern Ethiopia.  

PubMed

Three thousand tef (Eragrostis tef (Zucc.) Trotter) lines representing 60 germplasm populations from western and southern Ethiopia were sown on pellic Vertisols at Debre Zeit Agricultural Research Center during the 1999/2000 main season. The objectives were to assess the variation with respect to regions and altitude zones of origin and to study the inter-relationships of 17 pheno-morphic and agronomic traits. The populations showed significant (p < or = 0.05) regional variation in 10 (59%) of the quantitative traits, but clinal variation among altitude zones was significant (p < or = 0.05) only for six (35%) of the traits. On the other hand, the populations revealed consistent variation (p < or = 0.05) within both regions and altitude zones in all the traits evaluated. Likewise, the variation among lines within populations of both regions and altitude zones was significant (p < or = 0.05) in most of the traits. The number of characters showing substantial correlation depicted regional and clinal variation mainly depending on the number of populations. Based on the mean of the populations, grain yield panicle and shoot phytomass plant showed negative correlation with harvest index, and positive correlation with most of the remaining traits. Individual plant grain yield was positively correlated with all the other traits except harvest index, days to maturity, grain filling period and number of primary panicle branches. Overall, the tef germplasm populations showed substantial phenotypic variation which can be utilized in the genetic improvement of the crop. PMID:12369096

Assefa, Kebebew; Tefera, Hailu; Merker, Arnulf

2002-01-01

125

Quantitative Genomics of 30 Complex Phenotypes in Wagyu x Angus F1 Progeny  

PubMed Central

In the present study, a total of 91 genes involved in various pathways were investigated for their associations with six carcass traits and twenty-four fatty acid composition phenotypes in a Wagyu×Angus reference population, including 43 Wagyu bulls and their potential 791 F1 progeny. Of the 182 SNPs evaluated, 102 SNPs that were in Hardy-Weinberg equilibrium with minor allele frequencies (MAF>0.15) were selected for parentage assignment and association studies with these quantitative traits. The parentage assignment revealed that 40 of 43 Wagyu sires produced over 96.71% of the calves in the population. Linkage disequilibrium analysis identified 75 of 102 SNPs derived from 54 genes as tagged SNPs. After Bonferroni correction, single-marker analysis revealed a total of 113 significant associations between 44 genes and 29 phenotypes (adjusted P<0.05). Multiple-marker analysis confirmed single-gene associations for 10 traits, but revealed two-gene networks for 9 traits and three-gene networks for 8 traits. Particularly, we observed that TNF (tumor necrosis factor) gene is significantly associated with both beef marbling score (P=0.0016) and palmitic acid (C16:0) (P=0.0043), RCAN1 (regulator of calcineurin 1) with rib-eye area (P=0.0103), ASB3 (ankyrin repeat and SOCS box-containing 3) with backfat (P=0.0392), ABCA1 (ATP-binding cassette A1) with both palmitic acid (C16:0) (P=0.0025) and oleic acid (C18:1n9) (P=0.0114), SLC27A1(solute carrier family 27 A1) with oleic acid (C18:1n9) (P=0.0155), CRH (corticotropin releasing hormone) with both linolenic acid (OMEGA-3) (P=0.0200) and OMEGA 6:3 RATIO (P=0.0054), SLC27A2 (solute carrier family 27 A2) with both linoleic acid (OMEGA-6) (P=0.0121) and FAT (P=0.0333), GNG3 (guanine nucleotide binding protein gamma 3 with desaturase 9 (P=0.0115), and EFEMP1 (EGF containing fibulin-like extracellular matrix protein 1), PLTP (phospholipid transfer protein) and DSEL (dermatan sulfate epimerase-like) with conjugated linoleic acid (P=0.0042-0.0044), respectively, in the Wagyu x Angus F1 population. In addition, we observed an interesting phenomenon that crossbreeding of different breeds might change gene actions to dominant and overdominant modes, thus explaining the origin of heterosis. The present study confirmed that these important families or pathway-based genes are useful targets for improving meat quality traits and healthful beef products in cattle. PMID:22745575

Zhang, Lifan; Michal, Jennifer J.; O'Fallon, James V.; Pan, Zengxiang; Gaskins, Charles T.; Reeves, Jerry J.; Busboom, Jan R.; Zhou, Xiang; Ding, Bo; Dodson, Michael V.; Jiang, Zhihua

2012-01-01

126

Databases of genomic variation and phenotypes: existing resources and future needs  

PubMed Central

Massively parallel sequencing (MPS) has become an important tool for identifying medically significant variants in both research and the clinic. Accurate variation and genotype–phenotype databases are critical in our ability to make sense of the vast amount of information that MPS generates. The purpose of this review is to summarize the state of the art of variation and genotype–phenotype databases, how they can be used, and opportunities to improve these resources. Our working assumption is that the objective of the clinical genomicist is to identify highly penetrant variants that could explain existing disease or predict disease risk for individual patients or research participants. We have detailed how current databases contribute to this goal providing frequency data, literature reviews and predictions of causation for individual variants. For variant annotation, databases vary greatly in their ease of use, the use of standard mutation nomenclature, the comprehensiveness of the variant cataloging and the degree of expert opinion. Ultimately, we need a dynamic and comprehensive reference database of medically important variants that is easily cross referenced to exome and genome sequence data and allows for an accumulation of expert opinion. PMID:23962721

Johnston, Jennifer J.; Biesecker, Leslie G.

2013-01-01

127

Causes of variation in biotic interaction strength and phenotypic selection along an altitudinal gradient.  

PubMed

Understanding the causes of variation in biotic interaction strength and phenotypic selection remains one of the outstanding goals of evolutionary ecology. Here we examine the variation in strength of interactions between two seed predators, common crossbills (Loxia curvirostra) and European red squirrels (Sciurus vulgaris), and mountain pine (Pinus uncinata) at and below tree limit in the Pyrenees, and how this translates into phenotypic selection. Seed predation by crossbills increased whereas seed predation by squirrels decreased with increasing elevation and as the canopy became more open. Overall, seed predation by crossbills averaged about twice that by squirrels, and the intensity of selection exerted by crossbills averaged between 2.6 and 7.5 times greater than by squirrels. The higher levels of seed predation by crossbills than squirrels were related to the relatively open nature of most of the forests, and the higher intensity of selection exerted by crossbills resulted from their higher levels of seed predation. However, most of the differences in selection intensity between crossbills and squirrels were the result of habitat features having a greater effect on the foraging behavior of squirrels than of crossbills, causing selection to be much lower for squirrels than for crossbills. PMID:24593660

Mezquida, Eduardo T; Benkman, Craig W

2014-06-01

128

Behavioral variation in pelvic phenotypes of brook stickleback, Culaea inconstans , in response to predation by northern pike, Esox lucius  

Microsoft Academic Search

Populations ofCulaea inconstans, from Alberta and Saskatchewan, Canada exhibit phenotypic variation in expression of the pelvic skeleton and associated spines, from complete presence (with) through intermediate forms to complete absence (without). Such variation influences predation byEsox lucius which prefer the least spiny prey. Behavioral differences were investigated before and during pike predation. These differences may be associated either with the

James D. Reist

1983-01-01

129

International Association for Ecology Relationship of Phenotypic and Genetic Variation in Plantago lanceolata to Disease Caused by  

E-print Network

COiOgla ? Springer-Verlag1984 Relationshipof phenotypicand genetic variation in Plantago lanceolata to disease caused a population of Plantago lanceolata L. (the ribwort plantain) in which approximately 10% of the floweringInternational Association for Ecology Relationship of Phenotypic and Genetic Variation in Plantago

Antonovics, Janis

130

J Allergy Clin Immunol. Author manuscript Interrelationships of quantitative asthma-related phenotypes in the  

E-print Network

; Eosinophils ; immunology ; Female ; Forced Expiratory Volume ; Genetic Predisposition to Disease ; Humans ; Hypersensitivity, Immediate ; Immunoglobulin E ; blood ; Male ; Phenotype ; Sex Factors ; Skin Tests Author

Paris-Sud XI, Université de

131

Simple Sequence Repeats Provide a Substrate for Phenotypic Variation in the Neurospora crassa Circadian Clock  

PubMed Central

Background WHITE COLLAR-1 (WC-1) mediates interactions between the circadian clock and the environment by acting as both a core clock component and as a blue light photoreceptor in Neurospora crassa. Loss of the amino-terminal polyglutamine (NpolyQ) domain in WC-1 results in an arrhythmic circadian clock; this data is consistent with this simple sequence repeat (SSR) being essential for clock function. Methodology/Principal Findings Since SSRs are often polymorphic in length across natural populations, we reasoned that investigating natural variation of the WC-1 NpolyQ may provide insight into its role in the circadian clock. We observed significant phenotypic variation in the period, phase and temperature compensation of circadian regulated asexual conidiation across 143 N. crassa accessions. In addition to the NpolyQ, we identified two other simple sequence repeats in WC-1. The sizes of all three WC-1 SSRs correlated with polymorphisms in other clock genes, latitude and circadian period length. Furthermore, in a cross between two N. crassa accessions, the WC-1 NpolyQ co-segregated with period length. Conclusions/Significance Natural variation of the WC-1 NpolyQ suggests a mechanism by which period length can be varied and selected for by the local environment that does not deleteriously affect WC-1 activity. Understanding natural variation in the N. crassa circadian clock will facilitate an understanding of how fungi exploit their environments. PMID:17726525

Michael, Todd P.; Park, Sohyun; Kim, Tae-Sung; Booth, Jim; Byer, Amanda; Sun, Qi; Chory, Joanne; Lee, Kwangwon

2007-01-01

132

Molecular genetics of growth and development in Populus (Salicaceae). V. Mapping quantitative trait loci affecting leaf variation  

SciTech Connect

The genetic variation of leaf morphology and development was studied in the 2-yr-old replicated plantation of an interspecific hybrid pedigree of Populus trichocarpa T. & G. and P. deltoides Marsh. via both molecular and quantitative genetic methods. Leaf traits chosen showed pronounced differences between the original parents, including leaf size, shape, orientation, color, structure, petiole size, and petiole cross section. In the F{sub 2} generation, leaf traits were all significantly different among genotypes, but with significant effects due to genotype X crown-position interaction. Variation in leaf pigmentation, petiole length, and petiole length proportion appeared to be under the control of few quantitative trait loci (QTLs). More QTLs were associated with single leaf area, leaf shape, lamina angle, abaxial color, and petiole flatness, and in these traits the number of QTLs varied among crown positions. In general the estimates of QTL numbers from Wright`s biometric method were close to those derived from molecular markers. For those traits with few underlying QTLs, a single marker interval could explain from 30-60% of the observed phenotypic variance. For multigenic traits, certain markers contributed more substantially to the observed variation than others. Genetic cluster analysis showed developmentally related traits to be more strongly associated with each other than with unrelated traits. This finding was also supported by the QTL mapping. For example, the same chromosomal segment of linkage group L seemed to account for 20% of the phenotypic variation of all dimension-related traits, leaf size, petiole length, and midrib angle. In both traits, the P. deltoides alleles had positive effects and were dominant to the P. trichocarpa alleles. Similar relationships were also found for lamina angle, abaxial greenness, and petiole flatness. 72 refs., 3 figs., 2 tabs.

Wu, R.; Bradshaw, H.D. Jr.; Stettler, R.F. [Univ. of Washington, Seattle, WA (United States)

1997-02-01

133

Rapid and reliable detection of ?-globin copy number variations by quantitative real-time PCR  

PubMed Central

Background Alpha-thalassemia is the most common human genetic disease worldwide. Copy number variations in the form of deletions of ?-globin genes lead to ?-thalassemia while duplications of ?-globin genes can cause a severe phenotype in ?-thalassemia carriers due to accentuation of globin chain imbalance. It is important to have simple and reliable methods to identify unknown or rare deletions and duplications in cases in which thalassemia is suspected but cannot be confirmed by multiplex gap-PCR. Here we describe a copy number variation assay to detect deletions and duplications in the ?-globin gene cluster (HBA-CNV). Results Quantitative real-time PCR was performed using four TaqMan® assays which specifically amplify target sequences representing both the ?-globin genes, the –?3.7 deletion and the HS-40 region. The copy number for each target was determined by the 2-??Cq method. To validate our method, we compared the HBA-CNV method with traditional gap-PCR in 108 samples from patients referred to our laboratory for hemoglobinopathy evaluation. To determine the robustness of the four assays, we analyzed samples with and without deletions diluted to obtain different DNA concentrations. The HBA-CNV method identified the correct copy numbers in all 108 samples. All four assays showed the correct copy number within a wide range of DNA concentrations (3.2-100 ng/?L), showing that it is a robust and reliable method. By using the method in routine diagnostics of hemoglobinopathies we have also identified several deletions and duplications that are not detected with conventional gap-PCR. Conclusions HBA-CNV is able to detect all known large deletions and duplications affecting the ?-globin genes, providing a flexible and simple workflow with rapid and reliable results. PMID:24456650

2014-01-01

134

Phenotypic flexibility in passerine birds: seasonal variation in fuel storage, mobilization and transport.  

PubMed

Winter acclimatization in small birds living in cold climates produces a winter phenotype characterized by upregulation of metabolic rates to meet enhanced thermoregulatory demands. We measured several key aspects of fuel storage, mobilization and transport in summer and winter to determine whether black-capped chickadees (Poecile atricapillus), white-breasted nuthatches (Sitta carolinensis), and house sparrows (Passer domesticus) seasonally modulate these attributes to meet enhanced winter thermoregulatory demands. In addition, we exposed birds to thermoneutral (control) and severe cold exposure treatments to determine whether acute cold exposure influenced fuel storage, mobilization or transport. Carcass lipid mass and pectoralis intramuscular lipid did not vary significantly between seasons or temperature treatments for any of the study species. Muscle glycogen varied significantly seasonally only for chickadee supracoracoideus and leg muscles, and did not vary among warm or cold treatments for any species. Pectoralis fatty acid binding protein (FABPc) was significantly elevated in winter for chickadees and nuthatches, but not for sparrows. Plasma metabolites showed little consistent variation in response to season or acute cold exposure. Thus, fuel storage and mobilization do not appear to be major targets of adjustment associated with seasonal metabolic flexibility in these species, but modulation of intracellular lipid transport by FABPc may be an important contributor to seasonal phenotypes in some species of small birds. PMID:24704472

Liknes, Eric T; Guglielmo, Christopher G; Swanson, David L

2014-08-01

135

Phenotypic variations in re-lysogenization of Bacillus licheniformis with temperate phage.  

PubMed

A bacitracin-producing strain Bacillus licheniformis ATCC 10716 harbors two types of inducible phages (LP52 and DLP 10716). 156 strains re-lysogenized with phage LP52 were independently isolated from a cured strain UM12 of B. licheniformis. Those strains were divided into 12 groups based on colony morphology and pigment production. Some of the re-lysogenized strains grew faster than UM12 and others produced more bacitracin than the cured strain. For example, the production of bacitracin by one of the re-lysogenized strains, L89, was enhanced by about 70% in comparison with UM12. The phenotypic variations observed with re-lysogenized strains might be due to the re-insertion of the phage genome at different sites of the chromosome in addition to the pleiotropic effect assumed. PMID:7125801

Imanaka, T; Uchida, K; Aiba, S

1982-07-01

136

Cone and seed trait variation in whitebark pine (Pinus albicaulis; Pinaceae) and the potential for phenotypic selection.  

PubMed

Phenotypic variation among individuals is necessary for natural selection to operate and is therefore essential for adaptive evolution. However, extensive variation within individuals can mask variation among individuals and weaken the potential for selection. Here we quantify variation among and within individuals in female cone and seed traits of whitebark pine (Pinus albicaulis). In many plants, the production of numerous reproductive structures creates the potential for considerable variation within a plant, but these same traits should also undergo strong selection because of their direct link to plant fitness. We found about twice as much variation among individuals (overall mean = 65.3 ± 4.5% SE) than within individuals (overall mean = 34.7 ± 4.5%). One only needs to sample three to five cones per tree to accurately assess variation among trees in most cone and seed traits. The ease at which trees can be assessed helps account for the strong and consistent patterns of phenotypic selection exerted by seed predators and dispersers of whitebark pine and many other conifers. In contrast, the few traits where variation within trees equaled or exceeded that among trees underwent weak if any phenotypic selection. PMID:21628255

Garcia, Roberto; Siepielski, Adam M; Benkman, Craig W

2009-05-01

137

Quantitative multi-parametric evaluation of centrosome declustering drugs: centrosome amplification, mitotic phenotype, cell cycle and death  

PubMed Central

Unlike normal cells, cancer cells contain amplified centrosomes and rely on centrosome clustering mechanisms to form a pseudobipolar spindle that circumvents potentially fatal spindle multipolarity (MP). Centrosome clustering also promotes low-grade chromosome missegregation, which can drive malignant transformation and tumor progression. Putative ‘centrosome declustering drugs' represent a cancer cell-specific class of chemotherapeutics that produces a common phenotype of centrosome declustering and spindle MP. However, differences between individual agents in terms of efficacy and phenotypic nuances remain unexplored. Herein, we have developed a conceptual framework for the quantitative evaluation of centrosome declustering drugs by investigating their impact on centrosomes, clustering, spindle polarity, cell cycle arrest, and death in various cancer cell lines at multiple drug concentrations over time. Surprisingly, all centrosome declustering drugs evaluated in our study were also centrosome-amplifying drugs to varying extents. Notably, all declustering drugs induced spindle MP, and the peak extent of MP positively correlated with the induction of hypodiploid DNA-containing cells. Our data suggest acentriolar spindle pole amplification as a hitherto undescribed activity of some declustering drugs, resulting in spindle MP in cells that may not have amplified centrosomes. In general, declustering drugs were more toxic to cancer cell lines than non-transformed ones, with some exceptions. Through a comprehensive description and quantitative analysis of numerous phenotypes induced by declustering drugs, we propose a novel framework for the assessment of putative centrosome declustering drugs and describe cellular characteristics that may enhance susceptibility to them. PMID:24787016

Ogden, A; Cheng, A; Rida, P C G; Pannu, V; Osan, R; Clewley, R; Aneja, R

2014-01-01

138

PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease  

PubMed Central

Rats have been used extensively as animal models to study physiological and pathological processes involved in human diseases. Numerous rat strains have been selectively bred for certain biological traits related to specific medical interests. Recently, the Rat Genome Database (http://rgd.mcw.edu) has initiated the PhenoMiner project to integrate quantitative phenotype data from the PhysGen Program for Genomic Applications and the National BioResource Project in Japan as well as manual annotations from biomedical literature. PhenoMiner, the search engine for these integrated phenotype data, facilitates mining of data sets across studies by searching the database with a combination of terms from four different ontologies/vocabularies (Rat Strain Ontology, Clinical Measurement Ontology, Measurement Method Ontology and Experimental Condition Ontology). In this study, salt-induced hypertension was used as a model to retrieve blood pressure records of Brown Norway, Fawn-Hooded Hypertensive (FHH) and Dahl salt-sensitive (SS) rat strains. The records from these three strains served as a basis for comparing records from consomic/congenic/mutant offspring derived from them. We examined the cardiovascular and renal phenotypes of consomics derived from FHH and SS, and of SS congenics and mutants. The availability of quantitative records across laboratories in one database, such as these provided by PhenoMiner, can empower researchers to make the best use of publicly available data. Database URL: http://rgd.mcw.edu PMID:25632109

Wang, Shur-Jen; Laulederkind, Stanley J. F.; Hayman, G. Thomas; Petri, Victoria; Liu, Weisong; Smith, Jennifer R.; Nigam, Rajni; Dwinell, Melinda R.; Shimoyama, Mary

2015-01-01

139

PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease.  

PubMed

Rats have been used extensively as animal models to study physiological and pathological processes involved in human diseases. Numerous rat strains have been selectively bred for certain biological traits related to specific medical interests. Recently, the Rat Genome Database (http://rgd.mcw.edu) has initiated the PhenoMiner project to integrate quantitative phenotype data from the PhysGen Program for Genomic Applications and the National BioResource Project in Japan as well as manual annotations from biomedical literature. PhenoMiner, the search engine for these integrated phenotype data, facilitates mining of data sets across studies by searching the database with a combination of terms from four different ontologies/vocabularies (Rat Strain Ontology, Clinical Measurement Ontology, Measurement Method Ontology and Experimental Condition Ontology). In this study, salt-induced hypertension was used as a model to retrieve blood pressure records of Brown Norway, Fawn-Hooded Hypertensive (FHH) and Dahl salt-sensitive (SS) rat strains. The records from these three strains served as a basis for comparing records from consomic/congenic/mutant offspring derived from them. We examined the cardiovascular and renal phenotypes of consomics derived from FHH and SS, and of SS congenics and mutants. The availability of quantitative records across laboratories in one database, such as these provided by PhenoMiner, can empower researchers to make the best use of publicly available data. Database URL: http://rgd.mcw.edu. PMID:25632109

Wang, Shur-Jen; Laulederkind, Stanley J F; Hayman, G Thomas; Petri, Victoria; Liu, Weisong; Smith, Jennifer R; Nigam, Rajni; Dwinell, Melinda R; Shimoyama, Mary

2015-01-01

140

A general framework for robust and efficient association analysis in family-based designs: quantitative and dichotomous phenotypes.  

PubMed

Although transmission disequilibrium tests (TDT) and the FBAT statistic are robust against population substructure, they have reduced statistical power, as compared with fully efficient tests that are not guarded against confounding because of population substructure. This has often limited the application of transmission disequilibrium tests/FBATs to candidate gene analysis, because, in a genome-wide association study, population substructure can be adjusted by approaches such as genomic control and EIGENSTRAT. Here, we provide new statistical methods for the analysis of quantitative and dichotomous phenotypes in extended families. Although the approach utilizes the polygenic model to maximize the efficiency, it still preserves the robustness to non-normality and misspecified covariance structures. In addition, the proposed method performs better than the existing methods for dichotomous phenotype, and the new transmission disequilibrium test for candidate gene analysis is more efficient than FBAT statistics. PMID:23740776

Won, Sungho; Lange, Christoph

2013-11-10

141

Temporal patterns of genetic and phenotypic variation in the epidemiologically important drone fly, Eristalis tenax.  

PubMed

Eristalis tenax L. (Diptera: Syrphidae) is commonly known as the drone fly (adult) or rat-tailed maggot (immature). Both adults and immature stages are identified as potential mechanical vectors of mycobacterial pathogens, and early-stage maggots cause accidental myiasis. We compared four samples from Mount Fruška Gora, Serbia, with the aim of obtaining insights into the temporal variations and sexual dimorphism in the species. This integrative approach was based on allozyme loci, morphometric wing parameters (shape and size) and abdominal colour patterns. Consistent sexual dimorphism was observed, indicating that male specimens had lighter abdomens and smaller and narrower wings than females. The distribution of genetic diversity at polymorphic loci indicated genetic divergence among collection dates. Landmark-based geometric morphometrics revealed, contrary to the lack of divergence in wing size, significant wing shape variation throughout the year. In addition, temporal changes in the frequencies of the abdominal patterns observed are likely to relate to the biology of the species and ecological factors in the locality. Hence, the present study expands our knowledge of the genetic diversity and phenotypic plasticity of E. tenax. The quantification of such variability represents a step towards the evaluation of the adaptive potential of this species of medical and epidemiological importance. PMID:21414022

Francuski, Lj; Mati?, I; Ludoški, J; Milankov, V

2011-06-01

142

Phenotypic variation and vulnerability to predation in juvenile bluegill sunfish (Lepomis macrochirus)  

USGS Publications Warehouse

Bluegill sunfish (Lepomis macrochirus) are known to diversify into two forms specialized for foraging on either limnetic or littoral prey. Because juvenile bluegills seek vegetative cover in the presence of largemouth bass (Micropterus salmoides) predators, natural selection should favor the littoral body design at size ranges most vulnerable to predation. Yet within bluegill populations, both limnetic and littoral forms occur where vegetation and predators are present. While adaptive for foraging in different environments, does habitat-linked phenotypic variation also influence predator evasiveness for juvenile bluegills? We evaluate this question by quantifying susceptibility to predation for two groups of morphologically distinct bluegills; a limnetic form characteristic of bluegills inhabiting open water areas (limnetic bluegill) and a littoral form characteristic of bluegills inhabiting dense vegetation (littoral bluegill). In a series of predation trials, we found that bluegill behaviors differed in open water habitat but not in simulated vegetation. In open water habitat, limnetic bluegills formed more dense shoaling aggregations, maintained a larger distance from the predator, and required longer amounts of time to capture than littoral bluegill. When provided with simulated vegetation, largemouth bass spent longer amounts of time pursuing littoral bluegill and captured significantly fewer littoral bluegills than limnetic fish. Hence, morphological and behavioral variation in bluegills was linked to differential susceptibility to predation in open water and vegetated environments. Combined with previous studies, these findings show that morphological and behavioral adaptations enhance both foraging performance and predator evasiveness in different lake habitats.

Chipps, S.R.; Dunbar, J.A.; Wahl, David H.

2004-01-01

143

Phenotypic variation and vulnerability to predation in juvenile bluegill sunfish (Lepomis macrochirus).  

PubMed

Bluegill sunfish (Lepomis macrochirus) are known to diversify into two forms specialized for foraging on either limnetic or littoral prey. Because juvenile bluegills seek vegetative cover in the presence of largemouth bass (Micropterus salmoides) predators, natural selection should favor the littoral body design at size ranges most vulnerable to predation. Yet within bluegill populations, both limnetic and littoral forms occur where vegetation and predators are present. While adaptive for foraging in different environments, does habitat-linked phenotypic variation also influence predator evasiveness for juvenile bluegills? We evaluate this question by quantifying susceptibility to predation for two groups of morphologically distinct bluegills; a limnetic form characteristic of bluegills inhabiting open water areas (limnetic bluegill) and a littoral form characteristic of bluegills inhabiting dense vegetation (littoral bluegill). In a series of predation trials, we found that bluegill behaviors differed in open water habitat but not in simulated vegetation. In open water habitat, limnetic bluegills formed more dense shoaling aggregations, maintained a larger distance from the predator, and required longer amounts of time to capture than littoral bluegill. When provided with simulated vegetation, largemouth bass spent longer amounts of time pursuing littoral bluegill and captured significantly fewer littoral bluegills than limnetic fish. Hence, morphological and behavioral variation in bluegills was linked to differential susceptibility to predation in open water and vegetated environments. Combined with previous studies, these findings show that morphological and behavioral adaptations enhance both foraging performance and predator evasiveness in different lake habitats. PMID:14517677

Chipps, Steven R; Dunbar, Jessica A; Wahl, David H

2004-01-01

144

Quantitative genetic modeling of variation in human brain morphology  

Microsoft Academic Search

The degree to which individual variation in brain structure in humans is genetically or environmentally determined is as yet not well understood. We studied the brains of 54 monozygotic (33 male, 21 female) and 58 dizygotic (17 male, 20 female, 21 opposite sex) pairs of twins and 34 of their full siblings (19 male, 15 female) by means of high

W. F. C. Baare; H. E. Hulshoff-Poll; Dorret I. Boomsma; Daniëlle Posthuma; Geus de E. J. C; H. G. Snack; Haren van N. E. M; Oel van C. J; René S. Kahn

2001-01-01

145

Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals.  

PubMed

Advances in our understanding of genome structure provide consistent evidence for the existence of a core genome representing species classically defined by phenotype, as well as conditionally dispensable components of the genome that shows extensive variation between individuals of a given species. Generally, conservation of phenotypic features between species reflects conserved features of the genome; however, this is evidently not necessarily always the case as demonstrated by the analysis of the tunicate chordate Oikopleura dioica. In both plants and animals, the methylation activity of DNA and histones continues to present new variables for modifying (eventually) the phenotype of an organism and provides for structural variation that builds on the point mutations, rearrangements, indels, and amplification of retrotransposable elements traditionally considered. The translation of the advances in the structure/function analysis of the genome to industry is facilitated through the capture of research outputs in "toolboxes" that remain accessible in the public domain. PMID:23494190

Appels, R; Barrero, R; Bellgard, M

2013-03-01

146

A theory of developmental change in quantitative phenotypes applied to cognitive development  

Microsoft Academic Search

A model is presented for the changes in familial resemblance as a function of age. The model allows for separate developmental components of genetic and environmental effects and for the influence of earlier phenotypic values on current measurements. Genetic and environmental effects may be specific to occasions or constant over time. Expected covariances are derived within individuals and between relatives

L. J. Eaves; J. Long; A. C. Heath

1986-01-01

147

Genotype-Phenotype-Mapping and Neutral Variation - A Case Study in Genetic Programming  

Microsoft Academic Search

. We propose the application of a genotype-phenotype mappingto the solution of constrained optimization problems. The methodconsists of strictly separating the search space of genotypes from the solutionspace of phenotypes. A mapping from genotypes into phenotypesprovides for the appropriate expression of information represented bythe genotypes. The mapping is constructed as to guarantee feasibilityof phenotypic solutions for the problem under study.

Wolfgang Banzhaf

1994-01-01

148

Mapping quantitative-trait loci in humans by use of extreme concordant sib pairs: selected sampling by parental phenotypes.  

PubMed Central

In two previous articles, we have considered sample sizes required to detect linkage for mapping quantitative-trait loci in humans, using extreme discordant sib pairs. Here, we examine further the use of extreme concordant sib pairs but consider the effect of parents' phenotypes. Sample sizes necessary to obtain a power of 80% with concordant sib pairs at a significance level of .0001 are given, stratified by parental phenotypes. When there is no residual correlation between sibs, the parental phenotypes have little impact on the sample sizes. When residual correlations between sibs exist, we show, however, that power can be considerably reduced by including extreme sib pairs when the parents also have similarly extreme values. Thus, we recommend the exclusion of such pairs from linkage studies. This recommendation reduces the required sample sizes by 3- to 28-fold. The degree of saving in the required sample sizes varies among different models and allele frequencies. The reduction is most dramatic (a 28-fold reduction) for a rare recessive gene. PMID:8808613

Zhang, H.; Risch, N.

1996-01-01

149

Autozygome Sequencing Expands the Horizon of Human Knockout Research and Provides Novel Insights into Human Phenotypic Variation  

PubMed Central

The use of autozygosity as a mapping tool in the search for autosomal recessive disease genes is well established. We hypothesized that autozygosity not only unmasks the recessiveness of disease causing variants, but can also reveal natural knockouts of genes with less obvious phenotypic consequences. To test this hypothesis, we exome sequenced 77 well phenotyped individuals born to first cousin parents in search of genes that are biallelically inactivated. Using a very conservative estimate, we show that each of these individuals carries biallelic inactivation of 22.8 genes on average. For many of the 169 genes that appear to be biallelically inactivated, available data support involvement in modulating metabolism, immunity, perception, external appearance and other phenotypic aspects, and appear therefore to contribute to human phenotypic variation. Other genes with biallelic inactivation may contribute in yet unknown mechanisms or may be on their way to conversion into pseudogenes due to true recent dispensability. We conclude that sequencing the autozygome is an efficient way to map the contribution of genes to human phenotypic variation that goes beyond the classical definition of disease. PMID:24367280

Anazi, Shamsa; Alshamekh, Shomoukh; Alkuraya, Fowzan S.

2013-01-01

150

From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development.  

PubMed

Tremendous natural variation of growth and development exists within species. Uncovering the molecular mechanisms that tune growth and development promises to shed light on a broad set of biological issues including genotype to phenotype relations, regulatory mechanisms of biological processes and evolutionary questions. Recent progress in sequencing and data processing capabilities has enabled Genome Wide Association Studies (GWASs) to identify DNA sequence polymorphisms that underlie the variation of biological traits. In the last years, GWASs have proven powerful in revealing the complex genetic bases of many phenotypes in various plant species. Here we highlight successful recent GWASs that uncovered mechanistic and sequence bases of trait variation related to plant growth and development and discuss important considerations for conducting successful GWASs. PMID:25449733

Ogura, Takehiko; Busch, Wolfgang

2015-02-01

151

Phenotypic variation and ploidy level of plants regenerated from protoplasts of tetraploid potato (Solanum tuberosum L. cv. 'Bintje').  

PubMed

A wide range of phenotypic variation occurred among protoplast - derived plants of tetraploid potato cultivar 'Bintje'. The variant plants had alterations in growth and vigour, and in leaf and stem characteristics. The results suggest that the altered morphologies are caused predominantly by changes in ploidy levels. Some alterations could be attributed typically to octoploidy and aneuploidy. The occurrence of mixoploidy indicates that at least part of the observed variation arose during culture stage. The exogeneous cytokinin or auxin level and their combination during in vitro phase influenced the frequency of the variants observed. The origin of variation is discussed. PMID:24263544

Sree Ramulu, K; Dijkhuis, P; Roest, S

1983-06-01

152

Localized versus generalist phenotypes in a broadly distributed tropical mammal: how is intraspecific variation distributed across disparate environments?  

PubMed Central

Background The extent of phenotypic differentiation in response to local environmental conditions is a key component of species adaptation and persistence. Understanding the structuring of phenotypic diversity in response to local environmental pressures can provide important insights into species evolutionary dynamics and responses to environmental change. This work examines the influence of steep environmental gradients on intraspecific phenotypic variation and tests two hypotheses about how the tropical soft grass mouse, Akodon mollis (Cricetidae, Rodentia), contends with the disparate environmental conditions encompassed by its broad distribution. Specifically, we test if the species expresses a geographically unstructured, or generalist, phenotype throughout its range or if it shows geographically localized morphological differentiation across disparate environments. Results Using geometric morphometric and ecomorphological analyses of skull shape variation we found that despite distinct environmental conditions, geographically structured morphological variation is limited, with the notable exception of a distinct morphological disjunction at the high-elevation forest-grassland transition in the southern portion of A. mollis distribution. Based on genetic analyses, geographic isolation alone does not explain this localized phenotype, given that similar levels of genetic differentiation were also observed among individuals inhabiting other ecosystems that are nonetheless not distinct morphologically. Conclusions Instead of phenotypic specialization across environments in these tropical mountains, there was limited differentiation of skull shape and size across the broad range of A. mollis, with the exception of individuals from the puna, the highest-elevation ecosystem. The high morphological variance among individuals, together with a weak association with local environmental conditions, not only highlights the flexibility of A. mollis’ skull, but also highlights the need for further study to understand what maintains the observed morphological patterns. The work also indicates that mechanisms other than processes linked to local ecological specialization as a driver of diversification may contribute to the high diversity of this tropical region. PMID:23899319

2013-01-01

153

Genetic and phenotypic correlations among size-related traits, and heritability variation between body parts in Drosophila buzzatii.  

PubMed

Recent studies have shown that body size is a heritable trait phenotypically correlated with several fitness components in wild populations of the cactophilic fly Drosophila buzzatii. To obtain further information on size-related variation, heritabilities as well as genetic and phenotypic correlations among size-related traits of several body parts (head, thorax and wings) were estimated. The study was carried out on an Argentinean natural population in which size-related selection was previously detected. The genetic parameters were estimated using offspring-parent regressions (105 families) in the laboratory G2 generation of a sample of wild flies. The traits were also scored in Wild-Caught Flies (WCF). Laboratory-Reared Flies (LRF) were larger and less variable than WCF. Although heritability estimates were significant for all traits, heritabilities were higher for thorax-wing traits than for head traits. Phenotypic and genetic correlations were all positive. The highest genetic correlations were found between traits which are both functionally and developmentally related. Genetic and phenotypic correlations estimated in the lab show similar correlation pattern (r = 0.49; P = 0.02, Mantel's test). However, phenotypic correlations were found to be typically larger in WCF than in LRF. The genetic correlation matrix estimated in the relatively homogeneous lab environment is not simply a constant multiplicative factor of the phenotypic correlation matrix estimated in WCF. PMID:9465404

Norry, F M; Vilardi, J C; Hasson, E

1997-01-01

154

Consistency and variation in phenotypic selection exerted by a community of seed predators.  

PubMed

Phenotypic selection that is sustained over time underlies both anagenesis and cladogenesis, but the conditions that lead to such selection and what causes variation in selection are not well known. We measured the selection exerted by three species of predispersal seed predators of lodgepole pine (Pinus contorta latifolia) in the South Hills, Idaho, and found that net selection on different cone and seed traits exerted by red crossbills (Loxia curvirostra) and cone borer moths (Eucosma recissoriana) over 10 years of seed crops was similar to that measured in another mountain range. We also found that the strength of selection increased as seed predation increased, which provides a mechanism for the correlation between the escalation of seed defenses and the density of seed predators. Red crossbills consume the most seeds and selection they exert accounts for much of the selection experienced by lodgepole pine, providing additional support for a coevolutionary arms race between crossbills and lodgepole pine in the South Hills. The third seed predator, hairy woodpeckers (Picoides villosus), consumed less than one-sixth as many seeds as crossbills. Across the northern Rocky Mountains, woodpecker abundance and therefore selective impact appears limited by the elevated seed defenses of lodgepole pine. PMID:23289569

Benkman, Craig W; Smith, Julie W; Maier, Monika; Hansen, Leif; Talluto, Matt V

2013-01-01

155

Phenotypic variation in metamorphosis and paedomorphosis in the salamander Ambystoma talpoideum  

SciTech Connect

Phenotypic variation in metamorphosis and paedomorphosis in the salamander Ambystoma talpoideum was examined to determine its environmental or genetic basis. Eight artificial ponds were maintained, four at each of two environmental treatments: constant water level, to simulate fish-free permanent breeding ponds, and gradual drying out, to simulate temporary breeding ponds. Two populations of salamanders were used, derived from two breeding ponds having different frequencies of paedomorphosis. The water level in the drying treatment was lowered during the last 10 wk of the experimental period with no apparent differences in water chemistry parameters between treatments and only a slight change in water temperature during the last 2 wk. The effects of water level were potentially confounded by those of water temperature, density of larvae, and amount food. Population differences in the frequency of metamorphosis and paedomorphosis could potentially represent genetic differences resulting from the different selective regimes that individuals encounter in breeding ponds varying in drying frequency. 35 references, 3 figures, 4 tables.

Semlitsch, R.D.; Gibbons, J.W.

1985-08-01

156

Speciation, Phenotypic Variation and Plasticity: What Can Endocrine Disruptors Tell Us?  

PubMed Central

Phenotype variability, phenotypic plasticity, and the inheritance of phenotypic traits constitute the fundamental ground of processes such as individuation, individual and species adaptation and ultimately speciation. Even though traditional evolutionary thinking relies on genetic mutations as the main source of intra- and interspecies phenotypic variability, recent studies suggest that the epigenetic modulation of gene transcription and translation, epigenetic memory, and epigenetic inheritance are by far the most frequent reliable sources of transgenerational variability among viable individuals within and across organismal species. Therefore, individuation and speciation should be considered as nonmutational epigenetic phenomena. PMID:23762055

Ayala-García, Braulio; López-Santibáñez Guevara, Marta; Marcos-Camacho, Lluvia I.; Fuentes-Farías, Alma L.; Meléndez-Herrera, Esperanza; Gutiérrez-Ospina, Gabriel

2013-01-01

157

An experimental method for evaluating the contribution of deleterious mutations to quantitative trait variation  

E-print Network

by comparing the relative magnitudes of two genetic variance components: the covariance of additive and homozygous dominance effects (C ad ) and the additive genetic variance (V a ). If genetic variation is due to rare recessives, then the ratio of C ad to V a... should be equal to or greater than 1. In contrast, C ad }V a should be close to zero or even negative if variation is caused by alleles at intermediate frequencies. The ratio of C ad to V a can be estimated from phenotypic comparisons between inbred...

