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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

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 Central

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

Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dósa, Katalin; Pfammatter, Jesse

2014-01-01

5

Phenotypic variation and quantitative trait locus identification for osmotic potential in an interspecific hybrid inbred F2 poplar pedigree grown in contrasting environments  

SciTech Connect

Elucidation of the mechanisms of dehydration tolerance in popular (Populus sp.) trees will permit development of biochemical and molecular indicators to indentify dehydration-tolerant genotypes during genetic selection. The objectives of the study were to characterize the degree of phenotypic variation in osmotic potential (a determinant of dehydration tolerance), determine the relationship between osmotic potential at full turgor and relative growth rate, and identify quantitative trait loci (QTL) for osmotic potential in an advanced-generation, interpsecific popular pedigree established in contrasting environments.

Tschaplinski, Timothy J [ORNL; Tuskan, Gerald A [ORNL; Sewell, Mitchell [ORNL; Gebre, G [ORNL; Todd Jr, Donald E [ORNL; Pendley, Carrie D [ORNL

2006-01-01

6

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.

7

Admixture and clinical phenotypic variation.  

PubMed

All human populations exhibit some level of genetic differentiation. This differentiation, or population stratification, has many interacting sources, including historical migrations, population isolation over time, genetic drift, and selection and adaptation. If differentiated populations remained isolated from each other over a long period of time such that there is no mating of individuals between those populations, then some level of global consanguinity within those populations will lead to the formation of gene pools that will become more and more distinct over time. Global genetic differentiation of this sort can lead to overt phenotypic differences between populations if phenotypically relevant variants either arise uniquely within those populations or begin to exhibit frequency differences across the populations. This can occur at the single variant level for monogenic phenotypes or at the level of aggregate variant frequency differences across the many loci that contribute to a phenotype with a multifactorial or polygenic basis. However, if individuals begin to interbreed (or 'admix') from populations with different frequencies of phenotypically relevant genetic variants, then these admixed individuals will exhibit the phenotype to varying degrees. The level of phenotypic expression will depend on the degree to which the admixed individuals have inherited causative variants that have descended from the ancestral population in which those variants were present (or, more likely, simply more frequent). We review studies that consider the association between the degree of admixture (or ancestry) and phenotypes of clinical relevance. We find a great deal of literature-based evidence for associations between the degree of admixture and phenotypic variation for a number of admixed populations and phenotypes, although not all this evidence is confirmatory. We also consider the implications of such associations for gene-mapping initiatives as well as general clinical epidemiology studies and medical practice. We end with some thoughts on the future of studies exploring phenotypic differences among admixed individuals as well as individuals with different ancestral backgrounds. PMID:25060271

Goetz, Laura H; Uribe-Bruce, Liliana; Quarless, Danjuma; Libiger, Ondrej; Schork, Nicholas J

2014-01-01

8

Retrotransposons as epigenetic mediators of phenotypic variation in mammals  

Microsoft Academic Search

Phenotypic variation in mammals is frequently attributed to the action of quantitative trait loci (QTL) or the environment, but may also be epigenetic in origin. Here we consider a mechanism for phenotypic variation based on interference of transcription by somatically active retrotransposons. Transcriptionally competent retrotransposons may number in the tens of thousands in mammalian genomes. We propose that silencing of

Emma Whitelaw; David I. K. Martin

2001-01-01

9

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

10

Phenotypic variation in LADD syndrome.  

PubMed Central

A mother and son are reported with chronic dacrocystitis, cup shaped ears, hearing loss, abnormal teeth, and poor formation of saliva and tears. They are similar to previously reported cases of lacrimo-auriculo-dento-digital (LADD) syndrome. The variability of expression of this autosomal dominant syndrome is discussed, and it is suggested that poor saliva and tear formation be added to the phenotype. Images PMID:4078868

Thompson, E; Pembrey, M; Graham, J M

1985-01-01

11

What Role Does Heritable Epigenetic Variation Play in Phenotypic Evolution?  

NSDL National Science Digital Library

To explore the potential evolutionary relevance of heritable epigenetic variation, the National Evolutionary Synthesis Center recently hosted a catalysis meeting that brought together molecular epigeneticists, experimental evolutionary ecologists, and theoretical population and quantitative geneticists working across a wide variety of systems. The group discussed the methods available to investigate epigenetic variation and epigenetic inheritance, and how to evaluate their importance for phenotypic evolution. We found that understanding the relevance of epigenetic effects in phenotypic evolution will require clearly delineating epigenetics within existing terminology and expanding research efforts into ecologically relevant circumstances across model and nonmodel organisms. In addition, a critical component of understanding epigenetics will be the development of new and current statistical approaches and expansion of quantitative and population genetic theory. Although the importance of heritable epigenetic effects on evolution is still under discussion, investigating them in the context of a multidisciplinary approach could transform the field.

Christina Richards (University of South Florida;Department of Integrative Biology)

2010-03-01

12

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

13

Epigenetics and phenotypic variation in mammals Anne E. Peaston,1  

E-print Network

Epigenetics and phenotypic variation in mammals Anne E. Peaston,1 * Emma Whitelaw2 1 School and environment, in addition to variation not readily attributable to either. Epigenetic phe- nomena associated and are likely to contribute to the ``intangible variation'' alluded to. While it is clear that epigenetic

14

Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast  

PubMed Central

Background Most quantitative measures of phenotypic traits represent macroscopic contributions of large numbers of cells. Yet, cells of a tissue do not behave similarly, and molecular studies on several organisms have shown that regulations can be highly stochastic, sometimes generating diversified cellular phenotypes within tissues. Phenotypic noise, defined here as trait variability among isogenic cells of the same type and sharing a common environment, has therefore received a lot of attention. Given the potential fitness advantage provided by phenotypic noise in fluctuating environments, the possibility that it is directly subjected to evolutionary selection is being considered. For selection to act, phenotypic noise must differ between contemporary genotypes. Whether this is the case or not remains, however, unclear because phenotypic noise has very rarely been quantified in natural populations. Results Using automated image analysis, we describe here the phenotypic diversity of S. cerevisiae morphology at single-cell resolution. We profiled hundreds of quantitative traits in more than 1,000 cells of 37 natural strains, which represent various geographical and ecological origins of the species. We observed abundant trait variation between strains, with no correlation with their ecological origin or population history. Phenotypic noise strongly depended on the strain background. Noise variation was largely trait-specific (specific strains showing elevated noise for subset of traits) but also global (a few strains displaying elevated noise for many unrelated traits). Conclusions Our results demonstrate that phenotypic noise does differ quantitatively between natural populations. This supports the possibility that, if noise is adaptive, microevolution may tune it in the wild. This tuning may happen on specific traits or by varying the degree of global phenotypic buffering. PMID:23822767

2013-01-01

15

Quantifying the impact of development on phenotypic variation and evolution.  

PubMed

A primary goal of evolutionary biology is to identify the factors that shape phenotypic evolution. According to the theory of natural selection, phenotypic evolution occurs through the differential survival and reproduction of individuals whose traits are selectively advantageous relative to other individuals in the population. This implies that evolution by natural selection is contingent upon the distribution and magnitude of phenotypic variation among individuals, which are in turn the products of developmental processes. Development therefore has the potential to affect the trajectory and rate of phenotypic evolution. Recent research in diverse systems (e.g., mammalian teeth, cichlid skulls, butterfly wings, and marsupial limbs) supports the hypothesis that development biases phenotypic variation and evolution, but suggests that these biases might be system-specific. PMID:25393554

Sears, Karen E

2014-12-01

16

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.

17

The genetics of phenotypic plasticity. X. Variation versus uncertainty  

PubMed Central

Despite the apparent advantages of adaptive plasticity, it is not common. We examined the effects of variation and uncertainty on selection for plasticity using an individual-based computer simulation model. In the model, the environment consisted of a linear gradient of 50 demes with dispersal occurring either before or after selection. Individuals consisted of multiple loci whose phenotypic expression either are affected (plastic) or are not affected (nonplastic) by the environment. Typically, evolution occurred first as genetic differentiation, which was then replaced by the evolution of adaptive plasticity, opposite to the evolutionary trend that is often assumed. Increasing dispersal rates selected for plasticity, if selection occurred before dispersal. If selection occurred after dispersal, the highest plasticity was at intermediate dispersal rates. Temporal variation in the environment occurring after development, but before selection, favored the evolution of plasticity. With dispersal before selection, such temporal variation resulted in hyperplasticity, with a reaction norm much steeper than the optimum. This effect was enhanced with negative temporal autocorrelation and can be interpreted as representing a form of bet hedging. As the number of nonplastic loci increased, plasticity was disfavored due to an increase in the uncertainty of the genomic environment. This effect was reversed with temporal variation. Thus, variation and uncertainty affect whether or not plasticity is favored with different sources of variation—arising from the amount and timing of dispersal, from temporal variation, and even from the genetic architecture underlying the phenotype—having contrasting, interacting, and at times unexpected effects. PMID:22837824

Scheiner, Samuel M; Holt, Robert D

2012-01-01

18

Evolution of adaptive phenotypic variation patterns by direct selection for evolvability  

PubMed Central

A basic assumption of the Darwinian theory of evolution is that heritable variation arises randomly. In this context, randomness means that mutations arise irrespective of the current adaptive needs imposed by the environment. It is broadly accepted, however, that phenotypic variation is not uniformly distributed among phenotypic traits, some traits tend to covary, while others vary independently, and again others barely vary at all. Furthermore, it is well established that patterns of trait variation differ among species. Specifically, traits that serve different functions tend to be less correlated, as for instance forelimbs and hind limbs in bats and humans, compared with the limbs of quadrupedal mammals. Recently, a novel class of genetic elements has been identified in mouse gene-mapping studies that modify correlations among quantitative traits. These loci are called relationship loci, or relationship Quantitative Trait Loci (rQTL), and affect trait correlations by changing the expression of the existing genetic variation through gene interaction. Here, we present a population genetic model of how natural selection acts on rQTL. Contrary to the usual neo-Darwinian theory, in this model, new heritable phenotypic variation is produced along the selected dimension in response to directional selection. The results predict that selection on rQTL leads to higher correlations among traits that are simultaneously under directional selection. On the other hand, traits that are not simultaneously under directional selection are predicted to evolve lower correlations. These results and the previously demonstrated existence of rQTL variation, show a mechanism by which natural selection can directly enhance the evolvability of complex organisms along lines of adaptive change. PMID:21106581

Pavlicev, Mihaela; Cheverud, James M.; Wagner, Günter P.