Kelly, John K.

1999-06-01

158

Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse models.  

PubMed

A large fraction of genome variation between individuals is comprised of submicroscopic copy number variation of genomic DNA segments. We assessed the relative contribution of structural changes and gene dosage alterations on phenotypic outcomes with mouse models of Smith-Magenis and Potocki-Lupski syndromes. We phenotyped mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+), and balanced 2n compound heterozygous (Deletion/Duplication) copies of the same region. Parallel to the observations made in humans, such variation in gene copy number was sufficient to generate phenotypic consequences: in a number of cases diametrically opposing phenotypes were associated with gain versus loss of gene content. Surprisingly, some neurobehavioral traits were not rescued by restoration of the normal gene copy number. Transcriptome profiling showed that a highly significant propensity of transcriptional changes map to the engineered interval in the five assessed tissues. A statistically significant overrepresentation of the genes mapping to the entire length of the engineered chromosome was also found in the top-ranked differentially expressed genes in the mice containing rearranged chromosomes, regardless of the nature of the rearrangement, an observation robust across different cell lineages of the central nervous system. Our data indicate that a structural change at a given position of the human genome may affect not only locus and adjacent gene expression but also "genome regulation." Furthermore, structural change can cause the same perturbation in particular pathways regardless of gene dosage. Thus, the presence of a genomic structural change, as well as gene dosage imbalance, contributes to the ultimate phenotype. PMID:21124890

Ricard, Guénola; Molina, Jessica; Chrast, Jacqueline; Gu, Wenli; Gheldof, Nele; Pradervand, Sylvain; Schütz, Frédéric; Young, Juan I; Lupski, James R; Reymond, Alexandre; Walz, Katherina

2010-01-01

159

Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity.  

PubMed

Predicting the impact of genetic variation on human health remains an important and difficult challenge. Often, algorithmic classifiers are tasked with predicting binary traits (e.g. positive or negative for a disease) from missense variation. Though useful, this arrangement is limiting and contrived, because human diseases often comprise a spectrum of severities, rather than a discrete partitioning of patient populations. Furthermore, labeling variants as causal or benign can be error prone, which is problematic for training supervised learning algorithms (the so-called garbage in, garbage out phenomenon). We explore the potential value of training classifiers using continuous-valued quantitative measurements, rather than binary traits. Using 20 variants from cystic fibrosis transmembrane conductance regulator (CFTR) nucleotide-binding domains and six quantitative measures of cystic fibrosis (CF) severity, we trained classifiers to predict CF severity from CFTR variants. Employing cross validation, classifier prediction and measured clinical/functional values were significantly correlated for four of six quantitative traits (correlation P-values from 1.35 × 10(-4) to 4.15 × 10(-3)). Classifiers were also able to stratify variants by three clinically relevant risk categories with 85-100% accuracy, depending on which of the six quantitative traits was used for training. Finally, we characterized 11 additional CFTR variants using clinical sweat chloride testing, two functional assays, or all three diagnostics, and validated our classifier using blind prediction. Predictions were within the measured sweat chloride range for seven of eight variants, and captured the differential impact of specific variants on the two functional assays. This work demonstrates a promising and novel framework for assessing the impact of genetic variation. PMID:25489051

Masica, David L; Sosnay, Patrick R; Raraigh, Karen S; Cutting, Garry R; Karchin, Rachel

2015-04-01

160

24?Common and Rare Variation in the T Helper 2 Gene Pathway Predicts Allergic Asthma Phenotypes  

PubMed Central

Background The T helper 2 (Th2) inflammatory pathway, including the Th2-activating cytokine interleukin 33 and its receptor interleukin 1 receptor-like 1 have been strongly implicated in asthma susceptibility (Moffatt MF, et al NEJM 2010). However, the role of Th2 pathway genetic variation in asthma progression and severity is not well understood. Our research group recently developed a clustering algorithm based on comprehensive phenotype information to assign subjects with asthma in the Severe Asthma Research Program (SARP) to 5 primary clusters; 3 of which represent increasing severe allergic asthma (Moore WC, et al AJRCCM, 2010). We hypothesized that common and potentially deleterious rare variation in this pathway would be associated with severe asthma based on SARP cluster designation. Methods To evaluate common variants (minor allele frequency or MAF >5%), 419 SARP non-Hispanic white participants with a cluster assignment were genotyped for 182 single nucleotide polymorphisms (SNPs) in Th2 pathway genes using whole-genome SNP data. Individual SNPs and a cumulative model of significant SNPs were evaluated using contingency tables with a chi-square test for trend and ordinal regression models adjusted for age, sex, and principal components. Rare (MAF <5%) amino acid changes and splice site alterations in this pathway were tested for association with asthma severity outcomes in 20 SARP subjects with whole exome sequence data. Results Individual Th2 pathway variants were associated with overall SARP cluster assignment, and allergic clusters of increasing severity (1, 2, and 4), including GATA3 polymorphism rs1244186 (P = 0.005). In an 18-SNP additive model, an increasing number of Th2 pathway risk genotypes were highly associated with severe allergic asthma (P = 3.9 × 10?6). For example, in cluster 4, the percentage of subjects with at least 9 risk genotypes was 83% compared to 35% in cluster 1. Additionally, there was evidence that subjects with rare variants in this pathway were more likely to report allergy symptoms (P = 0.006), especially in the fall (P = 0.003), compared to subjects with no rare variants. Conclusions Common Th2 pathway variants predict an increased likelihood of severe allergic asthma and rare variants were associated with increased seasonal allergy symptoms.

Slager, Rebecca; Moore, Wendy; Li, Huashi; Busse, William; Castro, Mario; Erzurum, Serpil; Fitzpatrick, Anne; Wenzel, Sally; Meyers, Deborah; Bleecker, Eugene R.

2012-01-01

161

The quantitative genetic basis of sex ratio variation in Nasonia vitripennis: a QTL study  

E-print Network

The quantitative genetic basis of sex ratio variation in Nasonia vitripennis: a QTL study B. A The study of sex allocation and sex ratios has produced many of the best tests of evolutionary theory and Evolutionary Studies, University of Groningen, Groningen, The Netherlands àDepartment of Zoology, University

Shuker, David

162

Genetic variation in mountain hemlock ( Tsuga mertensiana Bong.): quantitative and adaptive attributes  

Microsoft Academic Search

Patterns of genetic variation for adaptive and quantitative attributes in mountain hemlock (Tsuga mertensiana (Bong.)) seedlings from British Columbia were examined at the population (provenance) and family levels. The population and family levels were represented by 12 provenances and 10 families from a single location, respectively. The adaptive attributes were related to gas exchange (net photosynthesis, transpiration rate, intercellular-to-ambient CO2

Andy Benowicz; Yousry A. El-Kassaby

1999-01-01

163

A Mendelian polymorphism underlying quantitative variations of goat ?s1-casein  

E-print Network

A Mendelian polymorphism underlying quantitative variations of goat ?s1-casein F. GROSCLAUDE- les, designated a,,-Cn'-, ?s1-CnF and ?s1-Cno, were identified at the goat a!-Cn locus superiority in casein content of milks from goats possessing the allele

Boyer, Edmond

164

Identification of genes related to the phenotypic variations of a synthesized Paulownia (Paulownia tomentosa×Paulownia fortunei) autotetraploid.  

PubMed

Paulownia is a fast-growing deciduous tree native to China. It has great economic importance for the pulp and paper industries, as well as ecological prominence in forest ecosystems. Paulownia is of much interest to plant breeder keen to explore new plant varieties by selecting on the basis of phenotype. A newly synthesized autotetraploid Paulownia exhibited advanced characteristics, such as greater yield, and higher resistance than the diploid tree. However, tissue-specific transcriptome and genomic data in public databases are not sufficient to understand the molecular mechanisms associated with genome duplication. To evaluate the effects of genome duplication on the phenotypic variations in Paulownia tomentosa×Paulownia fortunei, the transcriptomes of the autotetraploid and diploid Paulownia were compared. Using Illumina sequencing technology, a total of 82,934 All-unigenes with a mean length of 1109 bp were assembled. The data revealed numerous differences in gene expression between the two transcriptomes, including 718 up-regulated and 667 down-regulated differentially expressed genes between the two Paulownia trees. An analysis of the pathway and gene annotations revealed that genes involved in nucleotide sugar metabolism in plant cell walls were down-regulated, and genes involved in the light signal pathway and the biosynthesis of structural polymers were up-regulated in autotetraploid Paulownia. The differentially expressed genes may contribute to the observed phenotypic variations between diploid and autotetraploid Paulownia. These results provide a significant resource for understanding the variations in Paulownia polyploidization and will benefit future breeding work. PMID:25300252

Li, Yongsheng; Fan, Guoqiang; Dong, Yanpeng; Zhao, Zhenli; Deng, Minjie; Cao, Xibing; Xu, Enkai; Niu, Suyan

2014-12-15

165

A Thirty-Year Study of Phenotypic and Genetic Variation of Blue Tits in Mediterranean Habitat Mosaics  

NSDL National Science Digital Library

This peer reviewed article from BioScience investigate phenotypic variation in blue tits. In recent years, the study of phenotypic and genetic variation has been enhanced by combining genetic, physiological, demographic, and behavioral components of life histories. Using these new approaches, we address the problem of adaptation to environmental heterogeneity by examining in detail the variation of several fitness-related traits in a small passerine bird, the blue tit, which has been extensively studied in habitat mosaics of the Mediterranean region. The response of blue tits to spatial habitat heterogeneity depends on their range of dispersal relative to the size of habitat patches. Dispersal over short distances leads to local specialization, whereas dispersal over long distances leads to phenotypic plasticity. Gene flow between habitats of different quality may produce local maladaptation and a source-sink population structure. However, when habitat-specific divergent selection regimes are strong enough to oppose the effects of gene flow, local adaptation may arise on a scale that is much smaller than the scale of dispersal.

JACQUES BLONDEL, DONALD W. THOMAS, ANNE CHARMANTIER, PHILIPPE PERRET, PATRICE BOURGAULT, and MARCEL M. LAMBRECHTS (; )

2006-08-01

166

The contributions of evolutionary divergence and phenotypic plasticity to geographic variation in the  

E-print Network

in the western fence lizard, Sceloporus occidentalis CHRISTINE R. BUCKLEY1 *, DUNCAN J. IRSCHICK2 and STEPHEN C ontogeny to shape organismal phenotypes. We incubated eggs of the western fence lizard, Sceloporus

Irschick, Duncan J.

167

Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping  

E-print Network

The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test ...

Vaysse, Amaury

168

Phenotypic variation and associated predation risk of juvenile common carp Cyprinus carpio.  

PubMed

Juvenile common carp Cyprinus carpio were collected from 10 lakes with variable predator abundance over 4 months to evaluate if morphological defences increased with increasing predation risk. Cyprinus carpio dorsal and pectoral spines were longer and body depth was deeper when predators were more abundant, with differences becoming more pronounced from July to October. To determine if morphological plasticity successfully reduced predation risk, prey selection of largemouth bass Micropterus salmoides foraging on deep- and shallow-bodied C. carpio was evaluated in open and vegetated environments. Predators typically selected deep- over shallow-bodied phenotypes in open habitats and neutrally selected both phenotypes in vegetated habitats. When exposed to predators, shallow-bodied C. carpio phenotypes shoaled in open habitat, whereas deep-bodied phenotypes occupied vegetation. Although deep-bodied phenotypes required additional handling time, shallow-bodied phenotypes were more difficult to capture. These results suggest that juvenile C. carpio gradually develop deeper bodies and larger spines as predation risk increases. Morphological defences made it more difficult for predators to consume these prey but resulted in higher vulnerability to predation in some instances. PMID:22220889

Weber, M J; Rounds, K D; Brown, M L

2012-01-01

169

The effect of temperature and wing morphology on quantitative genetic variation in the cricket Gryllus firmus, with an appendix  

E-print Network

The effect of temperature and wing morphology on quantitative genetic variation in the cricket focuses on two factors that may induce G matrix variation within a population of field crickets on the quantitative genetic variances and covariances of five size-related traits in the sand cricket, Gryllus firmus

Debat, Vincent

170

A Quantitative Framework for Flower Phenotyping in Cultivated Carnation (Dianthus caryophyllus L.)  

PubMed Central

Most important breeding goals in ornamental crops are plant appearance and flower characteristics where selection is visually performed on direct offspring of crossings. We developed an image analysis toolbox for the acquisition of flower and petal images from cultivated carnation (Dianthus caryophyllus L.) that was validated by a detailed analysis of flower and petal size and shape in 78 commercial cultivars of D. caryophyllus, including 55 standard, 22 spray and 1 pot carnation cultivars. Correlation analyses allowed us to reduce the number of parameters accounting for the observed variation in flower and petal morphology. Convexity was used as a descriptor for the level of serration in flowers and petals. We used a landmark-based approach that allowed us to identify eight main principal components (PCs) accounting for most of the variance observed in petal shape. The effect and the strength of these PCs in standard and spray carnation cultivars are consistent with shared underlying mechanisms involved in the morphological diversification of petals in both subpopulations. Our results also indicate that neighbor-joining trees built with morphological data might infer certain phylogenetic relationships among carnation cultivars. Based on estimated broad-sense heritability values for some flower and petal features, different genetic determinants shall modulate the responses of flower and petal morphology to environmental cues in this species. We believe our image analysis toolbox could allow capturing flower variation in other species of high ornamental value. PMID:24349209

Chacón, Borja; Ballester, Roberto; Birlanga, Virginia; Rolland-Lagan, Anne-Gaëlle; Pérez-Pérez, José Manuel

2013-01-01

171

Maintenance of phenotypic variation: repeatability, heritability and size-dependent processes in a wild brook trout population.  

PubMed

Phenotypic variation in body size can result from within-cohort variation in birth dates, among-individual growth variation and size-selective processes. We explore the relative effects of these processes on the maintenance of wide observed body size variation in stream-dwelling brook trout (Salvelinus fontinalis). Based on the analyses of multiple recaptures of individual fish, it appears that size distributions are largely determined by the maintenance of early size variation. We found no evidence for size-dependent compensatory growth (which would reduce size variation) and found no indication that size-dependent survival substantially influenced body size distributions. Depensatory growth (faster growth by larger individuals) reinforced early size variation, but was relatively strong only during the first sampling interval (age-0, fall). Maternal decisions on the timing and location of spawning could have a major influence on early, and as our results suggest, later (>age-0) size distributions. If this is the case, our estimates of heritability of body size (body length = 0.25) will be dominated by processes that generate and maintain early size differences. As a result, evolutionary responses to environmental change that are mediated by body size may be largely expressed via changes in the timing and location of reproduction. PMID:25568008

Letcher, Benjamin H; Coombs, Jason A; Nislow, Keith H

2011-07-01

172

Phenotypic Variations and Dynamic Topography of Transformed Cells in an Experimental Model of Diethylstilbestrol-Induced Renal Tumour in Male Syrian Hamster  

Microsoft Academic Search

This work explores the phenotypic changes affecting transformed cells in an experimental model of diethylstilbestrol (DES)-induced renal tumours in male Syrian hamster. This estrogen-induced neoplasm presents an important cytological pleomorphism and its origin remains largely controversial. In order to characterize phenotypic variations during tumour progression, the occurrence of seven lineage markers was analysed by a morphometric approach in kidney sections

Denis Nonclercq; Vanessa Liénard; Jacqueline Zanen; Guy Laurent; Gérard Toubeau

2002-01-01

173

Determining the linkage of quantitative trait loci to RFLP markers using extreme phenotypes of recombinant inbreds of soybean ( Glycine max L. Merr.)  

Microsoft Academic Search

An experimental test is described for linkages between RFLP markers and quantitative trait loci (QTL). Two hundred and eighty-four F7-derived recombinant inbred lines (RIL) obtained from crossing the soybean cultivars (Glycine max L. Merr.) ‘Minsoy’ and ‘Noir 1’ were evaluated for maturity, plant height, lodging, and seed yield. RIL exhibiting an extreme phenotype for each trait (earliest and latest plants

L. M. Mansur; J. Orf; K. G. Lark

1993-01-01

174

Quantitative measurement of phase variation amplitude of ultrasonic diffraction grating based on diffraction spectral analysis  

SciTech Connect

A new method based on diffraction spectral analysis is proposed for the quantitative measurement of the phase variation amplitude of an ultrasonic diffraction grating. For a traveling wave, the phase variation amplitude of the grating depends on the intensity of the zeroth- and first-order diffraction waves. By contrast, for a standing wave, this amplitude depends on the intensity of the zeroth-, first-, and second-order diffraction waves. The proposed method is verified experimentally. The measured phase variation amplitude ranges from 0 to 2?, with a relative error of approximately 5%. A nearly linear relation exists between the phase variation amplitude and driving voltage. Our proposed method can also be applied to ordinary sinusoidal phase grating.

Pan, Meiyan, E-mail: yphantomohive@gmail.com; Zeng, Yingzhi; Huang, Zuohua, E-mail: zuohuah@163.com [Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou, Guangdong 510006 (China)

2014-09-15

175

Quantitative measurement of phase variation amplitude of ultrasonic diffraction grating based on diffraction spectral analysis.  

PubMed

A new method based on diffraction spectral analysis is proposed for the quantitative measurement of the phase variation amplitude of an ultrasonic diffraction grating. For a traveling wave, the phase variation amplitude of the grating depends on the intensity of the zeroth- and first-order diffraction waves. By contrast, for a standing wave, this amplitude depends on the intensity of the zeroth-, first-, and second-order diffraction waves. The proposed method is verified experimentally. The measured phase variation amplitude ranges from 0 to 2?, with a relative error of approximately 5%. A nearly linear relation exists between the phase variation amplitude and driving voltage. Our proposed method can also be applied to ordinary sinusoidal phase grating. PMID:25273712

Pan, Meiyan; Zeng, Yingzhi; Huang, Zuohua

2014-09-01

176

Phenotypic variation in nurse traits and community feedbacks define an alpine community.  

PubMed

Much is known about facilitation, but virtually nothing about the underlying genetic and evolutionary consequences of this important interaction. We assessed the potential of phenotypic differences in facilitative effects of a foundation species to determine the composition of an Alpine community in Arizona. Two phenotypes of Geum rossii occur along a gradient of disturbance, with 'tight' competitive cushions in stable conditions and 'loose' facilitative cushions in disturbed conditions. A common-garden study suggested that field-based traits may have a genetic basis. Field experiments showed that the reproductive fitness of G. rossii cushions decreased with increasing facilitation. Finally, using a dual-lattice model we showed that including the cost and benefit of facilitation may contribute to the co-occurrence of genotypes with contrasting facilitative effects. Our results indicate that changes in community composition due to phenotypic differences in facilitative effects of a foundation species may in turn affect selective pressures on the foundation species. PMID:21366815

Michalet, Richard; Xiao, Sa; Touzard, Blaise; Smith, David S; Cavieres, Lohengrin A; Callaway, Ragan M; Whitham, Thomas G

2011-05-01

177

Phenotypic variation of Staphylococcus epidermidis in infection of transvenous endocardial pacemaker electrodes.  

PubMed Central

Coagulase-negative staphylococci isolated from a patient with a pacemaker electrode infection were extensively evaluated by phenotypic and genotypic characterization. Findings from this evaluation were striking because different colony morphologic subtypes were recovered from blood and resected pacemaker electrodes. Staphylococci from each colony subtype (LBL, LBV, LBP, LBS) were identified as slime-producing strains of Staphylococcus epidermidis sensu stricto. Direct plating of isolates from a restricted electrode revealed a mixture of colony phenotypes when examined on a high-salt, low-glucose medium, Memphis agar. Bacteriophage typing employing 17 different phages and plasmid profile analysis were largely unsuccessful in further characterizing bacterial cells of each of the four colony morphotypes. On the other hand, restriction endonuclease analysis by EcoRI digestion of the chromosomal DNA demonstrated the probable common clonal origin of the four colony phenotypes. Images PMID:2332465

Baddour, L M; Barker, L P; Christensen, G D; Parisi, J T; Simpson, W A

1990-01-01

178

Phenotypic Variation across Chromosomal Hybrid Zones of the Common Shrew (Sorex araneus) Indicates Reduced Gene Flow  

PubMed Central

Sorex araneus, the Common shrew, is a species with more than 70 karyotypic races, many of which form parapatric hybrid zones, making it a model for studying chromosomal speciation. Hybrids between races have reduced fitness, but microsatellite markers have demonstrated considerable gene flow between them, calling into question whether the chromosomal barriers actually do contribute to genetic divergence. We studied phenotypic clines across two hybrid zones with especially complex heterozygotes. Hybrids between the Novosibirsk and Tomsk races produce chains of nine and three chromosomes at meiosis, and hybrids between the Moscow and Seliger races produce chains of eleven. Our goal was to determine whether phenotypes show evidence of reduced gene flow at hybrid zones. We used maximum likelihood to fit tanh cline models to geometric shape data and found that phenotypic clines in skulls and mandibles across these zones had similar centers and widths as chromosomal clines. The amount of phenotypic differentiation across the zones is greater than expected if it were dissipating due to unrestricted gene flow given the amount of time since contact, but it is less than expected to have accumulated from drift during allopatric separation in glacial refugia. Only if heritability is very low, Ne very high, and the time spent in allopatry very short, will the differences we observe be large enough to match the expectation of drift. Our results therefore suggest that phenotypic differentiation has been lost through gene flow since post-glacial secondary contact, but not as quickly as would be expected if there was free gene flow across the hybrid zones. The chromosomal tension zones are confirmed to be partial barriers that prevent differentiated races from becoming phenotypically homogenous. PMID:23874420

Polly, P. David; Polyakov, Andrei V.; Ilyashenko, Vadim B.; Onischenko, Sergei S.; White, Thomas A.; Shchipanov, Nikolay A.; Bulatova, Nina S.; Pavlova, Svetlana V.; Borodin, Pavel M.; Searle, Jeremy B.

2013-01-01

179

A Genome-Wide Association Study of Schizophrenia Using Brain Activation as a Quantitative Phenotype  

PubMed Central

Background: Genome-wide association studies (GWASs) are increasingly used to identify risk genes for complex illnesses including schizophrenia. These studies may require thousands of subjects to obtain sufficient power. We present an alternative strategy with increased statistical power over a case-control study that uses brain imaging as a quantitative trait (QT) in the context of a GWAS in schizophrenia. Methods: Sixty-four subjects with chronic schizophrenia and 74 matched controls were recruited from the Functional Biomedical Informatics Research Network (FBIRN) consortium. Subjects were genotyped using the Illumina HumanHap300 BeadArray and were scanned while performing a Sternberg Item Recognition Paradigm in which they learned and then recognized target sets of digits in an functional magnetic resonance imaging protocol. The QT was the mean blood oxygen level–dependent signal in the dorsolateral prefrontal cortex during the probe condition for a memory load of 3 items. Results: Three genes or chromosomal regions were identified by having 2 single-nucleotide polymorphisms (SNPs) each significant at P < 10?6 for the interaction between the imaging QT and the diagnosis (ROBO1-ROBO2, TNIK, and CTXN3-SLC12A2). Three other genes had a significant SNP at <10?6 (POU3F2, TRAF, and GPC1). Together, these 6 genes/regions identified pathways involved in neurodevelopment and response to stress. Conclusion: Combining imaging and genetic data from a GWAS identified genes related to forebrain development and stress response, already implicated in schizophrenic dysfunction, as affecting prefrontal efficiency. Although the identified genes require confirmation in an independent sample, our approach is a screening method over the whole genome to identify novel SNPs related to risk for schizophrenia. PMID:19023125

Potkin, Steven G.; Turner, Jessica A.; Guffanti, Guia; Lakatos, Anita; Fallon, James H.; Nguyen, Dana D.; Mathalon, Daniel; Ford, Judith; Lauriello, John; Macciardi, Fabio

2009-01-01

180

Multi-character approach reveals a discordant pattern of phenotypic variation during ontogeny in Culex pipiens biotypes (Diptera: Culicidae).  

PubMed

Culex (Culex) pipiens s.l. (Diptera: Culicidae) comprises two distinct biotypes, pipiens ('rural') and molestus ('urban'), both of which are thought to have differing capacities due to different host preferences. To better understand West Nile encephalitis epidemiology and improve risk assessment, local distinction between these forms is essential. This study assesses phenotypic variation at larval and adult stages of 'urban' and 'rural' biotypes of the species by complementary use of meristic, univariate and multivariate traits analyzed by traditional and geometric morphometrics. Third- and fourth-instar larvae from a broad area of the city of Novi Sad (Serbia) were collected and reared in the laboratory. After adult eclosion, the sex of each larva was recorded based on the sex of the corresponding adult. Examination of the association between variations of larval traits revealed contrasting variations regarding pecten spines vs. siphonal size and siphonal shape in the 'rural' biotype. Siphons of larvae collected in marshes and forest ecosystems outside urban areas were found to be the largest, but possessed the smallest number of pecten spines. In addition, statistically significant female-biased sexual dimorphism was observed in siphonal size, wing size and wing shape. Finally, we propose that an integrative approach is essential in delimitation of Cx. pipiens s.l. biotypes, since their differentiation was not possible based solely on larval and adult traits. Our findings shed light on the phenotypic plasticity important for population persistence in the changing environment of these medically important taxa. PMID:25424880

Krtini?, B; Ludoški, J; Milankov, V

2015-02-01

181

Clonal Expansion of the Pseudogymnoascus destructans Genotype in North America Is Accompanied by Significant Variation in Phenotypic Expression  

PubMed Central

Pseudogymnoascus destructans is the causative agent of an emerging infectious disease that threatens populations of several North American bat species. The fungal disease was first observed in 2006 and has since caused the death of nearly six million bats. The disease, commonly known as white-nose syndrome, is characterized by a cutaneous infection with P. destructans causing erosions and ulcers in the skin of nose, ears and/or wings of bats. Previous studies based on sequences from eight loci have found that isolates of P. destructans from bats in the US all belong to one multilocus genotype. Using the same multilocus sequence typing method, we found that isolates from eastern and central Canada also had the same genotype as those from the US, consistent with the clonal expansion of P. destructans into Canada. However, our PCR fingerprinting revealed that among the 112 North American isolates we analyzed, three, all from Canada, showed minor genetic variation. Furthermore, we found significant variations among isolates in mycelial growth rate; the production of mycelial exudates; and pigment production and diffusion into agar media. These phenotypic differences were influenced by culture medium and incubation temperature, indicating significant variation in environmental condition - dependent phenotypic expression among isolates of the clonal P. destructans genotype in North America. PMID:25122221

Khankhet, Jordan; Vanderwolf, Karen J.; McAlpine, Donald F.; McBurney, Scott; Overy, David P.; Slavic, Durda; Xu, Jianping

2014-01-01

182

Quantitative variation in ecological and hormonal variables correlates with spatial organization of pronghorn ( Antilocapra americana ) males  

Microsoft Academic Search

Whereas variation in pronghorn (Antilocapra americana) spatial organization is well documented, underlying ecological or physiological explanations are not well understood. This\\u000a study quantitatively describes spacing systems of pronghorn males and correlates of their spatial organization. I collected\\u000a behavioral data from two populations in South Dakota (Wind Cave) and Montana (Bar Diamond) to determine if males differed\\u000a in space use, response

C. R. Maher

2000-01-01

183

Variation in human brains may facilitate evolutionary change toward a limited range of phenotypes  

PubMed Central

Individual variation is the foundation for evolutionary change, but little is known about the nature of normal variation between brains. Phylogenetic variation across mammalian brains is characterized by high inter-correlations in brain region volumes, distinct allometric scaling for each brain region and the relative independence in olfactory and limbic structures volumes from the rest of the brain. Previous work examining brain variation in individuals of some domesticated species showed that these three features of phylogenetic variation were mirrored in individual variation. We extend this analysis to the human brain and 10 of its subdivisions (e.g., isocortex, hippocampus) by using magnetic resonance imaging scans of 90 human brains ranging between 16 to 25 years of age. Human brain variation resembles both the individual variation seen in other species, and variation observed across mammalian species. That is, the relative differences in the slopes of each brain region compared to medulla size within humans and between mammals are concordant, and limbic structures scale with relative independence from other brain regions. This non-random pattern of variation suggests that developmental programs channel the variation available for selection. PMID:23363667

Charvet, Christine J.; Darlington, Richard B.; Finlay, Barbara L.

2013-01-01

184

Deficiencies in Jasmonate-Mediated Plant Defense Reveal Quantitative Variation in Botrytis cinerea Pathogenesis  

E-print Network

Despite the described central role of jasmonate signaling in plant defense against necrotrophic pathogens, the existence of intraspecific variation in pathogen capacity to activate or evade plant jasmonate-mediated defenses is rarely considered. Experimental infection of jasmonate-deficient and jasmonate-insensitive Arabidopsis thaliana with diverse isolates of the necrotrophic fungal pathogen Botrytis cinerea revealed pathogen variation for virulence inhibition by jasmonate-mediated plant defenses and induction of plant defense metabolites. Comparison of the transcriptional effects of infection by two distinct B. cinerea isolates showed only minor differences in transcriptional responses of wild-type plants, but notable isolate-specific transcript differences in jasmonate-insensitive plants. These transcriptional differences suggest B. cinerea activation of plant defenses that require plant jasmonate signaling for activity in response to only one of the two B. cinerea isolates tested. Thus, similar infection phenotypes observed in wild-type plants result from different signaling interactions

Heather C. Rowe ¤a; Justin W. Walley ¤b; Jason Corwin; Eva K. -f. Chan ¤c; Katayoon Dehesh; Daniel J

2010-01-01

185

Landscape patterns of phenotypic variation and population structuring in a selfing grass, Elymus glaucus (blue wildrye)  

Microsoft Academic Search

Source-related phenotypic variance was investigated in a common garden study of populations of Elymus glaucus Buckley (blue wildrye) from the Blue Mountain Ecological Province of northeastern Oregon and adjoining Washington. The primary objective of this study was to assess geographic patterns of potentially adaptive differentia- tion in this self-fertile allotetraploid grass, and use this information to develop a framework for

Vicky J. Erickson; Nancy L. Mandel; Frank C. Sorensen

2004-01-01

186

Mining natural variation for maize improvement: Selection on phenotypes and genes  

Technology Transfer Automated Retrieval System (TEKTRAN)

Maize is highly genetically and phenotypically diverse. Tropical maize and teosinte are important genetic resources that harbor unique alleles not found in temperate maize hybrids. To access these resources, breeders must be able to extract favorable unique alleles from tropical maize and teosinte f...

187

Phenotypic variation in susceptibility of honey bees, Apis mellifera , to infestation by tracheal mites, Acarapis woodi  

Microsoft Academic Search

A laboratory bioassay was used to study phenotypic differences in susceptibility of honey bees,Apis mellifera L., to tracheal mites,Acarapis woodi Rennie. Significantly different infestation frequencies were found in bees from 23 colonies containing queens that were instrumentally inseminated with single drones. Queens and drones originated from a closed population composed of commercial stock from various areas of the United States.

Norman E. Gary; Robert E. Page

1987-01-01

188

Phenotypically Concordant and Discordant Monozygotic Twins Display Different DNA Copy-Number-Variation Profiles  

Microsoft Academic Search

in the genetic makeup between twins derived from the same zygote represent an irrefutable example of somatic mosaicism. We studied 19 pairs of monozygotic twins with either concordant or discordant phenotype by using two platforms for genome-wide CNV analyses and showed that CNVs exist within pairs in both groups. These findings have an impact on our views of genotypic and

Carl E. G. Bruder; Arkadiusz Piotrowski; Antoinet A. C. J. Gijsbers; Robin Andersson; Stephen Erickson; Teresita Diaz de Ståhl; Uwe Menzel; Johanna Sandgren; Desiree von Tell; Andrzej Poplawski; Michael Crowley; Chiquito Crasto; E. Christopher Partridge; Hemant Tiwari; David B. Allison; Jan Komorowski; Gert-Jan B. van Ommen; Dorret I. Boomsma; Nancy L. Pedersen; Johan T. den Dunnen; Karin Wirdefeldt; Jan P. Dumanski

2008-01-01

189

Pharmacogenetics of antidepressants and antipsychotics: the contribution of allelic variations to the phenotype of drug response  

Microsoft Academic Search

Genetic factors contribute to the phenotype of drug response. We systematically analyzed all available pharmacogenetic data from Medline databases (1970–2003) on the impact that genetic polymorphisms have on positive and adverse reactions to antidepressants and antipsychotics. Additionally, dose adjustments that would compensate for genetically caused differences in blood concentrations were calculated. To study pharmacokinetic effects, data for 36 antidepressants were

J Kirchheiner; K Nickchen; M Bauer; M-L Wong; J Licinio; I Roots; J Brockmöller

2004-01-01

190

recA mediated spontaneous deletions of the icaADBC operon of clinical Staphylococcus epidermidis isolates: a new mechanism of phenotypic variations  

PubMed Central

Phenotypic variation of Staphylococcus epidermidis involving the slime related ica operon results in heterogeneity in surface characteristics of individual bacteria in axenic cultures. Five clinical S. epidermidis isolates demonstrated phenotypic variation, i.e. both black and red colonies on Congo Red agar. Black colonies displayed bi-modal electrophoretic mobility distributions at pH 2, but such phenotypic variation was absent in red colonies of the same strain as well as in control strains without phenotypic variation. All red colonies had lost ica and the ability to form biofilms, in contrast to black colonies of the same strain. Real time PCR targeting icaA indicated a reduction in gene copy number within cultures exhibiting phenotypic variation, which correlated with phenotypic variations in biofilm formation and electrophoretic mobility distribution of cells within a culture. Loss of ica was irreversible and independent of the mobile element IS256. Instead, in high frequency switching strains, spontaneous mutations in lexA were found which resulted in deregulation of recA expression, as shown by real time PCR. RecA is involved in genetic deletions and rearrangements and we postulate a model representing a new mechanism of phenotypic variation in clinical isolates of S. epidermidis. This is the first report of S. epidermidis strains irreversibly switching from biofilm-positive to biofilm-negative phenotype by spontaneous deletion of icaADBC. Electronic supplementary material The online version of this article (doi:10.1007/s10482-008-9249-8) contains supplementary material, which is available to authorized users. PMID:18454346

Nuryastuti, Titik; van der Mei, Henny C.; Busscher, Henk J.; Kuijer, Roel; Aman, Abu T.

2008-01-01

191

Environmental effects on molecular and phenotypic variation in populations of Eruca sativa across a steep climatic gradient.  

PubMed

In Israel Eruca sativa has a geographically narrow distribution across a steep climatic gradient that ranges from mesic Mediterranean to hot desert environments. These conditions offer an opportunity to study the influence of the environment on intraspecific genetic variation. For this, we combined an analysis of neutral genetic markers with a phenotypic evaluation in common-garden experiments, and environmental characterization of populations that included climatic and edaphic parameters, as well as geographic distribution. A Bayesian clustering of individuals from nine representative populations based on amplified fragment length polymorphism (AFLP) divided the populations into a southern and a northern geographic cluster, with one admixed population at the geographic border between them. Linear mixed models, with cluster added as a grouping factor, revealed no clear effects of environment or geography on genetic distances, but this may be due to a strong association of geography and environment with genetic clusters. However, environmental factors accounted for part of the phenotypic variation observed in the common-garden experiments. In addition, candidate loci for selection were identified by association with environmental parameters and by two outlier methods. One locus, identified by all three methods, also showed an association with trichome density and herbivore damage, in net-house and field experiments, respectively. Accordingly, we propose that because trichomes are directly linked to defense against both herbivores and excess radiation, they could potentially be related to adaptive variation in these populations. These results demonstrate the value of combining environmental and phenotypic data with a detailed genetic survey when studying adaptation in plant populations. This article describes the use of several types of data to estimate the influence of the environment on intraspecific genetic variation in populations originating from a steep climatic gradient. In addition to molecular marker data, we made use of phenotypic evaluation from common garden experiments, and a broad GIS based environmental data with edaphic information gathered in the field. This study, among others, lead to the identification of an outlier locus with an association to trichome formation and herbivore defense, and its ecological adaptive value is discussed. PMID:24567822

Westberg, Erik; Ohali, Shachar; Shevelevich, Anatoly; Fine, Pinchas; Barazani, Oz

2013-08-01

192

Determining the linkage of quantitative trait loci to RFLP markers using extreme phenotypes of recombinant inbreds of soybean (Glycine max L. Merr.).  