2011-01-01

19

Phenotypic Variation in the Plant Pathogenic Bacterium Acidovorax citrulli  

PubMed Central

Acidovorax citrulli causes bacterial fruit blotch (BFB) of cucurbits, a disease that threatens the cucurbit industry worldwide. Despite the economic importance of BFB, little is known about pathogenicity and fitness strategies of the bacterium. We have observed the phenomenon of phenotypic variation in A. citrulli. Here we report the characterization of phenotypic variants (PVs) of two strains, M6 and 7a1, isolated from melon and watermelon, respectively. Phenotypic variation was observed following growth in rich medium, as well as upon isolation of bacteria from inoculated plants or exposure to several stresses, including heat, salt and acidic conditions. When grown on nutrient agar, all PV colonies possessed a translucent appearance, in contrast to parental strain colonies that were opaque. After 72 h, PV colonies were bigger than parental colonies, and had a fuzzy appearance relative to parental strain colonies that are relatively smooth. A. citrulli colonies are generally surrounded by haloes detectable by the naked eye. These haloes are formed by type IV pilus (T4P)-mediated twitching motility that occurs at the edge of the colony. No twitching haloes could be detected around colonies of both M6 and 7a1 PVs, and microscopy observations confirmed that indeed the PVs did not perform twitching motility. In agreement with these results, transmission electron microscopy revealed that M6 and 7a1 PVs do not produce T4P under tested conditions. PVs also differed from their parental strain in swimming motility and biofilm formation, and interestingly, all assessed variants were less virulent than their corresponding parental strains in seed transmission assays. Slight alterations could be detected in some DNA fingerprinting profiles of 7a1 variants relative to the parental strain, while no differences at all could be seen among M6 variants and parental strain, suggesting that, at least in the latter, phenotypic variation is mediated by slight genetic and/or epigenetic alterations. PMID:24023830

Shrestha, Ram Kumar; Rosenberg, Tally; Makarovsky, Daria; Eckshtain-Levi, Noam; Zelinger, Einat; Kopelowitz, June; Sikorski, Johannes; Burdman, Saul

2013-01-01

20

Quantitative phenotyping of bone fracture repair: a review.  

PubMed

Fracture repair is a complex process that involves the interaction of numerous molecular factors, cell lineages and tissue types. These biological processes allow for an impressive feat of engineering: an elastic soft callus is progressively replaced by a more rigid and mineralized callus. During this reparative phase, the healing bone is exposed to a risk of re-fracture. Bone volume and bone quality are the two major factors determining the strength of the callus. Although both factors are important, often only bone volume is analyzed and reported in preclinical studies. Recent developments in techniques for examining bone quality in the callus will enable the rapid and detailed analysis of its material properties and its microstructure. This review aims to give an overview of the methods available for quantitatively phenotyping the bone callus in preclinical studies such as Raman spectroscopy, nanoindentation, scanning acoustic microscopy, in vivo micro-computed tomography (micro-CT) and high-resolution micro-CT. Consolidated and emerging experimental methods are described with a focus on their applicability, and with examples of their utilization. PMID:25120907

Casanova, Michele; Schindeler, Aaron; Little, David; Müller, Ralph; Schneider, Philipp

2014-01-01

21

Genetic Variations Strongly Influence Phenotypic Outcome in the Mouse Retina  

PubMed Central

Variation in genetic background can significantly influence the phenotypic outcome of both disease and non-disease associated traits. Additionally, differences in temporal and strain specific gene expression can also contribute to phenotypes in the mammalian retina. This is the first report of microarray based cross-strain analysis of gene expression in the retina investigating genetic background effects. Microarray analyses were performed on retinas from the following mouse strains: C57BL6/J, AKR/J, CAST/EiJ, and NOD.NON-H2-nb1 at embryonic day 18.5 (E18.5) and postnatal day 30.5 (P30.5). Over 3000 differentially expressed genes were identified between strains and developmental stages. Differential gene expression was confirmed by qRT-PCR, Western blot, and immunohistochemistry. Three major gene networks were identified that function to regulate retinal or photoreceptor development, visual perception, cellular transport, and signal transduction. Many of the genes in these networks are implicated in retinal diseases such as bradyopsia, night-blindness, and cone-rod dystrophy. Our analysis revealed strain specific variations in cone photoreceptor cell patterning and retinal function. This study highlights the substantial impact of genetic background on both development and function of the retina and the level of gene expression differences tolerated for normal retinal function. These strain specific genetic variations may also be present in other tissues. In addition, this study will provide valuable insight for the development of more accurate models for human retinal diseases. PMID:21779340

Jelcick, Austin S.; Yuan, Yang; Leehy, Barrett D.; Cox, Lakeisha C.; Silveira, Alexandra C.; Qiu, Fang; Schenk, Sarah; Sachs, Andrew J.; Morrison, Margaux A.; Nystuen, Arne M.; DeAngelis, Margaret M.; Haider, Neena B.

2011-01-01

22

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

23

Pregnancy-induced metabolic phenotype variations in maternal plasma.  

PubMed

Metabolic variations occur during normal pregnancy to provide the growing fetus with a supply of nutrients required for its development and to ensure the health of the woman during gestation. Mass spectrometry-based metabolomics was employed to study the metabolic phenotype variations in the maternal plasma that are induced by pregnancy in each of its three trimesters. Nontargeted metabolomics analysis showed that pregnancy significantly altered the profile of metabolites in maternal plasma. The levels of six metabolites were found to change significantly throughout pregnancy, with related metabolic pathway variations observed in biopterin metabolism, phospholipid metabolism, amino acid derivatives, and fatty acid oxidation. In particular, there was a pronounced elevation of dihydrobiopterin (BH?), a compound produced in the synthesis of dopa, dopamine, norepinephrine, and epinephrine, in the second trimester, whereas it was markedly decreased in the third trimester. The turnover of BH? and tryptophan catabolites indicated that the fluctuations of neurotransmitters throughout pregnancy might reveal the metabolic adaption in the maternal body for the growth of the fetus. Furthermore, 11 lipid classes and 41 carnitine species were also determined and this showed variations in the presence of long-chain acylcarnitines and lysophospholipids in later pregnancy, suggesting changes of acylcarnitines and lysophospholipids to meet the energy demands in pregnant women. To our knowledge, this work is the first report of dynamic metabolic signatures and proposed related metabolic pathways in the maternal plasma for normal pregnancies and provided the basis for time-dependent metabolic trajectory against which disease-related disorders may be contrasted. PMID:24450375

Luan, Hemi; Meng, Nan; Liu, Ping; Feng, Qiang; Lin, Shuhai; Fu, Jin; Davidson, Robert; Chen, Xiaomin; Rao, Weiqiao; Chen, Fang; Jiang, Hui; Xu, Xun; Cai, Zongwei; Wang, Jun

2014-03-01

24

Phenotypic and genotypic variations within a single bacteriophage species  

PubMed Central

Background Although horizontal gene transfer plays a pivotal role in bacteriophage evolution, many lytic phage genomes are clearly shaped by vertical evolution. We investigated the influence of minor genomic deletions and insertions on various phage-related phenotypic and serological properties. Findings We collected ten different isolates of Pseudomonas aeruginosa bacteriophage ?KMV. All sequenced genomes (42-43 kb, long direct terminal repeats) are nearly identical, which intuitively implied strongly similar infections cycles. However, their latent periods vary between 21 and 28 minutes and they are able to lyse between 5 and 58% of a collection of 107 clinical P. aeruginosa strains. We also noted that phages with identical tail structures displayed profound differences in host spectra. Moreover, point mutations in tail and spike proteins were sufficient to evade neutralization by two phage-specific antisera, isolated from rabbits. Conclusion Although all analyzed phages are 83-97% identical at the genome level, they display a surprisingly large variation in various phenotypic properties. The small overlap in host spectrum and their ability to readily escape immune defences against a nearly identical phage are promising elements for the application of these phages in phage therapy. PMID:21429206

2011-01-01

25

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

26

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

27

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

28

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

29

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

30

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

31

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

32

Adrenocortical responses in zebra finches ( Taeniopygia guttata): Individual variation, repeatability, and relationship to phenotypic quality  

Microsoft Academic Search

Although individual variation is a key requirement for natural selection, little is known about the magnitude and patterns of individual variation in endocrine systems or the functional significance of that variation. Here we describe (1) the extent and repeatability of inter-individual variation in adrenocortical responses and (2) its relationship to sex-specific phenotypic quality, such as song duration and frequency and

Haruka Wada; Katrina G. Salvante; Christine Stables; Emily Wagner; Tony D. Williams; Creagh W. Breuner

2008-01-01

33

Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data.  

PubMed

Evolutionary biologists have long sought a way to determine whether a phenotypic difference between two taxa was caused by natural selection or random genetic drift. Here I argue that data from quantitative trait locus (QTL) analyses can be used to test the null hypothesis of neutral phenotypic evolution. I propose a sign test that compares the observed number of plus and minus alleles in the "high line" with that expected under neutrality, conditioning on the known phenotypic difference between the taxa. Rejection of the null hypothesis implies a role for directional natural selection. This test is applicable to any character in any organism in which QTL analysis can be performed. PMID:9691061

Orr, H A

1998-08-01

34

Quantitative Genetic Variation in Daphnia: Temporal Changes in Genetic Architecture  

E-print Network

Quantitative Genetic Variation in Daphnia: Temporal Changes in Genetic Architecture Michael E IN DAPHNIA: TEMPORAL CHANGES IN GENETIC ARCHITECTURE MICHAELE. PFRENDER~ LYNCHAND MICHAEL Ecology-pond-dwelling population of Daphnia pulex over a full season to examine the role of nonadditive genetic variation

Lynch, Michael

35

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

36

Influence of micropropagation through somatic embryogenesis on somaclonal variation in coffee (Coffea arabica) : assessment of variations at the phenotypical, cytological, genetic and epigenetic level.  

E-print Network

??Influence of micropropagation through somatic embryogenesis on somaclonal variation in coffee (Coffea arabica): assessment of variations at the phenotypical, cytological, genetic and epigenetic level Somaclonal… (more)

Bobadilla Landey, Roberto

2013-01-01

37

Alzheimer's Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans  

E-print Network

Alzheimer's Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core C. Greenj , Lars Bertramk , Clifford R. Jack, Jr.l , Michael W. Weinerm,n,o,p ; and the Alzheimer of Veterans Affairs Medical Center, San Francisco, CA, USA Abstract The role of the Alzheimer's Disease

Thompson, Paul

38

Quantitative molecular phenotyping of gill remodeling in a cichlid fish responding to salinity stress.  

PubMed

A two-tiered label-free quantitative (LFQ) proteomics workflow was used to elucidate how salinity affects the molecular phenotype, i.e. proteome, of gills from a cichlid fish, the euryhaline tilapia (Oreochromis mossambicus). The workflow consists of initial global profiling of relative tryptic peptide abundances in treated versus control samples followed by targeted identification (by MS/MS) and quantitation (by chromatographic peak area integration) of validated peptides for each protein of interest. Fresh water acclimated tilapia were independently exposed in separate experiments to acute short-term (34 ppt) and gradual long-term (70 ppt, 90 ppt) salinity stress followed by molecular phenotyping of the gill proteome. The severity of salinity stress can be deduced with high technical reproducibility from the initial global label-free quantitative profiling step alone at both peptide and protein levels. However, an accurate regulation ratio can only be determined by targeted label-free quantitative profiling because not all peptides used for protein identification are also valid for quantitation. Of the three salinity challenges, gradual acclimation to 90 ppt has the most pronounced effect on gill molecular phenotype. Known salinity effects on tilapia gills, including an increase in the size and number of mitochondria-rich ionocytes, activities of specific ion transporters, and induction of specific molecular chaperones are reflected in the regulation of abundances of the corresponding proteins. Moreover, specific protein isoforms that are responsive to environmental salinity change are resolved and it is revealed that salinity effects on the mitochondrial proteome are nonuniform. Furthermore, protein NDRG1 has been identified as a novel key component of molecular phenotype restructuring during salinity-induced gill remodeling. In conclusion, besides confirming known effects of salinity on gills of euryhaline fish, molecular phenotyping reveals novel insight into proteome changes that underlie the remodeling of tilapia gill epithelium in response to environmental salinity change. PMID:24065692

Kültz, Dietmar; Li, Johnathon; Gardell, Alison; Sacchi, Romina

2013-12-01

39

Resource variation and the evolution of phenotypic plasticity in fishes  

E-print Network

variation. The first empirical study addresses trophic plasticity, population divergence, and the effect of fine-scale environmental variation in western mosquitofish (Gambusia affinis). Offspring from two populations were fed either attached or unattached...

Ruehl, Clifton Benjamin

2004-09-30

40

The Evolution of Continuous Variation. III. Joint Transmission of Genotype, Phenotype and Environment  

PubMed Central

Evolutionary models of continuous traits are developed. The models are based on the ideas that: (1) the phenotype is the result of the interaction between genotype and environment; (2) the phenotype is the object of natural selection; (3) not only the genotype but also environmental variables and even phenotypes can be directly transmitted. The phenotype of an offspring at birth is a linear combination of its genotypic value, the phenotypic values of its parents, and their environmental values, all measured on the phenotypic scale. The genetic effects are additive polygenic, and a mutation contribution to the within family variance is admitted.—The values of the offspring phenotype and environment before selection are each linear combinations of these values at birth, the coefficients defining what we call "development." Selection is mostly stabilizing of the Gaussian type, but directional selection is introduced using a Gaussian fitness function with a large variance and a mean far from the current population.—Assortative mating for both phenotype and environment are considered. The analysis in all cases is made by iteration of the means, variances and covariances of the trivariate random variable (genotype, phenotype, environment) whose changes over time completely specify the evolution. In most cases numerical methods are used. The problems of estimating the relative roles of each of the variates in the parents in determining the variates in the offspring are discussed. The major results concern the relative magnitudes of the variances and correlations of the three variates, genotype, phenotype and environment, in a variety of selective, developmental and assorting situations with complex transmission in which G-(genetic), F-(phenotypic), E-(environment) inheritance mechanisms operate jointly. The transmission rules and development patterns (i.e., interactions between phenotype and environment during development) are of major importance in determining qualitative features of the equilibrium distribution. PMID:17248869

Cavalli-Sforza, L. L.; Feldman, M. W.

1978-01-01

41

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

42

Molecular ABO phenotyping in cynomolgus macaques using real-time quantitative PCR.  

PubMed

Macaques are commonly used in biomedical research as animal models of human disease. The ABO phenotype of donors and recipients plays an important role in the success of transplantation and stem cell research of both human and macaque tissue. Traditional serological methods for ABO phenotyping can be time consuming, provide ambiguous results and/or require tissue that is unavailable or unsuitable. We developed a novel method to detect the A, B, and AB phenotypes of macaques using real-time quantitative polymerase chain reaction. This method enables the simple and rapid screening of these phenotypes in macaques without the need for fresh blood or saliva. This study reports the distribution of the A, B, and AB phenotypes of captive cynomolgus macaques that, while regionally variable, closely resembles that of rhesus macaques. Blood group B, as in rhesus macaques, predominates in cynomolgus macaques and its frequency distribution leads to a probability of major incompatibility of 41%. No silencing mutations have been identified in exon 6 or 7 in macaques that could be responsible for the O phenotype, that, although rare, have been reported. The excess homozygosity of rhesus and cynomolgus macaque genotypes in this study, that assumes the absence of the O allele, suggests the possibility of some mechanism preventing the expression of the A and B transferases. PMID:22861170

Premasuthan, A; Ng, J; Kanthaswamy, S; Trask, J S; Houghton, P; Farkas, T; Sestak, K; Smith, D G

2012-10-01

43

MOLECULAR ABO PHENOTYPING IN CYNOMOLGUS MACAQUES USING REAL TIME QUANTITATIVE PCR (QPCR)  

PubMed Central

Macaques are commonly used in biomedical research as animal models of human disease. The ABO phenotype of donors and recipients plays an important role in the success of transplantation and stem cell research of both human and macaque tissue. Traditional serological methods for ABO phenotyping can be time consuming, provide ambiguous results and/or require tissue that is unavailable or unsuitable. We developed a novel method to detect the A, B, and AB phenotypes of macaques using real-time quantitative PCR. This method enables the simple and rapid screening of these phenotypes in macaques without the need for fresh blood or saliva. This study reports the distribution of the A, B, and AB phenotypes of captive cynomolgus macaques that, while regionally variable, closely resembles that of rhesus macaques. Blood group B, as in rhesus macaques, predominates in cynomolgus macaques and its frequency distribution leads to a probability of major incompatibility of 41%. No silencing mutations have been identified in exons 6 or 7 in macaques that could be responsible for the O phenotype, that, although rare, have been reported. The excess homozygosity of rhesus and cynomolgus macaque genotypes in the present study, that assumes the absence of the O allele, suggests the possibility of some mechanism preventing the expression of the A and B transferases. PMID:22861170

Premasuthan, Amritha; Ng, Jillian; Kanthaswamy, Sreetharan; Trask, Jessica Satkoski; Houghton, Paul; Farkas, Tibor; Sestak, Karol; Smith, David Glenn

2012-01-01

44

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

45

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

46

Multiple-trait quantitative trait locus mapping with incomplete phenotypic data  

PubMed Central

Background Conventional multiple-trait quantitative trait locus (QTL) mapping methods must discard cases (individuals) with incomplete phenotypic data, thereby sacrificing other phenotypic and genotypic information contained in the discarded cases. Under standard assumptions about the missing-data mechanism, it is possible to exploit these cases. Results We present an expectation-maximization (EM) algorithm, derived for recombinant inbred and F2 genetic models but extensible to any mating design, that supports conventional hypothesis tests for QTL main effect, pleiotropy, and QTL-by-environment interaction in multiple-trait analyses with missing phenotypic data. We evaluate its performance by simulations and illustrate with a real-data example. Conclusion The EM method affords improved QTL detection power and precision of QTL location and effect estimation in comparison with case deletion or imputation methods. It may be incorporated into any least-squares or likelihood-maximization QTL-mapping approach. PMID:19061502

Guo, Zhigang; Nelson, James C

2008-01-01

47

Variation in phenotype and proteins in plants regenerated from cell suspensions of potato cv. BP1  

Microsoft Academic Search

Phenotypic variation, SDS-PAGE and protein-DNA binding were used to determine variation during the in vitro phase of potato plantlets derived from callus and cell suspensions. Of the 27 plantlets assessed. 3 displayed a low or abnormal growth, 16 normal growth which correlated well with the original explant and 9 showed strong or vigorous growth. Differences were not observed in the

J. M. Lindeque; Ader Mescht; M. M. Slabbert; G. Henn

1991-01-01

48

Developmental contributions to phenotypic variation in functional leaf traits within quaking aspen clones.  

PubMed

Phenotypic variation in plant traits is strongly influenced by genetic and environmental factors. Over the life span of trees, developmental factors may also strongly influence leaf phenotypes. The objective of this study was to fill gaps in our understanding of developmental influences on patterns of phenotypic trait variation among different-aged ramets within quaking aspen (Populus tremuloides Michx.) clones. We hypothesized that phenotypic variation in leaf functional traits is strongly influenced by developmental cues as trees age. We surveyed eight aspen clones, each with eight distinct age classes ranging from 1 to 160 years in age, and selected three ramets per age class for sample collection. Leaf traits measured included photosynthesis, stomatal conductance, water use efficiency, specific leaf area, and concentrations of N, phosphorus, sucrose, starch, condensed tannins and phenolic glycosides. Using regression analysis, we examined the relationships between ramet age and expression of leaf functional traits. The data showed significant correlations between ramet age and 10 of the 12 phenotypic traits measured. Eight of the phenotypic traits demonstrated a non-linear relationship in which large changes in phenotype occurred in the early stages of ramet development and stabilized thereafter. Water relations, nutrient concentration, leaf gas exchange and phenolic glycosides tended to decrease from early to late development, whereas sucrose, condensed tannin concentrations and water use efficiency increased with ramet age. We hypothesize that ontogenetically derived phenotypic variation leads to fitness differentials among different-aged ramets, which may have important implications for clone fitness. Age-related increases in phenotypic diversity may partially underlie aspen's ability to tolerate the large environmental gradients that span its broad geographical range. PMID:21389003

Smith, Eric A; Collette, Sean B; Boynton, Thomas A; Lillrose, Tiffany; Stevens, Mikel R; Bekker, Matthew F; Eggett, Dennis; St Clair, Samuel B

2011-01-01

49

Phenotypic and genotypic variations within a single bacteriophage species  

Microsoft Academic Search

Background  Although horizontal gene transfer plays a pivotal role in bacteriophage evolution, many lytic phage genomes are clearly shaped\\u000a by vertical evolution. We investigated the influence of minor genomic deletions and insertions on various phage-related phenotypic\\u000a and serological properties.\\u000a \\u000a \\u000a \\u000a \\u000a Findings  We collected ten different isolates of Pseudomonas aeruginosa bacteriophage ?KMV. All sequenced genomes (42-43 kb, long direct terminal repeats) are nearly identical,

Pieter-Jan Ceyssens; Thea Glonti; ndrew M Kropinski; Rob Lavigne; Nina Chanishvili; Leonid Kulakov; Nino Lashkhi; Marina Tediashvili; Maya Merabishvili

2011-01-01

50

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

51

Mechanisms for phenotypic variation in Lesch-Nyhan disease and its variants.  

PubMed

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; Jinnah, H A

2011-01-01

52

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

53

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

54

Genotypic variation among different phenotypes within aphid clones.  