PubMed

An experimental test is described for linkages between RFLP markers and quantitative trait loci (QTL). Two hundred and eighty-four F7-derived recombinant inbred lines (RIL) obtained from crossing the soybean cultivars (Glycine max L. Merr.) 'Minsoy' and 'Noir 1' were evaluated for maturity, plant height, lodging, and seed yield. RIL exhibiting an extreme phenotype for each trait (earliest and latest plants for maturity, etc.) were selected, and two bulked DNA samples were prepared for each trait. A Southern transfer of the digested bulked DNA was hybridized with restriction fragement length polymorphism (RFLP) probes, and linkages with QTL were established by quantitating the amount of radioactive probe that bound to fragments defining alternative parental RFLP alleles. When an RFLP marker was linked to a QTL, one parental allele predominated in the bulked DNA from a particular phenotype; the other allele was associated with the opposite phenotype. When linkage was absent, radioactivity was associated equally with both alleles for a given phenotype (or with both phenotypes for a given allele). These results confirmed RFLP-QTL associations previously discovered by interval mapping on a smaller segregating population from the same cross. New linkages to QTL were also verified. PMID:24193997

Mansur, L M; Orf, J; Lark, K G

1993-09-01

193

Continuous Variation Rather than Specialization in the Egg Phenotypes of Cuckoos (Cuculus canorus) Parasitizing Two Sympatric Reed Warbler Species  

PubMed Central

The evolution of brood parasitism has long attracted considerable attention among behavioural ecologists, especially in the common cuckoo system. Common cuckoos (Cuculus canorus) are obligatory brood parasites, laying eggs in nests of passerines and specializing on specific host species. Specialized races of cuckoos are genetically distinct. Often in a given area, cuckoos encounter multiple hosts showing substantial variation in egg morphology. Exploiting different hosts should lead to egg-phenotype specialization in cuckoos to match egg phenotypes of the hosts. Here we test this assumption using a wild population of two sympatrically occurring host species: the great reed warbler (Acrocephalus arundinaceus) and reed warbler (A. scirpaceus). Using colour spectrophotometry, egg shell dynamometry and egg size measurements, we studied egg morphologies of cuckoos parasitizing these two hosts. In spite of observing clear differences between host egg phenotypes, we found no clear differences in cuckoo egg morphologies. Interestingly, although chromatically cuckoo eggs were more similar to reed warbler eggs, after taking into account achromatic differences, cuckoo eggs seemed to be equally similar to both host species. We hypothesize that such pattern may represent an initial stage of an averaging strategy of cuckoos, that – instead of specializing for specific hosts or exploiting only one host – adapt to multiple hosts. PMID:25180796

Drobniak, Szymon M.; Dyrcz, Andrzej; Sudyka, Joanna; Cicho?, Mariusz

2014-01-01

194

Quantitative genetics of floral traits in a gynodioecious wild strawberry Fragaria virginiana: implications for the independent evolution of female and hermaphrodite floral phenotypes  

Microsoft Academic Search

The independent evolution of floral phenotype is an important part of the process of gender specialization during the evolution of dioecy from hermaphroditism. However, we have little information on the genetic variation of floral traits in species with separate genders. Gynodioecious species (co-occurrence of females and hermaphrodites) have a breeding system intermediate between hermaphroditism and complete separation of the sexes

TIA-LYNN ASHMAN

1999-01-01

195

Genetic variation in twin calving incidence in herds with a high phenotypic mean  

Microsoft Academic Search

Twin calving data were analysed from five private New Zealand dairy and beef cattle herds, and from the Ruakura experimental twin?research herd founded from industry cows screened?in on their twin calving history. The objective of the study was to estimate the heritability of twin calving rate in herds with a high phenotypic mean for non?identical twin calving. The annual twin

C. A. Morris; M. Wheeler

2002-01-01

196

Intraspecfic variation in cold-temperature metabolic phenotypes of Arabidopsis lyrata ssp. petraea  

Microsoft Academic Search

Atmospheric temperature is a key factor in determining the distribution of a plant species. Alongside this, plant populations\\u000a growing at the margin of their range may exhibit traits that indicate genetic differentiation and adaptation to their local\\u000a abiotic environment. We investigated whether geographically separated marginal populations of Arabidopsis lyrata ssp. petraea have distinct metabolic phenotypes associated with exposure to cold

Matthew P. Davey; F. Ian Woodward; W. Paul Quick

2009-01-01

197

The relative contribution of environmental and genetic factors to phenotypic variation in familial Mediterranean fever (FMF)  

Microsoft Academic Search

IntroductionFamilial Mediterranean fever (FMF) is an autosomal recessive disease, caused by mutations in the FMF gene MEFV (MEditerranean FeVer). It has a large phenotypic diversity even in patients with similar genotypes. Despite evidence that environmental factors (EFs) and genetic factors, including MEFV mutations (such as M694V, E148Q) and background modifier genes (MGs), affect the clinical manifestations of FMF, the relative

Ilan Ben-Zvi; Benny Brandt; Yackov Berkun; Merav Lidar; Avi Livneh

198

Susceptibility to Phytophthora ramorum in a key infectious host: landscape variation in host genotype, host phenotype, and environmental factors.  

PubMed

Sudden oak death is an emerging forest disease caused by the invasive pathogen Phytophthora ramorum. Genetic and environmental factors affecting susceptibility to P. ramorum in the key inoculum-producing host tree Umbellularia californica (bay laurel) were examined across a heterogeneous landscape in California, USA. Laboratory susceptibility trials were conducted on detached leaves and assessed field disease levels for 97 host trees from 12 225-m(2) plots. Genotype and phenotype characteristics were assessed for each tree. Effects of plot-level environmental conditions (understory microclimate, amount of solar radiation and topographic moisture potential) on disease expression were also evaluated. Susceptibility varied significantly among U. californica trees, with a fivefold difference in leaf lesion size. Lesion size was positively related to leaf area, but not to other phenotypic traits or to field disease level. Genetic diversity was structured at three spatial scales, but primarily among individuals within plots. Lesion size was significantly related to amplified fragment length polymorphism (AFLP) markers, but local environment explained most variation in field disease level. Thus, substantial genetic variation in susceptibility to P. ramorum occurs in its principal foliar host U. californica, but local environment mediates expression of susceptibility in nature. PMID:18069961

Anacker, Brian L; Rank, Nathan E; Hüberli, Daniel; Garbelotto, Matteo; Gordon, Sarah; Harnik, Tami; Whitkus, Richard; Meentemeyer, Ross

2008-01-01

199

Contrasting the distribution of phenotypic and molecular variation in the freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni  

PubMed Central

Population differentiation was investigated by confronting phenotypic and molecular variation in the highly selfing freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni. We sampled seven natural populations separated by a few kilometers, and characterized by different habitat regimes (permanent/temporary) and openness (open/closed). A genetic analysis based on five microsatellite markers confirms that B. pfeifferi is a selfer (s?0.9) and exhibits limited variation within populations. Most pairwise FST were significant indicating marked population structure, though no isolation by distance was detected. Families from the seven populations were monitored under laboratory conditions over two generations (G1 and G2), allowing to record several life-history traits, including growth, fecundity and survival, over 25 weeks. Marked differences were detected among populations for traits expressed early in the life cycle (up to sexual maturity). Age and size at first reproduction had high heritability values, but such a trend was not found for early reproductive traits. In most populations, G1 snails matured later and at a larger size than G2 individuals. Individuals from permanent habitats matured at a smaller size and were more fecund than those from temporary habitats. The mean phenotypic differentiation over all populations (QST) was lower than the mean genetic differentiation (FST), suggesting stabilizing selection. However, no difference was detected between QST and FST for both habitat regime and habitat openness. PMID:23321708

Tian-Bi, Y-NT; Jarne, P; Konan, J-NK; Utzinger, J; N'Goran, E K

2013-01-01

200

Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis.  

PubMed

Little is known about the range and the genetic bases of naturally occurring variation for flavonoids. Using Arabidopsis thaliana seed as a model, the flavonoid content of 41 accessions and two recombinant inbred line (RIL) sets derived from divergent accessions (Cvi-0×Col-0 and Bay-0×Shahdara) were analysed. These accessions and RILs showed mainly quantitative rather than qualitative changes. To dissect the genetic architecture underlying these differences, a quantitative trait locus (QTL) analysis was performed on the two segregating populations. Twenty-two flavonoid QTLs were detected that accounted for 11-64% of the observed trait variations, only one QTL being common to both RIL sets. Sixteen of these QTLs were confirmed and coarsely mapped using heterogeneous inbred families (HIFs). Three genes, namely TRANSPARENT TESTA (TT)7, TT15, and MYB12, were proposed to underlie their variations since the corresponding mutants and QTLs displayed similar specific flavonoid changes. Interestingly, most loci did not co-localize with any gene known to be involved in flavonoid metabolism. This latter result shows that novel functions have yet to be characterized and paves the way for their isolation. PMID:22442426

Routaboul, Jean-Marc; Dubos, Christian; Beck, Gilles; Marquis, Catherine; Bidzinski, Przemyslaw; Loudet, Olivier; Lepiniec, Loïc

2012-06-01

201

Phenotypic CYP2A6 Variation and the Risk of Pancreatic Cancer  

PubMed Central

Objective Cytochrome P450 2A6 (CYP2A6) is an important metabolic enzyme capable of activating several procarcinogens, including dietary and tobacco-specific nitrosamines, which have been linked to pancreatic cancer. Positive associations between high CYP2A6 activity and lung and colorectal cancers have been reported. This is the first investigation of CYP2A6 activity and pancreatic cancer. Design In this case-control study of cancer of the exocrine pancreas, phenotypic CYP2A6 activity was measured using a ratio of urinary caffeine metabolites. Demographic, smoking, dietary and medical information were obtained by questionnaire. CYP2A6 phenotype, which is not influenced by smoking status, was measured for 90 cases and 470 controls. Results When modeled as a continuous variable, and adjusted for age, sex, race, education, current smoking status and chronic pancreatitis, the odds ratio (OR) per one unit of the natural log of the CYP2A6 ratio was 1.52 (95% confidence interval, CI: 1.09-2.12). In an adjusted categorical analysis, subjects in the uppermost quartile (based on controls) of CYP2A6 activity, when compared to the lower three quartiles, carried an 80% greater risk of pancreatic cancer (OR=1.80; 95% CI: 1.07-3.02). Conclusions High levels of CYP2A6 activity, as measured by a caffeine phenotyping assay, were positively associated with pancreatic cancer in this case-control study among a Midwestern U.S. population. PMID:19454817

Kadlubar, Susan; Anderson, Jeffrey P; Sweeney, Carol; Gross, Myron D; Lang, Nicholas P; Kadlubar, Fred F; Anderson, Kristin E

2015-01-01

202

SNP array mapping of 20p deletions: Genotypes, Phenotypes and Copy Number Variation  

PubMed Central

The use of array technology to define chromosome deletions and duplications is bringing us closer to establishing a genotype/phenotype map of genomic copy number alterations. We studied 21 patients and 5 relatives with deletions of the short arm of chromosome 20 using the Illumina HumanHap550 SNP array to 1) more accurately determine the deletion sizes, 2) identify and compare breakpoints, 3) establish genotype/phenotype correlations and 4) investigate the use of the HumanHap550 platform for analysis of chromosome deletions. Deletions ranged from 95kb to 14.62Mb, and all of the breakpoints were unique. Eleven patients had deletions between 95kb and 4Mb and these individuals had normal development, with no anomalies outside of those associated with Alagille syndrome. The proximal and distal boundaries of these eleven deletions constitute a 5.4MB region, and we propose that haploinsufficiency for only 1 of the 12 genes in this region causes phenotypic abnormalities. This defines the JAG1 associated critical region, in which deletions do not confer findings other than those associated with Alagille syndrome. The other 10 patients had deletions between 3.28Mb and 14.62Mb, which extended outside the critical region, and notably, all of these patients, had developmental delay. This group had other findings such as autism, scoliosis and bifid uvula. We identified 47 additional polymorphic genome-wide copy number variants (>20 SNPs), with 0–5 variants called per patient. Deletions of the short arm of chromosome 20 are associated with relatively mild and limited clinical anomalies. The use of SNP arrays provides accurate high-resolution definition of genomic abnormalities. PMID:19058200

Kamath, Binita M.; Thiel, Brian D.; Gai, Xiaowu; Conlin, Laura K.; Munoz, Pedro S.; Glessner, Joseph; Clark, Dinah; Warthen, Daniel M.; Shaikh, Tamim H.; Mihci, Ercan; Piccoli, David A.; Grant, Struan F.A.; Hakonarson, Hakon; Krantz, Ian D.; Spinner, Nancy B.

2008-01-01

203

Coat Color Variation in Rock Pocket Mice (Chaetodipus intermedius): From Genotype to Phenotype  

E-print Network

that this crypsis is an adaptation to avoid predation. Motivated by the wealth of data on the genetics, biochemistry been some controversy concerning the importance of crypsis in maintaining this kind of variation

Hoekstra, Hopi E.

204

Quantitative variation in obesity-related traits and insulin precursors linked to the OB gene region on human chromosome 7  

SciTech Connect

Despite the evidence that human obesity has strong genetic determinants, efforts at identifying specific genes that influence human obesity have largely been unsuccessful. Using the sibship data obtained from 32 low-income Mexican American pedigrees ascertained on a type II diabetic proband and a multipoint variance-components method, we tested for linkage between various obesity-related traits plus associated metabolic traits and 15 markers on human chromosome 7. We found evidence for linkage between markers in the OB gene region and various traits, as follows: D7S514 and extremity skinfolds (LOD = 3.1), human carboxypeptidase A1 (HCPA1) and 32,33-split proinsulin level (LOD = 4.2), and HCPA1 and proinsulin level (LOD = 3.2). A putative susceptibility locus linked to the marker D7S514 explained 56% of the total phenotypic variation in extremity skinfolds. Variation at the HCPA1 locus explained 64% of phenotypic variation in proinsulin level and {approximately}73% of phenotypic variation in split proinsulin concentration, respectively. Weaker evidence for linkage to several other obesity-related traits (e.g., waist circumference, body-mass index, fat mass by bioimpedance, etc.) was observed for a genetic location, which is {approximately}15 cM telomeric to OB. In conclusion, our study reveals that the OB region plays a significant role in determining the phenotypic variation of both insulin precursors and obesity-related traits, at least in Mexican Americans. 66 refs., 3 figs., 4 tabs.

Duggirala, R.; Stern, M.P.; Reinhart, L.J. [Univ. of Texas Health Science Center, San Antonio, TX (United States)] [and others

1996-09-01

205

No association between insulin gene variation and adult metabolic phenotypes in a large Finnish birth cohort  

Microsoft Academic Search

Aims\\/hypothesis  Although the variable number tandem repeat (VNTR) minisatellite 5 to the insulin gene is among the most studied polymorphisms in diabetes, the relationships between VNTR variation, diabetes-related traits and predisposition to type 2 diabetes remain unclear. Since inadequate sample size is likely to have been an obstacle to reliable inference, we examined the relationship between VNTR variation and a range

A. Bennett; U. Sovio; A. Ruokonen; H. Martikainen; A. Pouta; S. Taponen; A.-L. Hartikainen; S. Franks; L. Peltonen; P. Elliott; M.-R. Järvelin; M. I. McCarthy

2005-01-01

206

Phenotypic Variation Among Seven Members of One Family with Deficiency of Hypoxanthine-Guanine Phosphoribosyltransferase  

PubMed Central

We describe a family of seven boys affected by Lesch-Nyhan disease with various phenotypes. Further investigations revealed a mutation c.203T>C in the gene encoding HGprt of all members, with substitution of leucine to proline at residue 68 (p.Leu68Pro). Thus patients from this family display a wide variety of symptoms although sharing the same mutation. Mutant HGprt enzyme was prepared by site-directed mutagenesis and the kinetics of the enzyme revealed that the catalytic activity of the mutant was reduced, in association with marked reductions in the affinity towards phosphoribosylpyrophosphate (PRPP). Its Km for PRPP was increased 215-fold with hypoxanthine as substrate and 40-fold with guanine as substrate with associated reduced catalytic potential. Molecular modeling confirmed that the most prominent defect was the dramatically reduced affinity towards PRPP. Our studies suggest that the p.Leu68Pro mutation has a strong impact on PRPP binding and on stability of the active conformation. This suggests that factors other than HGprt activity per se may influence the phenotype of Lesch-Nyhan patients. PMID:24075303

Ceballos-Picot, Irène; Augé, Franck; Fu, Rong; Olivier-Bandini, Anne; Cahu, Julie; Chabrol, Brigitte; Aral, Bernard; de Martinville, Bérengère; Lecain, Jean-Paul; Jinnah, H. A.

2013-01-01

207

Phenotypic variation among seven members of one family with deficiency of hypoxanthine-guanine phosphoribosyltransferase.  

PubMed

We describe a family of seven boys affected by Lesch-Nyhan disease with various phenotypes. Further investigations revealed a mutation c.203T>C in the gene encoding HGprt of all members, with substitution of leucine to proline at residue 68 (p.Leu68Pro). Thus patients from this family display a wide variety of symptoms although sharing the same mutation. Mutant HGprt enzyme was prepared by site-directed mutagenesis and the kinetics of the enzyme revealed that the catalytic activity of the mutant was reduced, in association with marked reductions in the affinity towards phosphoribosylpyrophosphate (PRPP). Its Km for PRPP was increased 215-fold with hypoxanthine as substrate and 40-fold with guanine as substrate with associated reduced catalytic potential. Molecular modeling confirmed that the most prominent defect was the dramatically reduced affinity towards PRPP. Our studies suggest that the p.Leu68Pro mutation has a strong impact on PRPP binding and on stability of the active conformation. This suggests that factors other than HGprt activity per se may influence the phenotype of Lesch-Nyhan patients. PMID:24075303

Ceballos-Picot, Irène; Augé, Franck; Fu, Rong; Olivier-Bandini, Anne; Cahu, Julie; Chabrol, Brigitte; Aral, Bernard; de Martinville, Bérengère; Lecain, Jean-Paul; Jinnah, H A

2013-11-01

208

Quantitative correction of the rate constant in the improved variational master equation for excitation energy transfer.  

PubMed

Understanding the excitation energy transfer (EET) mechanism is a ubiquitous field of study in photosynthetic antennas. Recently, we qualitatively improved the theory of the variational master equation by introducing the second Bogoliubov inequality to determine the proper perturbative term. However, there were quantitative differences in the EET rate compared with the results from exact numerical calculations. In this study, we attempt to correct the differences in the intermediate coupling region. As a result, we found two methods to reproduce more exact results than those previously reported. PMID:25416877

Kimura, Akihiro; Fujihashi, Yuta

2014-11-21

209

Age-related variation in quantitative ultrasound at the tibia and prevalence of osteoporosis in native Chinese women  

Microsoft Academic Search

This study investigated the variations in age-related speed of sound (SOS) at the tibia and prevalence of osteoporosis in native Chinese women, and establishment of a reference database by quantitative ultrasound. SOS at the right midtibia was measured using a quantitative ultrasound device (SoundScan 2000, Myriad Ultrasound Systems, Israel) in 1596 healthy Chinese women ranging from 12 years to 96

X-P Wu; E-Y LIAO; X-H LUO; R-C DAI; H ZHANG; J PENG

2003-01-01

210

Physiological and morphological variation in Metrosideros polymorpha , a dominant Hawaiian tree species, along an altitudinal gradient: the role of phenotypic plasticity  

Microsoft Academic Search

Metrosideros polymorpha, a dominant tree species in Hawaiian ecosystems, occupies a wide range of habitats. Complementary field and common-garden\\u000a studies of M. polymorpha populations were conducted across an altitudinal gradient at two different substrate ages to ascertain if the large phenotypic\\u000a variation of this species is determined by genetic differences or by phenotypic modifications resulting from environmental\\u000a conditions. Several characteristics,

S. Cordell; G. Goldstein; D. Mueller-Dombois; D. Webb; P. M. Vitousek

1998-01-01

211

Variation in phenotypic characters of pale flax ( Linum bienne Mill.) from Turkey  

Microsoft Academic Search

The diversity of pale flax (Linum bienne Mill.) as the progenitor of cultivated flax (L. usitatissimum L.) has not been well documented and the domestication syndromes in cultivated flax are poorly understood. An attempt was\\u000a made to characterize 34 pale flax accessions and six cultivated flax accessions collected during 2007 summer in Turkey. A\\u000a total of 12 quantitative and 7

Hüseyin Uysal; Orhan Kurt; Yong-Bi Fu; Axel Diederichsen; Peter Kusters

212

Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait.  

PubMed

Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci. PMID:25833857

Husby, Arild; Kawakami, Takeshi; Rönnegård, Lars; Smeds, Linnéa; Ellegren, Hans; Qvarnström, Anna

2015-05-01

213

Genetic and Phenotypic Variation of FMDV During Serial Passages in a Natural Host  

Technology Transfer Automated Retrieval System (TEKTRAN)

Foot-and-Mouth Disease Virus (FMDV) exhibits high mutation rates during replication that have been suggested to be of adaptive value. However, even though genetic variation in RNA viruses has been extensively examined during virus replication in a wide variety of in vitro cell cultures, very little ...

214

Effect of trinucleotide repeat length and parental sex on phenotypic variation in spinocerebellar ataxia I  

Microsoft Academic Search

Trinucleotide repeat expansion has been found in 64 subjects from 19 families: 57 patients with SCA1 and 7 subjects predicted, by haplotype analysis, to carry the mutation. Comparison with a large set of normal chromosomes shows two distinct distributions, with a much wider variation among expanded chromosomes. The sex of transmitting parent plays a major role in the size distribution

C. Jodice; P. Malaspina; F. Persichetti; A. Novelletto; L. Terrenato; M. Spadaro; C. Morocutti; P. Giunti; A. E. Harding; M. Frontali

1994-01-01

215

Allometric influence on phenotypic variation in the Song Sparrow ( Melospiza melodia )  

Microsoft Academic Search

Song Sparrow (Melospiza melodia) populations found along the Pacific Coast of North America, from Baja California to the islands off the coast of Alaska, exhibit extensive morphological variation. With a multivariate analysis of size and shape, I describe a portion of this pattern and examine how it could be maintained despite gene flow among the populations. Because shape differences fall

JULIA I. SMITH

1998-01-01

216

The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene  

E-print Network

The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State to date, which have used measurements of steady- state gene expression levels, is the inability that steady-state expression levels are significantly correlated with variation in decay rates in 10% of genes

Nachman, Michael

217

[Quantitive variation of polysaccharides and alcohol-soluble extracts in F1 generation of Dendrobium officinale].  

PubMed

Using phenol-sulfuric acid method and hot-dip method of alcohol-soluble extracts, the contents of polysaccharides and alcohol-soluble extracts in 11 F1 generations of Dendrobium officinale were determined. The results showed that the polysaccharides contents in samples collected in May and February were 32.89%-43.07% and 25.77%-35.25%, respectively, while the extracts contents were 2.81%-4.85% and 7.90%-17.40%, respectively. They were significantly different among families. The content of polysaccharides in offspring could be significantly improved by hybridization between parents with low and high polysaccharides contents, and the hybrid vigor was obvious. Cross breeding was an effective way for breeding new varieties with higher polysaccharides contents. Harvest time would significantly affect the contents of polysaccharides and alcohol-soluble extracts. The contents of polysaccharides in families collected in May were higher than those of polysaccharides in families collected in February, but the extracts content had the opposite variation. The extents of quantitative variation of polysaccharides and alcohol-soluble extracts were different among families, and each family had its own rules. It would be significant in giving full play to their role as the excellent varieties and increasing effectiveness by studying on the quantitative accumulation regularity of polysaccharides and alcohol-soluble extracts in superior families (varieties) of D. officinale to determine the best harvesting time. PMID:24494555

Zhang, Xiao-Ling; Liu, Jing-Jing; Wu, Ling-Shang; Si, Jin-Ping; Guo, Ying-Ying; Yu, Jie; Wang, Lin-Hua

2013-11-01

218

DNA variation in the phenotypically-diverse brown alga Saccharina japonica  

PubMed Central

Background Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the “longipes” (LON) and “shallow-water” (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica. Results The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286?bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5’- and 3’- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5’- or 3’-) used for tree reconstruction. Consequently, the 5’-COI “barcoding” region (~ 650?bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events. Conclusion Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered. PMID:22784095

2012-01-01

219

LIFE-HISTORY VARIATION IN THE SAGEBRUSH LIZARD: PHENOTYPIC PLASTICITY OR LOCAL ADAPTATION?  

Microsoft Academic Search

We performed a laboratory common-environment study to determine the genetic and environmental sources of variation in growth rates of the sagebrush lizard (Sceloporus graciosus). Hatchling lizards were reared from gravid females collected from three study populations along an elevational gradient in southern Utah, USA. Hatchlings were fed ad libidum and were maintained on a 14:10 light:dark cycle, with temperatures at

Michael W. Sears

2003-01-01

220

Phenotypic Variation in Senescence in Miscanthus : Towards Optimising Biomass Quality and Quantity  

Microsoft Academic Search

Senescence impacts the harvestable biomass yield and quality in Miscanthus. Very early autumn senescence shortens the canopy duration reducing yield potential. When senescence is too late or slow,\\u000a the crop does not ripen sufficiently before harvest, resulting in high moisture and nutrient offtakes that reduce biomass\\u000a quality. In this study, variation in senescence was monitored over 3 years in a trial

Paul Robson; Michal Mos; John Clifton-Brown; Iain Donnison

221

Phenotypic variation of agronomic traits among coyote gourd accessions and their progeny  

Microsoft Academic Search

As a prelude to domestication efforts, variation of agronomic traits was determined among accessions of the polytypic, xerophytic\\u000a cucurbit, coyote gourd [Cucurbita digitata subsp. digitata (DIG), palmata (PAL), cylindrata (CYL), and cordata (COR)] and\\u000a among and within their progeny. Oil content in 60 accession seed lots (x = 27.8%, CV 21.4%) was more variable than protein\\u000a content (x = 33.1%,

Joseph C. Scheerens; Andrew E. Ralowicz; Terry L. McGriff; Keith A. Bee; John M. Nelson; Allen C. Gathman

1991-01-01

222

Phenotypic flexibility in migrating bats: seasonal variation in body composition, organ sizes and fatty acid profiles.  

PubMed

Many species of bats migrate long distances, but the physiological challenges of migration are poorly understood. We tested the hypothesis that migration is physiologically demanding for bats by examining migration-related phenotypic flexibility. Both bats and birds are endothermic, flying vertebrates; therefore, we predicted that migration would result in similar physiological trade-offs. We compared hoary bats (Lasiurus cinereus) during spring migration and summer non-migratory periods, comparing our results with previous observations of birds. Migrating bats had reduced digestive organs, enlarged exercise organs, and fat stores had higher proportions of polyunsaturated fatty acids (PUFAs). These results are consistent with previous studies of migrating birds; however, we also found sex differences not typically associated with bird migration. Migrating female hoary bats increased the relative size of fat stores by reducing lean body components, while males maintained the same relative amount of fat in both seasons. The ratio of n-6 to n-3 PUFA in flight muscle membrane increased in migrating males and decreased in migrating females, consistent with males using torpor more frequently than females during spring migration. Enlarged exercise organs, reduced digestive organs and changes in adipose tissue composition reflect the elevated energetic demands of migration. Sex-specific patterns of fat storage and muscle membrane composition likely reflect challenges faced by females that migrate while pregnant. Our results provide some of the first insights into the physiological demands of bat migration and highlight key differences between bats and birds. PMID:23408801

McGuire, Liam P; Fenton, M Brock; Guglielmo, Christopher G

2013-03-01

223

Application of quantitative trait locus mapping and transcriptomics to studies of the senescence-accelerated phenotype in rats  

PubMed Central

Background Etiology of complex disorders, such as cataract and neurodegenerative diseases including age-related macular degeneration (AMD), remains poorly understood due to the paucity of animal models, fully replicating the human disease. Previously, two quantitative trait loci (QTLs) associated with early cataract, AMD-like retinopathy, and some behavioral aberrations in senescence-accelerated OXYS rats were uncovered on chromosome 1 in a cross between OXYS and WAG rats. To confirm the findings, we generated interval-specific congenic strains, WAG/OXYS-1.1 and WAG/OXYS-1.2, carrying OXYS-derived loci of chromosome 1 in the WAG strain. Both congenic strains displayed early cataract and retinopathy but differed clinically from OXYS rats. Here we applied a high-throughput RNA sequencing (RNA-Seq) strategy to facilitate nomination of the candidate genes and functional pathways that may be responsible for these differences and can contribute to the development of the senescence-accelerated phenotype of OXYS rats. Results First, the size and map position of QTL-derived congenic segments were determined by comparative analysis of coding single-nucleotide polymorphisms (SNPs), which were identified for OXYS, WAG, and congenic retinal RNAs after sequencing. The transferred locus was not what we expected in WAG/OXYS-1.1 rats. In rat retina, 15442 genes were expressed. Coherent sets of differentially expressed genes were identified when we compared RNA-Seq retinal profiles of 20-day-old WAG/OXYS-1.1, WAG/OXYS-1.2, and OXYS rats. The genes most different in the average expression level between the congenic strains included those generally associated with the Wnt, integrin, and TGF-? signaling pathways, widely involved in neurodegenerative processes. Several candidate genes (including Arhgap33, Cebpg, Gtf3c1, Snurf, Tnfaip3, Yme1l1, Cbs, Car9 and Fn1) were found to be either polymorphic in the congenic loci or differentially expressed between the strains. These genes may contribute to the development of cataract and retinopathy. Conclusions This study is the first RNA-Seq analysis of the rat retinal transcriptome generated with 40 mln sequencing read depth. The integration of QTL and transcriptomic analyses in our study forms the basis of future research into the relationship between the candidate genes within the congenic regions and specific changes in the retinal transcriptome as possible causal mechanisms that underlie age-associated disorders. PMID:25563673

2014-01-01

224

Phenotypic and genotypic background underlying variations in fatty acid composition and sensory parameters in European bovine breeds  

PubMed Central

Background Consuming moderate amounts of lean red meat as part of a balanced diet valuably contributes to intakes of essential nutrients. In this study, we merged phenotypic and genotypic information to characterize the variation in lipid profile and sensory parameters and to represent the diversity among 15 cattle populations. Correlations between fat content, organoleptic characteristics and lipid profiles were also investigated. Methods A sample of 436 largely unrelated purebred bulls belonging to 15 breeds and reared under comparable management conditions was analyzed. Phenotypic data -including fatness score, fat percentage, individual fatty acids (FA) profiles and sensory panel tests- and genotypic information from 11 polymorphisms was used. Results The correlation coefficients between muscle total lipid measurements and absolute vs. relative amounts of polyunsaturated FA (PUFA) were in opposite directions. Increasing carcass fat leads to an increasing amount of FAs in triglycerides, but at the same time the relative amount of PUFAs is decreasing, which is in concordance with the negative correlation obtained here between the percentage of PUFA and fat measurements, as well as the weaker correlation between total phospholipids and total lipid muscle content compared with neutral lipids. Concerning organoleptic characteristics, a negative correlation between flavour scores and the percentage of total PUFA, particularly to n-6 fraction, was found. The correlation between juiciness and texture is higher than with flavour scores. The distribution of SNPs plotted by principal components analysis (PCA) mainly reflects their known trait associations, although influenced by their specific breed allele frequencies. Conclusions The results presented here help to understand the phenotypic and genotypic background underlying variations in FA composition and sensory parameters between breeds. The wide range of traits and breeds studied, along with the genotypic information on polymorphisms previously associated with different lipid traits, provide a broad characterization of beef meat, which allows giving a better response to the variety of consumers’ preferences. Also, the development and implementation of low-density SNP panels with predictive value for economically important traits, such as those summarized here, may be used to improve production efficiency and meat quality in the beef industry. PMID:24735897

2014-01-01

225

Biogeographic discordance of molecular phylogenetic and phenotypic variation in a continental archipelago radiation of land snails  

PubMed Central

Background In island archipelagos, where islands have experienced repeated periods of fragmentation and connection through cyclic changes in sea level, complex among-island distributions might reflect historical distributional changes or local evolution. We test the relative importance of these mechanisms in an endemic radiation of Rhagada land snails in the Dampier Archipelago, a continental archipelago off the coast of Western Australia, where ten morphospecies have complex, overlapping distributions. Results We obtained partial mtDNA sequence (COI) for 1015 snails collected from 213 locations across 30 Islands, and used Bayesian phylogenetic analysis and Analysis of Molecular Variance (AMOVA) to determine whether geography or the morphological taxonomy best explains the pattern of molecular evolution. Rather than forming distinct monophyletic groups, as would be expected if they had single, independent origins, all of the widely distributed morphospecies were polyphyletic, distributed among several well-supported clades, each of which included several morphospecies. Each mitochondrial clade had a clear, cohesive geographic distribution, together forming a series of parapatric replacements separated by narrow contact zones. AMOVA revealed further incongruence between mtDNA diversity and morphological variation within clades, as the taxonomic hypothesis always explained a low or non-significant proportion of the molecular variation. In contrast, the pattern of mtDNA evolution closely reflected contemporary and historical marine barriers. Conclusions Despite opportunities for distributional changes during periods when the islands were connected, there is no evidence that dispersal has contributed to the geographic variation of shell form at the broad scale. Based on an estimate of dispersal made previously for Rhagada, we conclude that the periods of connection have been too short in duration to allow for extensive overland dispersal or deep mitochondrial introgression. The result is a sharp and resilient phylogeographic pattern. The distribution of morphotypes among clades and distant islands is explained most simply by their parallel evolution. PMID:24393567

2014-01-01

226

Genetic variation in GPBAR1 predisposes to quantitative changes in colonic transit and bile acid excretion.  

PubMed

The pathobiology of irritable bowel syndrome (IBS) is multifaceted. We aimed to identify candidate genes predisposing to quantitative traits in IBS. In 30 healthy volunteers, 30 IBS-constipation, and 64 IBS-diarrhea patients, we measured bowel symptoms, bile acid (BA) synthesis (serum 7?-hydroxy-4-cholesten-3-one and FGF19), fecal BA and fat, colonic transit (CT by scintigraphy), and intestinal permeability (IP by 2-sugar excretion). We assessed associations of candidate genes controlling BA metabolism (KLB rs17618244 and FGFR4 rs351855), BA receptor (GPBAR1 rs11554825), serotonin (5-HT) reuptake (SLC6A4 through rs4795541 which encodes for the 44-bp insert in 5HTTLPR), or immune activation (TNFSF15 rs4263839) with three primary quantitative traits of interest: colonic transit, BA synthesis, and fecal BA excretion. There were significant associations between fecal BA and CT at 48 h (r = 0.43; P < 0.001) and IP (r = 0.23; P = 0.015). GPBAR1 genotype was associated with CT48 (P = 0.003) and total fecal BA [P = 0.030, false detection rate (FDR) P = 0.033]. Faster CT48 observed with both CC and TT GPBAR1 genotypes was due to significant interaction with G allele of KLB, which increases BA synthesis and excretion. Other univariate associations (P < 0.05, without FDR correction) observed between GPBAR1 and symptom phenotype and gas sensation ratings support the role of GPBAR1 receptor. Associations between SLC6A4 and stool consistency, ease of passage, postprandial colonic tone, and total fecal BA excretion provide data in support of future hypothesis-testing studies. Genetic control of GPBAR1 receptor predisposing to pathobiological mechanisms in IBS provides evidence from humans in support of the importance of GPBAR1 to colonic motor and secretory functions demonstrated in animal studies. PMID:25012842

Camilleri, Michael; Shin, Andrea; Busciglio, Irene; Carlson, Paula; Acosta, Andres; Bharucha, Adil E; Burton, Duane; Lamsam, Jesse; Lueke, Alan; Donato, Leslie J; Zinsmeister, Alan R

2014-09-01

227

Genetic variation within the Chrna7 gene modulates nicotine reward-like phenotypes in mice.  

PubMed

Mortality from tobacco smoking remains the leading cause of preventable death in the world, yet current cessation therapies are only modestly successful, suggesting new molecular targets are needed. Genetic analysis of gene expression and behavior identified Chrna7 as potentially modulating nicotine place conditioning in the BXD panel of inbred mice. We used gene targeting and pharmacological tools to confirm the role of Chrna7 in nicotine conditioned place preference (CPP). To identify molecular events downstream of Chrna7 that may modulate nicotine preference, we performed microarray analysis of ?7 knock-out (KO) and wild-type (WT) nucleus accumbens (NAc) tissue, followed by confirmation with quantitative polymerase chain reaction (PCR) and immunoblotting. In the BXD panel, we found a putative cis expression quantitative trait loci (eQTL) for Chrna7 in NAc that correlated inversely to nicotine CPP. We observed that gain-of-function ?7 mice did not display nicotine preference at any dose tested, whereas conversely, ?7 KO mice demonstrated nicotine place preference at a dose below that routinely required to produce preference. In B6 mice, the ?7 nicotinic acetylcholine receptor (nAChR)-selective agonist, PHA-543613, dose-dependently blocked nicotine CPP, which was restored using the ?7 nAChR-selective antagonist, methyllycaconitine citrate (MLA). Our genomic studies implicated a messenger RNA (mRNA) co-expression network regulated by Chrna7 in NAc. Mice lacking Chrna7 demonstrate increased insulin signaling in the NAc, which may modulate nicotine place preference. Our studies provide novel targets for future work on development of more effective therapeutic approaches to counteract the rewarding properties of nicotine for smoking cessation. PMID:24289814

Harenza, J L; Muldoon, P P; De Biasi, M; Damaj, M I; Miles, M F

2014-02-01

228

Quantitative NMR Metabolite Profiling of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Discriminates between Biofilm and Planktonic Phenotypes  

PubMed Central

Wound bioburden in the form of colonizing biofilms is a major contributor to nonhealing wounds. Staphylococcus aureus is a Gram-positive, facultative anaerobe commonly found in chronic wounds; however, much remains unknown about the basic physiology of this opportunistic pathogen, especially with regard to the biofilm phenotype. Transcriptomic and proteomic analysis of S. aureus biofilms have suggested that S. aureus biofilms exhibit an altered metabolic state relative to the planktonic phenotype. Herein, comparisons of extracellular and intracellular metabolite profiles detected by 1H NMR were conducted for methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) S. aureus strains grown as biofilm and planktonic cultures. Principal component analysis distinguished the biofilm phenotype from the planktonic phenotype, and factor loadings analysis identified metabolites that contributed to the statistical separation of the biofilm from the planktonic phenotype, suggesting that key features distinguishing biofilm from planktonic growth include selective amino acid uptake, lipid catabolism, butanediol fermentation, and a shift in metabolism from energy production to assembly of cell-wall components and matrix deposition. These metabolite profiles provide a basis for the development of metabolite biomarkers that distinguish between biofilm and planktonic phenotypes in S. aureus and have the potential for improved diagnostic and therapeutic use in chronic wounds. PMID:24809402

Ammons, Mary Cloud B.; Tripet, Brian P.; Carlson, Ross P.; Kirker, Kelly R.; Gross, Michael A.; Stanisich, Jessica J.; Copié, Valerie

2014-01-01

229

Plastic and Heritable Components of Phenotypic Variation in Nucella lapillus: An Assessment Using Reciprocal Transplant and Common Garden Experiments  

PubMed Central

Assessment of plastic and heritable components of phenotypic variation is crucial for understanding the evolution of adaptive character traits in heterogeneous environments. We assessed the above in relation to adaptive shell morphology of the rocky intertidal snail Nucella lapillus by reciprocal transplantation of snails between two shores differing in wave action and rearing snails of the same provenance in a common garden. Results were compared with those reported for similar experiments conducted elsewhere. Microsatellite variation indicated limited gene flow between the populations. Intrinsic growth rate was greater in exposed-site than sheltered-site snails, but the reverse was true of absolute growth rate, suggesting heritable compensation for reduced foraging opportunity at the exposed site. Shell morphology of reciprocal transplants partially converged through plasticity toward that of native snails. Shell morphology of F2s in the common garden partially retained characteristics of the P-generation, suggesting genetic control. A maternal effect was revealed by greater resemblance of F1s than F2s to the P-generation. The observed synergistic effects of plastic, maternal and genetic control of shell-shape may be expected to maximise fitness when environmental characteristics become unpredictable through dispersal. PMID:22299035

Pascoal, Sonia; Carvalho, Gary; Creer, Simon; Rock, Jenny; Kawaii, Kei; Mendo, Sonia; Hughes, Roger

2012-01-01

230

Effect of trinucleotide repeat length and parental sex on phenotypic variation in spinocerebellar ataxia I  

SciTech Connect

Trinucleotide repeat expansion has been found in 64 subjects from 19 families: 57 patients with SCA1 and 7 subjects predicted, by haplotype analysis, to carry the mutation. Comparison with a large set of normal chromosomes shows two distinct distributions, with a much wider variation among expanded chromosomes. The sex of transmitting parent plays a major role in the size distribution of expanded alleles, those with >54 repeats being transmitted by affected fathers exclusively. The data suggest that alleles with >54 repeats have a reduced chance of survival; these appear to be replaced in each generation by further expansion of alleles in the low- to medium-expanded repeat range, preferentially in male transmission. Detailed clinical follow-up of a subset of patients demonstrates significant relationships between increasing repeat number on expanded chromosomes and earlier age at onset, faster progression of the disease, and earlier age at death.