PubMed Central

Most aphid species Hemiptera: Aphididae are parthenogenetic between periods of sexual reproduction. They are also highly polyphenic, with different adult morphs occurring in the life cycle, piz. winged, wingless, asexual and sexual. It is assumed that aphids born in a parthenogenetic clonal lineage are genetically identical regardless of the final adult form with the exception of sexual forms). Using the randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) we have found that different asexual adult phenotypes winged and wingless of some clones of two cereal aphid species (the grain aphid, Sitobion avenae (F.) and the bird-cherry aphid. Rhopalosiphum padi (L.) may be distinguished by the presence or absence of one or more RAPD-PCR bands. In three of nine clones examined, such differences were found, and Southern blotting and hybridization of the discriminating bands confirmed these to be of aphid origin, rather than due to endosymbiotic bacteria or contaminating fungi. The main 248 and 296 bp bands, in the two species respectively, were sequenced and found to be A/T rich. The smaller band showed 57% homology with white striated muscle over a stretch of 90 bp. Genomic DNA treated with dimethyl sulphoxide to remove secondary structures still showed differences in RAPD-PCR profiles between winged and wingless morphs within the unusual clones. This discovery may be widespread and therefore it is important to understand the phenomenon in relation to clonal organisms. PMID:9178543

Lushai, G; Loxdale, H D; Brookes, C P; von Mende, N; Harrington, R; Hardie, J

1997-01-01

55

Body Mass Index as a Phenotypic Expression of Adiposity: Quantitative Contribution of Muscularity in a Population-Based Sample  

PubMed Central

Objective Although widely applied as a phenotypic expression of adiposity in population and gene-search studies, body mass index (BMI) is also acknowledged to reflect muscularity even though relevant studies directly measuring skeletal muscle (SM) mass are lacking. The current study aimed to fill this important gap by applying advanced imaging methods to test the hypothesis that, after controlling first for adiposity, SM mass is also a significant determinant of BMI in a population-based sample. Design Whole-body magnetic resonance imaging scans were completed in CARDIA Study subjects aged 33-45 years. Physical activity (PA) levels, alcohol intake, and adequacy of food intake were assessed by standardized questionnaires. Subjects 58 African-American (AA) and 78 Caucasian (C) men; 63 AA and 64 C women. Measurements Whole-body AT and SM volumes. Results AT was significantly predicted by not only BMI, but PA and alcohol intake with total model R2s of 0.68 (p<0.0001) for men and 0.89 (p<0.0001) for women. Men had more SM than AT at all levels of BMI while SM predominated in women at lower BMIs (C <26 kg/m2; AA <28 kg/m2). Both AT and SM contributed a similar proportion of between-subject variation in BMI in men. In contrast, AT contributed ~30% more than SM to the variation in BMI in women. Developed allometric models indicated SM associations with AT, PA, and race after adjusting for height. There was little association of age, lifestyle factors, or race with BMI after controlling for both AT and SM. Conclusion Variation in muscularity provides a mechanistic basis for the previously observed non-specificity of BMI as a phenotypic expression of adiposity. These quantitative observations have important implications when choosing adiposity measures in population and gene-search studies. PMID:19773739

Heymsfield, Steven B.; Scherzer, Rebecca; Pietrobelli, Angelo; Lewis, Cora E.; Grunfeld, Carl

2010-01-01

56

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

57

Selection on quantitative colour variation in Centaurea cyanus: the role of the pollinator's visual system.  

PubMed

Even though the importance of selection for trait evolution is well established, we still lack a functional understanding of the mechanisms underlying phenotypic selection. Because animals necessarily use their sensory system to perceive phenotypic traits, the model of sensory bias assumes that sensory systems are the main determinant of signal evolution. Yet, it has remained poorly known how sensory systems contribute to shaping the fitness surface of selected individuals. In a greenhouse experiment, we quantified the strength and direction of selection on floral coloration in a population of cornflowers exposed to bumblebees as unique pollinators during 4 days. We detected significant selection on the chromatic and achromatic (brightness) components of floral coloration. We then studied whether these patterns of selection are explicable by accounting for the visual system of the pollinators. Using data on bumblebee colour vision, we first showed that bumblebees should discriminate among quantitative colour variants. The observed selection was then compared to the selection predicted by psychophysical models of bumblebee colour vision. The achromatic but not the chromatic channel of the bumblebee's visual system could explain the observed pattern of selection. These results highlight that (i) pollinators can select quantitative variation in floral coloration and could thus account for a gradual evolution of flower coloration, and (ii) stimulation of the visual system represents, at least partly, a functional mechanism potentially explaining pollinators' selection on floral colour variants. PMID:24070120

Renoult, J P; Thomann, M; Schaefer, H M; Cheptou, P-O

2013-11-01

58

Variation of phenotype, ploidy level, and organogenic potential of in vitro regenerated polyploids of Pyrus communis  

Technology Transfer Automated Retrieval System (TEKTRAN)

A wide range of phenotypic variation was observed among neopolyploids obtained from diploid pear cultivar ‘Fertility’ by in vitro colchicine treatment. The variant plantlets had alterations in leaf and stem characteristics, and in growth. Neopolyploids had a significantly decreased ratio of leaf l...

59

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 ...

60

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

61

Classification of Human Chromosome 21 Gene-Expression Variations in Down Syndrome: Impact on Disease Phenotypes  

Microsoft Academic Search

Down syndrome caused by chromosome 21 trisomy is the most common genetic cause of mental retardation in humans. Disruption of the phenotype is thought to be the result of gene-dosage imbalance. Variations in chromosome 21 gene expression in Down syndrome were analyzed in lymphoblastoid cells derived from patients and control individuals. Of the 359 genes and predictions displayed on a

E. Aït Yahya-Graison; J. Aubert; L. Dauphinot; I. Rivals; M. Prieur; G. Golfier; J. Rossier; L. Personnaz; N. Créau; H. Bléhaut; S. Robin; J. M. Delabar; M.-C. Potier

2007-01-01

62

Patterns of phenotypic and genetic variation in three species of endemic Mesoamerican Peromyscus (Rodentia: Cricetidae)  

E-print Network

Patterns of phenotypic and genetic variation in three species of endemic Mesoamerican Peromyscus) * Correspondent: nicte.ordonez-garza@ttu.edu Three species of Mexican deer mice of the Peromyscus mexicanus-A-167.1. Key words: cytochrome b, morphometrics, Peromyscus, Peromyscus mexicanus species group E 2010

Strauss, Richard E.

63

Temperature-dependent phenotypic variation of Campylobacter jejuni lipooligosaccharides  

PubMed Central

Background Campylobacter jejuni is a major bacterial cause of food-borne enteritis, and its lipooligosaccharide (LOS) plays an initiating role in the development of the autoimmune neuropathy, Guillain-Barré syndrome, by induction of anti-neural cross-reactive antibodies through ganglioside molecular mimicry. Results Herein we describe the existence and heterogeneity of multiple LOS forms in C. jejuni strains of human and chicken origin grown at 37°C and 42°C, respectively, as determined on sodium dodecyl sulphate-polyacrylamide electrophoresis gels with carbohydrate-specific silver staining and blotting with anti-ganglioside ligands, and confirmed by nuclear magnetic resonance (NMR) spectroscopy. The C. jejuni NCTC 11168 original isolate (11168-O) was compared to its genome-sequenced variant (11168-GS), and both were found to have a lower-Mr LOS form, which was different in size and structure to the previously characterized higher-Mr form bearing GM1 mimicry. The lower-Mr form production was found to be dependent on the growth temperature as the production of this form increased from ~5%, observed at 37°C to ~35% at 42°C. The structure of the lower-Mr form contained a ?-D-Gal-(1?3)-?-D-GalNAc disaccharide moiety which is consistent with the termini of the GM1, asialo-GM1, GD1, GT1 and GQ1 gangliosides, however, it did not display GM1 mimicry as assessed in blotting studies but was shown in NMR to resemble asialo-GM1. The production of multiple LOS forms and lack of GM1 mimicry was not a result of phase variation in the genes tested of NCTC 11168 and was also observed in most of the human and chicken isolates of C. jejuni tested. Conclusion The presence of differing amounts of LOS forms at 37 and 42°C, and the variety of forms observed in different strains, indicate that LOS form variation may play a role in an adaptive mechanism or a stress response of the bacterium during the colonization of different hosts. PMID:21118497

2010-01-01

64

Interactive Effects of Geography and Host Plant Species on Genetic and Phenotypic Variation of Cotton Fleahopper Populations  

E-print Network

in the southern United States. No studies have addressed intraspecific genetic and phenotypic variation of this insect pest at a large geographic scale. I examined genetic variation among cotton fleahopper populations associated with cotton in different...

Barman, Apurba

2012-02-14

65

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

66

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

67

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

68

Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach  

PubMed Central

Human cancers exhibit strong phenotypic differences that can be visualized noninvasively by medical imaging. Radiomics refers to the comprehensive quantification of tumour phenotypes by applying a large number of quantitative image features. Here we present a radiomic analysis of 440 features quantifying tumour image intensity, shape and texture, which are extracted from computed tomography data of 1,019 patients with lung or head-and-neck cancer. We find that a large number of radiomic features have prognostic power in independent data sets of lung and head-and-neck cancer patients, many of which were not identified as significant before. Radiogenomics analysis reveals that a prognostic radiomic signature, capturing intratumour heterogeneity, is associated with underlying gene-expression patterns. These data suggest that radiomics identifies a general prognostic phenotype existing in both lung and head-and-neck cancer. This may have a clinical impact as imaging is routinely used in clinical practice, providing an unprecedented opportunity to improve decision-support in cancer treatment at low cost. PMID:24892406

Aerts, Hugo J. W. L.; Velazquez, Emmanuel Rios; Leijenaar, Ralph T. H.; Parmar, Chintan; Grossmann, Patrick; Cavalho, Sara; Bussink, Johan; Monshouwer, René; Haibe-Kains, Benjamin; Rietveld, Derek; Hoebers, Frank; Rietbergen, Michelle M.; Leemans, C. René; Dekker, Andre; Quackenbush, John; Gillies, Robert J.; Lambin, Philippe

2014-01-01

69

Contrasting patterns of divergence in quantitative traits and neutral DNA markers: analysis of clinal variation.  

PubMed

Clinal variation in quantitative traits is often attributed to the effects of spatially varying selection. However, identical patterns can be produced by the interplay between purely stochastic processes (i.e. drift in combination with spatially restricted gene flow). One means of distinguishing between adaptive and nonadaptive causes of geographical variation is to compare relative levels of between-population divergence in quantitative traits and neutral DNA markers. Such comparisons can be used to test whether levels of trait divergence attributable to additive genetic effects (as measured by QST) exceed null expectations based on the level of divergence at neutral marker loci (as measured by FST). The purpose of this study was to use an approach based on 'QST vs. FST' contrasts to test for evidence of diversifying selection on body size of an Indian fruit bat, Cynopterus sphinx (Chiroptera: Pteropodidae). Specifically, relative levels of between-population divergence in body size and microsatellite DNA markers were compared to assess whether the observed pattern of clinal size variation could be explained by a neutral model of isolation by distance. QST for body size was calculated using unbiased estimators of within- and between-population variance of principal component scores. The association between body size variation and geographical/environmental distance was tested using pairwise and partial matrix correspondence tests (MCTs). Independent variables (representing causal hypotheses) were constructed as between-locality distance matrices. The effects of neutral genetic divergence were assessed by including a matrix of pairwise FST as an independent variable. Partial MCTs revealed highly significant associations between phenotypic divergence (QST) and both geographical and environmental distance, even when the effects of neutral genetic divergence (FST) were partialled out. Results of the tests confirmed that migration-drift equilibrium is not a sufficient explanation for the latitudinal pattern of clinal size variation in C. sphinx. The geographical patterning of pairwise QST is most likely attributable to spatially varying selection and/or the direct influence of latitudinally ordered environmental effects. PMID:12453238

Storz, Jay F

2002-12-01

70

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

71

Stressful environments induce novel phenotypic variation: hierarchical reaction norms for sperm performance of a pervasive invader  

PubMed Central

Genetic variation for phenotypic plasticity is ubiquitous and important. However, the scale of such variation including the relative variability present in reaction norms among different hierarchies of biological organization (e.g., individuals, populations, and closely related species) is unknown. Complicating interpretation is a trade-off in environmental scale. As plasticity can only be inferred over the range of environments tested, experiments focusing on fine tuned responses to normal or benign conditions may miss cryptic phenotypic variation expressed under novel or stressful environments. Here, we sought to discern the presence and shape of plasticity in the performance of brown trout sperm as a function of optimal to extremely stressful river pH, and demarcate if the reaction norm varies among genotypes. Our overarching goal was to determine if deteriorating environmental quality increases expressed variation among individuals. A more applied aim was to ascertain whether maintaining sperm performance over a wide pH range could help explain how brown trout are able to invade diverse river systems when transplanted outside of their native range. Individuals differed in their reaction norms of phenotypic expression of an important trait in response to environmental change. Cryptic variation was revealed under stressful conditions, evidenced through increasing among-individual variability. Importantly, data on population averages masked this variability in plasticity. In addition, canalized reaction norms in sperm swimming velocities of many individuals over a very large range in water chemistry may help explain why brown trout are able to colonize a wide variety of habitats. PMID:23145341

Purchase, Craig F; Moreau, Darek T R

2012-01-01

72

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

73

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

74

Divergence in a master variator generates distinct phenotypes and transcriptional responses  

PubMed Central

Genetic basis of phenotypic differences in individuals is an important area in biology and personalized medicine. Analysis of divergent Saccharomyces cerevisiae strains grown under different conditions revealed extensive variation in response to both drugs (e.g., 4-nitroquinoline 1-oxide [4NQO]) and different carbon sources. Differences in 4NQO resistance were due to amino acid variation in the transcription factor Yrr1. Yrr1YJM789 conferred 4NQO resistance but caused slower growth on glycerol, and vice versa with Yrr1S96, indicating that alleles of Yrr1 confer distinct phenotypes. The binding targets of Yrr1 alleles from diverse yeast strains varied considerably among different strains grown under the same conditions as well as for the same strain under different conditions, indicating that distinct molecular programs are conferred by the different Yrr1 alleles. Our results demonstrate that genetic variations in one important control gene (YRR1), lead to distinct regulatory programs and phenotypes in individuals. We term these polymorphic control genes “master variators.” PMID:24532717

Gallagher, Jennifer E.G.; Zheng, Wei; Rong, Xiaoqing; Miranda, Noraliz; Lin, Zhixiang; Dunn, Barbara; Zhao, Hongyu; Snyder, Michael P.

2014-01-01

75

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

76

MSH1-induced non-genetic variation provides a source of phenotypic diversity in Sorghum bicolor.  

PubMed

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

de la Rosa Santamaria, Roberto; Shao, Mon-Ray; Wang, Guomei; Nino-Liu, David O; Kundariya, Hardik; Wamboldt, Yashitola; Dweikat, Ismail; Mackenzie, Sally A

2014-01-01

77

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

78

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

79

Adaptive basis of geographic variation: genetic, phenotypic and environmental differences among beach mouse populations  

PubMed Central

A major goal in evolutionary biology is to understand how and why populations differentiate, both genetically and phenotypically, as they invade a novel habitat. A classical example of adaptation is the pale colour of beach mice, relative to their dark mainland ancestors, which colonized the isolated sandy dunes and barrier islands on Florida's Gulf Coast. However, much less is known about differentiation among the Gulf Coast beach mice, which comprise five subspecies linearly arrayed on Florida's shoreline. Here, we test the role of selection in maintaining variation among these beach mouse subspecies at multiple levels—phenotype, genotype and the environments they inhabit. While all beach subspecies have light pelage, they differ significantly in colour pattern. These subspecies are also genetically distinct: pair-wise Fst-values range from 0.23 to 0.63 and levels of gene flow are low. However, we did not find a correlation between phenotypic and genetic distance. Instead, we find a significant association between the average ‘lightness’ of each subspecies and the brightness of the substrate it inhabits: the two most genetically divergent subspecies occupy the most similar habitats and have converged on phenotype, whereas the most genetically similar subspecies occupy the most different environments and have divergent phenotypes. Moreover, allelic variation at the pigmentation gene, Mc1r, is statistically correlated with these colour differences but not with variation at other genetic loci. Together, these results suggest that natural selection for camouflage—via changes in Mc1r allele frequency—contributes to pigment differentiation among beach mouse subspecies. PMID:19656790

Mullen, Lynne M.; Vignieri, Sacha N.; Gore, Jeffery A.; Hoekstra, Hopi E.

2009-01-01

80

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

81

Regional quantitative histological variations in human oral mucosa.  

PubMed

Oral mucosa demonstrates regional variations that reflect contact with food during mastication. Though known qualitatively, our aim was to quantitatively assess regions to establish a measurable baseline from which one could compare in pathological and comparative studies, in which the abrasiveness of diets may differ. We assessed variations in the epithelial-connective tissue junction (rete ridges counts), collagen organization within the lamina propria, and elastin composition of the lamina propria of 15 regions of the labial (buccal) gingiva, lingual gingiva, vestibule, and palate. All characteristics varied more between regions within the same individual than between individuals. Lingual gingiva had high rete ridges counts, high level of collagen organization, and moderate elastin composition compared to other regions. The labial gingiva had few rete ridges, high collagen organization, and low elastin. The vestibule had the fewest average of rete ridges, least organized collagen, and high elastin. The hard palate had the highest average of rete ridges, high collagen organization, and the lowest elastin content. The soft palate conversely had the smallest average of rete ridges, moderate collagen organization, and the highest elastin composition. Our results indicate that comparison of these quantitative histological differences is warranted only for collagen organization and elastin composition. Differences in rete ridges counts were not statistically significant. Most histological characteristics observed were not significantly different between dentulous and edentulous cadavers, and the group containing all individuals. An exception was the level of collagen fiber organization within the lamina propria, which was higher in most regions when teeth were present. Anat Rec, 298:562-578, 2015. © 2014 Wiley Periodicals, Inc. PMID:25402000

Ciano, Joseph; Beatty, Brian Lee

2015-03-01

82

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

83

Ploidy-regulated variation in biofilm-related phenotypes in natural isolates of Saccharomyces cerevisiae.  

PubMed

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

2014-09-01

84

Diurnal variation in the quantitative EEG in healthy adult volunteers  

PubMed Central

Aims To define the change in power in standard waveband frequencies of quantitative cortical electroencephalogram (EEG) data over a 24 h period, in a drug free representative healthy volunteer population. Methods This was an open, non randomised study in which 18 volunteers (9 male and 9 female) were studied on 1 study day, over a 24 h period. Volunteers had a cortical EEG recording taken at 0, 2, 4, 6, 8, 10, 12, 16 and 24 h. Each recording lasted for 6 min (3 min eyes open, 3 min eyes closed). All EEG recordings were taken in a quietened ward environment with the curtains drawn round the bed and the volunteer supine. During the 3 min eyes open, volunteers were asked to look at a red circle on a screen at the foot of the bed, and refrain from talking. Results Plots produced of geometric mean power by time of the standard wave band frequencies gave some indication of a circadian rhythm over the 24 h period for ? (4.75–6.75 Hz), ?1 (7.0–9.5 Hz) and ?1 (12.75–18.50 Hz) wavebands. Mixed models were fitted to both the eyes open and eyes closed data which confirmed a change in mean waveband power with time with statistical significance at the conventional 5% level (P < 0.05). Conclusions These data indicate the presence of a diurnal variation in the cortical quantitative EEG. They support the use of a placebo control group when designing clinical trials which utilize quantitative EEG to screen for central nervous system (CNS) activity of pharmaceutical agents, to control for the confounding variable of time of day at which the EEG recordings were made. PMID:10886113

Cummings, L; Dane, A; Rhodes, J; Lynch, P; Hughes, A M

2000-01-01

85

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

86

Adiponectin in renal disease: Relationship to phenotype and genetic variation in the gene encoding adiponectin  

Microsoft Academic Search

Adiponectin in renal disease: Relationship to phenotype and genetic variation in the gene encoding adiponectin.BackgroundThe prevalence of cardiovascular disease (CVD) and inflammation is high in patients with end-stage renal disease (ESRD). Adiponectin is an adipocytokine that may have significant anti-inflammatory and anti-atherosclerotic effects. Low adiponectin levels have previously been found in patients with high risk for CVD.MethodsIn a cohort of

PETER STENVINKEL; ALICIA MARCHLEWSKA; ROBERTO PECOITS-FILHO; OLOF HEIMBÜRGER; ZHENGZHONG ZHANG; CATHERINE HOFF; CLIFF HOLMES; JONAS AXELSSON; SIVONNE ARVIDSSON; MARTIN SCHALLING; PETER BARANY; BENGT LINDHOLM; LOUISE NORDFORS

2004-01-01

87

Fractal and Transgenerational Genetic Effects on Phenotypic Variation and Disease Risk  

NASA Astrophysics Data System (ADS)

To understand human biology and to manage heritable diseases, a complete picture of the genetic basis for phenotypic variation and disease risk is needed. Unexpectedly however, most of these genetic variants, even for highly heritable traits, continue to elude discovery for poorly understood reasons. The genetics community is actively exploring the usual explanations for missing heritability. But given the extraordinary work that has already been done and the exceptional magnitude of the problem, it seems likely that unconventional genetic properties are involved.

Nadeau, Joe

88

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

89

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

90

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

91

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

92

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

Technology Transfer Automated Retrieval System (TEKTRAN)

The choice of populations for quantitative genetics experiments impacts inferences about genetic architecture and prospective selection gains. Plant breeding and quantitative genetics studies are often conducted in one or a few among many possible biparental families. Trait genotypic variation withi...

93

Natural diversity in daily rhythms of gene expression contributes to phenotypic variation.  