Jodice, C.; Malaspina, P.; Persichetti, F.; Novelletto, A.; Terrenato, L. (Universita Tor Vergata, Rome (Italy)); Spadaro, M.; Morocutti, C. (Universita La Sapienza, Rome (Italy)); Giunti, P. (Universita La Sapienza, Rome (Italy) Institute of Neurology, London (United Kingdom)); Harding, A.E. (Institute of Neurology, London (United Kingdom)); Frontali, M. (Istituto di Medicina Sperimentale, Rome (Italy))

1994-06-01

231

The quantitative genetic basis of sex ratio variation in Nasonia vitripennis: a QTL study  

PubMed Central

Our understanding of how natural selection should shape sex allocation is perhaps more developed than for any other trait. However, this understanding is not matched by our knowledge of the genetic basis of sex allocation. Here, we examine the genetic basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, a species well known for its response to local mate competition (LMC). We identified a quantitative trait locus (QTL) for sex ratio on chromosome 2 and three weaker QTL on chromosomes 3 and 5. We tested predictions that genes associated with sex ratio should be pleiotropic for other traits by seeing if sex ratio QTL co-occurred with clutch size QTL. We found one clutch size QTL on chromosome 1, and six weaker QTL across chromosomes 2, 3 and 5, with some overlap to regions associated with sex ratio. The results suggest rather limited scope for pleiotropy between these traits. PMID:20977519

Pannebakker, B A; Watt, R; Knott, S A; West, S A; Shuker, D M

2011-01-01

232

Genetic and Phenotypic Variation through the Migratory Season Provides Evidence for Multiple Populations of Wild Steelhead in the Dean River, British Columbia  

Microsoft Academic Search

We provide evidence for previously undetected population structure in a wild run of summer steelhead Oncorhynchus mykisswithin a river that has considerable recreational importance (Dean River, British Columbia). Data were gathered from an existing catch-and-release fishery and examined for phenotypic and genetic variation through the migratory season. Specifically, we compared fish captured in different periods during the migration: early (July

Michael A. Hendry; John K. Wenburg; Katherine W. Myers; Andrew P. Hendry

2002-01-01

233

Genetic and Phenotypic Variation through the Migratory Season Provides Evidence for Multiple Populations of Wild Steelhead in the Dean River, British Columbia  

Microsoft Academic Search

We provide evidence for previously undetected population structure in a wild run of summer steelhead Oncorhynchus mykiss within a river that has considerable recreational importance (Dean River, British Columbia). Data were gathered from an existing catch-and-release fishery and examined for phenotypic and genetic variation through the migratory season. Specifically, we compared fish captured in different periods during the migration: early

Michael A. Hendry; John K. Wenburg; Katherine W. Myers; Andrew P. Hendry

2002-01-01

234

Two Subsets of HLA-DQA1 Alleles Mark Phenotypic Variation in Levels of Insulin Autoantibodies in First Degree Relatives at Risk for Insulin-dependent Diabetes  

E-print Network

Two Subsets of HLA-DQA1 Alleles Mark Phenotypic Variation in Levels of Insulin Autoantibodies Genetics Department, Roche Molecular Systems, Alameda, California 94501 Abstract Levels of insulin in First Degree Relatives at Risk for Insulin-dependent Diabetes Alberto Pugliese, * Teodorica Bugawan,11

Alper, Chester A.

235

Effects of environmental disturbance on phenotypic variation: an integrated assessment of canalization, developmental stability, modularity, and allometry in lizard head shape.  

PubMed

When populations experience suboptimal conditions, the mechanisms involved in the regulation of phenotypic variation can be challenged, resulting in increased phenotypic variance. This kind of disturbance can be diagnosed by using morphometric tools to study morphological patterns at different hierarchical levels and evaluate canalization, developmental stability, integration, modularity, and allometry. We assess the effect of urbanization on phenotypic variation in the common wall lizard (Podarcis muralis) by using geometric morphometrics to assess disturbance to head shape development. The head shapes of urban lizards were more variable and less symmetric, suggesting that urban living is more likely to disturb development. Head shape variation was congruent within and across individuals, which indicated that canalization and developmental stability are two related phenomena in these organisms. Furthermore, urban lizards exhibited smaller mean head sizes, divergent size-shape allometries, and increased deviation from within-group allometric lines. This suggests that mechanisms regulating head shape allometry may also be disrupted. The integrated evaluation of several measures of developmental instability at different hierarchical levels, which provided in this case congruent results, can be a powerful methodological guide for future studies, as it enhances the detection of environmental disturbances on phenotypic variation and aids biological interpretation of the results. PMID:25560552

Lazi?, Marko M; Carretero, Miguel A; Crnobrnja-Isailovi?, Jelka; Kaliontzopoulou, Antigoni

2015-01-01

236

Genetic variation within the Chrna7 gene modulates nicotine reward-like phenotypes in mice  

PubMed Central

Mortality from tobacco smoking remains the leading cause of preventable death in the world, yet current cessation therapies are only modestly successful, suggesting new molecular targets are needed. Genetic analysis of gene expression and behavior identified Chrna7 as potentially modulating nicotine place conditioning in the BXD panel of inbred mice. We used gene targeting and pharmacological tools to confirm the role of Chrna7 in nicotine CPP. To identify molecular events downstream of Chrna7 that may modulate nicotine preference, we performed microarray analysis of ?7 KO and WT nucleus accumbens tissue, followed by confirmation with quantitative PCR and immunoblotting. In the BXD panel, we found a putative cis eQTL for Chrna7 in nucleus accumbens that correlated inversely to nicotine CPP. We observed that gain-of-function ?7 mice did not display nicotine preference at any dose tested, while conversely, ?7 KO mice showed nicotine place preference at a dose below that routinely required to produce preference. In B6 mice, the ?7 nAChR-selective agonist, PHA-543613, dose-dependently blocked nicotine CPP, which was restored using the ?7 nAChR-selective antagonist, MLA. Our genomic studies implicated an mRNA co-expression network regulated by Chrna7 in nucleus accumbens. Mice lacking Chrna7 demonstrate increased insulin signaling in the nucleus accumbens, which may modulate nicotine place preference. Our studies provide novel targets for future work on development of more effective therapeutic approaches to counteract the rewarding properties of nicotine for smoking cessation. PMID:24289814

Harenza, Jo Lynne; Muldoon, Pretal P.; De Biasi, Mariella; Damaj, M. Imad; Miles, Michael F.

2014-01-01

237

Quantitative Estimation of Temperature Variations in Plantar Angiosomes: A Study Case for Diabetic Foot  

PubMed Central

Thermography is a useful tool since it provides information that may help in the diagnostic of several diseases in a noninvasive and fast way. Particularly, thermography has been applied in the study of the diabetic foot. However, most of these studies report only qualitative information making it difficult to measure significant parameters such as temperature variations. These variations are important in the analysis of the diabetic foot since they could bring knowledge, for instance, regarding ulceration risks. The early detection of ulceration risks is considered an important research topic in the medicine field, as its objective is to avoid major complications that might lead to a limb amputation. The absence of symptoms in the early phase of the ulceration is conceived as the main disadvantage to provide an opportune diagnostic in subjects with neuropathy. Since the relation between temperature and ulceration risks is well established in the literature, a methodology that obtains quantitative temperature differences in the plantar area of the diabetic foot to detect ulceration risks is proposed in this work. Such methodology is based on the angiosome concept and image processing. PMID:24688595

Peregrina-Barreto, H.; Morales-Hernandez, L. A.; Rangel-Magdaleno, J. J.; Avina-Cervantes, J. G.; Ramirez-Cortes, J. M.; Morales-Caporal, R.

2014-01-01

238

Genetic and phenotypic variation of Fusarium proliferatum isolates from different host species.  

PubMed

Fusarium proliferatum (Matsushima) Nirenberg is a common pathogen infecting numerous crop plants and occurring in various climatic zones. It produces large amounts of fumonisins, a group of polyketide-derived mycotoxins. Fumonisin biosynthesis is determined by the presence and activity of the FUM cluster, several co-regulated genes with a common expression pattern. In the present work, we analyzed 38 F. proliferatum isolates from different host plant species, demonstrating host-specific polymorphisms in partial sequences of the key FUM1 gene (encoding polyketide synthase). We also studied growth rates across different temperatures and sample origin and tried to establish the relationships between DNA sequence polymorphism and toxigenic potential. Phylogenetic analysis was conducted based on FUM1 and tef-1? sequences for all isolates. The results indicated the greatest variations of both toxigenic potential and growth patterns found across the wide selection of isolates derived from maize. Fumonisin production for maize isolates ranged from 3.74 to 4,500 ?g/g of fumonisin B(1). The most efficient producer isolates obtained from other host plants were only able to synthesize 1,820-2,419 ?g/g of this metabolite. A weak negative rank correlation between fumonisin content and isolate growth rates was observed. All garlic-derived isolates formed a distinct group on a FUM1-based dendrogram. A second clade consisted of tropical and sub-tropical strains (isolated from pineapple and date palm). Interestingly, isolates with the fastest growth patterns were also grouped together and included both isolates originating from rice. The sequence of the FUM1 gene was found to be useful in revealing the intraspecific polymorphism, which is, to some extent, specifically correlated with the host plant. PMID:21796391

St?pie?, Lukasz; Koczyk, Grzegorz; Wa?kiewicz, Agnieszka

2011-11-01

239

Quantitative Assessment of Autism Symptom-Related Traits in Probands and Parents: Broader Phenotype Autism Symptom Scale  

ERIC Educational Resources Information Center

Autism susceptibility genes likely have effects on continuously distributed autism-related traits, yet few measures of such traits exist. The Broader Phenotype Autism Symptom Scale (BPASS), developed for use with affected children and family members, measures social motivation, social expressiveness, conversational skills, and flexibility. Based…

Dawson, Geraldine; Estes, Annette; Munson, Jeffrey; Schellenberg, Gerard; Bernier, Raphael; Abbott, Robert

2007-01-01

240

Geographical patterns of morphological variation in sorghum ( Sorghum bicolor (L.) Moench) germplasm from Ethiopia and Eritrea: Quantitative characters  

Microsoft Academic Search

A total of 415 sorghum (Sorghum bicolor (L.) Moench) accessions representing different regions of Ethiopia, Eritrea and a group of introduced lines were evaluated\\u000a for 15 quantitative characters to determine the extent and geographical pattern of morphological variation. The extent of\\u000a variation was highly pronounced for agronomically important characters for sorghum. These characters included plant height,\\u000a days for 50% flowering,

Amsalu Ayana; Endashaw Bekele

2000-01-01

241

Linkage Analysis of a Cluster-Based Quantitative Phenotype Constructed from Pulmonary Function Test Data in 27 Multigenerational Families with Multiple Asthmatic Members  

PubMed Central

Objective To identify genes involved in phenotypes that increase one's risk for developing asthma, a complex disease that is likely genetically heterogeneous. Unlike other approaches to locus discovery in the presence of heterogeneity, this method seeks loci that segregate in all or most ascertained families while recognizing that other genes and environmental factors that modify the action of the common gene may vary across families. Methods The method is based on seeking groups of families that differ, between groups, in the way affected idndividuals express the genotype. Then we use the distance of each individual to the cluster center for his family to define a quantitative trait. This quantitative trait is then subjected to a genome scan using variance components methods. Results The method is applied to a data set of 27 multigenerational families with asthma, and a novel locus at 2q33 (at 210 cM) is identified. Conclusions The proposed method has the potential to identify loci near genes that increase risk for asthma related phenotypes. The method could be used for other complex disorders that exhibit locus heterogeneity. PMID:17476113

Reilly, Cavan; Miller, Michael B.; Liu, Yuhong; Oetting, William S.; King, Richard; Blumenthal, Malcolm

2007-01-01

242

Assessment of the ratio of pollen to seed flow in a cline for genetic variation in a quantitative trait  

Microsoft Academic Search

A dispersal–selection cline model is analysed to evaluate the role of the ratio of pollen to seed flow (r) in spatial genetic variation, with a focus on clines in additive and dominant variances of major genes affecting a quantitative trait, assuming one locus with two alleles, no genetic drift and no mutation. It is shown that under weak selection, steady-state

Xin-Sheng Hu; Bailian Li

2001-01-01

243

Variation in quantitative sensory testing and epidermal nerve fiber density in repeated measurements.  

PubMed

Quantitative sensory testing (QST) is commonly used to evaluate peripheral sensory function in neuropathic conditions. QST measures vary in repeated measurements of normal subjects but it is not known whether QST can reflect small changes in epidermal nerve fiber density (ENFd). This study evaluated QST measures (touch, mechanical pain, heat pain and innocuous cold sensations) for differences between genders and over time using ENFd as an objective-independent measure. QST was performed on the thighs of 36 healthy volunteers on four occasions between December and May. ENFd in skin biopsies was determined on three of those visits. Compared to men, women had a higher ENFd, a difference of 12.2 ENFs/mm. They also had lower tactile and innocuous cold thresholds, and detected mechanical pain (pinprick) at a higher frequency. Heat pain thresholds did not differ between genders. By the end of the 24-week study, men and women showed a small reduction (p<0.05) in the frequency of sharp mechanical pain evoked by pinprick whereas tactile and thermal thresholds showed no change. This coincided with a small decrease in ENFd, 4.18 ENFs/mm. Variation in measurements over time was large in a fraction of normal subjects. We conclude that most QST measures detect relatively large differences in epidermal innervation (12.2 ENFs/mm), but response to mechanical pain was the only sensory modality tested with the sensitivity to detect small changes in innervation (4.18 ENFs/mm). Since some individuals had large unsystematic variations, unexpected test results should therefore alert clinicians to test additional locations. PMID:20851518

Selim, Mona M; Wendelschafer-Crabb, Gwen; Hodges, James S; Simone, Donald A; Foster, Shawn X Y-L; Vanhove, Geertrui F; Kennedy, William R

2010-12-01

244

Fast quantitative susceptibility mapping using 3D EPI and total generalized variation.  

PubMed

Quantitative susceptibility mapping (QSM) allows new insights into tissue composition and organization by assessing its magnetic property. Previous QSM studies have already demonstrated that magnetic susceptibility is highly sensitive to myelin density and fiber orientation as well as to para- and diamagnetic trace elements. Image resolution in QSM with current approaches is limited by the long acquisition time of 3D scans and the need for high signal to noise ratio (SNR) to solve the dipole inversion problem. We here propose a new total-generalized-variation (TGV) based method for QSM reconstruction, which incorporates individual steps of phase unwrapping, background field removal and dipole inversion in a single iteration, thus yielding a robust solution to the reconstruction problem. This approach has beneficial characteristics for low SNR data, allowing for phase data to be rapidly acquired with a 3D echo planar imaging (EPI) sequence. The proposed method was evaluated with a numerical phantom and in vivo at 3 and 7T. Compared to total variation (TV), TGV-QSM enforced higher order smoothness which yielded solutions closer to the ground truth and prevented stair-casing artifacts. The acquisition time for images with 1mm isotropic resolution and whole brain coverage was 10s on a clinical 3Tesla scanner. In conclusion, 3D EPI acquisition combined with single-step TGV reconstruction yields reliable QSM images of the entire brain with 1mm isotropic resolution in seconds. The short acquisition time combined with the robust reconstruction may enable new QSM applications in less compliant populations, clinical susceptibility tensor imaging, and functional resting state examinations. PMID:25731991

Langkammer, Christian; Bredies, Kristian; Poser, Benedikt A; Barth, Markus; Reishofer, Gernot; Fan, Audrey Peiwen; Bilgic, Berkin; Fazekas, Franz; Mainero, Caterina; Ropele, Stefan

2015-05-01

245

Genes and quantitative genetic variation involved with senescence in cells, organs, and the whole plant  

PubMed Central

Senescence, the deterioration of morphological, physiological, and reproductive functions with age that ends with the death of the organism, was widely studied in plants. Genes were identified that are linked to the deterioration of cells, organs and the whole plant. It is, however, unclear whether those genes are the source of age dependent deterioration or get activated to regulate such deterioration. Furthermore, it is also unclear whether such genes are active as a direct consequence of age or because they are specifically involved in some developmental stages. At the individual level, it is the relationship between quantitative genetic variation, and age that can be used to detect the genetic signature of senescence. Surprisingly, the latter approach was only scarcely applied to plants. This may be the consequence of the demanding requirements for such approaches and/or the fact that most research interest was directed toward plants that avoid senescence. Here, I review those aspects in turn and call for an integrative genetic theory of senescence in plants. Such conceptual development would have implications for the management of plant genetic resources and generate progress on fundamental questions raised by aging research. PMID:25755664

Pujol, Benoit

2015-01-01

246

Natural variation for carbohydrate content in Arabidopsis. Interaction with complex traits dissected by quantitative genetics.  

PubMed

Besides being a metabolic fuel, carbohydrates play important roles in plant growth and development, in stress responses, and as signal molecules. We exploited natural variation in Arabidopsis (Arabidopsis thaliana) to decipher the genetic architecture determining carbohydrate content. A quantitative trait locus (QTL) approach in the Bay-0 x Shahdara progeny grown in two contrasting nitrogen environments led to the identification of 39 QTLs for starch, glucose, fructose, and sucrose contents representing at least 14 distinct polymorphic loci. A major QTL for fructose content (FR3.4) and a QTL for starch content (ST3.4) were confirmed in heterogeneous inbred families. Several genes associated with carbon (C) metabolism colocalize with the identified QTL. QTLs for senescence-related traits, and for flowering time, water status, and nitrogen-related traits, previously detected with the same genetic material, colocalize with C-related QTLs. These colocalizations reflect the complex interactions of C metabolism with other physiological processes. QTL fine-mapping and cloning could thus lead soon to the identification of genes potentially involved in the control of different connected physiological processes. PMID:16798941

Calenge, Fanny; Saliba-Colombani, Véra; Mahieu, Stéphanie; Loudet, Olivier; Daniel-Vedele, Françoise; Krapp, Anne

2006-08-01

247

Quantitative genetics of sugarcane : I. Analysis of variation in a commercial hybrid sugarcane population.  

PubMed

1. The statistical techniques of quantitative genetic analysis have been applied to the study of variation in a sugarcane breeding population of interspecific hybrid origin. 2. A comparison has been made of estimates of heritability based on sire or dam components of variance alone. The overall equality of these two statistics has been taken as evidence that pollen contamination, self-fertilization and parthenogenetic reproduction are unimportant sources of disturbance in the genetic analysis of the population. 3. From an analysis of plot means it has been concluded that all twenty-four primary characters show significant clonal variation, the overall mean value for clonal repeatability being 0.48. For sixteen of the variables, the estimate of heritability based on the component of variance among full-sib family groups was also significant, the mean value of this parameter being 0.29. 4. For ten of the primary characters, the estimate of clonal repeatability differed significantly from the estimate of heritability. In every case the repeatability value was the greater of the two. It cannot be concluded that nonadditive genetic variance is the major factor responsible, since the use of selected clones as parental material, and disassortative mating for some easily observed characters, appear to provide a sufficient explanation of the disparity. 5. The irregular transmission of unpaired chromosomes derived fromS. spontaneum, S. robustum andS. sinense may possibly contribute to the observed difference between heritability and repeatability. No other serious departure was observed from expectations based on diploid inheritance. 6. The analyses show fibre percent fresh weight and sucrose percent dry matter to be particularly strong clonal characters. The measure of sucrose per plot, which includes variability for yield of cane, has a heritability of 0.24, a repeatability of 0.43, and a high coefficient of variation (46%). 7. Comparisons of the breeding population with two commercial standards have indicated that selection among genotypes within the present population could lead to significant improvement in any one of the commercially important characters. Further gains with subsequent cycles of hybridization and selection are also strongly indicated. No information has as yet been obtained on the magnitude of genotype×years interaction effects. PMID:24442394

Brown, A H; Daniels, J; Latter, B D

1968-08-01

248

Resolving within- and between-population variation in feeding ecology with a biomechanical model  

Microsoft Academic Search

Studies of phenotypic plasticity have emphasized the effect of the environment on the phenotype, but plasticity can also be used as a tool to study the functional significance of key traits. By inducing variation in phenotypes and testing quantitative models that predict performance based on biological mechanisms, we can develop functionally general models of performance. Pumpkinseed sunfish from lakes with

Craig W. Osenberg; Casey J F. Huckins; Anthony Kaltenberg; Ari Martinez

2004-01-01

249

Sources of interindividual variation in the quantitative levels of apolipoprotein B in pedigrees ascertained through a lipid clinic.  

PubMed Central

The quantitative level of apolipoprotein (apo) B associated with low-density lipoprotein (LDL) varies among individuals within the population. This variation in level of the LDL receptor ligand appears to have predictive value, and may have an etiologic role, in coronary artery disease. Complex segregation analysis was used to compare eight different models of transmission. This study confirms the existence of allelic variations at a single genetic locus with large effects on the interindividual variation in the level of the serum apo B associated with LDL. This is the first study to consider the possible effects of inherited polymorphic variation in the apo E molecule when analyzing the components of variation in apo B associated with LDL. Our analyses suggest that the common alleles coding for the apo E polymorphism act independently of the unmeasured single-gene locus characterized by this study. PMID:3414686

Pairitz, G; Davignon, J; Mailloux, H; Sing, C F

1988-01-01

250

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice.  

PubMed

Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits. PMID:25295980

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

2014-01-01

251

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice  

PubMed Central

Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits. PMID:25295980

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

2014-01-01

252

Effect of Genetic Variation in STXBP5 and STX2 on von Willebrand Factor and Bleeding Phenotype in Type 1 von Willebrand Disease Patients  

PubMed Central

Background In type 1 von Willebrand Disease (VWD) patients, von Willebrand Factor (VWF) levels and bleeding symptoms are highly variable. Recently, the association between genetic variations in STXBP5 and STX2 with VWF levels has been discovered in the general population. We assessed the relationship between genetic variations in STXBP5 and STX2, VWF levels, and bleeding phenotype in type 1 VWD patients. Methods In 158 patients diagnosed with type 1 VWD according to the current ISTH guidelines, we genotyped three tagging-SNPs in STXBP5 and STX2 and analyzed their relationship with VWF:Ag levels and the severity of the bleeding phenotype, as assessed by the Tosetto bleeding score. Results In STX2, rs7978987 was significantly associated with VWF:Ag levels (bèta-coefficient (?)?=??0.04 IU/mL per allele, [95%CI ?0.07;?0.001], p?=?0.04) and VWF:CB activity (??=??0.12 IU/mL per allele, [95%CI ?0.17;?0.06], p<0.0001). For rs1039084 in STXBP5 a similar trend with VWF:Ag levels was observed: (??=??0.03 IU/mL per allele [95% CI ?0.06;0.003], p?=?0.07). In women, homozygous carriers of the minor alleles of both SNPs in STXBP5 had a significantly higher bleeding score than homozygous carriers of the major alleles. (Rs1039084 p?=?0.01 and rs9399599 p?=?0.02). Conclusions Genetic variation in STX2 is associated with VWF:Ag levels in patients diagnosed with type 1 VWD. In addition, genetic variation in STXBP5 is associated with bleeding phenotype in female VWD patients. Our findings may partly explain the variable VWF levels and bleeding phenotype in type 1 VWD patients. PMID:22792389

van Loon, Janine E.; Sanders, Yvonne V.; de Wee, Eva M.; Kruip, Marieke J. H. A.; de Maat, Moniek P. M.; Leebeek, Frank W. G.

2012-01-01

253

High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate.  

PubMed

Embryogenic suspensions that involve extensive cell division are risky in respect to genome and epigenome instability. Elevated frequencies of somaclonal variation in embryogenic suspension-derived plants were reported in many species, including coffee. This problem could be overcome by using culture conditions that allow moderate cell proliferation. In view of true-to-type large-scale propagation of C. arabica hybrids, suspension protocols based on low 2,4-D concentrations and short proliferation periods were developed. As mechanisms leading to somaclonal variation are often complex, the phenotypic, genetic and epigenetic changes were jointly assessed so as to accurately evaluate the conformity of suspension-derived plants. The effects of embryogenic suspensions and secondary embryogenesis, used as proliferation systems, on the genetic conformity of somatic embryogenesis-derived plants (emblings) were assessed in two hybrids. When applied over a 6 month period, both systems ensured very low somaclonal variation rates, as observed through massive phenotypic observations in field plots (0.74% from 200,000 plant). Molecular AFLP and MSAP analyses performed on 145 three year-old emblings showed that polymorphism between mother plants and emblings was extremely low, i.e. ranges of 0-0.003% and 0.07-0.18% respectively, with no significant difference between the proliferation systems for the two hybrids. No embling was found to cumulate more than three methylation polymorphisms. No relation was established between the variant phenotype (27 variants studied) and a particular MSAP pattern. Chromosome counting showed that 7 of the 11 variant emblings analyzed were characterized by the loss of 1-3 chromosomes. This work showed that both embryogenic suspensions and secondary embryogenesis are reliable for true-to-type propagation of elite material. Molecular analyses revealed that genetic and epigenetic alterations are particularly limited during coffee somatic embryogenesis. The main change in most of the rare phenotypic variants was aneuploidy, indicating that mitotic aberrations play a major role in somaclonal variation in coffee. PMID:23418563

Bobadilla Landey, Roberto; Cenci, Alberto; Georget, Frédéric; Bertrand, Benoît; Camayo, Gloria; Dechamp, Eveline; Herrera, Juan Carlos; Santoni, Sylvain; Lashermes, Philippe; Simpson, June; Etienne, Hervé

2013-01-01

254

Changes in T-DNA methylation and expression are associated with phenotypic variation and plant regeneration in a crown gall tumor line  

Microsoft Academic Search

Phenotypic variation of an octopine-type crown gall tumor line resulting from changes in the pattern of T-DNA methylation and expression is described. Variants that grow as unorganized callus always express T-DNA transcripts 1 and 2. In shoot-forming variants (teratomas) only T-DNA transcript 4 is expressed. This line also regenerates normal-appearing, rooted plants in which all T-DNA expression is suppressed. Tissues

Richard M. Amasino; Ann L. T. Powell; Milton P. Gordon

1984-01-01

255

Quantitative Phenotyping-Based In Vivo Chemical Screening in a Zebrafish Model of Leukemia Stem Cell Xenotransplantation  

PubMed Central

Zebrafish-based chemical screening has recently emerged as a rapid and efficient method to identify important compounds that modulate specific biological processes and to test the therapeutic efficacy in disease models, including cancer. In leukemia, the ablation of leukemia stem cells (LSCs) is necessary to permanently eradicate the leukemia cell population. However, because of the very small number of LSCs in leukemia cell populations, their use in xenotransplantation studies (in vivo) and the difficulties in functionally and pathophysiologically replicating clinical conditions in cell culture experiments (in vitro), the progress of drug discovery for LSC inhibitors has been painfully slow. In this study, we developed a novel phenotype-based in vivo screening method using LSCs xenotransplanted into zebrafish. Aldehyde dehydrogenase-positive (ALDH+) cells were purified from chronic myelogenous leukemia K562 cells tagged with a fluorescent protein (Kusabira-orange) and then implanted in young zebrafish at 48 hours post-fertilization. Twenty-four hours after transplantation, the animals were treated with one of eight different therapeutic agents (imatinib, dasatinib, parthenolide, TDZD-8, arsenic trioxide, niclosamide, salinomycin, and thioridazine). Cancer cell proliferation, and cell migration were determined by high-content imaging. Of the eight compounds that were tested, all except imatinib and dasatinib selectively inhibited ALDH+ cell proliferation in zebrafish. In addition, these anti-LSC agents suppressed tumor cell migration in LSC-xenotransplants. Our approach offers a simple, rapid, and reliable in vivo screening system that facilitates the phenotype-driven discovery of drugs effective in suppressing LSCs. PMID:24454867

Zhang, Beibei; Shimada, Yasuhito; Kuroyanagi, Junya; Umemoto, Noriko; Nishimura, Yuhei; Tanaka, Toshio

2014-01-01

256

Quantitative phenotyping-based in vivo chemical screening in a zebrafish model of leukemia stem cell xenotransplantation.  

PubMed

Zebrafish-based chemical screening has recently emerged as a rapid and efficient method to identify important compounds that modulate specific biological processes and to test the therapeutic efficacy in disease models, including cancer. In leukemia, the ablation of leukemia stem cells (LSCs) is necessary to permanently eradicate the leukemia cell population. However, because of the very small number of LSCs in leukemia cell populations, their use in xenotransplantation studies (in vivo) and the difficulties in functionally and pathophysiologically replicating clinical conditions in cell culture experiments (in vitro), the progress of drug discovery for LSC inhibitors has been painfully slow. In this study, we developed a novel phenotype-based in vivo screening method using LSCs xenotransplanted into zebrafish. Aldehyde dehydrogenase-positive (ALDH+) cells were purified from chronic myelogenous leukemia K562 cells tagged with a fluorescent protein (Kusabira-orange) and then implanted in young zebrafish at 48 hours post-fertilization. Twenty-four hours after transplantation, the animals were treated with one of eight different therapeutic agents (imatinib, dasatinib, parthenolide, TDZD-8, arsenic trioxide, niclosamide, salinomycin, and thioridazine). Cancer cell proliferation, and cell migration were determined by high-content imaging. Of the eight compounds that were tested, all except imatinib and dasatinib selectively inhibited ALDH+ cell proliferation in zebrafish. In addition, these anti-LSC agents suppressed tumor cell migration in LSC-xenotransplants. Our approach offers a simple, rapid, and reliable in vivo screening system that facilitates the phenotype-driven discovery of drugs effective in suppressing LSCs. PMID:24454867

Zhang, Beibei; Shimada, Yasuhito; Kuroyanagi, Junya; Umemoto, Noriko; Nishimura, Yuhei; Tanaka, Toshio

2014-01-01

257

Quantitative proteomic profiling reveals photosynthesis responsible for inoculum size dependent variation in Chlorella sorokiniana.  

PubMed

High density cultivation is essential to industrial production of biodiesel from microalgae, which involves in variations of micro-environment around individual cells, including light intensity, nutrition distribution, other abiotic stress and so on. To figure out the main limit factor in high inoculum cultivation, a quantitative proteomic analysis (iTRAQ-on-line 2-D nano-LC/MS) in a non-model green microalga, Chlorella sorokiniana, under different inoculum sizes was conducted. The resulting high-quality proteomic dataset consisted of 695 proteins. Using a cutoff of P < 0.05, 241 unique proteins with differential expression levels were identified between control and different inoculum sizes. Functional analysis showed that proteins participating in photosynthesis (light reaction) and Calvin cycle (carbon reaction pathway) had highest expression levels under inoculum size of 1 × 10(6) cells mL(-1), and lowest levels under 1 × 10(7) cells mL(-1). Canonical correlation analysis of the photosynthesis related proteins and metabolites biomarkers showed that a good correlation existed between them (canonical coefficient was 0.987), suggesting photosynthesis process greatly affected microalgae biodiesel productivity and quality. Proteomic study of C. sorokiniana under different illuminations was also conducted to confirm light intensity as a potential limit factor of high inoculum size. Nearly two thirds of proteins showed up-regulation under the illumination of 70-110 µmol m(-2) s(-1), compared to those of 40 µmol m(-2) s(-1). This result suggested that by elegantly adjusting light conditions, high cell density cultivation and high biodiesel production might be achieved. PMID:23096779

Ma, Qian; Wang, Jiangxin; Lu, Shuhuan; Lv, Yajin; Yuan, Yingjin

2013-03-01

258

A pyramid breeding of eight grain-yield related quantitative trait loci based on marker-assistant and phenotype selection in rice (Oryza sativa L.).  

PubMed

1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci (QTLs) conferring spikelet number per panicle and 1000-grain weight were mapped through sequencing-based genotyping of 150 rice recombinant inbred lines (RILs). In this study, we validated the effects of four QTLs from Nipponbare using chromosome segment substitution lines (CSSLs), and pyramided eight grain yield related QTLs. The new lines containing the eight QTLs with positive effects showed increased panicle and spikelet size as compared with the parent variety 93-11. We further proposed a novel pyramid breeding scheme based on marker-assistant and phenotype selection (MAPS). This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding. PMID:22835980

Zong, Guo; Wang, Ahong; Wang, Lu; Liang, Guohua; Gu, Minghong; Sang, Tao; Han, Bin

2012-07-20

259

Exploring the quantitative relationship between metabolism and enzymatic phenotype by physiological modeling of glucose metabolism and lactate oxidation in solid tumors  

NASA Astrophysics Data System (ADS)

Molecular imaging using PET or hyperpolarized MRI can characterize tumor phenotypes by assessing the related metabolism of certain substrates. However, the interpretation of the substrate turnover in terms of a pathophysiological understanding is not straightforward and only semiquantitative. The metabolism of imaging probes is influenced by a number of factors, such as the microvascular structure or the expression of key enzymes. This study aims to use computational simulation to investigate the relationship between the metabolism behind molecular imaging and the underlying tumor phenotype. The study focused on the pathways of glucose metabolism and lactate oxidation in order to establish the quantitative relationship between the expression of several transporters (GLUT, MCT1 and MCT4), expression of the enzyme hexokinase (HK), microvasculature and the metabolism of glucose or lactate and the extracellular pH distribution. A computational model for a 2D tumor tissue phantom was constructed and the spatio-temporal evolution of related species (e.g. oxygen, glucose, lactate, protons, bicarbonate ions) was estimated by solving reaction-diffusion equations. The proposed model was tested by the verification of the simulation results using in vivo and in vitro literature data. The influences of different expression levels of GLUT, MCT1, MCT4, HK and microvessel distribution on substrate concentrations were analyzed. The major results are consistent with experimental data (e.g. GLUT is more influential to glycolytic flux than HK; extracellular pH is not correlated with MCT expressions) and provide theoretical interpretation of the co-influence of multiple factors of the tumor microenvironment. This computational simulation may assist the generation of hypotheses to bridge the discrepancy between tumor metabolism and the functions of transporters and enzymes. It has the potential to accelerate the development of multi-modal imaging strategies for assessment of tumor phenotypes.

Wang, Qian; Vaupel, Peter; Ziegler, Sibylle I.; Shi, Kuangyu

2015-03-01

260

Phenotypic and functional properties of murine thymocytes. II. Quantitation of host- and donor-derived cytolytic T lymphocyte precursors in regenerating radiation bone marrow chimeras  

SciTech Connect

Thymocytes from radiation bone marrow chimeras, in which donor bone marrow and irradiated recipient differed at the Thy-1 locus, were stained by indirect immunofluorescence with monoclonal anti-Thy-1 antibodies and analyzed by flow microfluorometry (FMF). Kinetic studies indicated an early appearance of host-derived (CBA, Thy-1.2/sup +/) thymocytes, which reaches maximum number of 10 to 20 x 10/sup 6/ cells at 12 to 16 days after bone marrow reconstitution. Donor-derived (AKR, Thy-1.1/sup +/) cells were not detectable until 10 to 12 days after reconstitution; subsequently, they increased exponentially in number until 28 days, when they accounted for essentially all cells in the thymus (50 x 10/sup 6/). Concomitant with the appearance and disappearance of host-derived cells was a change in their Thy-1 surface phenotype. In particular, the proportion of host cells having a ''mature'' phenotype (weakly Thy-1.2 staining) increased progressively with time after irradiation. Functional studies using a sensitive mixed leukocyte microculture system to quantitate cytolytic T lymphocyte precursors (CTL-P) were also carried out in regenerating chimeric thymuses. Initially, the regenerating thymus contained few CTL-P, but by 4 wk after reconstitution, frequencies similar to control adult thymuses were obtained. Analysis of the CTL-P content of host and donor-derived subpopulations, separated either by appropriate anti-Thy-1 antibody plus complement or by direct cell sorting, indicated that both host- and donor-derived cells contained appreciable numbers of CTL-P. Furthermore, increases in CTL-P frequency of both host and donor subpopulations correlated with changes in their surface Thy-1 phenotype.

Ceredig, R.; McDonald, H.R.

1982-02-01

261

Genetics, phosphorus availability, and herbivore-derived induction as sources of phenotypic variation of leaf volatile terpenes in a pine species  

PubMed Central

Oleoresin produced and stored in pine tree leaves provides direct resistance to herbivores, while leaf volatile terpenes (LVT) in the resin are also powerful airborne infochemicals. Resin concentration and profile show considerable spatial and temporal phenotypic variation within and among pine populations. LVT biochemistry is known to be under genetic control, and although LVT should be plastic to diverse abiotic and biotic environmental factors such as nutrient availability and herbivore attack, little is known about their relative contributions and interactive effects. The aim of this paper was to clarify whether reduced phosphorus availability could increase the LVT concentration and affect the expression of herbivore-derived induced defences, and how plasticity would contribute to the phenotypic variation of LVT. The constitutive and methyl-jasmonate (MeJa) induced LVT concentration and profile were analysed in 17 half-sib Pinus pinaster families growing under two levels of P-availability (complete and P-limited fertilization). Individual terpene concentrations showed large additive genetic variation, which was more pronounced in the control than in MeJa-induced pines. MeJa application did not affect the LVT concentration, but significantly modified the LVT profile by depleting the ?-pinene content and reducing the sesquiterpene fraction. Low P-availability strongly reduced plant growth and foliar nutrient concentrations, but did not affect LVT concentration and profile, and did not interact with MeJa-induction. Results indicate a strong homeostasis of LVT concentration to P-availability, and minor changes in the LVT profile due to MeJa-induction. Genetic variation appears to be the main source of phenotypic variation affecting the LVT concentration in this pine species. PMID:20952630

Sampedro, Luis; Llusia, Joan; Peñuelas, Josep; Zas, Rafael

2010-01-01

262

Genetics, phosphorus availability, and herbivore-derived induction as sources of phenotypic variation of leaf volatile terpenes in a pine species.  

PubMed

Oleoresin produced and stored in pine tree leaves provides direct resistance to herbivores, while leaf volatile terpenes (LVT) in the resin are also powerful airborne infochemicals. Resin concentration and profile show considerable spatial and temporal phenotypic variation within and among pine populations. LVT biochemistry is known to be under genetic control, and although LVT should be plastic to diverse abiotic and biotic environmental factors such as nutrient availability and herbivore attack, little is known about their relative contributions and interactive effects. The aim of this paper was to clarify whether reduced phosphorus availability could increase the LVT concentration and affect the expression of herbivore-derived induced defences, and how plasticity would contribute to the phenotypic variation of LVT. The constitutive and methyl-jasmonate (MeJa) induced LVT concentration and profile were analysed in 17 half-sib Pinus pinaster families growing under two levels of P-availability (complete and P-limited fertilization). Individual terpene concentrations showed large additive genetic variation, which was more pronounced in the control than in MeJa-induced pines. MeJa application did not affect the LVT concentration, but significantly modified the LVT profile by depleting the ?-pinene content and reducing the sesquiterpene fraction. Low P-availability strongly reduced plant growth and foliar nutrient concentrations, but did not affect LVT concentration and profile, and did not interact with MeJa-induction. Results indicate a strong homeostasis of LVT concentration to P-availability, and minor changes in the LVT profile due to MeJa-induction. Genetic variation appears to be the main source of phenotypic variation affecting the LVT concentration in this pine species. PMID:20952630

Sampedro, Luis; Moreira, Xoaquín; Llusia, Joan; Peñuelas, Josep; Zas, Rafael

2010-10-01

263

Skin Expression of Metalloproteinases and Tissue Inhibitor of Metalloproteinases in Sibling Patients with Recessive Dystrophic Epidermolysis and Intrafamilial Phenotypic Variation  

Microsoft Academic Search

A number of COL7A1 mutations have now been reported in recessive dystrophic epidermolysis bullosa patients, and the analysis of phenotype?genotype correlations showed evidence for interfamilial and intrafamilial phenotypic variability, occurring for the same mutation. Collagenase and stromelysin activities have been found to be overexpressed in skin cultures of some recessive dystrophic epidermolysis bullosa patients, and tissue destruction in the disease

Christine Bodemer; Sylvie Igondjo Tchen; Sabah Ghomrasseni; Sylvie Séguier; Frédérick Gaultier; Sylvie Fraitag; Yves de Prost; Gaston Godeau

2003-01-01

264

Limited phylogeographic signal in sex-linked and autosomal loci despite geographically, ecologically, and phenotypically concordant structure of mtDNA variation in the Holarctic avian genus Eremophila.  

PubMed

Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early-Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris) with respect to the Temminck's lark (E. bilopha). In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species. PMID:24498139

Drovetski, Sergei V; Rakovi?, Marko; Semenov, Georgy; Fadeev, Igor V; Red'kin, Yaroslav A

2014-01-01

265

Limited Phylogeographic Signal in Sex-Linked and Autosomal Loci Despite Geographically, Ecologically, and Phenotypically Concordant Structure of mtDNA Variation in the Holarctic Avian Genus Eremophila  

PubMed Central

Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early - Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris) with respect to the Temminck's lark (E. bilopha). In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species. PMID:24498139

Drovetski, Sergei V.; Rakovi?, Marko; Semenov, Georgy; Fadeev, Igor V.; Red’kin, Yaroslav A.

2014-01-01

266

A single nucleotide polymorphism tags variation in the arylamine N-acetyltransferase 2 phenotype in populations of European background  

PubMed Central

Objective The arylamine N-acetyltransferase 2 (NAT2) slow acetylation phenotype is an established risk factor for urinary bladder cancer. We previously reported on this risk association using NAT2 phenotypic categories inferred from NAT2 haplotypes based on 7 single nucleotide polymorphisms (SNPs) in a study in Spain. In a subsequent genome-wide scan, we have identified a single common tag SNP (rs1495741) located in the 3? end of NAT2 that is also associated with bladder cancer risk. The aim of this report is to evaluate the agreement between the common tag SNP and the 7-SNP NAT2 inferred phenotype. Methods The agreement between the 7-SNP NAT2 inferred phenotype and the tag SNP, rs1495741, was initially assessed in 2,174 subjects from the Spanish Bladder Cancer Study (SBCS), and confirmed in a subset of subjects from the Main and Vermont component the New England Bladder Cancer Study (NEBCS). We also investigated the association of rs1495741 genotypes with NAT2 catalytic activity in cryopreserved hepatocytes from 154 individuals of European background. Results We observed very strong agreement between rs1495741 and the 7-SNP inferred NAT2 phenotype: sensitivity and specificity for the NAT2 slow phenotype was 99% and 95%, respectively. Our findings were replicated in an independent population from the United States. Estimates for the association between NAT2 slow phenotype and bladder cancer risk in the SBCS and its interaction with cigarette smoking were comparable for the 7-SNP inferred NAT2 phenotype and rs1495741. In addition, rs1495741 genotypes were strongly related to NAT2 activity measured in hepatocytes (P<0.0001). Conclusion A novel NAT2 tag SNP (rs1495741) predicts with high accuracy the 7- SNP inferred NAT2 phenotype, and thus can be used as a sole marker in pharmacogenetic or epidemiological studies of populations of European background. These findings illustrate the utility of tag SNPs, often employed in genome-wide association studies (GWAS), to identify novel phenotypic markers. Further studies are required to determine the functional implications of this novel SNP and the structure and evolution of the haplotype on which it resides. PMID:20739907

García-Closas, Montserrat; Hein, David W.; Silverman, Debra; Malats, Núria; Yeager, Meredith; Jacobs, Kevin; Doll, Mark A; Figueroa, Jonine D; Baris, Dalsu; Schwenn, Molly; Kogevinas, Manolis; Johnson, Alison; Chatterjee, Nilanjan; Moore, Lee E.; Moeller, Timothy; Real, Francisco X.; Chanock, Stephen; Rothman, Nathaniel

2010-01-01

267

SNP signatures of selection on standing genetic variation and their association with adaptive phenotypes along gradients of ecological speciation in lake whitefish species pairs (Coregonus spp.).  

PubMed

As populations adapt to novel environments, divergent selection will promote heterogeneous genomic differentiation via reductions in gene flow for loci underlying adaptive traits. Using a data set of over 100 SNP markers, genome scans were performed to investigate the effect of natural selection maintaining differentiation in five lakes harbouring sympatric pairs of normal and dwarf lake whitefish (Coregonus clupeaformis). A variable proportion of SNPs (between 0% and 12%) was identified as outliers, which corroborated the predicted intensity of competitive interactions unique to each lake. Moreover, strong reduction in heterozygosity was typically observed for outlier loci in dwarf but not in normal whitefish, indicating that directional selection has been acting on standing genetic variation more intensively in dwarf whitefish. SNP associations in backcross hybrid progeny identified 16 genes exhibiting genotype-phenotype associations for four adaptive traits (growth, swimming activity, gill rakers and condition factor). However, neither simple relationship between elevated levels of genetic differentiation with adaptive phenotype nor conspicuous genetic signatures for parallelism at outlier loci were detected, which underscores the importance of independent evolution among lakes. The integration of phenotypic, transcriptomic and functional genomic information identified two candidate genes (sodium potassium ATPase and triosephosphate isomerase) involved in the recent ecological divergence of lake whitefish. Finally, the identification of several markers under divergent selection suggests that many genes, in an environment-specific manner, are recruited by selection and ultimately contributed to the repeated ecological speciation of a dwarf phenotype. PMID:21143332

Renaut, Sébastien; Nolte, Arne W; Rogers, Sean M; Derome, Nicolas; Bernatchez, Louis

2011-02-01

268

Natural variation of barley vernalization requirements: implication of quantitative variation of winter growth habit as an adaptive trait in East Asia.  

PubMed

In many temperate plant species, prolonged cold treatment, known as vernalization, is one of the most critical steps in the transition from the vegetative to the reproductive stage. In contrast to recent advances in understanding the molecular basis of vernalization in Arabidopsis non-vernalization mutants or the spring growth habits of cereal crops such as wheat and barley, natural variations in winter growth habits and their geographic distribution are poorly understood. We analyzed varietal variation and the geographic distribution of the degree of vernalization requirements in germplasms of domesticated barley and wild barley collections. We found a biased geographic distribution of vernalization requirements in domesticated barley: Western regions were strongly associated with a higher degree of spring growth habits, and the extreme winter growth habits were localized to Far Eastern regions including China, Korea and Japan. Both wild accessions and domesticated landraces, the regions of distribution of which overlapped each other, mainly belonged to the moderate class of winter growth habit. As a result of quantitative evaluations performed in this study, we provide evidence that the variation in the degree of winter growth habit in recombinant inbred lines was controlled by quantitative trait loci including three vernalization genes (VRN1, VRN2 and VRN3) that account for 37.9% of the variation in vernalization requirements, with unknown gene(s) explaining the remaining two-thirds of the variation. This evidence implied that the Far Eastern accessions might be a genetically differentiated group derived for an evolutionary reason, resulting in their greater tendency towards a winter growth habit. PMID:21482579

Saisho, Daisuke; Ishii, Makoto; Hori, Kiyosumi; Sato, Kazuhiro

2011-05-01

269

Quantitative genetics of floral traits in a gynodioecious wild strawberry Fragaria virginiana: implications for the independent evolution of female and hermaphrodite floral phenotypes.  

PubMed

The independent evolution of floral phenotype is an important part of the process of gender specialization during the evolution of dioecy from hermaphroditism. However, we have little information on the genetic variation of floral traits in species with separate genders. Gynodioecious species (co-occurrence of females and hermaphrodites) have a breeding system intermediate between hermaphroditism and complete separation of the sexes (dioecy) and thus can provide insight into the genetic architecture underlying floral phenotype with respect to both primary (stamens and carpels) and secondary (petals) sexual traits. I used a nested breeding design to examine the potential for response to selection on floral traits and to examine whether this response would be similar in the two sex morphs of gynodioecious Fragaria virginiana. There was significant genetic variation underlying all floral traits, although narrow-sense heritabilities (ranging from -0.25 to 0.44) were, in most cases, much lower than broad-sense ones (ranging from 0.28 to 1. 53). Moreover, the sex morphs differed significantly in their heritabilities for shared traits, such as stamen length, and showed a tendency towards differing significantly in others, like carpel number and petal length. In addition, correlations between the sex morphs for these traits (ranging from 0.41 to 0.58) were significantly greater than 0, but less than 1. These results indicate that greater sexual dimorphism could evolve in this population of F. virginiana, even if selection on these traits is not divergent. However, strong developmental integration of floral traits (e.g. stamen length and petal length) and high levels of nonadditive genetic variance may represent barriers to the evolution of complete sexual dimorphism. PMID:10651918

Ashman, T L

1999-12-01

270

Phenotypic variation of Val1589Met mutation in a four-generation Chinese pedigree with mild paramyotonia congenitia: case report  

PubMed Central

Four generations of a Chinese family with a mild form of paramyotonia congenital was characterized in phenotype and genotype. For each member, clinical history, physical examination, laboratory tests, electrophysiological and gene analyses were recorded and carried out. A potassium loading, exercise and cold provocation were further tested to diagnose the clinical differentiation. All members shared the characteristics of mild muscle cramp and stiffness induced by exercise or exposed to cold. The symptoms were relieved after rest and warming. A Val1589Met mutation at exon 24 of the SCN4A gene appears in affected subjects, while healthy members had a point mutation at position 1513 at exon 24 of the SCN4A gene. The mild phenotype of the paramyotonia congenital in the family had a Val1589Met mutation in the SCN4A gene. Various phenotypes can exist among different families, indicating that family, individual, genetic or environmental factors influence symptoms. PMID:25755818

Xu, Changshui; Qi, Junjia; Shi, Yingying; Feng, Yan; Zang, Weizhou; Zhang, Jiewen

2015-01-01

271

Copy Number Variations Burden on miRNA Genes Reveals Layers of Complexities Involved in the Regulation of Pathways and Phenotypic Expression  

PubMed Central

MicroRNAs are involved in post-transcriptional down-regulation of gene expression. Variations in miRNA genes can severely affect downstream-regulated genes and their pathways. However, population-specific burden of CNVs on miRNA genes and the complexities created towards the phenotype is not known. From a total of 44109 CNVs investigated from 1715 individuals across 12 populations using high-throughput arrays, 4007 miRNA-CNVs (?9%) consisting 6542 (?5%) miRNA genes with a total of 333 (?5%) singleton miRNA genes were identified. We found miRNA-CNVs across the genomes of individuals showing multiple hits in many targets, co-regulated under the same pathway. This study proposes four mechanisms unraveling the many complexities in miRNA genes, targets and co-regulated miRNA genes towards establishment of phenotypic diversity. PMID:24587348

Veerappa, Avinash M.; Nachappa, Somanna Ajjamada; Prashali, Nelchi; Yadav, Sangeetha Nuggehalli; Srikanta, Manjula Arsikere; Manjegowda, Dinesh S.; Seshachalam, Keshava B.; Ramachandra, Nallur B.

2014-01-01

272

Genetic Markers and Quantitative Genetic Variation in Medicago Truncatula (Leguminosae): A Comparative Analysis of Population Structure  

PubMed Central

Two populations of the selfing annual Medicago truncatula Gaertn. (Leguminoseae), each subdivided into three subpopulations, were studied for both metric traits (quantitative characters) and genetic markers (random amplified polymorphic DNA and one morphological, single-locus marker). Hierarchical analyses of variance components show that (1) populations are more differentiated for quantitative characters than for marker loci, (2) the contribution of both within and among subpopulations components of variance to overall genetic variance of these characters is reduced as compared to markers, and (3) at the population level, within population structure is slightly but not significantly larger for markers than for quantitative traits. Under the hypothesis that most markers are neutral, such comparisons may be used to make hypotheses about the strength and heterogeneity of natural selection in the face of genetic drift and gene flow. We thus suggest that in these populations, quantitative characters are under strong divergent selection among populations, and that gene flow is restricted among populations and subpopulations. PMID:8844165

Bonnin, I.; Prosperi, J. M.; Olivieri, I.

1996-01-01

273

Temporal Variations of Skin Pigmentation in C57Bl\\/6 Mice Affect Optical Bioluminescence Quantitation  

Microsoft Academic Search

Purpose  Depilation-induced skin pigmentation in C57Bl\\/6 mice is a known occurrence, and presents a unique problem for quantitative\\u000a optical imaging of small animals, especially for bioluminescence. The work reported here quantitatively investigated the optical\\u000a attenuation of bioluminescent light due to melanin pigmentation in the skin of transgenic C57Bl\\/6 mice, modified such that\\u000a luciferase expression is under the transcription control of a

Allison Curtis; Katherine Calabro; Jean-Rene Galarneau; Irving J. Bigio; Thomas Krucker

274

Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae).  

PubMed

Adaptive evolution requires both raw genetic material and an accessible path of high fitness from one fitness peak to another. In this study, we used an introgression line (IL) population to map quantitative trait loci (QTL) for leaf traits thought to be associated with adaptation to precipitation in wild tomatoes (Solanum sect. Lycopersicon; Solanaceae). A QTL sign test showed that several traits likely evolved under directional natural selection. Leaf traits correlated across species do not share a common genetic basis, consistent with a scenario in which selection maintains trait covariation unconstrained by pleiotropy or linkage disequilibrium. Two large effect QTL for stomatal distribution colocalized with key genes in the stomatal development pathway, suggesting promising candidates for the molecular bases of adaptation in these species. Furthermore, macroevolutionary transitions between vastly different stomatal distributions may not be constrained when such large-effect mutations are available. Finally, genetic correlations between stomatal traits measured in this study and data on carbon isotope discrimination from the same ILs support a functional hypothesis that the distribution of stomata affects the resistance to CO2 diffusion inside the leaf, a trait implicated in climatic adaptation in wild tomatoes. Along with evidence from previous comparative and experimental studies, this analysis indicates that leaf traits are an important component of climatic niche adaptation in wild tomatoes and demonstrates that some trait transitions between species could have involved few, large-effect genetic changes, allowing rapid responses to new environmental conditions. PMID:25298519

Muir, Christopher D; Pease, James B; Moyle, Leonie C

2014-12-01

275

Genetic linkage map of the guppy, Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation  

PubMed Central

We report construction of a genetic linkage map of the guppy genome using 790 single nucleotide polymorphism markers, integrated from six mapping crosses. The markers define 23 linkage groups (LGs), corresponding to the known haploid number of guppy chromosomes. The map, which spans a genetic length of 899?cM, includes 276 markers linked to expressed genes (expressed sequence tag), which have been used to derive broad syntenic relationships of guppy LGs with medaka chromosomes. This combined linkage map should facilitate the advancement of genetic studies for a wide variety of complex adaptive phenotypes relevant to natural and sexual selection in this species. We have used the linkage data to predict quantitative trait loci for a set of variable male traits including size and colour pattern. Contributing loci map to the sex LG for many of these traits. PMID:19324769

Tripathi, Namita; Hoffmann, Margarete; Willing, Eva-Maria; Lanz, Christa; Weigel, Detlef; Dreyer, Christine

2009-01-01

276

Epigenome dynamics: a quantitative genetics perspective  

Microsoft Academic Search

Classically, quantitative geneticists have envisioned DNA sequence variants as the only source of heritable phenotypes. This view should be revised in light of accumulating evidence for widespread epigenetic variation in natural and experimental populations. Here we argue that it is timely to consider novel experimental strategies and analysis models to capture the potentially dynamic interplay between chromatin and DNA sequence

Vincent Colot; Ritsert C. Jansen; Frank Johannes

2008-01-01

277

Phenotypic variation and leaf fluctuating asymmetry in isolated populations of an endangered dwarf birch Betula ovalifolia in Hokkaido, Japan  

Microsoft Academic Search

Betula ovalifolia is an endangered tetraploid that is restricted to two isolated sites, Betsukai and Sarabetsu, in Hokkaido, Japan. Among 50 ramets sampled along transect(s) in the each site, 45 genets in Betsukai and 49 in Sarabetsu were discriminated by simple sequence repeat (SSR) phenotypes. Multivariate patterns in seven measurements for leaf morphology and frequency distributions of fragment lengths in

TERUYOSHI NAGAMITSU; TAKAYUKI KAWAHARA; MAYUKO HOTTA

2004-01-01

278

Worm variation made accessible  

PubMed Central

In Caenorhabditis elegans, the recent advances in high-throughput quantitative analyses of natural genetic and phenotypic variation have led to a wealth of data on genotype phenotype relations. This data has resulted in the discovery of genes with major allelic effects and insights in the effect of natural genetic variation on a whole range of complex traits as well as how this variation is distributed across the genome. Regardless of the advances presented in specific studies, the majority of the data generated in these studies had yet to be made easily accessible, allowing for meta-analysis. Not only data in figures or tables but meta-data should be accessible for further investigation and comparison between studies. A platform was created where all the data, phenotypic measurements, genotypes, and mappings can be stored, compared, and new linkages within and between published studies can be discovered. WormQTL focuses on quantitative genetics in Caenorhabditis and other nematode species, whereas WormQTLHD quantitatively links gene expression quantitative trait loci (eQTL) in C. elegans to gene–disease associations in humans. PMID:24843834

Snoek, L Basten; Joeri van der Velde, K; Li, Yang; Jansen, Ritsert C; Swertz, Morris A; Kammenga, Jan E

2014-01-01

279

Seasonal variation in pectoralis muscle and heart myostatin and tolloid-like proteinases in small birds: a regulatory role for seasonal phenotypic flexibility?  

PubMed

Seasonally variable environments produce seasonal phenotypes in small birds such that winter birds have higher thermogenic capacities and pectoralis and heart masses. One potential regulator of these seasonal phenotypes is myostatin, a muscle growth inhibitor, which may be downregulated under conditions promoting increased energy demand. We examined summer-to-winter variation in skeletal muscle and heart masses and used qPCR and Western blots to measure levels of myostatin and its metalloproteinase activators TLL-1 and TLL-2 for two small temperate-zone resident birds, American goldfinches (Spinus tristis) and black-capped chickadees (Poecile atricapillus). Winter pectoralis and heart masses were significantly greater than in summer for American goldfinches. Neither myostatin expression nor protein levels differed significantly between seasons for goldfinch pectoralis. However, myostatin levels in goldfinch heart were significantly greater in summer than in winter, although heart myostatin expression was seasonally stable. In addition, expression of both metalloproteinase activators was greater in summer than in winter goldfinches for both pectoralis and heart, significantly so except for heart TLL-2 (P = 0.083). Black-capped chickadees showed no significant seasonal variation in muscle or heart masses. Seasonal patterns of pectoralis and heart expression and/or protein levels for myostatin and its metalloproteinase activators in chickadees showed no consistent seasonal trends, which may help explain the absence of significant seasonal variation in muscle or heart masses for chickadees in this study. These data are partially consistent with a regulatory role for myostatin, and especially myostatin processing capacity, in mediating seasonal metabolic phenotypes of small birds. PMID:24395519

Swanson, David L; King, Marisa O; Harmon, Erin

2014-02-01

280

Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort.  

PubMed

A genome-wide, whole brain approach to investigate genetic effects on neuroimaging phenotypes for identifying quantitative trait loci is described. The Alzheimer's Disease Neuroimaging Initiative 1.5 T MRI and genetic dataset was investigated using voxel-based morphometry (VBM) and FreeSurfer parcellation followed by genome-wide association studies (GWAS). One hundred forty-two measures of grey matter (GM) density, volume, and cortical thickness were extracted from baseline scans. GWAS, using PLINK, were performed on each phenotype using quality-controlled genotype and scan data including 530,992 of 620,903 single nucleotide polymorphisms (SNPs) and 733 of 818 participants (175 AD, 354 amnestic mild cognitive impairment, MCI, and 204 healthy controls, HC). Hierarchical clustering and heat maps were used to analyze the GWAS results and associations are reported at two significance thresholds (p<10(-7) and p<10(-6)). As expected, SNPs in the APOE and TOMM40 genes were confirmed as markers strongly associated with multiple brain regions. Other top SNPs were proximal to the EPHA4, TP63 and NXPH1 genes. Detailed image analyses of rs6463843 (flanking NXPH1) revealed reduced global and regional GM density across diagnostic groups in TT relative to GG homozygotes. Interaction analysis indicated that AD patients homozygous for the T allele showed differential vulnerability to right hippocampal GM density loss. NXPH1 codes for a protein implicated in promotion of adhesion between dendrites and axons, a key factor in synaptic integrity, the loss of which is a hallmark of AD. A genome-wide, whole brain search strategy has the potential to reveal novel candidate genes and loci warranting further investigation and replication. PMID:20100581

Shen, Li; Kim, Sungeun; Risacher, Shannon L; Nho, Kwangsik; Swaminathan, Shanker; West, John D; Foroud, Tatiana; Pankratz, Nathan; Moore, Jason H; Sloan, Chantel D; Huentelman, Matthew J; Craig, David W; Dechairo, Bryan M; Potkin, Steven G; Jack, Clifford R; Weiner, Michael W; Saykin, Andrew J

2010-11-15

281

Population Substructure and Patterns of Quantitative Variation among the Gollas of Southern Andhra Pradesh, India  

E-print Network

of mean heterozygosity/phenotypic variance on the distance of populations from the centroid (Harpending and Ward 1982; Relethford and Blangero 1990), is supposed to offer useful insights in this regard. The above proponents of the mod- el and many other... variability in Sub-Saharan Africa. Ann. Hum. Biol. 6:41–53. Jantz, R.L., and L. Meadows. 1995. Population structure of the Algonquian speakers. Hum. Biol. 67:375–386. Karve, I., and K.C. Malhotra. 1968. Biological comparison of eight endogamous groups...

Reddy, B. Mohan; Pfeffer, Alexa; Crawford, Michael H.; Langstieh, Banrida T.

2001-04-01

282

Population frequencies of alternative male phenotypes in tree lizards: geographic variation and common-garden rearing studies  

Microsoft Academic Search

Tree lizards (Urosaurus ornatus) vary in throat fan (dewlap) color. Earlier, we described five dewlap types (Orange, Orange-Blue, Yellow, Yellow-Blue, and\\u000a Blue), and reported that only males had blue in the dewlap and that presence or absence of a discrete blue patch was correlated\\u000a with male alternative reproductive phenotypes in a central Arizona population. Here, with a modified scheme characterizing

Diana K. Hews; Christopher W. Thompson; Ignacio T. Moore; Michael C. Moore

1997-01-01

283

Individual quality, survival variation and patterns of phenotypic selection on body condition and timing of nesting in birds  

Microsoft Academic Search

Questions about individual variation in “quality” and fitness are of great interest to evolutionary and population ecologists. Such variation can be investigated using either a random effects approach or an approach that relies on identifying observable traits that are themselves correlated with fitness components. We used the latter approach with data from 1,925 individual females of three species of ducks

Peter Blums; James D Nichols; James E. Hines; Mark S. Lindberg; Aivars Mednis

2005-01-01

284

Use of quantitative ultrasound to detect temperature variations in biological phantoms due to heating  

E-print Network

the envelope statistics (k parameter and µ parameter) of the backscattered echoes versus temperature of an ultrasonic imaging technique for monitoring HIFU treatment is highly medically significant. Quantitative the phantoms. Sound speed and attenuation were estimated in the phantoms versus temperature using insertion

Illinois at Urbana-Champaign, University of

285

Validation and Estimation of Additive Genetic Variation Associated with DNA Tests for Quantitative Beef Cattle Traits  

Technology Transfer Automated Retrieval System (TEKTRAN)

The U.S. National Beef Cattle Evaluation Consortium (NBCEC) has been involved in the validation of commercial DNA tests for quantitative beef quality traits since their first appearance on the U.S. market in the early 2000s. The NBCEC Advisory Council initially requested that the NBCEC set up a syst...

286

Genic and non-genic contributions to natural variation of quantitative traits in maize  

Technology Transfer Automated Retrieval System (TEKTRAN)

The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design...

287

Statistical Genetics of an Annual Plant, Impatiens capensis. I. Genetic Basis of Quantitative Variation  

Microsoft Academic Search

Analysis of quantitative genetics in natural populations has been hindered by computational and methodological problems in statistical analysis. We developed and validated a jackknife procedure to test for existence of broad sense heritabilities and dominance or maternal effects influencing quanti- tative characters in Impatiens capensis. Early life cycle characters showed evidence of dominance and\\/ or maternal effects, while later characters

Thomas Mitchell-Olds; Joy Bergelson

1990-01-01

288

3D geometry and quantitative variation of the cervico-thoracic region in Crocodylia.  

PubMed

This study aims to interpret the axial patterning of the crocodylian neck, and to find a potential taxonomic signal that corresponds to vertebral position. Morphological variation in the cervico-thoracic vertebrae is compared in fifteen different crocodylian species using 3D geometric morphometric methods. Multivariate analysis indicated that the pattern of intracolumnar variation was a gradual change in shape of the vertebral series (at the parapophyses, diapophyses, prezygapohyses, and postzygapohyses), in the cervical (C3 to C9) and dorsal (D1-D2) regions which was quite conservative among the crocodylians studied. In spite of this, we also found that intracolumnar shape variation allowed differentiation between two sub regions of the crocodylian neck. Growth is subtly correlated with vertebral shape variation, predicting changes in both the vertebral centrum and the neural spine. Interestingly, the allometric scaling for the pooled sample is equivalently shared by each vertebra studied. However, there were significant taxonomic differences, both in the average shape of the entire neck configuration (regional variation) and by shape variation at each vertebral position (positional variation) among the necks. The average neck vertebra of crocodylids is characterized by a relatively cranio-caudally short neural arch, whereby the spine is relatively longer and pointed orthogonal to the frontal plane. Conversely, the average vertebra in alligatorids has cranio-caudally longer neural spine and arch, with a relatively (dorso-ventrally) shorter spine. At each vertebral position there are significant differences between alligatorids and crocodylids. We discuss that the delayed timing of neurocentral fusion in Alligatoridae possibly explains the observed taxonomic differences. PMID:24753482

Chamero, Beatriz; Buscalioni, Angela D; Marugán-Lobón, Jesús; Sarris, Ioannis

2014-07-01

289

QUANTITATIVE MEASUREMENT OF THE ABILITY OF DIFFERENT MUTAGENS TO INDUCE AN INHERITED CHANGE IN PHENOTYPE TO ALLOW MALTOSE UTILIZATION IN SUSPENSION CULTURES OF THE SOYBEAN, GLYCZNE MAX (L.) MERR  

Microsoft Academic Search

Using a newly developed plating system, we have measured cell survival and the frequencies of variation in an inherited trait after treatment of soy- bean cell suspensions with different mutagens: ethyl methanesulfonate (EMS), methyl methanesulfonate (MMS) , N-Methyl-N'-nitro-N-nitroso- guanidine (MNNG), hycanthone (I-{ C2- (diethylamino) ethyl) amino}-4- (hydroxymethyl) -9H-thioxanthen-9-one and ultraviolet light (UV) .-The heritable variation selected for displays a phenotype

GERD WEBER; K. G. LARK

1980-01-01

290

Variation in psychosis gene ZNF804A is associated with a refined schizotypy phenotype but not neurocognitive performance in a large young male population.  

PubMed

Genetic variability within the ZNF804A gene has been recently found to be associated with schizophrenia and bipolar disorder, although the pathways by which this gene may confer risk remain largely unknown. We set out to investigate whether common ZNF804A variants affect psychosis-related intermediate phenotypes such as cognitive performance dependent on prefrontal and frontotemporal brain function, schizotypal traits, and attenuated psychotic experiences in a large young male population. Association analyses were performed using all 4 available self-rated schizotypy questionnaires and cognitive data retrospectively drawn from the Athens Study of Psychosis Proneness and Incidence of Schizophrenia (ASPIS). DNA samples from 1507 healthy young men undergoing induction to military training were genotyped for 4 previously studied polymorphic markers in the ZNF804A gene locus. Single-marker analysis revealed significant associations between 2 recently identified candidate schizophrenia susceptibility variants (rs1344706 and rs7597593) and a refined positive schizotypy phenotype characterized primarily by self-rated paranoia/ideas of reference. Nominal associations were noted with all positive, but not negative, schizotypy related factors. ZNF804A genotype effect on paranoia was confirmed at the haplotype level. No significant associations were noted with central indexes of sustained attention or working memory performance. In this study, ZNF804A variation was associated with a population-based self-rated schizotypy phenotype previously suggested to preferentially reflect genetic liability to psychosis and defined by a tendency to misinterpret otherwise neutral social cues and perceptual experiences in one's immediate environment, as personally relevant and significant information. This suggests a novel route by which schizophrenia-implicated ZNF804A genetic variation may confer risk to clinical psychosis at the general population level. PMID:23155182

Stefanis, Nicholas C; Hatzimanolis, Alex; Avramopoulos, Dimitrios; Smyrnis, Nikolaos; Evdokimidis, Ioannis; Stefanis, Costas N; Weinberger, Daniel R; Straub, Richard E

2013-11-01

291

Quantitative mapping of pore fraction variations in silicon nitride using an ultrasonic contact scan technique  

NASA Technical Reports Server (NTRS)

An ultrasonic scan procedure using the pulse-echo contact configuration was employed to obtain maps of pore fraction variations in sintered silicon nitride samples in terms of ultrasonic material properties. Ultrasonic velocity, attenuation coefficient, and reflection coefficient images were obtained simultaneously over a broad band of frequencies (e.g., 30 to 110 MHz) by using spectroscopic analysis. Liquid and membrane (dry) coupling techniques and longitudinal and shear-wave energies were used. The major results include the following: Ultrasonic velocity (longitudinal and shear wave) images revealed and correlated with the extent of average through-thickness pore fraction variations in the silicon nitride disks. Attenuation coefficient images revealed pore fraction nonuniformity due to the scattering that occurred at boundaries between regions of high and low pore fraction. Velocity and attenuation coefficient images were each nearly identical for machined and polished disks, making the method readily applicable to machined materials. Velocity images were similar for wet and membrane coupling. Maps of apparent Poisson's ratio constructed from longitudinal and shear-wave velocities quantified Poisson's ratio variations across a silicon nitride disk. Thermal wave images of a disk indicated transient thermal behavior variations that correlated with observed variations in pore fraction and velocity and attenuation coefficients.

Roth, Don J.; Kiser, James D.; Swickard, Suzanne M.; Szatmary, Steven A.; Kerwin, David P.

1993-01-01

292

Quantitative bounds for Markov chain convergence: Wasserstein and total variation distances  

E-print Network

We present a framework for obtaining explicit bounds on the rate of convergence to equilibrium of a Markov chain on a general state space, with respect to both total variation and Wasserstein distances. For Wasserstein bounds, our main tool is Steinsaltz's convergence theorem for locally contractive random dynamical systems. We describe practical methods for finding Steinsaltz's "drift functions" that prove local contractivity. We then use the idea of "one-shot coupling" to derive criteria that give bounds for total variation distances in terms of Wasserstein distances. Our methods are applied to two examples: a two-component Gibbs sampler for the Normal distribution and a random logistic dynamical system.

Madras, Neal; 10.3150/09-BEJ238

2011-01-01

293

Foliar ?13C response patterns along a moisture gradient arising from genetic variation and phenotypic plasticity in grassland species of Inner Mongolia  

PubMed Central

Plants depend upon both genetic differences and phenotypic plasticity to cope with environmental variation over different timescales. The spatial variation in foliar ?13C levels along a moisture gradient represents an overlay of genetic and plastic responses. We hypothesized that such a spatial variation would be more obvious than the variation arising purely from a plastic response to moisture change. Leymus chinensis and Stipa spp. were sampled from Inner Mongolia along a dry-wet transect, and some of these species were transplanted to an area with a moisture gradient. For Stipa spp., the slope of foliar ?13C and mean annual precipitation along the transect was significantly steeper than that of foliar ?13C and mean annual precipitation after the watering treatment. For L. chinensis, there was a general decreasing trend in foliar ?13C under the different (increasing) watering levels; however, its populations showed an irregular relationship between foliar ?13C and moisture origin. Therefore, support for our hypothesis was obtained from Stipa spp., but not from L. chinensis. PMID:23467429

Liu, Yanjie; Niu, Haishan; Xu, Xingliang

2013-01-01

294

Quantitative bounds for Markov chain convergence: Wasserstein and total variation distances  

Microsoft Academic Search

We present a framework for obtaining explicit bounds on the rate of convergence to equilibrium of a Markov chain on a general state space, with respect to both total variation and Wasserstein distances. For Wasserstein bounds, our main tool is Steinsaltz's convergence theorem for locally contractive random dynamical systems. We describe practical methods for finding Steinsaltz's \\

Neal Madras; Deniz Sezer

2011-01-01

295

Quantitative bounds for Markov chain convergence: Wasserstein and total variation distances  

Microsoft Academic Search

We present a framework for obtaining explicit bounds on the rate of convergence to equilibrium of a Markov chain on a general state space, with respect to both total variation and Wasserstein distances. For Wasserstein bounds, our main tool is Steinsaltz’s convergence theorem for locally contractive random dynamical systems. We describe practical methods for finding Steinsaltz’s “drift functions” that prove

Neal Madras; Deniz Sezer

2010-01-01

296

A quantitative evaluation of microstructure by electron back-scattered diffraction pattern quality variations.  

PubMed

Band contrast (BC) is a qualitative measure of electron back-scattered diffraction (EBSD), which is derived from the intensity of the Kikuchi bands. The BC is dependent upon several factors including scanning electron microscope measurement parameters, EBSD camera setup, and the specimen itself (lattice defect and grain orientation). In this study, the effective factors for BC variations and the feasibility of using BC variations for the quantification of microstructure evolutions have been investigated. In addition, the effects of the lattice defect and the grain orientation on the BC variations are studied. Next, a shear-deformed microstructure of 316L stainless steel, which contains nanosized grains and a large portion of twin boundaries, is revealed by BC map and histogram. Recovery and recrystallization of shear-deformed 316L stainless steel are displayed by BC variations during isothermal annealing at 700 and 800°C, respectively. It is observed that the BC turns bright as the shear-deformed crystal structure is recovered or recrystallized. PMID:23920181

Kang, Suk Hoon; Jin, Hyung-Ha; Jang, Jinsung; Choi, Yong Seok; Oh, Kyu Hwan; Foley, David C; Zhang, Xinghang

2013-08-01

297

Quantitative Genetic Variation for Oviposition Preference with Respect to Phenylthiocarbamide in Drosophila melanogaster  

Microsoft Academic Search

Seven isogenic strains of Drosophila melanogaster were assayed for oviposition preference on food with phenylthiocarbamide (PTC) versus plain food. There was significant variation among strains for the percentage of eggs oviposited on each medium, ranging from 70±4% (SE) preference for plain food to no significant preference. Reciprocal hybrid, backcross, and F2 generations derived from two extreme parent strains revealed significant

Bernard Possidente; Marianne Mustafa; Laura Collins

1999-01-01

298

Quantitative Statistical Analysis of Atomic Scale Structural and Chemical Variations in Complex Oxides Interfaces  

NASA Astrophysics Data System (ADS)

Grain boundaries (GBs) are known to have far-reaching effects on the electrical and mechanical properties of materials. Understanding the atomic scale mechanisms behind these effects requires an accurate determination of the interplay between GB structure and composition. Based on the analysis of a range of grain boundaries using aberration corrected scanning transmission electron microscopy (STEM), a general structural units model has been derived for the structure of grain boundaries in various dense packing cubic materials including FCC metals, perovskites and fluorites. The similarities in the observed grain boundary structures of these materials originate from related space (and point) group symmetries of the parent structures. The presence of structural variations away from the general structural units model may be caused by frustrations of certain symmetry operations that result from the incorporation of point defects (vacancies and impurities). A clear understanding of the similarity and variation in grain boundary atomic structures will not only provide a means to infer the structure-property relationships in broad classes of materials, but also enables us eventually to effectively manipulate the GB structures to achieve better materials properties. To understand these chemical induced variations, and further quantify exactly how atomic scale variations at the boundary plane extend to the practical mesoscale operating length of the system, statistical analysis has been applied to the aberration corrected STEM Z-contrast images acquired from a series of undoped and doped SrTiO3 GBs. In order to understand the effects of oxygen vacancies incorporation, in-situ characterization of GB atomic structures were performed using the Environmental TEM under the reduced gas and heating environment. This analysis of GB similarity and variation provides insights into the structure-composition relationship in GBs to understand the influence of nonstoichiometry and dopant segregations. It also helps to determine experimentally the energetics behind the formation of grain boundary structures to predict GB formation in various materials.

Yang, Hao

299

Vagaries in the delimitation of character states in quantitative variation--an experimental study.  

PubMed

An experimental study on the delimitation of character states in continuous variation indicates that (1) the way data are presented influences the assignment of character states and (2) states in the same data set are delimited in various ways by different individuals. Forty-nine individuals were given a set of graphs denoting variation of 10 characters in the genus Kalmia (Ericaceae) and outgroups, all identification having been removed from the graphs. The variation was represented in one of three ways: as 95% confidence intervals on a linear scale, as 95% confidence intervals on a log10 scale, or with bars showing SD x 2 on a linear scale. No two individuals scored a set of graphs in the same way, and only one character in one representation was scored identically by all individuals; the scoring for this character was completely different when the ordinate was changed from linear to logarithmic. Together, the 49 individuals delimited states within each character between 9 and 16 different ways. In general, variation represented by 2 x SD bars elicited the largest numbers of different scorings, yet with a relatively low number of states; the complexity of the patterns in the graphs in this representation was greatest. Expert knowledge appears to be of dubious value in delimiting states in such variation, and if such characters are to be used in phylogenetic analyses, states could be delimited by people who know nothing of the details of the study being scored; in any case, presentation of data and an explicit protocol to follow when delimiting states are essential. In converting data of this type into character states, psychological factors are particularly likely to come into play. Other implications of our experiments include the severe underdetermination of some phylogenetic hypotheses by observation and the heterogeneous nature of morphological data. PMID:11975349

Gift, N; Stevens, P F

1997-03-01

300

Quantitative genetic approach for assessing invasiveness: geographic and genetic variation in life-history traits  

Microsoft Academic Search

Predicting the spread of invasive species is a challenge for modern ecology. Although many invasive species undergo genetic\\u000a bottlenecks during introduction to new areas resulting in a loss of genetic diversity, successful invaders manage to flourish\\u000a in novel environments either because of pre-adaptations or because important traits contain adaptive variation enabling rapid\\u000a adaptation to changing conditions. To predict and understand

Sanna Boman; Alessandro Grapputo; Leena Lindström; Anne Lyytinen; Johanna Mappes

2008-01-01

301

Quantitative Genetic Variation of Enzyme Activities in Natural Populations of Drosophila melanogaster  

Microsoft Academic Search

The genetic component of variation of enzyme activity in natural populations of Drosophila melanogaster was investigated by using two sets of chromosome substitution lines. The constitution of a line of each type is: i1\\/i1; +2\\/+2; i3\\/i3 and i1\\/i1; i2\\/i2; +3\\/+3, where i refers to a chromosome from a highly inbred line and + refers to a chromosome from a natural

C. C. Laurie-Ahlberg; G. Maroni; G. C. Bewley; J. C. Lucchesi; B. S. Weir

1980-01-01

302

Quantitative genetic variation in populations of Amsinckia spectabilis that differ in rate of self-fertilization.  