PubMed

Daily rhythms of gene expression provide a benefit to most organisms by ensuring that biological processes are activated at the optimal time of day. Although temporal patterns of expression control plant traits of agricultural importance, how natural genetic variation modifies these patterns during the day and how precisely these patterns influence phenotypes is poorly understood. The circadian clock regulates the timing of gene expression, and natural variation in circadian rhythms has been described, but circadian rhythms are measured in artificial continuous conditions that do not reflect the complexity of biologically relevant day/night cycles. By studying transcriptional rhythms of the evening-expressed gene GIGANTEA (GI) at high temporal resolution and during day/night cycles, we show that natural variation in the timing of GI expression occurs mostly under long days in 77 Arabidopsis accessions. This variation is explained by natural alleles that alter light sensitivity of GI, specifically in the evening, and that act at least partly independent of circadian rhythms. Natural alleles induce precise changes in the temporal waveform of GI expression, and these changes have detectable effects on PHYTOCHROME INTERACTING FACTOR 4 expression and growth. Our findings provide a paradigm for how natural alleles act within day/night cycles to precisely modify temporal gene expression waveforms and cause phenotypic diversity. Such alleles could confer an advantage by adjusting the activity of temporally regulated processes without severely disrupting the circadian system. PMID:25548158

de Montaigu, Amaury; Giakountis, Antonis; Rubin, Matthew; Tóth, Réka; Cremer, Frédéric; Sokolova, Vladislava; Porri, Aimone; Reymond, Matthieu; Weinig, Cynthia; Coupland, George

2015-01-20

94

Natural diversity in daily rhythms of gene expression contributes to phenotypic variation  

PubMed Central

Daily rhythms of gene expression provide a benefit to most organisms by ensuring that biological processes are activated at the optimal time of day. Although temporal patterns of expression control plant traits of agricultural importance, how natural genetic variation modifies these patterns during the day and how precisely these patterns influence phenotypes is poorly understood. The circadian clock regulates the timing of gene expression, and natural variation in circadian rhythms has been described, but circadian rhythms are measured in artificial continuous conditions that do not reflect the complexity of biologically relevant day/night cycles. By studying transcriptional rhythms of the evening-expressed gene GIGANTEA (GI) at high temporal resolution and during day/night cycles, we show that natural variation in the timing of GI expression occurs mostly under long days in 77 Arabidopsis accessions. This variation is explained by natural alleles that alter light sensitivity of GI, specifically in the evening, and that act at least partly independent of circadian rhythms. Natural alleles induce precise changes in the temporal waveform of GI expression, and these changes have detectable effects on PHYTOCHROME INTERACTING FACTOR 4 expression and growth. Our findings provide a paradigm for how natural alleles act within day/night cycles to precisely modify temporal gene expression waveforms and cause phenotypic diversity. Such alleles could confer an advantage by adjusting the activity of temporally regulated processes without severely disrupting the circadian system. PMID:25548158

de Montaigu, Amaury; Giakountis, Antonis; Rubin, Matthew; Tóth, Réka; Cremer, Frédéric; Sokolova, Vladislava; Porri, Aimone; Reymond, Matthieu; Weinig, Cynthia; Coupland, George

2015-01-01

95

Candidate genes and thermal phenotypes: identifying ecologically important genetic variation for thermotolerance in the Australian Drosophila melanogaster cline.  

PubMed

Clinal variation in traits often reflects climatic adaptation; in Drosophila melanogaster clinal variation provides an opportunity to link variation in chromosomal inversions, microsatellite loci and various candidate genes to adaptive variation in traits. We undertook association studies with crosses from a single population of D. melanogaster from eastern Australia to investigate the association between genetic markers and traits showing clinal variation. By genotyping parents and phenotyping offspring, we minimized genotyping costs but had the power to detect association between markers and quantitative traits. Consistent with prior studies, we found strong associations between the clinal chromosomal inversion In(3R)Payne and markers within it, as well as among these markers. We also found an association between In(3L)Payne and one marker located within this inversion. Of the five predicted associations between markers and traits, four were detected (increased heat, decreased cold resistance and body size with the heat shock gene hsr-omega S, increased cold resistance with the inversion In(3L)Payne), while one was not detected (heat resistance and the heat shock gene hsp68). In a set of eight exploratory tests, we detected one positive association (between hsp23a and heat resistance) but no associations of heat resistance with alleles at the hsp26, hsp83, Desat 2, alpha-Gpdh, hsp70 loci, while cold resistance was not associated with Frost and Dca loci. These results confirm interactions between hsr-omega and thermal resistance, as well as between In(3L)Payne and cold resistance, but do not provide evidence for associations between thermal responses and alleles at other clinically varying marker genes. PMID:17614909

Rako, Lea; Blacket, Mark J; McKechnie, Stephen W; Hoffmann, Ary A

2007-07-01

96

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

2015-01-28

97

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

98

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

99

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

100

Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa.  

PubMed

• Populus trichocarpa is widespread across western North America spanning extensive variation in photoperiod, growing season and climate. We investigated trait variation in P. trichocarpa using over 2000 trees from a common garden at Vancouver, Canada, representing replicate plantings of 461 genotypes originating from 136 provenance localities. • We measured 40 traits encompassing phenological events, biomass accumulation, growth rates, and leaf, isotope and gas exchange-based ecophysiology traits. With replicated plantings and 29,354 single nucleotide polymorphisms (SNPs) from 3518 genes, we estimated both broad-sense trait heritability (H(2)) and overall population genetic structure from principal component analysis. • Populus trichocarpa had high phenotypic variation and moderate/high H(2) for many traits. H(2) ranged from 0.3 to 0.9 in phenology, 0.3 to 0.8 in biomass and 0.1 to 0.8 in ecophysiology traits. Most traits correlated strongly with latitude, maximum daylength and temperature of tree origin, but not necessarily with elevation, precipitation or heat : moisture indices. Trait H(2) values reflected trait correlation strength with geoclimate variables. The population genetic structure had one significant principal component (PC1) which correlated with daylength and showed enrichment for genes relating to circadian rhythm and photoperiod. • Robust relationships between traits, population structure and geoclimate in P. trichocarpa reflect patterns which suggest that range-wide geographical and environment gradients have shaped its genotypic and phenotypic variability. PMID:24491114

McKown, Athena D; Guy, Robert D; Klápšt?, Jaroslav; Geraldes, Armando; Friedmann, Michael; Cronk, Quentin C B; El-Kassaby, Yousry A; Mansfield, Shawn D; Douglas, Carl J

2014-03-01

101

A Pleiotropic Nonadditive Model of Variation in Quantitative Traits  

PubMed Central

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. These experiments suggest a leptokurtic distribution of effects with an intermediate correlation between effects on the trait and fitness. 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, in which the proportion of mutations with an effect on the trait is small, 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(4) to 10(6), and most of the variance for the metric trait in segregating populations is due to a small proportion of mutations (about 1% of the total number) with neutral or nearly neutral effects on fitness and intermediate effects on the trait (0.1-0.5?(P)). Much of the genetic variance is contributed by recessive or partially recessive mutants, but only a small proportion (about 10%) of the genetic variance is dominance variance. The amount of apparent selection on the trait itself generated by the model is very small. 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 viability, the heritability is about 0.1, independent of the population size. PMID:7851783

Caballero, A.; Keightley, P. D.

1994-01-01

102

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

103

Quantitative social dialectology: explaining linguistic variation geographically and socially.  

PubMed

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

104

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

105

Mitochondrial-Nuclear Epistasis Contributes to Phenotypic Variation and Coadaptation in Natural Isolates of Saccharomyces cerevisiae.  

PubMed

Mitochondria are essential multifunctional organelles whose metabolic functions, biogenesis, and maintenance are controlled through genetic interactions between mitochondrial and nuclear genomes. In natural populations, mitochondrial efficiencies may be impacted by epistatic interactions between naturally segregating genome variants. The extent that mitochondrial-nuclear epistasis contributes to the phenotypic variation present in nature is unknown. We have systematically replaced mitochondrial DNAs in a collection of divergent Saccharomyces cerevisiae yeast isolates and quantified the effects on growth rates in a variety of environments. We found that mitochondrial-nuclear interactions significantly affected growth rates and explained a substantial proportion of the phenotypic variances under some environmental conditions. Naturally occurring mitochondrial-nuclear genome combinations were more likely to provide growth advantages, but genetic distance could not predict the effects of epistasis. Interruption of naturally occurring mitochondrial-nuclear genome combinations increased endogenous reactive oxygen species in several strains to levels that were not always proportional to growth rate differences. Our results demonstrate that interactions between mitochondrial and nuclear genomes generate phenotypic diversity in natural populations of yeasts and that coadaptation of intergenomic interactions likely occurs quickly within the specific niches that yeast occupy. This study reveals the importance of considering allelic interactions between mitochondrial and nuclear genomes when investigating evolutionary relationships and mapping the genetic basis underlying complex traits. PMID:25164882

Paliwal, Swati; Fiumera, Anthony C; Fiumera, Heather L

2014-11-01

106

Quantitative Analysis of the Phenotypic Variability of Shoot Architecture in Two Grapevine (Vitis vinifera) Cultivars  

PubMed Central

Background and Aims Plant architecture and its interaction with agronomic practices and environmental constraints are determinants of the structure of the canopy, which is involved in carbon acquisition and fruit quality development. A framework for the quantitative analysis of grapevine (Vitis vinifera) shoot architecture, based on a set of topological and geometrical parameters, was developed for the identification of differences between cultivars and the origins of phenotypic variability. Methods Two commercial cultivars (‘Grenache N’, ‘Syrah’) with different shoot architectures were grown in pots, in well-irrigated conditions. Shoot topology was analysed, using a hidden semi-Markov chain and variable-order Markov chains to identify deviations from the normal pattern of succession of phytomer types (P0–P1–P2), together with kinematic analysis of shoot axis development. Shoot geometry was characterized by final internode and individual leaf area measurements. Key Results Shoot architecture differed significantly between cultivars. Secondary leaf area and axis length were greater for ‘Syrah’. Secondary leaf area distribution along the main axis also differed between cultivars, with secondary leaves preferentially located towards the basal part of the shoot in ‘Syrah’. The main factors leading to differences in leaf area between the cultivars were: (a) slight differences in main shoot structure, with the supplementary P0 phytomer on the lower part of the shoot in ‘Grenache N’, which bears a short branch; and (b) an higher rate and duration of development of branches bearing by P1–P2 phytomers related to P0 ones at the bottom of the shoot in ‘Syrah’. Differences in axis length were accounted for principally by differences in individual internode morphology, with ‘Syrah’ having significantly longer internodes. This trait, together with a smaller shoot diameter, may account for the characteristic ‘droopy’ habit of ‘Syrah’ shoots. Conclusions This study highlights the architectural parameters involved in the phenotypic variability of shoot architecture in two grapevine cultivars. Differences in primary shoot structure and in branch development potential accounted for the main differences in leaf area distribution between the two cultivars. By contrast, shoot shape seemed to be controlled by differences in axis length due principally to differences in internode length. PMID:17204533

Louarn, Gaëtan; Guedon, Yann; Lecoeur, Jeremie; Lebon, Eric

2007-01-01

107

SSR-marker analysis of the intracultivar phenotypic variation discovered within 3 soybean cultivars.  