PubMed

Self-fertilization is expected to reduce genetic diversity within populations and consequently to limit adaptability to changing environments. Little is known, however, about the way the evolution of self-fertilization changes the amount or pattern of the components of genetic variation in natural populations. In this study, a reciprocal North Carolina II design and maximum-likelihood methods were implemented to investigate the genetic basis of variation for 15 floral and vegetative traits in four populations of the annual plant Amsinckia spectabilis (Boraginaceae) differing in mating system. Six variance components were estimated according to Cockerham and Weir's "bio" model c. Compared to the three partially selfing populations, we found significantly lower levels of nuclear variance for several traits in the nearly completely self-fertilizing population. Furthermore, for 11 of 15 traits we did not detect nuclear variation to be significantly greater than zero. We also found high maternal variance in one of the partially selfing populations for several traits, and little dominance variance in any population. These results are in agreement with the evolutionary dead-end hypothesis for highly self-fertilizing taxa. PMID:19236472

Bartkowska, Magdalena P; Johnston, Mark O

2009-05-01

303

Conflicting selection from fire and seed predation drives fine-scaled phenotypic variation in a widespread North American conifer.  

PubMed

Recent work has demonstrated that evolutionary processes shape ecological dynamics on relatively short timescales (eco-evolutionary dynamics), but demonstrating these effects at large spatial scales in natural landscapes has proven difficult. We used empirical studies and modeling to investigate how selective pressures from fire and predispersal seed predation affect the evolution of serotiny, an ecologically important trait. Serotiny is a highly heritable key reproductive trait in Rocky Mountain lodgepole pine (Pinus contorta subsp. latifolia), a conifer that dominates millions of hectares in western North America. In these forests, the frequency of serotiny determines postfire seedling density with corresponding community- and ecosystem-level effects. We found that serotinous individuals have a selective advantage at high fire frequencies and low predation pressure; however, very high seed predation shifted the selective advantage to nonserotinous individuals even at high fire frequencies. Simulation modeling suggests that spatial variation in the frequency of serotiny results from heterogeneity in these two selective agents. These results, combined with previous findings showing a negative association between the density of seed predators and the frequency of serotiny at both landscape and continental scales, demonstrate that contemporary patterns in serotiny reflect an evolutionary response to conflicting selection pressures from fire and seed predation. Thus, we show that variation in the frequency of a heritable polygenic trait depends on spatial variation in two dominant selective agents, and, importantly, the effects of the local trait variation propagate with profound consequences to the structure and function of communities and ecosystems across a large landscape. PMID:24979772

Talluto, Matthew V; Benkman, Craig W

2014-07-01

304

Genetic and Phenotypic Variation of Foot-and-Mouth Disease Virus during Serial Passages in a Natural Host  

Microsoft Academic Search

Foot-and-mouth disease virus (FMDV), like other RNA viruses, exhibits high mutation rates during repli- cation that have been suggested to be of adaptive value. However, even though genetic variation in RNA viruses and, more specifically, FMDV has been extensively examined during virus replication in a wide variety of in vitro cell cultures, very little is known regarding the generation and

C. Carrillo; Z. Lu; M. V. Borca; A. Vagnozzi; G. F. Kutish; D. L. Rock

2007-01-01

305

Conflicting selection from fire and seed predation drives fine-scaled phenotypic variation in a widespread North American conifer  

PubMed Central

Recent work has demonstrated that evolutionary processes shape ecological dynamics on relatively short timescales (eco-evolutionary dynamics), but demonstrating these effects at large spatial scales in natural landscapes has proven difficult. We used empirical studies and modeling to investigate how selective pressures from fire and predispersal seed predation affect the evolution of serotiny, an ecologically important trait. Serotiny is a highly heritable key reproductive trait in Rocky Mountain lodgepole pine (Pinus contorta subsp. latifolia), a conifer that dominates millions of hectares in western North America. In these forests, the frequency of serotiny determines postfire seedling density with corresponding community- and ecosystem-level effects. We found that serotinous individuals have a selective advantage at high fire frequencies and low predation pressure; however, very high seed predation shifted the selective advantage to nonserotinous individuals even at high fire frequencies. Simulation modeling suggests that spatial variation in the frequency of serotiny results from heterogeneity in these two selective agents. These results, combined with previous findings showing a negative association between the density of seed predators and the frequency of serotiny at both landscape and continental scales, demonstrate that contemporary patterns in serotiny reflect an evolutionary response to conflicting selection pressures from fire and seed predation. Thus, we show that variation in the frequency of a heritable polygenic trait depends on spatial variation in two dominant selective agents, and, importantly, the effects of the local trait variation propagate with profound consequences to the structure and function of communities and ecosystems across a large landscape. PMID:24979772

Talluto, Matthew V.; Benkman, Craig W.

2014-01-01

306

Rapid and inexpensive screening of genomic copy number variations using a novel quantitative fluorescent PCR method.  

PubMed

Detection of human microdeletion and microduplication syndromes poses significant burden on public healthcare systems in developing countries. With genome-wide diagnostic assays frequently inaccessible, targeted low-cost PCR-based approaches are preferred. However, their reproducibility depends on equally efficient amplification using a number of target and control primers. To address this, the recently described technique called Microdeletion/Microduplication Quantitative Fluorescent PCR (MQF-PCR) was shown to reliably detect four human syndromes by quantifying DNA amplification in an internally controlled PCR reaction. Here, we confirm its utility in the detection of eight human microdeletion syndromes, including the more common WAGR, Smith-Magenis, and Potocki-Lupski syndromes with 100% sensitivity and 100% specificity. We present selection, design, and performance evaluation of detection primers using variety of approaches. We conclude that MQF-PCR is an easily adaptable method for detection of human pathological chromosomal aberrations. PMID:24288428

Stofanko, Martin; Han, Joan C; Elsea, Sarah H; Pena, Heloísa B; Gonçalves-Dornelas, Higgor; Pena, Sérgio Danilo Junho

2013-01-01

307

Rapid and Inexpensive Screening of Genomic Copy Number Variations Using a Novel Quantitative Fluorescent PCR Method  

PubMed Central

Detection of human microdeletion and microduplication syndromes poses significant burden on public healthcare systems in developing countries. With genome-wide diagnostic assays frequently inaccessible, targeted low-cost PCR-based approaches are preferred. However, their reproducibility depends on equally efficient amplification using a number of target and control primers. To address this, the recently described technique called Microdeletion/Microduplication Quantitative Fluorescent PCR (MQF-PCR) was shown to reliably detect four human syndromes by quantifying DNA amplification in an internally controlled PCR reaction. Here, we confirm its utility in the detection of eight human microdeletion syndromes, including the more common WAGR, Smith-Magenis, and Potocki-Lupski syndromes with 100% sensitivity and 100% specificity. We present selection, design, and performance evaluation of detection primers using variety of approaches. We conclude that MQF-PCR is an easily adaptable method for detection of human pathological chromosomal aberrations. PMID:24288428

Han, Joan C.; Elsea, Sarah H.; Pena, Heloísa B.; Pena, Sérgio Danilo Junho

2013-01-01

308

Qualitative and Quantitative Radio-Anatomical Variation of the Posterior Clinoid Process  

PubMed Central

This study was conducted to investigate the radiological anatomy of the posterior clinoid process (PCP) to highlight preoperative awareness of its variations and its relationships to other skull base landmarks. The PCPs of 36, three-dimensional computed tomographic cadaveric heads were evaluated by studying the gross anatomy of the PCP and by measuring the distances between the PCP and other skull base anatomical landmarks relevant to transnasal or transcranial skull base approaches. PCP variations were found in five specimens (14%): in two the dorsum sellae was absent, in one the PCP and the anterior clinoid process (ACP) were connected unilaterally and in two bilaterally. The mean distance between the right/left PCP and the crista galli was 45.14?±?4.0 standard deviation (SD_/46.24?±?4.5 SD, respectively, while the distance to the middle point of the basion at the level of the foramen magnum was 40.41?±?5.1 SD/41.0?±?5.2 SD, respectively. The mean distance between the PCP and the ACP was 12.03?±?3.18 SD on the right side and 12.11?±?2.77 SD on the left. The data provided highlights the importance of careful preoperative evaluation of the PCP and of its relationships to other commonly encountered skull base landmarks. This information may give an idea of the exposure achievable through different transcranial and transnasal approaches. This is especially relevant when neuronavigation is not available. PMID:22547963

Salma, Asem; Baidya, Nishanta B.; Wendt, Benjamin; Aguila, Francisco; Sammet, Steffen; Ammirati, Mario

2011-01-01

309

Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens  

PubMed Central

Pea-comb is a dominant mutation in chickens that drastically reduces the size of the comb and wattles. It is an adaptive trait in cold climates as it reduces heat loss and makes the chicken less susceptible to frost lesions. Here we report that Pea-comb is caused by a massive amplification of a duplicated sequence located near evolutionary conserved non-coding sequences in intron 1 of the gene encoding the SOX5 transcription factor. This must be the causative mutation since all other polymorphisms associated with the Pea-comb allele were excluded by genetic analysis. SOX5 controls cell fate and differentiation and is essential for skeletal development, chondrocyte differentiation, and extracellular matrix production. Immunostaining in early embryos demonstrated that Pea-comb is associated with ectopic expression of SOX5 in mesenchymal cells located just beneath the surface ectoderm where the comb and wattles will subsequently develop. The results imply that the duplication expansion interferes with the regulation of SOX5 expression during the differentiation of cells crucial for the development of comb and wattles. The study provides novel insight into the nature of mutations that contribute to phenotypic evolution and is the first description of a spontaneous and fully viable mutation in this developmentally important gene. PMID:19521496

Wright, Dominic; Boije, Henrik; Meadows, Jennifer R. S.; Bed'hom, Bertrand; Gourichon, David; Vieaud, Agathe; Tixier-Boichard, Michèle; Rubin, Carl-Johan; Imsland, Freyja; Hallböök, Finn; Andersson, Leif

2009-01-01

310

Decomposing variation in population growth into contributions from environment and phenotypes in an age-structured population.  

PubMed

Evaluating the relative importance of ecological drivers responsible for natural population fluctuations in size is challenging. Longitudinal studies where most individuals are monitored from birth to death and where environmental conditions are known provide a valuable resource to characterize complex ecological interactions. We used a recently developed approach to decompose the observed fluctuation in population growth of the red deer population on the Isle of Rum into contributions from climate, density and their interaction and to quantify their relative importance. We also quantified the contribution of individual covariates, including phenotypic and life-history traits, to population growth. Fluctuations in composition in age and sex classes ((st)age structure) of the population contributed substantially to the population dynamics. Density, climate, birth weight and reproductive status contributed less and approximately equally to the population growth. Our results support the contention that fluctuations in the population's (st)age structure have important consequences for population dynamics and underline the importance of including information on population composition to understand the effect of human-driven changes on population performance of long-lived species. PMID:21715404

Pelletier, Fanie; Moyes, Kelly; Clutton-Brock, Tim H; Coulson, Tim

2012-01-22

311

Decomposing variation in population growth into contributions from environment and phenotypes in an age-structured population  

PubMed Central

Evaluating the relative importance of ecological drivers responsible for natural population fluctuations in size is challenging. Longitudinal studies where most individuals are monitored from birth to death and where environmental conditions are known provide a valuable resource to characterize complex ecological interactions. We used a recently developed approach to decompose the observed fluctuation in population growth of the red deer population on the Isle of Rum into contributions from climate, density and their interaction and to quantify their relative importance. We also quantified the contribution of individual covariates, including phenotypic and life-history traits, to population growth. Fluctuations in composition in age and sex classes ((st)age structure) of the population contributed substantially to the population dynamics. Density, climate, birth weight and reproductive status contributed less and approximately equally to the population growth. Our results support the contention that fluctuations in the population's (st)age structure have important consequences for population dynamics and underline the importance of including information on population composition to understand the effect of human-driven changes on population performance of long-lived species. PMID:21715404

Pelletier, Fanie; Moyes, Kelly; Clutton-Brock, Tim H.; Coulson, Tim

2012-01-01

312

A comparison of isozyme and quantitative genetic variation in Pinus contorta ssp. latifolia by F{sub ST}  

SciTech Connect

We employed F-statistics to analyze quantitative and isozyme variation among five populations of Pinus contorta ssp. latifolia, a wind-pollinated outcrossing conifer with wide and continuous distribution in west North America. Estimates of population differentiation (F{sub ST}) for six quantitative traits were compared with the overall estimate of the differentiation (F*{sub ST}) from 19 isozymes that tested neutral to examine whether similar evolutionary processes were involved in morphological and isozyme differentiation. While the F{sub ST} estimates for specific gravity, stem diameter, stem height and branch length were significantly greater than the F*{sub ST} estimate, as judged from the 95% confidence intervals by bootstrapping, the F{sub ST} estimates for branch angle and branch diameter were indistinguishable from the F*{sub ST} estimate. Differentiation in stem height and stem diameter might reflect the inherent adaptation of the populations for rapid growth to escape suppression by neighboring plants during establishment and to regional differences in photoperiod, precipitation and temperature. In contrast, divergences in wood specific gravity and branch length might be correlated responses to population differentiation in stem growth. Possible bias in the estimation of F{sub ST} due to Hardy-Weinberg disequilibrium (F{sub IS} {ne} 0), linkage disequilibrium, maternal effects and nonadditive genetic effects was discussed with special reference to P. contorta ssp. latifolia. 48 refs., 1 fig., 3 tabs.

Yang, Rong-Cai; Yeh, F.C. [Univ. of Alberta, Edmonton (Canada); Yanchuk, A.D. [British Columbia Ministry of Forests (Canada)

1996-03-01

313

Age- and gender-dependent heterogeneous proportion of variation explained by SNPs in quantitative traits reflecting human health.  

PubMed

Age-related effects are often included as covariates in the analytical model for genome-wide association analysis of quantitative traits reflecting human health. Nevertheless, previous studies have hardly examined the effects of age on the proportion of variation explained by single nucleotide polymorphisms (PVSNP) in these traits. In this study, the PVSNP estimates of body mass index (BMI), waist-to-hip ratio, pulse pressure, high-density lipoprotein cholesterol level, triglyceride level (TG), low-density lipoprotein cholesterol level, and glucose level were obtained from Korean consortium metadata partitioned by gender or by age. Restricted maximum likelihood estimates of the PVSNP were obtained in a mixed model framework. Previous studies using pedigree data suggested possible differential heritability of certain traits with regard to gender, which we observed in our current study (BMI and TG; P?quantitative traits related to human health should be further examined. PMID:25701395

Lee, Dain; Lee, Chaeyoung

2015-04-01

314

Simple Absolute Quantification Method Correcting for Quantitative PCR Efficiency Variations for Microbial Community Samples  

PubMed Central

Real-time quantitative PCR (qPCR) is a widely used technique in microbial community analysis, allowing the quantification of the number of target genes in a community sample. Currently, the standard-curve (SC) method of absolute quantification is widely employed for these kinds of analysis. However, the SC method assumes that the amplification efficiency (E) is the same for both the standard and the sample target template. We analyzed 19 bacterial strains and nine environmental samples in qPCR assays, targeting the nifH and 16S rRNA genes. The E values of the qPCRs differed significantly, depending on the template. This has major implications for the quantification. If the sample and standard differ in their E values, quantification errors of up to orders of magnitude are possible. To address this problem, we propose and test the one-point calibration (OPC) method for absolute quantification. The OPC method corrects for differences in E and was derived from the ??CT method with correction for E, which is commonly used for relative quantification in gene expression studies. The SC and OPC methods were compared by quantifying artificial template mixtures from Geobacter sulfurreducens (DSM 12127) and Nostoc commune (Culture Collection of Algae and Protozoa [CCAP] 1453/33), which differ in their E values. While the SC method deviated from the expected nifH gene copy number by 3- to 5-fold, the OPC method quantified the template mixtures with high accuracy. Moreover, analyzing environmental samples, we show that even small differences in E between the standard and the sample can cause significant differences between the copy numbers calculated by the SC and the OPC methods. PMID:22492459

Bodenhausen, Natacha; Zeyer, Josef; Bürgmann, Helmut

2012-01-01

315

Quantitative Monitoring for Enhanced Geothermal Systems Using Double-Difference Waveform Inversion with Spatially-Variant Total-Variation Regularization  

SciTech Connect

Double-difference waveform inversion is a promising tool for quantitative monitoring for enhanced geothermal systems (EGS). The method uses time-lapse seismic data to jointly inverts for reservoir changes. Due to the ill-posedness of waveform inversion, it is a great challenge to obtain reservoir changes accurately and efficiently, particularly when using timelapse seismic reflection data. To improve reconstruction, we develop a spatially-variant total-variation regularization scheme into double-difference waveform inversion to improve the inversion accuracy and robustness. The new regularization scheme employs different regularization parameters in different regions of the model to obtain an optimal regularization in each area. We compare the results obtained using a spatially-variant parameter with those obtained using a constant regularization parameter. Utilizing a spatially-variant regularization scheme, the target monitoring regions are well reconstructed and the image noise is significantly reduced outside the monitoring regions. Our numerical examples demonstrate that the spatially-variant total-variation regularization scheme provides the flexibility to regularize local regions based on the a priori spatial information without increasing computational costs and the computer memory requirement.

Lin, Youzuo [Los Alamos National Laboratory; Huang, Lianjie [Los Alamos National Laboratory; Zhang, Zhigang [Los Alamos National Laboratory

2011-01-01

316

Genome-wide quantitative assessment of variation in DNA methylation patterns  

PubMed Central

Genomic DNA methylation contributes substantively to transcriptional regulations that underlie mammalian development and cellular differentiation. Much effort has been made to decipher the molecular mechanisms governing the establishment and maintenance of DNA methylation patterns. However, little is known about genome-wide variation of DNA methylation patterns. In this study, we introduced the concept of methylation entropy, a measure of the randomness of DNA methylation patterns in a cell population, and exploited it to assess the variability in DNA methylation patterns of Alu repeats and promoters. A few interesting observations were made: (i) within a cell population, methylation entropy varies among genomic loci; (ii) among cell populations, the methylation entropies of most genomic loci remain constant; (iii) compared to normal tissue controls, some tumors exhibit greater methylation entropies; (iv) Alu elements with high methylation entropy are associated with high GC content but depletion of CpG dinucleotides and (v) Alu elements in the intronic regions or far from CpG islands are associated with low methylation entropy. We further identified 12 putative allelic-specific methylated genomic loci, including four Alu elements and eight promoters. Lastly, using subcloned normal fibroblast cells, we demonstrated the highly variable methylation patterns are resulted from low fidelity of DNA methylation inheritance. PMID:21278160

Xie, Hehuang; Wang, Min; de Andrade, Alexandre; de F. Bonaldo, Maria; Galat, Vasil; Arndt, Kelly; Rajaram, Veena; Goldman, Stewart; Tomita, Tadanori; Soares, Marcelo B.

2011-01-01

317

Are we Genomic Mosaics? Variations of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes.  

PubMed

Theoretical and experimental evidences support the hypothesis that the genomes and the epigenomes may be different in the somatic cells of complex organisms. In the genome, the differences range from single base substitutions to chromosome number; in the epigenome, they entail multiple postsynthetic modifications of the chromatin. Somatic genome variations (SGV) may accumulate during development in response both to genetic programs, which may differ from tissue to tissue, and to environmental stimuli, which are often undetected and generally irreproducible. SGV may jeopardize physiological cellular functions, but also create novel coding and regulatory sequences, to be exposed to intraorganismal Darwinian selection. Genomes acknowledged as comparatively poor in genes, such as humans', could thus increase their pristine informational endowment. A better understanding of SGV will contribute to basic issues such as the "nature vs nurture" dualism and the inheritance of acquired characters. On the applied side, they may explain the low yield of cloning via somatic cell nuclear transfer, provide clues to some of the problems associated with transdifferentiation, and interfere with individual DNA analysis. SGV may be unique in the different cells types and in the different developmental stages, and thus explain the several hundred gaps persisting in the human genomes "completed" so far. They may compound the variations associated to our epigenomes and make of each of us an "(epi)genomic" mosaic. An ensuing paradigm is the possibility that a single genome (the ephemeral one assembled at fertilization) has the capacity to generate several different brains in response to different environments. PMID:21358981

Astolfi, P A; Salamini, F; Sgaramella, V

2010-09-01

318

Are we Genomic Mosaics? Variations of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes  

PubMed Central

Theoretical and experimental evidences support the hypothesis that the genomes and the epigenomes may be different in the somatic cells of complex organisms. In the genome, the differences range from single base substitutions to chromosome number; in the epigenome, they entail multiple postsynthetic modifications of the chromatin. Somatic genome variations (SGV) may accumulate during development in response both to genetic programs, which may differ from tissue to tissue, and to environmental stimuli, which are often undetected and generally irreproducible. SGV may jeopardize physiological cellular functions, but also create novel coding and regulatory sequences, to be exposed to intraorganismal Darwinian selection. Genomes acknowledged as comparatively poor in genes, such as humans’, could thus increase their pristine informational endowment. A better understanding of SGV will contribute to basic issues such as the “nature vs nurture” dualism and the inheritance of acquired characters. On the applied side, they may explain the low yield of cloning via somatic cell nuclear transfer, provide clues to some of the problems associated with transdifferentiation, and interfere with individual DNA analysis. SGV may be unique in the different cells types and in the different developmental stages, and thus explain the several hundred gaps persisting in the human genomes “completed” so far. They may compound the variations associated to our epigenomes and make of each of us an “(epi)genomic” mosaic. An ensuing paradigm is the possibility that a single genome (the ephemeral one assembled at fertilization) has the capacity to generate several different brains in response to different environments. PMID:21358981

Astolfi, P.A.; Salamini, F.; Sgaramella, V.

2010-01-01

319

Induction and stability of somaclonal variation in growth, leaf phenotype and gas exchange characteristics of poplar regenerated from callus culture.  

PubMed

Populus trichocarpa Torr. and Grey x P. balsamifera L. TT32 lines were regenerated from calli that had been maintained under differing in vitro conditions for sixteen months. In the final months, calli were maintained with one of six concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D, 0.1, 0.2, 0.3, 0.4, 0.5 or 0.6 mg l(-1))and regenerated with 0.25, 0.50 or 1.0 mg l(-1) benzylaminopurine (BA). Regenerant lines were obtained from 15 of these 18 treatments. The spectrum of variation in several morphological, physiological and leaf gas exchange traits was evaluated in the primary regenerants in 1986, and in their secondary vegetative propagules in the two subsequent years, in relation to differences in the original culture conditions. The results indicate that somoclonal variation was induced largely as a result of prolonged culture in the presence of 2,4-D, but that the terminal maintenance and regeneration phases also induced changes in the regenerants. Qualitative differences among the regenerant lines were detected by the end of 1986. For most traits, these differences were statistically confirmed within the 3-year period. The treatment lines ultimately diverged sufficiently to produce lines showing general performance that was either above or below that of the original TT32 clone. An early visible indicator of this divergence was variation in leaf shape (leaf length/width ratio), which could be related to 2,4-D-BA interactions in the final stages of culture. Graphic illustration of the independent effects of either 2,4-D or BA on stem height and gas exchange parameters suggested an inverse relationship with BA concentration and a complex interaction with 2,4-D. Significant correlations were detected between gas exchange parameters and morphological characteristics representing leaf form and stem development. Overall, the results indicate the presence of somaclonal lines that offer potential for the selective improvement of growth using morphological and gas exchange parameters as screening tools. PMID:14967629

Saieed, N T; Douglas, G C; Fry, D J

1994-01-01

320

Cranial ontogeny in Stegoceras validum (Dinosauria: Pachycephalosauria): a quantitative model of pachycephalosaur dome growth and variation.  

PubMed

Historically, studies of pachycephalosaurs have recognized plesiomorphically flat-headed taxa and apomorphically domed taxa. More recently, it has been suggested that the expression of the frontoparietal dome is ontogenetic and derived from a flat-headed juvenile morphology. However, strong evidence to support this hypothesis has been lacking. Here we test this hypothesis in a large, stratigraphically constrained sample of specimens assigned to Stegoceras validum, the best known pachycephalosaur, using multiple independent lines of evidence including conserved morphology of ornamentation, landmark-based allometric analyses of frontoparietal shape, and cranial bone histology. New specimens show that the diagnostic ornamentation of the parietosquamosal bar is conserved throughout the size range of the sample, which links flat-headed specimens to domed S. validum. High-resolution CT scans of three frontoparietals reveal that vascularity decreases with size and document a pattern that is consistent with previously proposed histological changes during growth. Furthermore, aspects of dome shape and size are strongly correlated and indicative of ontogenetic growth. These results are complementary and strongly support the hypothesis that the sample represents a growth series of a single taxon. Cranial dome growth is positively allometric, proceeds from a flat-headed to a domed state, and confirms the synonymy of Ornatotholus browni as a juvenile Stegoceras. This dataset serves as the first detailed model of growth and variation in a pachycephalosaur. Flat-headed juveniles possess three characters (externally open cranial sutures, tuberculate dorsal surface texture, and open supratemporal fenestrae) that are reduced or eliminated during ontogeny. These characters also occur in putative flat-headed taxa, suggesting that they may also represent juveniles of domed taxa. However, open cranial sutures and supratemporal fenestrae are plesiomorphic within Ornithischia, and thus should be expected in the adult stage of a primitive pachycephalosaur. Additional lines of evidence will be needed to resolve the taxonomic validity of flat-headed pachycephalosaur taxa. PMID:21738608

Schott, Ryan K; Evans, David C; Goodwin, Mark B; Horner, John R; Brown, Caleb Marshall; Longrich, Nicholas R

2011-01-01

321

Cranial Ontogeny in Stegoceras validum (Dinosauria: Pachycephalosauria): A Quantitative Model of Pachycephalosaur Dome Growth and Variation  

PubMed Central

Historically, studies of pachycephalosaurs have recognized plesiomorphically flat-headed taxa and apomorphically domed taxa. More recently, it has been suggested that the expression of the frontoparietal dome is ontogenetic and derived from a flat-headed juvenile morphology. However, strong evidence to support this hypothesis has been lacking. Here we test this hypothesis in a large, stratigraphically constrained sample of specimens assigned to Stegoceras validum, the best known pachycephalosaur, using multiple independent lines of evidence including conserved morphology of ornamentation, landmark-based allometric analyses of frontoparietal shape, and cranial bone histology. New specimens show that the diagnostic ornamentation of the parietosquamosal bar is conserved throughout the size range of the sample, which links flat-headed specimens to domed S. validum. High-resolution CT scans of three frontoparietals reveal that vascularity decreases with size and document a pattern that is consistent with previously proposed histological changes during growth. Furthermore, aspects of dome shape and size are strongly correlated and indicative of ontogenetic growth. These results are complementary and strongly support the hypothesis that the sample represents a growth series of a single taxon. Cranial dome growth is positively allometric, proceeds from a flat-headed to a domed state, and confirms the synonymy of Ornatotholus browni as a juvenile Stegoceras. This dataset serves as the first detailed model of growth and variation in a pachycephalosaur. Flat-headed juveniles possess three characters (externally open cranial sutures, tuberculate dorsal surface texture, and open supratemporal fenestrae) that are reduced or eliminated during ontogeny. These characters also occur in putative flat-headed taxa, suggesting that they may also represent juveniles of domed taxa. However, open cranial sutures and supratemporal fenestrae are plesiomorphic within Ornithischia, and thus should be expected in the adult stage of a primitive pachycephalosaur. Additional lines of evidence will be needed to resolve the taxonomic validity of flat-headed pachycephalosaur taxa. PMID:21738608

Schott, Ryan K.; Evans, David C.; Goodwin, Mark B.; Horner, John R.; Brown, Caleb Marshall; Longrich, Nicholas R.

2011-01-01

322

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast  

PubMed Central

To better understand the quantitative characteristics and structure of phenotypic diversity, we measured over 14,000 transcript, protein, metabolite, and morphological traits in 22 genetically diverse strains of Saccharomyces cerevisiae. More than 50% of all measured traits varied significantly across strains [false discovery rate (FDR) = 5%]. The structure of phenotypic correlations is complex, with 85% of all traits significantly correlated with at least one other phenotype (median = 6, maximum = 328). We show how high-dimensional molecular phenomics data sets can be leveraged to accurately predict phenotypic variation between strains, often with greater precision than afforded by DNA sequence information alone. These results provide new insights into the spectrum and structure of phenotypic diversity and the characteristics influencing the ability to accurately predict phenotypes. PMID:23720455

Skelly, Daniel A.; Merrihew, Gennifer E.; Riffle, Michael; Connelly, Caitlin F.; Kerr, Emily O.; Johansson, Marnie; Jaschob, Daniel; Graczyk, Beth; Shulman, Nicholas J.; Wakefield, Jon; Cooper, Sara J.; Fields, Stanley; Noble, William S.; Muller, Eric G.D.; Davis, Trisha N.; Dunham, Maitreya J.; MacCoss, Michael J.; Akey, Joshua M.

2013-01-01

323

Autistic-like behavioral phenotypes in a mouse model with copy number variation of the CAPS2/CADPS2 gene.  

PubMed

Ca²?-dependent activator protein for secretion 2 (CAPS2 or CADPS2) facilitates secretion and trafficking of dense-core vesicles. Recent genome-wide association studies of autism have identified several microdeletions due to copy number variation (CNV) in one of the chromosome 7q31.32 alleles on which the locus for CAPS2 is located in autistic patients. To evaluate the biological significance of reducing CAPS2 copy number, we analyzed CAPS2 heterozygous mice. Our present findings suggest that adequate levels of CAPS2 protein are critical for normal brain development and behavior, and that allelic changes due to CNV may contribute to autistic symptoms in combination with deficits in other autism-associated genes. PMID:23159942

Sadakata, Tetsushi; Shinoda, Yo; Oka, Megumi; Sekine, Yukiko; Furuichi, Teiichi

2013-01-01

324

Individual quality, survival variation and patterns of phenotypic selection on body condition and timing of nesting in birds  

USGS Publications Warehouse

Questions about individual variation in 'quality' and fitness are of great interest to evolutionary and population ecologists. Such variation can be investigated using either a random effects approach or an approach that relies on identifying observable traits that are themselves correlated with fitness components. We used the latter approach with data from 1,925 individual females of three species of ducks (tufted duck, Aythya fuligula; common pochard, Aythya ferina; northern shoveler, Anas clypeata) sampled on their breeding grounds at Engure Marsh, Latvia, for over 15 years. Based on associations with reproductive output, we selected two traits, one morphological (relative body condition) and one behavioral (relative time of nesting), that can be used to characterize individual females over their lifetimes. We then asked whether these traits were related to annual survival probabilities of nesting females. We hypothesized quadratic, rather than monotonic, relationships based loosely on ideas about the likely action of stabilizing selection on these two traits. Parameters of these relationships were estimated directly using ultrastructural models embedded within capture-recapture-band-recovery models. Results provided evidence that both traits were related to survival in the hypothesized manner. For all three species, females that tended to nest earlier than the norm exhibited the highest survival rates, but very early nesters experienced reduced survival and late nesters showed even lower survival. For shovelers, females in average body condition showed the highest survival, with lower survival rates exhibited by both heavy and light birds. For common pochard and tufted duck, the highest survival rates were associated with birds of slightly above-average condition, with somewhat lower survival for very heavy birds and much lower survival for birds in relatively poor condition. Based on results from this study and previous work on reproduction, we conclude that nest initiation date and body condition covary with both reproductive and survival components of fitness. These associations lead to a positive covariance of these two fitness components within individuals and to the conclusion that these two traits are indeed correlates of individual quality.

Blums, P.; Nichols, J.D.; Hines, J.E.; Lindberg, M.; Mednis, A.

2005-01-01

325

Individual quality, survival variation and patterns of phenotypic selection on body condition and timing of nesting in birds.  

PubMed

Questions about individual variation in "quality" and fitness are of great interest to evolutionary and population ecologists. Such variation can be investigated using either a random effects approach or an approach that relies on identifying observable traits that are themselves correlated with fitness components. We used the latter approach with data from 1,925 individual females of three species of ducks (tufted duck, Aythya fuligula; common pochard, Aythya ferina; northern shoveler, Anas clypeata) sampled on their breeding grounds at Engure Marsh, Latvia, for over 15 years. Based on associations with reproductive output, we selected two traits, one morphological (relative body condition) and one behavioral (relative time of nesting), that can be used to characterize individual females over their lifetimes. We then asked whether these traits were related to annual survival probabilities of nesting females. We hypothesized quadratic, rather than monotonic, relationships based loosely on ideas about the likely action of stabilizing selection on these two traits. Parameters of these relationships were estimated directly using ultrastructural models embedded within capture-recapture-band-recovery models. Results provided evidence that both traits were related to survival in the hypothesized manner. For all three species, females that tended to nest earlier than the norm exhibited the highest survival rates, but very early nesters experienced reduced survival and late nesters showed even lower survival. For shovelers, females in average body condition showed the highest survival, with lower survival rates exhibited by both heavy and light birds. For common pochard and tufted duck, the highest survival rates were associated with birds of slightly above-average condition, with somewhat lower survival for very heavy birds and much lower survival for birds in relatively poor condition. Based on results from this study and previous work on reproduction, we conclude that nest initiation date and body condition covary with both reproductive and survival components of fitness. These associations lead to a positive covariance of these two fitness components within individuals and to the conclusion that these two traits are indeed correlates of individual quality. PMID:15657762

Blums, Peter; Nichols, James D; Hines, James E; Lindberg, Mark S; Mednis, Aivars

2005-04-01

326

Quantitative genetic analyses of complex behaviours in Drosophila  

Microsoft Academic Search

Behaviours are exceptionally complex quantitative traits. Sensitivity to environmental variation and genetic background, the presence of sexual dimorphism, and the widespread functional pleiotropy that is inherent in behavioural phenotypes pose daunting challenges for unravelling their underlying genetics. Drosophila melanogaster provides an attractive system for elucidating the unifying principles of the genetic architectures that drive behaviours, as genetically identical individuals can

Trudy F. C. Mackay; Robert R. H. Anholt

2004-01-01

327

Quantitative trait transcripts for nicotine resistance in Drosophila melanogaster  

Microsoft Academic Search

Although most genetic association studies are performed with the intention of detecting nucleotide polymorphisms that are correlated with a complex trait, transcript abundance should also be expected to associate with diseases or phenotypes. We performed a scan for such quantitative trait transcripts in adult female heads of the fruit fly (Drosophila melanogaster) that might explain variation for nicotine resistance. The

Gisele Passador-Gurgel; Wen-Ping Hsieh; Priscilla Hunt; Nigel Deighton; Greg Gibson

2007-01-01

328

A phenotypic diversity analysis of foxtail millet (Setaria italica (L.) P. Beauv.) landraces of Chinese origin  

Microsoft Academic Search

A total of 23 381 foxtail millet landraces of Chinese origin were analysed for seven qualitative traits and four quantitative traits. The Shannon-Weaver diversity index was used to estimate the phenotypic diversity of each characteristic on the basis of administrative provinces and ecogeographical regions. Hierarchical analysis of variance indicated that most of the variation was due to differences among characteristics.

Yu Li; Shuzhi Wu; Yongsheng Cao; Xianzhen Zhang

1996-01-01

329

The genetic and molecular origin of natural variation for the fragrance trait in an elite Malaysian aromatic rice through quantitative trait loci mapping using SSR and gene-based markers.  

PubMed

MRQ74, a popular aromatic Malaysian landrace, allows for charging considerably higher prices than non-aromatic landraces. Thus, breeding this profitable trait has become a priority for Malaysian rice breeding. Despite many studies on aroma genetics, ambiguities considering its genetic basis remain. It has been observed that identifying quantitative trait loci (QTLs) based on anchor markers, particularly candidate genes controlling a trait of interest, can increase the power of QTL detection. Hence, this study aimed to locate QTLs that influence natural variations in rice scent using microsatellites and candidate gene-based sequence polymorphisms. For this purpose, an F2 mapping population including 189 individual plants was developed by MRQ74 crosses with 'MR84', a non-scented Malaysian accession. Additionally, qualitative and quantitative approaches were applied to obtain a phenotype data framework. Consequently, we identified two QTLs on chromosomes 4 and 8. These QTLs explained from 3.2% to 39.3% of the total fragrance phenotypic variance. In addition, we could resolve linkage group 8 by adding six gene-based primers in the interval harboring the most robust QTL. Hence, we could locate a putative fgr allele in the QTL found on chromosome 8 in the interval RM223-SCU015RM (1.63cM). The identified QTLs represent an important step toward recognition of the rice flavor genetic control mechanism. In addition, this identification will likely accelerate the progress of the use of molecular markers for gene isolation, gene-based cloning, and marker-assisted selection breeding programs aimed at improving rice cultivars. PMID:25445269

Golestan Hashemi, Farahnaz Sadat; Rafii, Mohd Y; Ismail, Mohd Razi; Mohamed, Mahmud Tengku Muda; Rahim, Harun A; Latif, Mohammad Abdul; Aslani, Farzad

2015-01-25

330

Quantifying genetic variations and phenotypic plasticity of leaf phenology and growth for two temperate Fagaceae species (sessile oak and european beech)  

NASA Astrophysics Data System (ADS)

Under current climate change, research on inherent adaptive capacities of organisms is crucial to assess future evolutionary changes of natural populations. Genetic diversity and phenotypic plasticity constitute adaptative capacities that could allow populations to respond to new environmental conditions. The aim of the present study was (i) to determine whether there are genetic variations among populations from altitudinal gradients using a lowland common garden experiment and (ii) to assess the magnitude of phenotypic plasticity using a reciprocal transplant experiment (5 elevations from 100 to 1600 m asl.) for leaf phenology (flushing and senescence) and growth of two fagaceae species (Fagus sylvatica and Quercus petraea). We found significant differences in phenology among provenances for most species, and evidenced that these among-population differences in phenology were related to annual temperature of the provenance sites for both species. It's noteworthy that, along the same climatic gradient, the species exhibited opposite genetic clines: beech populations from high elevation flushed earlier than those of low elevation, whereas we observed an opposite trend for oak. Finally, we highlighted that both phenology timing and growth rate were highly consistent year to year. The results demonstrated that in spite of the proximity of the populations in their natural area, altitude led to genetic differentiations in their phenology and growth. Moreover, a high phenological plasticity was found for both species. We evidenced that reaction norms of flushing timing to temperature followed linear clinal trends for both species with an average shift of 5.7 days per degree increase. Timing of leaf senescence exhibited hyperbolic trends for beech and no or slight trends for oak. Furthermore, within species, there was no difference in magnitude of phenological plasticity among populations neither for flushing, nor for senescence. Consequently, for both species, the growing season length increased to reach maximum values for annual temperature ranging from 10°C to 13°C according to the population. These adaptive capacities (genetic differentiations and high magnitude of plasticity) could allow populations to respond immediately to temperature variations in term of leaf phenology and then to cope with current climate change. Finally, we also highlight that current populations tend to occupy suboptimal environments, i.e, populations inhabit climates colder that their optimum.

Delzon, Sylvain; Vitasse, Yann; Alberto, Florian; Bresson, Caroline; Kremer, Antoine

2010-05-01

331

Quantitative reconstruction of climatic variations during the Bronze and early Iron ages based on pollen and lake-level data in  

E-print Network

Quantitative reconstruction of climatic variations during the Bronze and early Iron ages based-Alps, and to examine the possible impact of climatic changes on societies of the Bronze and early Iron Ages France) show a general expansion of population density from the middle Bronze Age to the early Iron Age

Boyer, Edmond

332

Effects of Quantitative Variation in Allelochemicals in Plantago lanceolata on Development of a Generalist and a Specialist Herbivore and their Endoparasitoids  

Microsoft Academic Search

Studies in crop species show that the effect of plant allelochemicals is not necessarily restricted to herbivores, but can extend to (positive as well as negative) effects on performance at higher trophic levels, including the predators and parasitoids of herbivores. We examined how quantitative variation in allelochemicals (iridoid glycosides) in ribwort plantain, Plantago lanceolata, affects the development of a specialist

Jeffrey A. Harvey; Saskya Van Nouhuys; Arjen Biere

2005-01-01

333

A quantitative trait locus for variation in dopamine metabolism mapped in a primate model using reference sequences from related species.  

PubMed

Non-human primates (NHP) provide crucial research models. Their strong similarities to humans make them particularly valuable for understanding complex behavioral traits and brain structure and function. We report here the genetic mapping of an NHP nervous system biologic trait, the cerebrospinal fluid (CSF) concentration of the dopamine metabolite homovanillic acid (HVA), in an extended inbred vervet monkey (Chlorocebus aethiops sabaeus) pedigree. CSF HVA is an index of CNS dopamine activity, which is hypothesized to contribute substantially to behavioral variations in NHP and humans. For quantitative trait locus (QTL) mapping, we carried out a two-stage procedure. We first scanned the genome using a first-generation genetic map of short tandem repeat markers. Subsequently, using >100 SNPs within the most promising region identified by the genome scan, we mapped a QTL for CSF HVA at a genome-wide level of significance (peak logarithm of odds score >4) to a narrow well delineated interval (<10 Mb). The SNP discovery exploited conserved segments between human and rhesus macaque reference genome sequences. Our findings demonstrate the potential of using existing primate reference genome sequences for designing high-resolution genetic analyses applicable across a wide range of NHP species, including the many for which full genome sequences are not yet available. Leveraging genomic information from sequenced to nonsequenced species should enable the utilization of the full range of NHP diversity in behavior and disease susceptibility to determine the genetic basis of specific biological and behavioral traits. PMID:17884980

Freimer, Nelson B; Service, Susan K; Ophoff, Roel A; Jasinska, Anna J; McKee, Kevin; Villeneuve, Amelie; Belisle, Alexandre; Bailey, Julia N; Breidenthal, Sherry E; Jorgensen, Matthew J; Mann, J John; Cantor, Rita M; Dewar, Ken; Fairbanks, Lynn A

2007-10-01

334

Quantitative estimation of density variation in high-speed flows through inversion of the measured wavefront distortion  

NASA Astrophysics Data System (ADS)

A simple method employing an optical probe is presented to measure density variations in a hypersonic flow obstructed by a test model in a typical shock tunnel. The probe has a plane light wave trans-illuminating the flow and casting a shadow of a random dot pattern. Local slopes of the distorted wavefront are obtained from shifts of the dots in the pattern. Local shifts in the dots are accurately measured by cross-correlating local shifted shadows with the corresponding unshifted originals. The measured slopes are suitably unwrapped by using a discrete cosine transform based phase unwrapping procedure and also through iterative procedures. The unwrapped phase information is used in an iterative scheme for a full quantitative recovery of density distribution in the shock around the model through refraction tomographic inversion. Hypersonic flow field parameters around a missile shaped body at a free-stream Mach number of 5.8 measured using this technique are compared with the numerically estimated values.

Medhi, Biswajit; Hegde, Gopalkrishna Mahadeva; Reddy, Kalidevapura Polareddy Jagannath; Roy, Debasish; Vasu, Ram Mohan

2014-12-01

335

Linkage Analysis of a Cluster-Based Quantitative Phenotype Constructed from Pulmonary Function Test Data in 27 Multigenerational Families with Multiple Asthmatic Members  

Microsoft Academic Search

Objective: To identify genes involved in phenotypes that increase one’s risk for developing asthma, a complex disease that is likely genetically heterogeneous. Unlike other approaches to locus discovery in the presence of heterogeneity, this method seeks loci that segregate in all or most ascertained families while recognizing that other genes and environmental factors that modify the action of the common

Cavan Reilly; Michael B. Miller; Yuhong Liu; William S. Oetting; Richard King; Malcolm Blumenthal

2007-01-01

336

Pseudohyphal variations of yeasts exposed to specific space flight parameters.  

PubMed

Phenotypes of Saccharomyces cerevisiae and Rhodotorula rubra exposed to specific parameters of space flight, which were measured both quantitatively and qualitatively, produced variations in pseudohyphal formation. Both the length of the parent and branch psuedohyphal filaments varied according to specific wavelengths and energy levels of UV light exposures when phenotypic isolates were compared with the parent or ground control isolate of each yeast species. PMID:9881461

Volz, P A; Hunter, R L

1998-01-01

337

Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry  

PubMed Central

Background Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have great potential for improving the efficiency of hop breeding. The success of MAS is reliant on the identification of reliable marker-trait associations. This study used quantitative trait loci (QTL) analysis to identify marker-trait associations for hop, focusing on traits related to expediting plant sex identification, increasing yield capacity and improving bittering, flavour and aroma chemistry. Results QTL analysis was performed on two new linkage maps incorporating transferable Diversity Arrays Technology (DArT) markers. Sixty-three QTL were identified, influencing 36 of the 50 traits examined. A putative sex-linked marker was validated in a different pedigree, confirming the potential of this marker as a screening tool in hop breeding programs. An ontogenetically stable QTL was identified for the yield trait dry cone weight; and a QTL was identified for essential oil content, which verified the genetic basis for variation in secondary metabolite accumulation in hop cones. A total of 60 QTL were identified for 33 secondary metabolite traits. Of these, 51 were pleiotropic/linked, affecting a substantial number of secondary metabolites; nine were specific to individual secondary metabolites. Conclusions Pleiotropy and linkage, found for the first time to influence multiple hop secondary metabolites, have important implications for molecular selection methods. The selection of particular secondary metabolite profiles using pleiotropic/linked QTL will be challenging because of the difficulty of selecting for specific traits without adversely changing others. QTL specific to individual secondary metabolites, however, offer unequalled value to selection programs. In addition to their potential for selection, the QTL identified in this study advance our understanding of the genetic control of traits of current economic and breeding significance in hop and demonstrate the complex genetic architecture underlying variation in these traits. The linkage information obtained in this study, based on transferable markers, can be used to facilitate the validation of QTL, crucial to the success of MAS. PMID:23718194

2013-01-01

338

SpA, ClfA, and FnbA Genetic Variations Lead to Staphaurex Test-Negative Phenotypes in Bovine Mastitis Staphylococcus aureus Isolates?  

PubMed Central

Staphylococcus aureus encodes many proteins that act as virulence factors, leading to a variety of diseases, including mastitis in cows. Among these virulence factors, SpA, ClfA, ClfB, FnbA, and FnbB are important for the ability of S. aureus to adhere to and invade host cells as well as to evade host immune responses. The interaction between these S. aureus surface proteins and human immunoglobulin G and fibrinogen that are coupled to latex particles is utilized to induce latex agglutination reactions, which are used widely in diagnostic kits for confirmation of presumptive S. aureus isolates. In this study, the Staphaurex latex agglutination test was performed on a collection of confirmed bovine mastitis S. aureus isolates. Notably, 54% (43/79 isolates) of these isolates exhibited latex agglutination-negative phenotypes (Staphaurex-negative result). To gain insights into the reasons for the high frequency of Staphaurex-negative bovine mastitis S. aureus isolates, the spa, clfA, clfB, fnbA, and fnbB genes were examined. Specific genetic changes in spa, clfA, and fnbA, as well as a loss of fnbB, which may impair SpA, ClfA, FnbA, and FnbB functions in latex agglutination reactions, were detected in Staphaurex-negative S. aureus isolates. The genetic changes included a premature stop codon in the spa gene, leading to a truncated SpA protein that is unable to participate in S. aureus cell-mediated agglutination of latex particles. In addition, clfA and fnbA genetic polymorphisms were detected that were linked to ClfA and FnbA amino acid changes that may significantly reduce fibrinogen-binding activity. The genetic variations in these S. aureus isolates might also have implications for their bovine mastitis virulence capacity. PMID:21147952

Stutz, Katrin; Stephan, Roger; Tasara, Taurai

2011-01-01

339

Phenotypic integration between antipredator behavior and camouflage pattern in juvenile sticklebacks.  

PubMed

Predation is a strong selective force that promotes the evolution of antipredator behaviors and camouflage in prey animals. However, the independent evolution of single traits cannot explain how observed phenotypic variations of these traits are maintained within populations. We studied genetic and phenotypic correlations between antipredator behaviors (shoaling and risk-taking) and morphology traits (pigmentation and size) in juvenile three-spined sticklebacks by using pedigree-based quantitative genetic analysis to test phenotypic integration (or complex phenotype) as an evolutionary response to predation risk. Individuals with strongly melanized (i.e., camouflaged) phenotype and genotype were less sociable to conspecifics, but bolder during foraging under predation risk. Individuals with faster growing phenotype and genotype were bolder, and those with lager eyes were more fearful. These phenotypic integrations were not confounded with correlated plastic responses to predation risk because the phenotypes were measured in naïve fish born in the laboratory, but originated from a natural population with predation pressure. Consistent selection for particular combinations of traits under predation pressure or pleiotropic genes might influence the maintenance of the genetic (co)variations and polymorphism in melanin color, growth trajectory, and behavior patterns. PMID:25572122

Kim, Sin-Yeon; Velando, Alberto

2015-03-01

340

Quantitative Autism Traits in First Degree Relatives: Evidence for the Broader Autism Phenotype in Fathers, but Not in Mothers and Siblings  

ERIC Educational Resources Information Center

Autism spectrum disorder (ASD) symptoms are present in unaffected relatives and individuals from the general population. Results are inconclusive, however, on whether unaffected relatives have higher levels of quantitative autism traits (QAT) or not. This might be due to differences in research populations, because behavioral data and molecular…

De la Marche, Wouter; Noens, Ilse; Luts, Jan; Scholte, Evert; Van Huffel, Sabine; Steyaert, Jean

2012-01-01

341

Rapid evolution of quantitative traits: theoretical perspectives  

PubMed Central

An increasing number of studies demonstrate phenotypic and genetic changes in natural populations that are subject to climate change, and there is hope that some of these changes will contribute to avoiding species extinctions (‘evolutionary rescue’). Here, we review theoretical models of rapid evolution in quantitative traits that can shed light on the potential for adaptation to a changing climate. Our focus is on quantitative-genetic models with selection for a moving phenotypic optimum. We point out that there is no one-to-one relationship between the rate of adaptation and population survival, because the former depends on relative fitness and the latter on absolute fitness. Nevertheless, previous estimates that sustainable rates of genetically based change usually do not exceed 0.1 haldanes (i.e., phenotypic standard deviations per generation) are probably correct. Survival can be greatly facilitated by phenotypic plasticity, and heritable variation in plasticity can further speed up genetic evolution. Multivariate selection and genetic correlations are frequently assumed to constrain adaptation, but this is not necessarily the case and depends on the geometric relationship between the fitness landscape and the structure of genetic variation. Similar conclusions hold for adaptation to shifting spatial gradients. Recent models of adaptation in multispecies communities indicate that the potential for rapid evolution is strongly influenced by interspecific competition. PMID:24454555

Kopp, Michael; Matuszewski, Sebastian

2014-01-01

342

Overlapping LQT1 and LQT2 phenotype in a patient with long QT syndrome associated with loss-of-function variations in KCNQ1 and KCNH2.  

PubMed

Long QT syndrome (LQTS) is an inherited disorder characterized by prolonged QT intervals and potentially life-threatening arrhythmias. Mutations in 12 different genes have been associated with LQTS. Here we describe a patient with LQTS who has a mutation in KCNQ1 as well as a polymorphism in KCNH2. The proband (MMRL0362), a 32-year-old female, exhibited multiple ventricular extrasystoles and one syncope. Her ECG (QT interval corrected for heart rate (QTc) = 518ms) showed an LQT2 morphology in leads V4-V6 and LQT1 morphology in leads V1-V2. Genomic DNA was isolated from lymphocytes. All exons and intron borders of 7 LQTS susceptibility genes were amplified and sequenced. Variations were detected predicting a novel missense mutation (V110I) in KCNQ1, as well as a common polymorphism in KCNH2 (K897T). We expressed wild-type (WT) or V110I Kv7.1 channels in CHO-K1 cells cotransfected with KCNE1 and performed patch-clamp analysis. In addition, WT or K897T Kv11.1 were also studied by patch clamp. Current-voltage (I-V) relations for V110I showed a significant reduction in both developing and tail current densities compared with WT at potentials >+20 mV (p < 0.05; n = 8 cells, each group), suggesting a reduction in IKs currents. K897T- Kv11.1 channels displayed a significantly reduced tail current density compared with WT-Kv11.1 at potentials >+10 mV. Interestingly, channel availability assessed using a triple-pulse protocol was slightly greater for K897T compared with WT (V0.5 = -53.1 ± 1.13 mV and -60.7 ± 1.15 mV for K897T and WT, respectively; p < 0.05). Comparison of the fully activated I-V revealed no difference in the rectification properties between WT and K897T channels. We report a patient with a loss-of-function mutation in KCNQ1 and a loss-of-function polymorphism in KCNH2. Our results suggest that a reduction of both IKr and IKs underlies the combined LQT1 and LQT2 phenotype observed in this patient. PMID:21164565

Cordeiro, Jonathan M; Perez, Guillermo J; Schmitt, Nicole; Pfeiffer, Ryan; Nesterenko, Vladislav V; Burashnikov, Elena; Veltmann, Christian; Borggrefe, Martin; Wolpert, Christian; Schimpf, Rainer; Antzelevitch, Charles

2010-12-01

343

Molecular and phenotypic characterization of near isogenic lines at QTL for quantitative resistance to Leptosphaeria maculans in oilseed rape (Brassica napus L.).  

PubMed

The most common and effective way to control phoma stem canker (blackleg) caused by Leptosphaeria maculans in oilseed rape (Brassica napus) is by breeding resistant cultivars. Specific resistance genes have been identified in B. napus and related species but in some B. napus cultivars resistance is polygenic [mediated by quantitative trait loci (QTL)], postulated to be race non-specific and durable. The genetic basis of quantitative resistance in the French winter oilseed rape 'Darmor', which was derived from 'Jet Neuf', was previously examined in two genetic backgrounds. Stable QTL involved in blackleg resistance across year and genetic backgrounds were identified. In this study, near isogenic lines (NILs) were produced in the susceptible background 'Yudal' for four of these QTL using marker-assisted selection. Various strategies were used to develop new molecular markers, which were mapped in these QTL regions. These were used to characterize the length and homozygosity of the 'Darmor-bzh' introgressed segment in the NILs. Individuals from each NIL were evaluated in blackleg disease field trials and assessed for their level of stem canker in comparison to the recurrent line 'Yudal'. The effect of QTL LmA2 was clearly validated and to a lesser extent, QTL LmA9 also showed an effect on the disease level. This work provides valuable material that can be used to study the mode of action of genetic factors involved in L. maculans quantitative resistance. PMID:18696043

Delourme, R; Piel, N; Horvais, R; Pouilly, N; Domin, C; Vallée, P; Falentin, C; Manzanares-Dauleux, M J; Renard, M

2008-11-01

344

Phenotype-genotype correlations of facial width and height proportions in patients with Class II malocclusion  

PubMed Central

Objectives To characterize soft tissue facial height and width variation in Class II malocclusion and test for correlations with genes HMGA2, AJUBA and ADK. Setting and Sample Population Nine facial proportions were estimated from 2D frontal repose photographs of 330 Caucasian adults with Class II malocclusion. Material & Methods After adjustments for age and gender, the facial proportions were submitted to a principal component analyses (PCA). The most meaningful phenotypic variations were correlated with SNPS rs7924176 (ADK), rs17101923 (HMGA2), and rs997154 (AJUBA) genotyped in 106 individuals. Results PCA resulted in 4 principal components (PCs) which explained 75% of total variation. PC1 captured variation in the intercanthus distance and explained 28% of total variation. PC2 explained 21% of the variations in facial taper and facial index. PC3 explained 14% and reflected variations in the vertical dimension of the lower face. PC4 explained 12% and captured variations in distance between the eyes, width of the commissures, and the length of the superior aspect of the lower face height, corresponding to the vertical dimension of the philtrum of the upper lip. A suggestive association (p<0.05) was observed between PC4 and rs997154 corroborating the role of AJUBA in variation of facial dimensions. Conclusion 2D frontal photographs can be used to derive quantitative measures of soft tissue phenotypes that are of clinical relevance. The methods described are suitable for discovery and replication of associations between genotypes and malocclusion phenotypes. PMID:25865538

Uribe, L.M. Moreno; Ray, A.; Blanchette, D. R.; Dawson, D.V.; Southard, T.E.

2015-01-01

345

Dissecting Genetic Networks Underlying Complex Phenotypes: The Theoretical Framework  

PubMed Central

Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate contemporary knowledge of signal transduction pathways with principles of quantitative and population genetics to characterize genetic networks underlying complex traits, using a model founded upon one-way functional dependency of downstream genes on upstream regulators (the principle of hierarchy) and mutual functional dependency among related genes (functional genetic units, FGU). Both simulated and real data suggest that complementary epistasis contributes greatly to quantitative trait variation, and obscures the phenotypic effects of many ‘downstream’ loci in pathways. The mathematical relationships between the main effects and epistatic effects of genes acting at different levels of signaling pathways were established using the quantitative and population genetic parameters. Both loss of function and “co-adapted” gene complexes formed by multiple alleles with differentiated functions (effects) are predicted to be frequent types of allelic diversity at loci that contribute to the genetic variation of complex traits in populations. Downstream FGUs appear to be more vulnerable to loss of function than their upstream regulators, but this vulnerability is apparently compensated by different FGUs of similar functions. Other predictions from the model may account for puzzling results regarding responses to selection, genotype by environment interaction, and the genetic basis of heterosis. PMID:21283795

Zhang, Fan; Zhai, Hu-Qu; Paterson, Andrew H.; Xu, Jian-Long; Gao, Yong-Ming; Zheng, Tian-Qing; Wu, Rong-Ling; Fu, Bin-Ying; Ali, Jauhar; Li, Zhi-Kang

2011-01-01

346

Explaining Quantitative Variation in the Rate of Optional Infinitive Errors across Languages: A Comparison of MOSAIC and the Variational Learning Model  

ERIC Educational Resources Information Center

In this study, we use corpus analysis and computational modelling techniques to compare two recent accounts of the OI stage: Legate & Yang's (2007) Variational Learning Model and Freudenthal, Pine & Gobet's (2006) Model of Syntax Acquisition in Children. We first assess the extent to which each of these accounts can explain the level of OI errors…

Freudenthal, Daniel: Pine, Julian; Gobet, Fernando

2010-01-01

347

Phenotypic plasticity of life history characteristics: quantitative analysis of delayed reproduction of green foxtail (Setaria viridis) in the Songnen Plain of China.  

PubMed

Green foxtail (Setaria viridis L.) is a common weed species in temperate regions. Research on the effect of delayed reproduction on the phenotypic plasticity and regularity of the vegetative and reproductive growth is of vital significance for understanding population regulation and control of the weed in the growing season. Green foxtail seeds were sown every 10 days from 25 June to 24 August of 2004. The growth and production metrics were measured via harvesting tufts and statistical analysis was carried out. The results showed that the reproductive tillers, seed number, seed biomass and one thousand-seed weight of plants at the first sowing (25 June) approximately increased 28.8, 7 827.0, 1 104.0 and 12.3 times compared with that at the last sowing (24 August), respectively. Total tillers, reproductive tillers and height increased linearly as the reproductive period delayed, however, biomass increased exponentially. Quadratic equations best explained the relationships between the delayed reproductive period and seed number, inflorescence length, one thousand-seed weight, seed biomass. Based on the quantity and quality of seed production, weeding young seedlings emerging before July can be the most effective weed-control strategy in the Songnen Plain. PMID:18713403

Li, Hai-Yan; Yang, Yun-Fei

2008-06-01

348

Population sub-structure and patterns of quantitative variation among the Gollas of Southern Andhra Pradesh, India  

E-print Network

of mean heterozygosity/phenotypic variance on the distance of populations from the centroid (Harpending and Ward 1982; Relethford and Blangero 1990), is supposed to offer useful insights in this regard. The above proponents of the mod- el and many other... variability in Sub-Saharan Africa. Ann. Hum. Biol. 6:41–53. Jantz, R.L., and L. Meadows. 1995. Population structure of the Algonquian speakers. Hum. Biol. 67:375–386. Karve, I., and K.C. Malhotra. 1968. Biological comparison of eight endogamous groups...

Reddy, B. Mohan; Pfeffer, Alexa; Crawford, Michael H.; Langstieh, Banrida T.

2001-08-01

349

Stilbenes: Quantitative extraction from grape skins, contribution of grape solids to wine and variation during wine maturation  

Microsoft Academic Search

With the objective of studying the relationship between stilbenic composition in grape skins and that in corresponding red wine, we have firstly optimized a method for quantitative extraction and purification of stilbenes from grape skins, used for posterior HPLC analysis. Stilbene levels in grape skins of three Vitis vinifera varieties (Castelão, Syrah and Tinta Roriz) and in their corresponding wines

Baoshan Sun; Ana M. Ribes; M. Conceição Leandro; A. Pedro Belchior; M. Isabel Spranger

2006-01-01

350

EVOLUTION OF COLOR VARIATION IN DRAGON LIZARDS: QUANTITATIVE TESTS OF THE ROLE OF CRYPSIS AND LOCAL ADAPTATION  

Microsoft Academic Search

Many animal species display striking color differences with respect to geographic location, sex, and body region. Traditional adaptive explanations for such complex patterns invoke an interaction between selection for conspicuous signals and natural selection for crypsis. Although there is now a substantial body of evidence supporting the role of sexual selection for signaling functions, quantitative studies of crypsis remain comparatively

Devi M. Stuart-Fox; Adnan Moussalli; Gregory R. Johnston; Ian P. F. Owens

2004-01-01

351

Understanding Variation in Treatment Effects in Education Impact Evaluations: An Overview of Quantitative Methods. NCEE 2014-4017  

ERIC Educational Resources Information Center

This report summarizes the complex research literature on quantitative methods for assessing how impacts of educational interventions on instructional practices and student learning differ across students, educators, and schools. It also provides technical guidance about the use and interpretation of these methods. The research topics addressed…

Schochet, Peter Z.; Puma, Mike; Deke, John

2014-01-01

352

Adaptive phenotypic plasticity and plant water use  

Microsoft Academic Search

The emergence of new techniques in plant science, including molecular and phenomic tools, presents a novel opportunitytore-evaluatethewayweexaminethephenotype.Ourincreasingcapacityforphenotypingmeansthatnotonly canweconsiderincreasingnumbersofspeciesorvarieties,butalsothatwecaneffectivelyquantifythephenotypesofthese differentgenotypesunderarangeofenvironmentalconditions.Thephenotypicplasticityofagivengenotype,ortherangeof phenotypes, that can be expressed dependent upon environment becomes something we can feasibly assess. Of particular importance is phenotypic variation that increases fitness or survival - adaptive phenotypic plasticity. Here, we examine the case of adaptive phenotypic plasticity in plant water

Adrienne B. NicotraA; Amy DavidsonA

2010-01-01

353

Neurochemical phenotype of corticocortical connections in the macaque monkey: quantitative analysis of a subset of neurofilament protein-immunoreactive projection neurons in frontal, parietal, temporal, and cingulate cortices  

NASA Technical Reports Server (NTRS)

The neurochemical characteristics of the neuronal subsets that furnish different types of corticocortical connections have been only partially determined. In recent years, several cytoskeletal proteins have emerged as reliable markers to distinguish subsets of pyramidal neurons in the cerebral cortex of primates. In particular, previous studies using an antibody to nonphosphorylated neurofilament protein (SMI-32) have revealed a consistent degree of regional and laminar specificity in the distribution of a subpopulation of pyramidal cells in the primate cerebral cortex. The density of neurofilament protein-immunoreactive neurons was shown to vary across corticocortical pathways in macaque monkeys. In the present study, we have used the antibody SMI-32 to examine further and to quantify the distribution of a subset of corticocortically projecting neurons in a series of long ipsilateral corticocortical pathways in comparison to short corticocortical, commissural, and limbic connections. The results demonstrate that the long association pathways interconnecting the frontal, parietal, and temporal neocortex have a high representation of neurofilament protein-enriched pyramidal neurons (45-90%), whereas short corticocortical, callosal, and limbic pathways are characterized by much lower numbers of such neurons (4-35%). These data suggest that different types of corticocortical connections have differential representation of highly specific neuronal subsets that share common neurochemical characteristics, thereby determining regional and laminar cortical patterns of morphological and molecular heterogeneity. These differences in neuronal neurochemical phenotype among corticocortical circuits may have considerable influence on cortical processing and may be directly related to the type of integrative function subserved by each cortical pathway. Finally, it is worth noting that neurofilament protein-immunoreactive neurons are dramatically affected in the course of Alzheimer's disease. The present results support the hypothesis that neurofilament protein may be crucially linked to the development of selective neuronal vulnerability and subsequent disruption of corticocortical pathways that lead to the severe impairment of cognitive function commonly observed in age-related dementing disorders.

Hof, P. R.; Nimchinsky, E. A.; Morrison, J. H.; Bloom, F. E. (Principal Investigator)

1995-01-01

354

Precision phenotyping of biomass accumulation in triticale reveals temporal genetic patterns of regulation  

PubMed Central

To extend agricultural productivity by knowledge-based breeding and tailor varieties adapted to specific environmental conditions, it is imperative to improve our ability to assess the dynamic changes of the phenome of crops under field conditions. To this end, we have developed a precision phenotyping platform that combines various sensors for a non-invasive, high-throughput and high-dimensional phenotyping of small grain cereals. This platform yielded high prediction accuracies and heritabilities for biomass of triticale. Genetic variation for biomass accumulation was dissected with 647 doubled haploid lines derived from four families. Employing a genome-wide association mapping approach, two major quantitative trait loci (QTL) for biomass were identified and the genetic architecture of biomass accumulation was found to be characterized by dynamic temporal patterns. Our findings highlight the potential of precision phenotyping to assess the dynamic genetics of complex traits, especially those not amenable to traditional phenotyping. PMID:23942574

Busemeyer, Lucas; Ruckelshausen, Arno; Möller, Kim; Melchinger, Albrecht E.; Alheit, Katharina V.; Maurer, Hans Peter; Hahn, Volker; Weissmann, Elmar A.; Reif, Jochen C.; Würschum, Tobias

2013-01-01

355

Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches  

DOEpatents

DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

McCutchen-Maloney, Sandra L. (Pleasanton, CA)

2002-01-01

356

Phenoscope: an automated large-scale phenotyping platform offering high spatial homogeneity.  

PubMed

Increased phenotyping accuracy and throughput are necessary to improve our understanding of quantitative variation and to be able to deconstruct complex traits such as those involved in growth responses to the environment. Still, only a few facilities are known to handle individual plants of small stature for non-destructive, real-time phenotype acquisition from plants grown in precisely adjusted and variable experimental conditions. Here, we describe Phenoscope, a high-throughput phenotyping platform that has the unique feature of continuously rotating 735 individual pots over a table. It automatically adjusts watering and is equipped with a zenithal imaging system to monitor rosette size and expansion rate during the vegetative stage, with automatic image analysis allowing manual correction. When applied to Arabidopsis thaliana, we show that rotating the pots strongly reduced micro-environmental disparity: heterogeneity in evaporation was cut by a factor of 2.5 and the number of replicates needed to detect a specific mild genotypic effect was reduced by a factor of 3. In addition, by controlling a large proportion of the micro-environmental variance, other tangible sources of variance become noticeable. Overall, Phenoscope makes it possible to perform large-scale experiments that would not be possible or reproducible by hand. When applied to a typical quantitative trait loci (QTL) mapping experiment, we show that mapping power is more limited by genetic complexity than phenotyping accuracy. This will help to draw a more general picture as to how genetic diversity shapes phenotypic variation. PMID:23452317

Tisné, Sébastien; Serrand, Yann; Bach, Liên; Gilbault, Elodie; Ben Ameur, Rachid; Balasse, Hervé; Voisin, Roger; Bouchez, David; Durand-Tardif, Mylène; Guerche, Philippe; Chareyron, Gaël; Da Rugna, Jérôme; Camilleri, Christine; Loudet, Olivier

2013-05-01

357

Additive genetic architecture underlying a rapidly evolving sexual signaling phenotype in the Hawaiian cricket genus Laupala.  

PubMed

Complex, quantitative traits are often the function of the coordinated action of many physically independent genetic factors. Interactive properties of multilocus genotypes, such as epistasis, are thought to be pervasive components of the genetic architecture of complex phenotypes. Here, we utilize a panel of interspecific backcross introgression lines to evaluate the genetic architecture of song variation, a quantitative sexual signaling phenotype, in the Hawaiian swordtail cricket genus Laupala. Allelic effects across five quantitative trait loci are consistent with a purely additive model of gene action, where alleles at multiple loci are found to have fully independent and discrete effects with respect to the sexual signaling phenotype. Whereas a more complex genetic architecture featuring non-additive dominance and epistasis components may constrain potential evolutionary trajectories and reduce the rate of evolutionary change, the polygenic, additive genetic architecture observed for sexual signaling in Laupala should respond rapidly to directional selection pressures and freely move throughout phenotypic space. This classic type I genetic architecture may facilitate the explosive radiation of song variation observed across the Laupala genus. PMID:23907616

Ellison, Christopher K; Shaw, Kerry L

2013-09-01

358

Transmission-disequilibrium tests for quantitative traits.  

PubMed Central

The transmission-disequilibrium test (TDT) of Spielman et al. is a family-based linkage-disequilibrium test that offers a powerful way to test for linkage between alleles and phenotypes that is either causal (i.e., the marker locus is the disease/trait allele) or due to linkage disequilibrium. The TDT is equivalent to a randomized experiment and, therefore, is resistant to confounding. When the marker is extremely close to the disease locus or is the disease locus itself, tests such as the TDT can be far more powerful than conventional linkage tests. To date, the TDT and most other family-based association tests have been applied only to dichotomous traits. This paper develops five TDT-type tests for use with quantitative traits. These tests accommodate either unselected sampling or sampling based on selection of phenotypically extreme offspring. Power calculations are provided and show that, when a candidate gene is available (1) these TDT-type tests are at least an order of magnitude more efficient than two common sib-pair tests of linkage; (2) extreme sampling results in substantial increases in power; and (3) if the most extreme 20% of the phenotypic distribution is selectively sampled, across a wide variety of plausible genetic models, quantitative-trait loci explaining as little as 5% of the phenotypic variation can be detected at the .0001 alpha level with <300 observations. PMID:9042929

Allison, D B

1997-01-01

359

Phenotypic Variation in Heterozygous Familial Hypercholesterolemia A Comparison of Chinese Patients With the Same or Similar Mutations in the LDL Receptor Gene in China or Canada  

Microsoft Academic Search

Familial hypercholesterolemia (FH) is caused by mutations in the LDL receptor (LDLR) gene and is usually associated with hypercholesterolemia, lipid deposition in tissues, and premature coronary artery disease (CAD). However, individuals with heterozygous FH in China exhibit a milder phenotype despite having deleterious mutations in the LDLR gene (X.-M. Sun et al, Arterioscler Thromb. 1994;14:85-94). Nineteen Chinese FH heterozygotes living

Simon N. Pimstone; Xi-Ming Sun; Jiri J. Frohlich; Michael R. Hayden; Anne K. Soutar

360

Shift in phenotypic variation coupled with rapid loss of genetic diversity in captive populations of Eristalis tenax (Diptera: Syrphidae): consequences for rearing and potential commercial use.  

PubMed

Because of its importance as a pollinator and its potential economic usefulness for the biodegradation of organic animal waste, the genetic and phenotypic diversity of the drone fly, Eristalis tenax L. (Diptera: Syrphidae), was studied in both wild and captive populations from southeastern Europe. Wild specimens from a natural protected habitat (with low human impact), field crop habitat (semisynanthropic condition), and intensive pig farming habitat (synanthropic condition) were compared with a laboratory colony reared on artificial media An integrative approach was applied based on allozyme loci, cytochrome c oxidase I mitochondrial DNA, wing traits (size and shape), and abdominal color patterns. Our results indicate that the fourth and eighth generations of the laboratory colony show a severe lack of genetic diversity compared with natural populations. Reduced genetic diversity in subsequent generations (F4 and F8) of the laboratory colony was found to be linked with phenotypic divergence. Loss of genetic variability associated with phenotypic differentiation in laboratory samples suggests a founder effect, followed by stochastic genetic processes and inbreeding. Hence, our results have implications for captive bred Eristalis flies, which have been used in crop pollination and biodegradation of organic waste under synanthropic conditions. PMID:24772566

Francuski, Ljubinka; Djurakic, Marko; Ludoski, Jasmina; Hurtado, Pilar; Pérez-Bañón, Celeste; Ståhls, Gunilla; Rojo, Santos; Milankov, Vesna

2014-04-01

361

Quantitative evaluation of the petal shape variation in Primula sieboldii caused by breeding process in the last 300 years.  

PubMed

Primula sieboldii: (E. Morren) has been a popular garden plant at least since the Edo period, about 300 years ago. We compared petal form between cultivars and wild populations in order to characterise the changes that have occurred during domestication. The comparison was made using EF-PCA analysis, which describes overall petal shape mathematically by transforming petal contour coordinates into elliptic Fourier descriptors; it subsequently summarises these descriptors by principal component analysis (PCA). Rearing cultivars in a common-garden experiment identified the PCs with a substantial genetic element. A clear heritable component was detected for the PCs characterising symmetrical variation in flower shape, but not the asymmetrical variation. Wild populations of this species have become endangered owing to habitat destruction by human activity, and many lowland floodplain habitats have been lost. Variation within the remaining wild populations was significantly lower than in the cultivars for PC1 (aspect ratio), PC3 (curvature of proximal and distal parts) and petal area; but not for PC2 (depth of head notch) and PC4 (position of the centre of gravity). The shifts in petal form from the wild populations to the cultivars parallel those seen in other crop-types following domestication, including an increase in size and diversity of forms: cultivars have shallower head notches, more fan-shaped petals and larger petals than do wild P. sieboldii. PMID:15829983

Yoshioka, Y; Iwata, H; Ohsawa, R; Ninomiya, S

2005-06-01

362

CT-based quantitative evaluation of radiation-induced lung fibrosis: a study of interobserver and intraobserver variations  

PubMed Central

Purpose The degree of radiation-induced lung fibrosis (RILF) can be measured quantitatively by fibrosis volume (VF) on chest computed tomography (CT) scan. The purpose of this study was to investigate the interobserver and intraobserver variability in CT-based measurement of VF. Materials and Methods We selected 10 non-small cell lung cancer patients developed with RILF after postoperative radiation therapy (PORT) and delineated VF on the follow-up chest CT scanned at more than 6 months after radiotherapy. Three radiation oncologists independently delineated VF to investigate the interobserver variability. Three times of delineation of VF was performed by two radiation oncologists for the analysis of intraobserver variability. We analysed the concordance index (CI) and inter/intraclass correlation coefficient (ICC). Results The median CI was 0.61 (range, 0.44 to 0.68) for interobserver variability and the median CIs for intraobserver variability were 0.69 (range, 0.65 to 0.79) and 0.61(range, 0.55 to 0.65) by two observers. The ICC for interobserver variability was 0.974 (p < 0.001) and ICCs for intraobserver variability were 0.996 (p < 0.001) and 0.991 (p < 0.001), respectively. Conclusion CT-based measurement of VF with patients who received PORT was a highly consistent and reproducible quantitative method between and within observers. PMID:24724050

Heo, Jaesung; Cho, Oyeon; Oh, Young-Taek; Chun, Mison; Kim, Mi-Hwa; Park, Hae-Jin

2014-01-01

363

Simple Quantitative PCR Approach to Reveal Naturally Occurring and Mutation-Induced Repetitive Sequence Variation on the Drosophila Y Chromosome  

PubMed Central

Heterochromatin is a significant component of the human genome and the genomes of most model organisms. Although heterochromatin is thought to be largely non-coding, it is clear that it plays an important role in chromosome structure and gene regulation. Despite a growing awareness of its functional significance, the repetitive sequences underlying some heterochromatin remain relatively uncharacterized. We have developed a real-time quantitative PCR-based method for quantifying simple repetitive satellite sequences and have used this technique to characterize the heterochromatic Y chromosome of Drosophila melanogaster. In this report, we validate the approach, identify previously unknown satellite sequence copy number polymorphisms in Y chromosomes from different geographic sources, and show that a defect in heterochromatin formation can induce similar copy number polymorphisms in a laboratory strain. These findings provide a simple method to investigate the dynamic nature of repetitive sequences and characterize conditions which might give rise to long-lasting alterations in DNA sequence. PMID:25285439

Aldrich, John C.; Maggert, Keith A.

2014-01-01

364

Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches  

DOEpatents

Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

McCutchen-Maloney, Sandra L. (Pleasanton, CA)

2002-01-01

365

A Quantitative-Trait Genome-Wide Association Study of Alcoholism Risk in the Community: Findings and  

E-print Network

A Quantitative-Trait Genome-Wide Association Study of Alcoholism Risk in the Community: Findings contributions to variation in alcoholism and heaviness of drinking (50% to 60% heritability) with high) for phenotypes related to alcohol use and dependence. Methods: Diagnostic interview and blood/buccal samples were

Nyholt, Dale R.

366

191J. Biosci. | Vol. 27|No. 3|June 2002|191193|Indian Academy of Sciences Analysing phenotypic variation: when old-fashioned  

E-print Network

morphological studies. Paleontology, zoology and anatomy then became (and remained frequently) considered as old decades has generated an increasing number of morphometric studies in fields ranging from paleontology (Crônier et al 1998) to developmental biology (Klingenberg and Zaklan 2000) and quantitative genetics

Debat, Vincent

367

Genome wide search for variation associated with micronutrient density of developing rice grains  

Technology Transfer Automated Retrieval System (TEKTRAN)

“Omic” tools are rapidly being employed to delineate the biological framework controlling phenotypes of interest in crop species. An advanced understanding of the genetic basis for quantitative trait variation has been made possible through genome wide association studies (GWAS) that make use of ge...