PubMed

Genetic variation within homogeneous gene pools in various crops is assumed to be very limited. One objective of this study was to use 144 simple sequence repeat (SSR) markers to determine if the single-plant lines selected at ultra-low plant density in honeycomb designs within the soybean cultivars Benning, Haskell, and Cook had unique SSR genetic fingerprints. Another objective was to investigate if the variation found was the result of residual genetic heterozygosity that could be detected in the original gene pool where selection initiated. Our results showed that the phenotypic variation for seed protein content and seed weight has a genotypic component identified by the SSR band variation. The 7 lines from Haskell had a total of 63 variant alleles, the 5 lines from Benning had 34 variant alleles, and the 7 lines from Cook had 34 variant alleles, therefore, possessing unique genetic fingerprints. Most of the intracultivar SSR band variation discovered was the result of residual heterozygosity in the initial plant selected to become the cultivar. More specifically, 82% of the SSR variant alleles were traced in the Benning Foundation seed source, 93% in the Haskell seed source, and 82% in the Cook seed source. The remaining variant bands (18% for Benning, 7% for Haskell, and 18% for Cook) could not be detected in the Foundation seed source and were likely the result of mutation or some other mechanism generating de novo variation. These results provide evidence that genetic variation among individual plants is present even in homogeneous gene pools and can be further utilized in breeding programs. PMID:22547666

Yates, Jennifer L; Boerma, H Roger; Fasoula, Vasilia A

2012-07-01

108

Hidden genetic variation evolves with ecological specialization: the genetic basis of phenotypic plasticity in Arctic charr ecomorphs.  

PubMed

The genetic variance that determines phenotypic variation can change across environments through developmental plasticity and in turn play a strong role in evolution. Induced changes in genotype-phenotype relationships should strongly influence adaptation by exposing different sets of heritable variation to selection under some conditions, while also hiding variation. Therefore, the heritable variation exposed or hidden from selection is likely to differ among habitats. We used ecomorphs from two divergent populations of Arctic charr (Salvelinus alpinus) to test the prediction that genotype-phenotype relationships would change in relation to environment. If present over several generations this should lead to divergence in genotype-phenotype relationships under common conditions, and to changes in the amount and type of hidden genetic variance that can evolve. We performed a common garden experiment whereby two ecomorphs from each of two Icelandic lakes were reared under conditions that mimicked benthic and limnetic prey to induce responses in craniofacial traits. Using microsatellite based genetic maps, we subsequently detected QTL related to these craniofacial traits. We found substantial changes in the number and type of QTL between diet treatments and evidence that novel diet treatments can in some cases provide a higher number of QTL. These findings suggest that selection on phenotypic variation, which is both genetically and environmentally determined, has shaped the genetic architecture of adaptive divergence in Arctic charr. However, while adaptive changes are occurring in the genome there also appears to be an accumulation of hidden genetic variation for loci not expressed in the contemporary environment. PMID:24920458

Küttner, Eva; Parsons, Kevin J; Easton, Anne A; Skúlason, Skuli; Danzmann, Roy G; Ferguson, Moira M

2014-01-01

109

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

110

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

111

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

112

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

113

3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture  

PubMed Central

Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala × Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24–37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops. PMID:23580618

Topp, Christopher N.; Iyer-Pascuzzi, Anjali S.; Anderson, Jill T.; Lee, Cheng-Ruei; Zurek, Paul R.; Symonova, Olga; Zheng, Ying; Bucksch, Alexander; Mileyko, Yuriy; Galkovskyi, Taras; Moore, Brad T.; Harer, John; Edelsbrunner, Herbert; Mitchell-Olds, Thomas; Weitz, Joshua S.; Benfey, Philip N.

2013-01-01

114

Genotypic and phenotypic variation as stress adaptations in temperate tree species: a review of several case studies.  

PubMed

Species that occupy large geographic ranges or a variety of habitats within a limited area deal with contrasting environmental conditions by genotypic and phenotypic variation. My students and I have studied these forms of ecophysiological variation in temperate tree species in eastern North America by means of a series of field and greenhouse experiments, including controlled studies with Cercis canadensis L., Fraxinus pennsylvanica Marsh., Acer rubrum L., Prunus serotina Ehrh. and Quercus rubra L., in relation to drought stress. These studies have included measurements of gas exchange, tissue water relations and leaf morphology, and have identified genotypic variation at the biome and individual community levels. Xeric genotypes generally had higher net photosynthesis and leaf conductance and lower osmotic and water potentials at incipient wilting than mesic genotypes during drought. Xeric genotypes also produced leaves with greater thickness, leaf mass per area and stomatal density and smaller area than the mesic genotypes, suggesting general coordination among leaf morphology, gas exchange and tissue water relations. Leaf phenotypic plasticity to different light environments occurred in virtually every study species, which represented a wide array of ecological tolerances. In a study of interactions of genotypes with environment, shade plants, but not sun plants, exhibited osmotic adjustment during drought and shade plants had smaller reductions in photosynthesis with decreasing leaf water potential. In that study, sun, but not shade, plants had significant genotypic differences in leaf structure, but with certain variables phenotypic variation exceeded genotype variation. Thus, genotypic variation was not expressed in all phenotypes, and phenotypes responded differentially to stress. Overall, these studies indicate the importance of genotypic and phenotypic variation as stress adaptations in temperate tree species among both distant and nearby sites of contrasting environmental conditions. PMID:14967652

Abrams, Marc D.

1994-01-01

115

A Genomewide Linkage Scan for Quantitative-Trait Loci for Obesity Phenotypes  

PubMed Central

Obesity is an increasingly serious health problem in the world. Body mass index (BMI), percentage fat mass, and body fat mass are important indices of obesity. For a sample of pedigrees that contains >10,000 relative pairs (including 1,249 sib pairs) that are useful for linkage analyses, we performed a whole-genome linkage scan, using 380 microsatellite markers to identify genomic regions that may contain quantitative-trait loci (QTLs) for obesity. Each pedigree was ascertained through a proband who has extremely low bone mass, which translates into a low BMI. A major QTL for BMI was identified on 2q14 near the marker D2S347 with a LOD score of 4.04 in two-point analysis and a maximum LOD score (MLS) of 4.44 in multipoint analysis. The genomic region near 2q14 also achieved an MLS >2.0 for percentage of fat mass and body fat mass. For the putative QTL on 2q14, as much as 28.2% of BMI variation (after adjustment for age and sex) may be attributable to this locus. In addition, several other genomic regions that may contain obesity-related QTLs are suggested. For example, 1p36 near the marker D1S468 may contain a QTL for BMI variation, with a LOD score of 2.75 in two-point analysis and an MLS of 2.09 in multipoint analysis. The genomic regions identified in this and earlier reports are compared for further exploration in extension studies that use larger samples and/or denser markers for confirmation and fine-mapping studies, to eventually identify major functional genes involved in obesity. PMID:11923910

Deng, Hong-Wen; Deng, Hongyi; Liu, Yong-Jun; Liu, Yao-Zhong; Xu, Fu-Hua; Shen, Hui; Conway, Theresa; Li, Jin-Long; Huang, Qing-Yang; Davies, K. M.; Recker, Robert R.

2002-01-01

116

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

117

Semi-quantitative and structural metabolic phenotyping by direct infusion ion trap mass spectrometry and its application in genetical metabolomics  

PubMed Central

The identification of quantitative trait loci (QTL) for plant metabolites requires the quantitation of these metabolites across a large range of progeny. We developed a rapid metabolic profiling method using both untargeted and targeted direct infusion tandem mass spectrometry (DIMSMS) with a linear ion trap mass spectrometer yielding sufficient precision and accuracy for the quantification of a large number of metabolites in a high-throughput environment. The untargeted DIMSMS method uses top-down data-dependent fragmentation yielding MS2 and MS3 spectra. We have developed software tools to assess the structural homogeneity of the MS2 and MS3 spectra hence their utility for phenotyping and genetical metabolomics. In addition we used a targeted DIMS(MS) method for rapid quantitation of specific compounds. This method was compared with targeted LC/MS/MS methods for these compounds. The DIMSMS methods showed sufficient precision and accuracy for QTL discovery. We phenotyped 200 individual Lolium perenne genotypes from a mapping population harvested in two consecutive years. Computational and statistical analyses identified 246 nominal m/z bins with sufficient precision and homogeneity for QTL discovery. Comparison of the data for specific metabolites obtained by DIMSMS with the results from targeted LC/MS/MS analysis showed that quantitation by this metabolic profiling method is reasonably accurate. Of the top 100 MS1 bins, 22 ions gave one or more reproducible QTL across the 2 years. Copyright © 2009 John Wiley & Sons, Ltd. PMID:19551846

Koulman, Albert; Cao, Mingshu; Faville, Marty; Lane, Geoff; Mace, Wade; Rasmussen, Susanne

2009-01-01

118

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

119

Phenotypic variation of Salmonella in host tissues delays eradication by antimicrobial chemotherapy.  

PubMed

Antibiotic therapy often fails to eliminate a fraction of transiently refractory bacteria, causing relapses and chronic infections. Multiple mechanisms can induce such persisters with high antimicrobial tolerance in vitro, but their in vivo relevance remains unclear. Using a fluorescent growth rate reporter, we detected extensive phenotypic variation of Salmonella in host tissues. This included slow-growing subsets as well as well-nourished fast-growing subsets driving disease progression. Monitoring of Salmonella growth and survival during chemotherapy revealed that antibiotic killing correlated with single-cell division rates. Nondividing Salmonella survived best but were rare, limiting their impact. Instead, most survivors originated from abundant moderately growing, partially tolerant Salmonella. These data demonstrate that host tissues diversify pathogen physiology, with major consequences for disease progression and control. PMID:25126781

Claudi, Beatrice; Spröte, Petra; Chirkova, Anna; Personnic, Nicolas; Zankl, Janine; Schürmann, Nura; Schmidt, Alexander; Bumann, Dirk

2014-08-14

120

Phenotype variations in Lafora progressive myoclonus epilepsy: possible involvement of genetic modifiers?  

PubMed

Lafora progressive myoclonus epilepsy, also known as Lafora disease (LD), is the most severe and fatal form of progressive myoclonus epilepsy with its typical onset during the late childhood or early adolescence. LD is characterized by recurrent epileptic seizures and progressive decline in intellectual function. LD can be caused by defects in any of the two known genes and the clinical features of these two genetic groups are almost identical. The past one decade has witnessed considerable success in identifying the LD genes, their mutations, the cellular functions of gene products and on molecular basis of LD. Here, we briefly review the current literature on the phenotype variations, on possible presence of genetic modifiers, and candidate modifiers as targets for therapeutic interventions in LD. PMID:22456482

Singh, Shweta; Ganesh, Subramaniam

2012-05-01

121

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

122

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

E-print Network

that the contribution of rare, partially recessive alleles to quantitative trait variation can be assessed by comparing the relative magnitudes of two genetic variance components: the covariance of additive and homozygous dominance effects (Cad) and the additive genetic...

Kelly, John K.

1999-06-01

123

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

Microsoft Academic Search

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\\u000a bi-modal electrophoretic mobility distributions at pH 2, but such phenotypic variation was absent in red colonies

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

2008-01-01

124

Population Structure in Daphnia obtusa: Quantitative Genetic and Allozymic Variation  

Microsoft Academic Search

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: GST = 0.28. No associations between electrophoretic genotype and pheno- typic characters were found, providing support

Ken Spitze

1993-01-01

125

Predicting quantitative variation within rice germplasm using molecular markers  

Microsoft Academic Search

Diverse Asian rice (Oryza sativa) germplasm has been used to identify associations between various quantitative traits and RAPD molecular markers using multiple regression analysis. This has allowed us to predict for other samples of germplasm their performance for traits such as culm length and number, days to flowering, grain width, and panicle and leaf length using only RAPD marker data.