368

Repeatability and variation of region-of-interest methods using quantitative diffusion tensor MR imaging of the brain  

PubMed Central

Background Diffusion tensor imaging (DTI) is increasingly used in various diseases as a clinical tool for assessing the integrity of the brain’s white matter. Reduced fractional anisotropy (FA) and an increased apparent diffusion coefficient (ADC) are nonspecific findings in most pathological processes affecting the brain’s parenchyma. At present, there is no gold standard for validating diffusion measures, which are dependent on the scanning protocols, methods of the softwares and observers. Therefore, the normal variation and repeatability effects on commonly-derived measures should be carefully examined. Methods Thirty healthy volunteers (mean age 37.8 years, SD 11.4) underwent DTI of the brain with 3T MRI. Region-of-interest (ROI) -based measurements were calculated at eleven anatomical locations in the pyramidal tracts, corpus callosum and frontobasal area. Two ROI-based methods, the circular method (CM) and the freehand method (FM), were compared. Both methods were also compared by performing measurements on a DTI phantom. The intra- and inter-observer variability (coefficient of variation, or CV%) and repeatability (intra-class correlation coefficient, or ICC) were assessed for FA and ADC values obtained using both ROI methods. Results The mean FA values for all of the regions were 0.663 with the CM and 0.621 with the FM. For both methods, the FA was highest in the splenium of the corpus callosum. The mean ADC value was 0.727 ×10-3 mm2/s with the CM and 0.747 ×10-3 mm2/s with the FM, and both methods found the ADC to be lowest in the corona radiata. The CV percentages of the derived measures were < 13% with the CM and < 10% with the FM. In most of the regions, the ICCs were excellent or moderate for both methods. With the CM, the highest ICC for FA was in the posterior limb of the internal capsule (0.90), and with the FM, it was in the corona radiata (0.86). For ADC, the highest ICC was found in the genu of the corpus callosum (0.93) with the CM and in the uncinate fasciculus (0.92) with FM. Conclusions With both ROI-based methods variability was low and repeatability was moderate. The circular method gave higher repeatability, but variation was slightly lower using the freehand method. The circular method can be recommended for the posterior limb of the internal capsule and splenium of the corpus callosum, and the freehand method for the corona radiata. PMID:23057584

2012-01-01

369

Genomic variation. Impact of regulatory variation from RNA to protein.  

PubMed

The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to their effects on protein expression levels. Yet the impact of genetic variation, including eQTLs, on protein levels remains poorly understood. To address this, we mapped genetic variants that are associated with eQTLs, ribosome occupancy (rQTLs), or protein abundance (pQTLs). We found that most QTLs are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, eQTLs tend to have significantly reduced effect sizes on protein levels, which suggests that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we identified a class of cis QTLs that affect protein abundance with little or no effect on messenger RNA or ribosome levels, which suggests that they may arise from differences in posttranslational regulation. PMID:25657249

Battle, Alexis; Khan, Zia; Wang, Sidney H; Mitrano, Amy; Ford, Michael J; Pritchard, Jonathan K; Gilad, Yoav

2015-02-01

370

On the capability of Swarm for surface mass variation monitoring: Quantitative assessment based on orbit information from CHAMP, GRACE and GOCE  

NASA Astrophysics Data System (ADS)

In the last decade, temporal variations of the gravity field from GRACE observations have become one of the most ubiquitous and valuable sources of information for geophysical and environmental studies. In the context of global climate change, mass balance of the Arctic and Antarctic ice sheets gained particular attention. Because GRACE has outlived its predicted lifetime by several years already, it is very likely that a gap between GRACE and its successor GRACE follow-on (supposed to be launched in 2017, at the earliest) occurs. The Swarm mission - launched on November 22, 2013 - is the most promising candidate to bridge this potential gap, i.e., to directly acquire large-scale mass variation information on the Earth's surface in case of a gap between the present GRACE and the upcoming GRACE follow-on projects. Although the magnetometry mission Swarm has not been designed for gravity field purposes, its three satellites have the characteristics for such an endeavor: (i) low, near-circular and near-polar orbits, (ii) precise positioning with high-quality GNSS receivers, (iii) on-board accelerometers to measure the influence of non-gravitational forces. Hence, from an orbit analysis point of view the Swarm satellites are comparable to the CHAMP, GRACE and GOCE spacecraft. Indeed and as data analysis from CHAMP has been shown, the detection of annual signals and trends from orbit analysis is possible for long-wavelength features of the gravity field, although the accuracy associated with the inter-satellite GRACE measurements cannot be reached. We assess the capability of the (non-dedicated) mission Swarm for mass variation detection in a real-case environment (opposed to simulation studies). For this purpose, we "approximate" the Swarm scenario by the GRACE+CHAMP and GRACE+GOCE constellations. In a first step, kinematic orbits of the individual satellites are derived from GNSS observations. From these orbits, we compute monthly combined GRACE+CHAMP and GRACE+GOCE time-variable gravity fields; sophisticated techniques based on Kalman filtering are applied to reduce noise in the time series. Finally, we infer mass variation in selected areas from to gravity signal. These results are compared to the findings obtained from mass variation detection exploiting CSR-RL05 gravity fields; due to their superior quality (which is due to the fact that they are derived from inter-satellite GRACE measurements), the CSR-RL05 solutions serve as benchmark. Our quantitative assessment shows the potential and limitations of what can be expected from Swarm with regard to surface mass variation monitoring.

Baur, Oliver; Weigelt, Matthias; Zehentner, Norbert; Mayer-Gürr, Torsten; Jäggi, Adrian

2014-05-01

371

Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice  

PubMed Central

To identify quantitative trait loci (QTLs) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (BILs) derived from crosses between temperate japonica rice cultivars Nipponbare and Koshihikari were evaluated for 50 agronomic traits at six experimental fields located throughout Japan. Thirty-three of the 50 traits were significantly correlated with heading date. Using a linkage map including 647 single-nucleotide polymorphisms (SNPs), a total of 122 QTLs for 38 traits were mapped on all rice chromosomes except chromosomes 5 and 9. Fifty-eight of the 122 QTLs were detected near the heading date QTLs Hd16 and Hd17 and the remaining 64 QTLs were found in other chromosome regions. QTL analysis of 51 BILs having homozygous for the Koshihikari chromosome segments around Hd16 and Hd17 allowed us to detect 40 QTLs associated with 27 traits; 23 of these QTLs had not been detected in the original analysis. Among the 97 QTLs for the 30 traits measured in multiple environments, the genotype-by-environment interaction was significant for 44 QTLs and not significant for 53 QTLs. These results led us to propose a new selection strategy to improve agronomic performance in temperate japonica rice cultivars. PMID:23226082

Hori, Kiyosumi; Kataoka, Tomomori; Miura, Kiyoyuki; Yamaguchi, Masayuki; Saka, Norikuni; Nakahara, Takahiro; Sunohara, Yoshihiro; Ebana, Kaworu; Yano, Masahiro

2012-01-01

372

Qualitative and quantitative variation among volatile profiles induced by Tetranychus urticae feeding on plants from various families.  

PubMed

Many plant species are known to emit herbivore-induced volatiles in response to herbivory. The spider mite Tetranychus urticae Koch is a generalist that can feed on several hundreds of host plant species. Volatiles emitted by T. urticae-infested plants of 11 species were compared: soybean (Glycine max), golden chain (Laburnum anagyroides), black locust (Robinia pseudo-acacia), cowpea (Vigna unguiculata), tobacco (Nicotiana tabacum), eggplant (Solanum melalonga), thorn apple (Datura stramonium), sweet pepper (Capsicum annuum), hop (Humulus lupulus), grapevine (Vitis vinifera), and ginkgo (Ginkgo biloba). The degree to which the plant species produced novel compounds was analyzed when compared to the odors of mechanically damaged leaves. Almost all of the investigated plant species produced novel compounds that dominated the volatile blend, such as methyl salicylate, terpenes, oximes, and nitriles. Only spider mite-infested eggplant and tobacco emitted a blend that was merely quantitatively different from the blend emitted by mechanically damaged or clean leaves. We hypothesized that plant species with a low degree of direct defense would produce more novel compounds. However, although plant species with a low direct defense level do use indirect defense to defend themselves, they do not always emit novel compounds. Plant species with a high level of direct defense seem to invest in the production of novel compounds. When plant species of the Fabaceae were compared to plant species of the Solanaceae, qualitative differences in spider mite-induced volatile blends seemed to be more prominent in the Fabaceae than in the Solanaceae. PMID:15074658

van den Boom, Cindy E M; van Beek, Teris A; Posthumus, Maarten A; de Groot, Aede; Dicke, Marcel

2004-01-01

373

Insect mating signal and mate preference phenotypes covary among host plant genotypes.  

PubMed

Sexual selection acting on small initial differences in mating signals and mate preferences can enhance signal-preference codivergence and reproductive isolation during speciation. However, the origin of initial differences in sexual traits remains unclear. We asked whether biotic environments, a source of variation in sexual traits, may provide a general solution to this problem. Specifically, we asked whether genetic variation in biotic environments provided by host plants can result in signal-preference phenotypic covariance in a host-specific, plant-feeding insect. We used a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae) to assess patterns of variation in male mating signals and female mate preferences induced by genetic variation in host plants. We employed a novel implementation of a quantitative genetics method, rearing field-collected treehoppers on a sample of naturally occurring replicated host plant clone lines. We found remarkably high signal-preference covariance among host plant genotypes. Thus, genetic variation in biotic environments influences the sexual phenotypes of organisms living on those environments in a way that promotes assortative mating among environments. This consequence arises from conditions likely to be common in nature (phenotypic plasticity and variation in biotic environments). It therefore offers a general answer to how divergent sexual selection may begin. PMID:25611556

Rebar, Darren; Rodríguez, Rafael L

2015-03-01

374

A quantitative trait locus on Bos taurus autosome 17 explains a large proportion of the genetic variation in de novo synthesized milk fatty acids.  

PubMed

A genomic region associated with milk fatty acid (FA) composition has been detected on Bos taurus autosome (BTA)17 based on 50,000 (50K) single nucleotide polymorphism (SNP) genotypes. The aim of our study was to fine-map BTA17 with imputed 777,000 (777 K) SNP genotypes to identify candidate genes associated with milk FA composition. Phenotypes consisted of gas chromatography measurements of 14 FA based on winter and summer milk samples. Phenotypes and genotypes were available on 1,640 animals in winter milk, and on 1,581 animals in summer milk samples. Single-SNP analyses showed that several SNP in a region located between 29.0 and 34.0 Mbp were in strong association with C6:0, C8:0, and C10:0. This region was further characterized based on haplotypes. In summer milk samples, for example, these haplotypes explained almost 10% of the genetic variance in C6:0, 9% in C8:0, 3.5% in C10:0, 1.8% in C12:0, and 0.9% in C14:0. Two groups of haplotypes with distinct predicted effects could be defined, suggesting the presence of one causal variant. Predicted haplotype effects tended to increase from C6:0 to C14:0; however, the proportion of genetic variance explained by the haplotypes tended to decrease from C6:0 to C14:0. This is an indication that the quantitative trait locus (QTL) region is involved either in the elongation process or in early termination of de novo synthesized FA. Although many genes are present in this QTL region, most of these genes on BTA17 have not been characterized yet. The strongest association was found close to the progesterone receptor membrane component 2 (PGRMC2) gene, which has not yet been associated with milk FA composition. Therefore, no clear candidate gene associated with milk FA composition could be identified for this QTL. PMID:25242430

Duchemin, S I; Visker, M H P W; Van Arendonk, J A M; Bovenhuis, H

2014-11-01

375

Relaxed selection is a precursor to the evolution of phenotypic plasticity  

Technology Transfer Automated Retrieval System (TEKTRAN)

Phenotypic plasticity represents one of the most important ways that organisms adaptively respond to environmental variation. Alternate phenotypes produced through phenotypic plasiticity generally arise through conditional gene expression, which is predicted to result in relaxed selective constrain...

376

Dissecting High-Dimensional Phenotypes with Bayesian Sparse Factor Analysis of Genetic Covariance Matrices  

PubMed Central

Quantitative genetic studies that model complex, multivariate phenotypes are important for both evolutionary prediction and artificial selection. For example, changes in gene expression can provide insight into developmental and physiological mechanisms that link genotype and phenotype. However, classical analytical techniques are poorly suited to quantitative genetic studies of gene expression where the number of traits assayed per individual can reach many thousand. Here, we derive a Bayesian genetic sparse factor model for estimating the genetic covariance matrix (G-matrix) of high-dimensional traits, such as gene expression, in a mixed-effects model. The key idea of our model is that we need consider only G-matrices that are biologically plausible. An organism’s entire phenotype is the result of processes that are modular and have limited complexity. This implies that the G-matrix will be highly structured. In particular, we assume that a limited number of intermediate traits (or factors, e.g., variations in development or physiology) control the variation in the high-dimensional phenotype, and that each of these intermediate traits is sparse – affecting only a few observed traits. The advantages of this approach are twofold. First, sparse factors are interpretable and provide biological insight into mechanisms underlying the genetic architecture. Second, enforcing sparsity helps prevent sampling errors from swamping out the true signal in high-dimensional data. We demonstrate the advantages of our model on simulated data and in an analysis of a published Drosophila melanogaster gene expression data set. PMID:23636737

Runcie, Daniel E.; Mukherjee, Sayan

2013-01-01

377

Quantitative Estimation of the Impact of European Teleconnections on Interannual Variation of East Asian Winter Temperature and Monsoon  

NASA Technical Reports Server (NTRS)

The impact of European teleconnections including the East AtlanticWest Russia (EA-WR), the Scandinavia (SCA), and the East Atlantic (EA) on East Asian winter temperature variability was quantified and compared with the combined effect of the Arctic Oscillation (AO), the Western Pacific (WP), and the El-Nino Southern Oscillation (ENSO), which are originated in the Northern Hemispheric high-latitudes or the Pacific. Three European teleconnections explained 22-25 percent of the total monthly upper-tropospheric height variance over Eurasia. Regression analysis revealed warming by EA-WR and EA and cooling by SCA over mid-latitude East Asia during their positive phase and vice versa. Temperature anomalies were largely explained by the advective temperature change process at the lower troposphere. The average spatial correlation over East Asia (90-180E, 10-80N) for the last 34 winters between observed and reconstructed temperature comprised of AO, WP and ENSO effect (AWE) was approximately 0.55, and adding the European teleconnection components (ESE) to the reconstructed temperature improved the correlation up to approximately 0.64. Lower level atmospheric structure demonstrated that approximately five of the last 34 winters were significantly better explained by ESE than AWE to determine East Asian seasonal winter temperatures. We also compared the impact between EA-WR and AO on the 1) East Asian winter monsoon, 2) cold surge, and 3) the Siberian high. These three were strongly coupled, and their spatial features and interannual variation were somewhat better explained by EA-WR than AO. Results suggest that the EA-WR impact must be treated more importantly than previously thought for a better understanding of East Asian winter temperature and monsoon variability.

Lim, Young-Kwon; Kim, Hae-Dong

2014-01-01

378

Quantitative variations of individual carotenoids in relationship with the leaflet development of six species of the genus Ceratozamia (Cycads).  

PubMed

The content and relative variations of individual carotenoids during the leaflet development stages (I, II, III, A and P) of six species of Ceratozamia (Cycads) were investigated. There is an unusual, transitory and marked presence of six red stroma keto-carotenoids in the first development stages, while the thylakoidal carotenoids showed a low concentration during the same period. As no official A1cm1% coefficients were available, it was necessary to calculate these for the following stroma carotenoids: semi-beta-carotenone (major component), triphasiaxanthin, ceratoxanthin, ceratozamiaxanthin, kuesteriaxanthin and ceratoxanthone. The stroma keto-carotenoids, which reached the highest content in the first development stage (average of 78% of total carotenoids), were always present in the five species: C. fuscoviridis, C. robusta, C. spinosa, C. kuesteriana and C. hildae, but never in C. mexicana. From stage II, the stroma keto-carotenoids decreased and finally disappeared in the green adult leaflets. The thylakoidal carotenoids showed a minimum at stage III, and then increased to a maximum in the perennial leaflets. Among these, beta-carotene showed an anomalous and characteristic behaviour, being a minor component during leaflet development (from stage I to A). In stage P it was markedly exceeded not only by lutein but also by alpha-carotene, neoxanthin and violaxanthin, and in C. robusta also by lutein-5,6-epoxide. Additionally, the alpha/beta ratio in these species is unusual: it increased from 0.3-0.5 to 1.5-3.0 during leaflet development. Moreover, antheraxanthin amounts are very small, while zeaxanthin was present only in the evergreen leaflets of C. mexicana in small quantities. Lutein-5,6-epoxide represented more than 5% of thylakoidal carotenoids in the leaflets of all the species. A revision of the taxonomic rank of C. fuscoviridis is recommended. PMID:16399003

Cardini, Franco; Pucci, Susanna; Calamassi, Roberto

2006-02-01

379

Quantitative phenotyping via deep barcode sequencing  

Microsoft Academic Search

Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or ''Bar-seq,'' outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput.

Andrew M. Smith; Lawrence E. Heisler; Joseph Mellor; Fiona Kaper; Michael J. Thompson; Mark Chee; Frederick P. Roth; Guri Giaever; Corey Nislow

2009-01-01

380

Plant chip for high-throughput phenotyping of Arabidopsis.  

PubMed

We report on the development of a vertical and transparent microfluidic chip for high-throughput phenotyping of Arabidopsis thaliana plants. Multiple Arabidopsis seeds can be germinated and grown hydroponically over more than two weeks in the chip, thus enabling large-scale and quantitative monitoring of plant phenotypes. The novel vertical arrangement of this microfluidic device not only allows for normal gravitropic growth of the plants but also, more importantly, makes it convenient to continuously monitor phenotypic changes in plants at the whole organismal level, including seed germination and root and shoot growth (hypocotyls, cotyledons, and leaves), as well as at the cellular level. We also developed a hydrodynamic trapping method to automatically place single seeds into seed holding sites of the device and to avoid potential damage to seeds that might occur during manual loading. We demonstrated general utility of this microfluidic device by showing clear visible phenotypes of the immutans mutant of Arabidopsis, and we also showed changes occurring during plant-pathogen interactions at different developmental stages. Arabidopsis plants grown in the device maintained normal morphological and physiological behaviour, and distinct phenotypic variations consistent with a priori data were observed via high-resolution images taken in real time. Moreover, the timeline for different developmental stages for plants grown in this device was highly comparable to growth using a conventional agar plate method. This prototype plant chip technology is expected to lead to the establishment of a powerful experimental and cost-effective framework for high-throughput and precise plant phenotyping. PMID:24510109

Jiang, Huawei; Xu, Zhen; Aluru, Maneesha R; Dong, Liang

2014-04-01

381

Structural variation in the Waxy gene and differentiation in foxtail millet [ Setaria italica (L.) P. Beauv.]: implications for multiple origins of the waxy phenotype  

Microsoft Academic Search

The origin and evolution of the waxy type of foxtail millet [Setaria italica (L.) P. Beauv] were studied by analyzing structural variation in the Waxy gene. Initially, the Waxy gene was amplified by RT-PCR, RACE and genomic PCR from a non-waxy strain to determine the structure of the wild-type gene. Secondly, we screened by PCR for polymorphisms at the Waxy

K. Fukunaga; M. Kawase; K. Kato

2002-01-01

382

Interindividual variation in relative CYP1A2/3A4 phenotype influences susceptibility of clozapine oxidation to cytochrome P450-specific inhibition in human hepatic microsomes.  

PubMed

The atypical antipsychotic drug clozapine (CLZ) is effective in a substantial number of patients who exhibit treatment-resistance to conventional agents. CYP1A2 is generally considered to be the major enzyme involved in the biotransformation of CLZ to its N-demethylated (norCLZ) and N-oxygenated (CLZ N-oxide) metabolites in liver, but several studies have also implicated CYP3A4. The present study assessed the interplay between these cytochrome P450s (P450s) in CLZ biotransformation in a panel of hepatic microsomal fractions from 14 individuals. The relative activity of P450s 1A2 and 3A4 in microsomes was found to be a major determinant of the relative susceptibility of norCLZ formation to inhibition by the P450-selective inhibitors fluvoxamine and ketoconazole. In contrast, the activity of CYP3A4 alone was correlated with the susceptibility of CLZ N-oxide formation to inhibition by these agents. These findings suggest that both P450s may be dominant CLZ oxidases in patients and that the relative activities of these enzymes may determine clearance pathways. In vivo assessment of CYP1A2 and CYP3A4 activities, perhaps by phenotyping approaches, could assist the optimization of CLZ dosage and minimize pharmacokinetic interactions with coadministered drugs. PMID:18809730

Zhang, Wei V; D'Esposito, Fabrizio; Edwards, Robert J; Ramzan, Iqbal; Murray, Michael

2008-12-01

383

[Phenotypes in chronic obstructive pulmonary disease].  

PubMed

Chronic Obstructive Pulmonary Disease (COPD) is a multi-dimensional disorder with multiple phenotypes. The GOLD guidelines, used for the diagnosis, staging and treatment of COPD, do not fully reflect the heterogeneous nature of the disease. Historically, the two most recognized clinical phenotypes of COPD are emphysema and chronic bronchitis. Most COPD patients encountered in practice actually share, both of these features. Genetic background, clinical presentation, variation in the response to treatment and propensity to exacerbations may also identify other phenotypes. Recently, using a mathematical approach, such as cluster analysis, which is based on pre-selected parameters, other interesting phenotypes were identified. A precise definition of COPD phenotypes should lead to a more targeted therapeutic approach based on these phenotypes. The purpose of this article is to point out that COPD is a heterogeneous disease and to summarize the current data available about the phenotypes of this disease. PMID:25158382

Corhay, J-L; Schleich, F; Louis, R

2014-01-01

384

Toxic hydrogen sulfide and dark caves: phenotypic and genetic divergence across two abiotic environmental gradients in Poecilia mexicana.  

PubMed

Divergent natural selection drives evolutionary diversification. It creates phenotypic diversity by favoring developmental plasticity within populations or genetic differentiation and local adaptation among populations. We investigated phenotypic and genetic divergence in the livebearing fish Poecilia mexicana along two abiotic environmental gradients. These fish typically inhabit nonsulfidic surface rivers, but also colonized sulfidic and cave habitats. We assessed phenotypic variation among a factorial combination of habitat types using geometric and traditional morphometrics, and genetic divergence using quantitative and molecular genetic analyses. Fish in caves (sulfidic or not) exhibited reduced eyes and slender bodies. Fish from sulfidic habitats (surface or cave) exhibited larger heads and longer gill filaments. Common-garden rearing suggested that these morphological differences are partly heritable. Population genetic analyses using microsatellites as well as cytochrome b gene sequences indicate high population differentiation over small spatial scale and very low rates of gene flow, especially among different habitat types. This suggests that divergent environmental conditions constitute barriers to gene flow. Strong molecular divergence over short distances as well as phenotypic and quantitative genetic divergence across habitats in directions classic to fish ecomorphology suggest that divergent selection is structuring phenotypic variation in this system. PMID:18637957

Tobler, Michael; Dewitt, Thomas J; Schlupp, Ingo; García de León, Francisco J; Herrmann, Roger; Feulner, Philine G D; Tiedemann, Ralph; Plath, Martin

2008-10-01

385

The phenotypic variance gradient – a novel concept  

PubMed Central

Evolutionary ecologists commonly use reaction norms, which show the range of phenotypes produced by a set of genotypes exposed to different environments, to quantify the degree of phenotypic variance and the magnitude of plasticity of morphometric and life-history traits. Significant differences among the values of the slopes of the reaction norms are interpreted as significant differences in phenotypic plasticity, whereas significant differences among phenotypic variances (variance or coefficient of variation) are interpreted as differences in the degree of developmental instability or canalization. We highlight some potential problems with this approach to quantifying phenotypic variance and suggest a novel and more informative way to plot reaction norms: namely “a plot of log (variance) on the y-axis versus log (mean) on the x-axis, with a reference line added”. This approach gives an immediate impression of how the degree of phenotypic variance varies across an environmental gradient, taking into account the consequences of the scaling effect of the variance with the mean. The evolutionary implications of the variation in the degree of phenotypic variance, which we call a “phenotypic variance gradient”, are discussed together with its potential interactions with variation in the degree of phenotypic plasticity and canalization. PMID:25540685

Pertoldi, Cino; Bundgaard, Jørgen; Loeschcke, Volker; Barker, James Stuart Flinton

2014-01-01

386

The phenotypic variance gradient - a novel concept.  

PubMed

Evolutionary ecologists commonly use reaction norms, which show the range of phenotypes produced by a set of genotypes exposed to different environments, to quantify the degree of phenotypic variance and the magnitude of plasticity of morphometric and life-history traits. Significant differences among the values of the slopes of the reaction norms are interpreted as significant differences in phenotypic plasticity, whereas significant differences among phenotypic variances (variance or coefficient of variation) are interpreted as differences in the degree of developmental instability or canalization. We highlight some potential problems with this approach to quantifying phenotypic variance and suggest a novel and more informative way to plot reaction norms: namely "a plot of log (variance) on the y-axis versus log (mean) on the x-axis, with a reference line added". This approach gives an immediate impression of how the degree of phenotypic variance varies across an environmental gradient, taking into account the consequences of the scaling effect of the variance with the mean. The evolutionary implications of the variation in the degree of phenotypic variance, which we call a "phenotypic variance gradient", are discussed together with its potential interactions with variation in the degree of phenotypic plasticity and canalization. PMID:25540685

Pertoldi, Cino; Bundgaard, Jørgen; Loeschcke, Volker; Barker, James Stuart Flinton

2014-11-01

387

phenosim - A software to simulate phenotypes for testing in genome-wide association studies  

PubMed Central

Background There is a great interest in understanding the genetic architecture of complex traits in natural populations. Genome-wide association studies (GWAS) are becoming routine in human, animal and plant genetics to understand the connection between naturally occurring genotypic and phenotypic variation. Coalescent simulations are commonly used in population genetics to simulate genotypes under different parameters and demographic models. Results Here, we present phenosim, a software to add a phenotype to genotypes generated in time-efficient coalescent simulations. Both qualitative and quantitative phenotypes can be generated and it is possible to partition phenotypic variation between additive effects and epistatic interactions between causal variants. The output formats of phenosim are directly usable as input for different GWAS tools. The applicability of phenosim is shown by simulating a genome-wide association study in Arabidopsis thaliana. Conclusions By using the coalescent approach to generate genotypes and phenosim to add phenotypes, the data sets can be used to assess the influence of various factors such as demography, genetic architecture or selection on the statistical power of association methods to detect causal genetic variants under a wide variety of population genetic scenarios. phenosim is freely available from the authors' website http://evoplant.uni-hohenheim.de PMID:21714868

2011-01-01

388

Variation in PAH-related DNA adduct levels among non-smokers: the role of multiple genetic polymorphisms and nucleotide excision repair phenotype  

PubMed Central

Polycyclic aromatic hydrocarbons (PAHs) likely play a role in many cancers even in never-smokers. We tried to find a model to explain the relationship between variation in PAH-related DNA adduct levels among people with similar exposures, multiple genetic polymorphisms in genes related to metabolic and repair pathways, and nucleotide excision repair (NER) capacity. In 111 randomly-selected female never-smokers from the Golestan Cohort Study in Iran, we evaluated 21 SNPs in 14 genes related to xenobiotic metabolism and 12 SNPs in 8 DNA repair genes. NER capacity was evaluated by a modified comet assay, and aromatic DNA adduct levels were measured in blood by 32P-postlabelling. Multivariable regression models were compared by Akaike’s information criterion (AIC). Aromatic DNA adduct levels ranged between 1.7 and 18.6 per 108 nucleotides (mean: 5.8±3.1). DNA adduct level was significantly lower in homozygotes for NAT2 slow alleles and ERCC5 non risk-allele genotype, and was higher in the MPO homozygote risk-allele genotype. The sum of risk alleles in these genes significantly correlated with the log-adduct level (r=0.4, p<0.001). Compared with the environmental model, adding phase I SNPs and NER capacity provided the best fit, and could explain 17% more of the variation in adduct levels. NER capacity was affected by polymorphisms in the MTHFR and ERCC1 genes. Female non-smokers in this population had PAH-related DNA adduct levels 3-4 times higher than smokers and occupationally-exposed groups in previous studies, with large inter-individual variation which could best be explained by a combination of phase I genes and NER capacity. PMID:23175176

Etemadi, Arash; Islami, Farhad; Phillips, David H.; Godschalk, Roger; Golozar, Asieh; Kamangar, Farin; Malekshah, Akbar Fazel-Tabar; Pourshams, Akram; Elahi, Seerat; Ghojaghi, Farhad; Strickland, Paul T; Taylor, Philip R; Boffetta, Paolo; Abnet, Christian C; Dawsey, Sanford M; Malekzadeh, Reza; van Schooten, Frederik J.

2012-01-01

389

Analysis of the impact of genetic variation on human gene expression.  

PubMed

Interindividual variation in gene expression has been convincingly shown to be controlled, in part, by genetic differences. Determining the architecture of genetic variation, the underlying gene expression may allow deeper insight into complex phenotypes, such as differences in disease susceptibility. Mapping genetic variants accounting for expression phenotypes in human cell and tissue panels has rapidly progressed from proof-of-principle experiments to general tools in biomedical discovery. We discuss the general approach and critical considerations for carrying out expression quantitative trait mapping in human tissues. PMID:20238090

Grundberg, Elin; Kwan, Tony; Pastinen, Tomi M

2010-01-01

390

Correlation Assessment among Clinical Phenotypes, Expression Analysis and Molecular Modeling of 14 Novel Variations in the Human Galactose-1-phosphate Uridylyltransferase Gene  

PubMed Central

Galactose-1-phosphate uridylyltransferase (GALT) catalyses the conversion of galactose-1-phosphate to UDP-galactose, a key step in the galactose metabolism. Deficiency of GALT activity in humans caused by deleterious variations in the GALT gene can cause a potentially lethal disease called Classic Galactosemia. In this study, we selected 14 novel nucleotide sequence changes in the GALT genes found in galactosemic patients for expression analysis and molecular modeling. Several variants showed decreased levels of expression and decreased abundance in the soluble fraction of the Escherichia coli cell extracts, suggesting altered stability and solubility. Only six variant GALT enzymes had detectable enzymatic activities. Kinetic studies showed that their Vmax decreased significantly. To further characterize the variants at molecular level, we performed static and dynamic molecular modeling studies. Effects of variations on local and/or global structural features of the enzyme were anticipated for the majority of variants. In-depth studies with molecular dynamic simulations on selected variants predicted the alteration of the protein structure even when static models apparently did not highlight any perturbation. Overall, these studies offered new insights on the molecular properties of GALT enzyme, with the aim of correlating them with the clinical outcome. PMID:22461411

Tang, Manshu; Facchiano, Angelo; Rachamadugu, Rakesh; Calderon, Fernanda; Mao, Rong; Milanesi, Luciano; Marabotti, Anna; Lai, Kent

2012-01-01

391

Lack of phenotypic effect of triallelic variation in SPATA7 in a family with Leber congenital amaurosis resulting from CRB1 mutations  

PubMed Central

Purpose To identify the causative gene for autosomal recessive Leber congenital amaurosis (LCA) in a Chinese family. Methods One Chinese LCA family was identified and an ophthalmologic examination was performed. The genetic defects were analyzed simultaneously by a genome-wide linkage scan with 382 polymorphic microsatellite markers, as well as by comprehensive mutational screening of 15 genes known to associate with LCA on the genomic DNA of this family. Results Suggestive linkages were found in 13 chromosomal regions, of which only one harbored a known causative gene, crumbs homolog 1 (CRB1), on chromosome 1. Sanger sequencing of CRB1 identified two novel heterozygous mutations, c.3221T>C (p.L1074S) and c.2677–2A>C. In addition, a novel missense heterozygous mutation, c.938C>A (p.A313D), in spermatogenesis associated 7 (SPATA7), was detected in the proband after screening of the other 14 LCA causative genes. All three affected individuals of the family had compound heterozygous CRB1 mutations, and one of the three (the proband) had an additional mutation in SPATA7. The unaffected mother had the heterozygous c.3221T>C mutation in CRB1 and the heterozygous c.938C>A mutation in SPATA7. The unaffected father could not be tested, but presumably had the heterozygous c.2677–2A>C mutation in CRB1. The proband, with triallelic mutations in CRB1 and SPATA7, had a phenotype similar to other two affected brothers, suggesting the additional mutant allele in SPATA7 might not contribute to the disease. Similarly, the mother, with digenic mutations in CRB1 and SPATA7, had normal vision and fundi, suggesting the digenic mutations in these two genes might not cause disease. Conclusions Digenic and triallelic mutations of CRB1 and SPATA7 were detected in a family with LCA. Our results imply that CRB1 and SPATA7 may not interact with each other directly. This emphasizes that care should be taken in invoking a mutation–disease association for digenic and triallelic mutations. PMID:22219627

Li, Lin; Xiao, Xueshan; Li, Shiqiang; Jiao, Xiaodong; Hejtmancik, J. Fielding

2011-01-01

392

Optofluidic Detection for Cellular Phenotyping  

PubMed Central

Quantitative analysis of the output of processes and molecular interactions within a single cell is highly critical to the advancement of accurate disease screening and personalized medicine. Optical detection is one of the most broadly adapted measurement methods in biological and clinical assays and serves cellular phenotyping. Recently, microfluidics has obtained increasing attention due to several advantages, such as small sample and reagent volumes, very high throughput, and accurate flow control in the spatial and temporal domains. Optofluidics, which is the attempt to integrate optics with microfluidic, shows great promise to enable on-chip phenotypic measurements with high precision, sensitivity, specificity, and simplicity. This paper reviews the most recent developments of optofluidic technologies for cellular phenotyping optical detection. PMID:22854915

Tung, Yi-Chung; Huang, Nien-Tsu; Oh, Bo-Ram; Patra, Bishnubrata; Pan, Chi-Chun; Qiu, Teng; Paul, K. Chu; Zhang, Wenjun; Kurabayashi, Katsuo

2012-01-01

393

Quantitative aspects of variations of 1.5-6.0 MeV electrons in the outer radiation belt during magnetic storms  

NASA Astrophysics Data System (ADS)

We have quantitatively investigated the radiation belt dynamic variations of 1.5-6.0 MeV electrons during 54 coronal mass ejection (CME)-driven storms from 1993 to 2003 and 26 corotating interaction region (CIR)-driven recurrent storms in 1995 by utilizing case and statistical studies based on the data from the SAMPEX satellite. It is found that the boundaries determined by fitting an exponential to the flux as a function of L shell obtained in this study agree with the observed outer and inner boundaries of the outer radiation belt. Furthermore, we have constructed the radiation belt content (RBC) index by integrating the number density of electrons between those inner and outer boundaries. According to the ratio of the maximum RBC index during the recovery phase to the prestorm average RBC index, we conclude that CME-driven storms produce more relativistic electrons than CIR-driven storms in the entire outer radiation belt, although the relativistic electron fluxes during CIR-related storms are much higher than those during CME-related storms at geosynchronous orbit.

Yuan, C. J.; Zong, Q.-G.

2012-11-01

394

Quantitative variation in water-use efficiency across water regimes and its relationship with circadian, vegetative, reproductive, and leaf gas-exchange traits.  

PubMed

Drought limits light harvesting, resulting in lower plant growth and reproduction. One trait important for plant drought response is water-use efficiency (WUE). We investigated (1) how the joint genetic architecture of WUE, reproductive characters, and vegetative traits changed across drought and well-watered conditions, (2) whether traits with distinct developmental bases (e.g. leaf gas exchange versus reproduction) differed in the environmental sensitivity of their genetic architecture, and (3) whether quantitative variation in circadian period was related to drought response in Brassica rapa. Overall, WUE increased in drought, primarily because stomatal conductance, and thus water loss, declined more than carbon fixation. Genotypes with the highest WUE in drought expressed the lowest WUE in well-watered conditions, and had the largest vegetative and floral organs in both treatments. Thus, large changes in WUE enabled some genotypes to approach vegetative and reproductive trait optima across environments. The genetic architecture differed for gas-exchange and vegetative traits across drought and well-watered conditions, but not for floral traits. Correlations between circadian and leaf gas-exchange traits were significant but did not vary across treatments, indicating that circadian period affects physiological function regardless of water availability. These results suggest that WUE is important for drought tolerance in Brassica rapa and that artificial selection for increased WUE in drought will not result in maladaptive expression of other traits that are correlated with WUE. PMID:22319207

Edwards, Christine E; Ewers, Brent E; McClung, C Robertson; Lou, Ping; Weinig, Cynthia

2012-05-01

395

The genetic architecture of psychophysiological phenotypes  

PubMed Central

It is now clear that almost all complex traits have a highly polygenic component; that is, their genetic basis consists of relatively frequent risk alleles at a very large number of loci, each making a small contribution to variation, or disease susceptibility. This general conclusion appears to hold for intermediate phenotypes. Therefore, we should not expect these phenotypes to be associated with substantially larger effect sizes than conventional phenotypes. Instead, their usefulness is likely to lie in understanding the mechanism underpinning associations identified via genome-wide association studies of conventional phenotypes. PMID:25387716

Munafò, Marcus R; Flint, Jonathan

2014-01-01

396

The genetic architecture of psychophysiological phenotypes.  

PubMed

It is now clear that almost all complex traits have a highly polygenic component; that is, their genetic basis consists of relatively frequent risk alleles at a very large number of loci, each making a small contribution to variation, or disease susceptibility. This general conclusion appears to hold for intermediate phenotypes. Therefore, we should not expect these phenotypes to be associated with substantially larger effect sizes than conventional phenotypes. Instead, their usefulness is likely to lie in understanding the mechanism underpinning associations identified via genome-wide association studies of conventional phenotypes. PMID:25387716

Munafò, Marcus R; Flint, Jonathan

2014-12-01

397

Adaptive evolution of molecular phenotypes  

NASA Astrophysics Data System (ADS)

Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.

Held, Torsten; Nourmohammad, Armita; Lässig, Michael

2014-09-01

398

Pharmacometabonomic characterization of xenobiotic and endogenous metabolic phenotypes that account for inter-individual variation in isoniazid-induced toxicological response.  

PubMed

An NMR-based pharmacometabonomic approach was applied to investigate inter-animal variation in response to isoniazid (INH; 200 and 400 mg/kg) in male Sprague-Dawley rats, alongside complementary clinical chemistry and histopathological analysis. Marked inter-animal variability in central nervous system (CNS) toxicity was identified following administration of a high dose of INH, which enabled characterization of CNS responders and CNS non-responders. High-resolution post-dose urinary ¹H NMR spectra were modeled both by their xenobiotic and endogenous metabolic information sets, enabling simultaneous identification of the differential metabolic fate of INH and its associated endogenous metabolic consequences in CNS responders and CNS non-responders. A