Parminder S Virk; Brian V Ford-Lloyd; Michael T Jackson; Harpal S Pooni; Tomas P Clemeno; H John Newbury

1996-01-01

126

Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila melanogaster  

Microsoft Academic Search

Predicting organismal phenotypes from genotype data is important for plant and animal breeding, medicine, and evolutionary biology. Genomic-based phenotype prediction has been applied for single-nucleotide polymorphism (SNP) genotyping platforms, but not using complete genome sequences. Here, we report genomic prediction for starvation stress resistance and startle response in Drosophila melanogaster, using ?2.5 million SNPs determined by sequencing the Drosophila Genetic

Ulrike Ober; Julien F. Ayroles; Eric A. Stone; Stephen Richards; Dianhui Zhu; Richard A. Gibbs; Christian Stricker; Daniel Gianola; Martin Schlather; Trudy F. C. Mackay; Henner Simianer

2012-01-01

127

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

128

A non-parametric test to detect quantitative trait loci where the phenotypic distribution differs by genotypes  

PubMed Central

Searching for genetic variants involved in gene-gene and gene-environment interactions in large scale data raises multiple methodological issues. Many existing methods have focused on the problem of dimensionality, trying to explore the largest number of combinations between risk factors while considering simple interaction models. Despite evidence demonstrating the efficacy of these methods in simulated data, their application in real data has been unsuccessful so far. The classical test of a linear marginal genetic effect has been widely used for agnostic genome-wide association studies, with the underlying idea that most variants involved in interactions might display marginal effect on the phenotypic mean. While this approach may allow for the identification of genetic variants involved in interactions in many scenarios, the linear marginal effects of some causal alleles on the phenotypic mean might not be always detectable at genome-wide significance level. We introduce in this study a general association test for quantitative trait loci that compare the distributions of phenotypic values by genotypic classes as opposed to most standard tests that compare phenotypic means by genotypic classes. Using simulation we show that in presence of an interaction, this approach can be more powerful than the standard test of the linear marginal exposures. We demonstrate the potential utility of our method on real data by analyzing mammographic density genome-wide data from the Nurses’ Health Study. PMID:23512279

Aschard, Hugues; Zaitlen, Noah; Tamimi, Rulla M.; Lindström, Sara; Kraft, Peter

2014-01-01

129

Developing a breeding strategy to exploit quantitative variation in symbiotic nitrogen fixation  

Microsoft Academic Search

Summary This paper examines evidence which quantifies the relative importance of legume and Rhizobium genotypes as determinants of phenotypic variation in symbiotic nitrogen fixation. It demonstrates potentially large and unpredictable effects of the Rhizobium genotype. The likely importance of such effects on crop yield is considered. The information is then used to assess ways in which legume breeding programmes may

L. R. Mytton

1984-01-01

130

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, D.H.

2004-01-01

131

Quantitative genetic analysis of natural variation in body size in Drosophila melanogaster  

Microsoft Academic Search

Latitudinal, genetic variation in body size is a commonly observed phenomenon in many invertebrate species and is shaped by natural selection. In this study, we use a chromosome substitution and a quantitative trait locus (QTL) mapping approach to identify chromosomes and genomic regions associated with adaptive variation in body size in natural populations of Drosophila melanogaster from the extreme ends

J Gockel; S J W Robinson; W J Kennington; D B Goldstein; L Partridge

2002-01-01

132

Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation  

PubMed Central

Background Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations (CNVs). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE. Results We performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0?1%. Conclusions Our study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing. PMID:19093001

Lee, Soohyun; Kasif, Simon; Weng, Zhiping; Cantor, Charles R.

2008-01-01

133

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

E-print Network

J Allergy Clin Immunol. Author manuscript Page /1 9 Interrelationships of quantitative asthma the interrelationships of quantitative asthma-related traits. Objective To study the interrelationships of allergy). Results Allergy parameters were significantly higher in asthmatic cases than in controls for children

Paris-Sud XI, Université de

134

Comparison of quantitative and molecular genetic variation of native vs. invasive populations of purple loosestrife (Lythrum salicaria L., Lythraceae).  

PubMed

Study of adaptive evolutionary changes in populations of invasive species can be advanced through the joint application of quantitative and population genetic methods. Using purple loosestrife as a model system, we investigated the relative roles of natural selection, genetic drift and gene flow in the invasive process by contrasting phenotypical and neutral genetic differentiation among native European and invasive North American populations (Q(ST) - F(ST) analysis). Our results indicate that invasive and native populations harbour comparable levels of amplified fragment length polymorphism variation, a pattern consistent with multiple independent introductions from a diverse European gene pool. However, it was observed that the genetic variation reduced during subsequent invasion, perhaps by founder effects and genetic drift. Comparison of genetically based quantitative trait differentiation (Q(ST)) with its expectation under neutrality (F(ST)) revealed no evidence of disruptive selection (Q(ST) > F(ST)) or stabilizing selection (Q(ST) < F(ST)). One exception was found for only one trait (the number of stems) showing significant sign of stabilizing selection across all populations. This suggests that there are difficulties in distinguishing the effects of nonadaptive population processes and natural selection. Multiple introductions of purple loosestrife may have created a genetic mixture from diverse source populations and increased population genetic diversity, but its link to the adaptive differentiation of invasive North American populations needs further research. PMID:19548895

Chun, Young Jin; Nason, John D; Moloney, Kirk A

2009-07-01

135

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

136

Mouse genomic variation and its effect on phenotypes and gene regulation  

PubMed Central

We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcripts show a significant tissue-specific expression bias. By identifying candidate functional variants at 718 quantitative trait loci we show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus. These sequences provide a starting point for a new era in the functional analysis of a key model organism. PMID:21921910

Keane, Thomas M.; Goodstadt, Leo; Danecek, Petr; White, Michael A.; Wong, Kim; Yalcin, Binnaz; Heger, Andreas; Agam, Avigail; Slater, Guy; Goodson, Martin; Furlotte, Nicholas A.; Eskin, Eleazar; Nellåker, Christoffer; Whitley, Helen; Cleak, James; Janowitz, Deborah; Hernandez-Pliego, Polinka; Edwards, Andrew; Belgard, T. Grant; Oliver, Peter L.; McIntyre, Rebecca E.; Bhomra, Amarjit; Nicod, Jérôme; Gan, Xiangchao; Yuan, Wei; van der Weyden, Louise; Steward, Charles A.; Balasubramaniam, Sendu; Stalker, Jim; Mott, Richard; Durbin, Richard; Jackson, Ian J.; Czechanski, Anne; Assunção, José Afonso Guerra; Donahue, Leah Rae; Reinholdt, Laura G.; Payseur, Bret A.; Ponting, Chris P.; Birney, Ewan; Flint, Jonathan; Adams, David J.

2012-01-01

137

Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin\\/TOR and associated phenotypes in Drosophila melanogaster  

Microsoft Academic Search

BACKGROUND: A molecular process based genotype-to-phenotype map will ultimately enable us to predict how genetic variation among individuals results in phenotypic alterations. Building such a map is, however, far from straightforward. It requires understanding how molecular variation re-shapes developmental and metabolic networks, and how the functional state of these networks modifies phenotypes in genotype specific way. We focus on the

Sergey V Nuzhdin; Jennifer A Brisson; Andrew Pickering; Marta L Wayne; Lawrence G Harshman; Lauren M McIntyre

2009-01-01

138

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

139

The Ability of Aneurinibacillus migulanus (Bacillus brevis) To Produce the Antibiotic Gramicidin S Is Correlated with Phenotype Variation?  

PubMed Central

Phenotype instability of bacterial strains can cause significant problems in biotechnological applications, since industrially useful properties may be lost. Here we report such degenerative dissociation for Aneurinibacillus migulanus (formerly known as Bacillus brevis) an established producer of the antimicrobial peptide gramicidin S (GS). Phenotypic variations within and between various strains maintained in different culture collections are demonstrated. The type strain, ATCC 9999, consists of six colony morphology variants, R, RC, RP, RT, SC, and SP, which were isolated and characterized as pure cultures. Correlations between colony morphology, growth, GS production, spore formation, and resistance to their own antimicrobial peptide were established in this study. We found the original R form to be the best producer, followed by RC, RP, and RT, while SC and SP yielded no GS at all. Currently available ATCC 9999T contains only 2% of the original R producer and is dominated by the newly described phenotypes RC and RP. No original R form is detected in the nominally equivalent strain DSM 2895T (=ATCC 9999T), which grows only as SC and SP phenotypes and has thus completely lost its value as a peptide producer. Two other strains from the same collection, DSM 5668 and DSM 5759, contain the unproductive SC variant and the GS-producing RC form, respectively. We describe the growth and maintenance conditions that stabilize certain colony phenotypes and reduce the degree of degenerative dissociation, thus providing a recommendation for how to revert the nonproducing smooth phenotypes to the valuable GS-producing rough ones. PMID:17720841

Berditsch, Marina; Afonin, Sergii; Ulrich, Anne S.

2007-01-01

140

The ability of Aneurinibacillus migulanus (Bacillus brevis) to produce the antibiotic gramicidin S is correlated with phenotype variation.  

PubMed

Phenotype instability of bacterial strains can cause significant problems in biotechnological applications, since industrially useful properties may be lost. Here we report such degenerative dissociation for Aneurinibacillus migulanus (formerly known as Bacillus brevis) an established producer of the antimicrobial peptide gramicidin S (GS). Phenotypic variations within and between various strains maintained in different culture collections are demonstrated. The type strain, ATCC 9999, consists of six colony morphology variants, R, RC, RP, RT, SC, and SP, which were isolated and characterized as pure cultures. Correlations between colony morphology, growth, GS production, spore formation, and resistance to their own antimicrobial peptide were established in this study. We found the original R form to be the best producer, followed by RC, RP, and RT, while SC and SP yielded no GS at all. Currently available ATCC 9999(T) contains only 2% of the original R producer and is dominated by the newly described phenotypes RC and RP. No original R form is detected in the nominally equivalent strain DSM 2895(T) (=ATCC 9999(T)), which grows only as SC and SP phenotypes and has thus completely lost its value as a peptide producer. Two other strains from the same collection, DSM 5668 and DSM 5759, contain the unproductive SC variant and the GS-producing RC form, respectively. We describe the growth and maintenance conditions that stabilize certain colony phenotypes and reduce the degree of degenerative dissociation, thus providing a recommendation for how to revert the nonproducing smooth phenotypes to the valuable GS-producing rough ones. PMID:17720841

Berditsch, Marina; Afonin, Sergii; Ulrich, Anne S

2007-10-01

141

Facial Phenotyping by Quantitative Photography Reflects Craniofacial Morphology Measured on Magnetic Resonance Imaging in Icelandic Sleep Apnea Patients  

PubMed Central

Study Objectives: (1) To determine whether facial phenotype, measured by quantitative photography, relates to underlying craniofacial obstructive sleep apnea (OSA) risk factors, measured with magnetic resonance imaging (MRI); (2) To assess whether these associations are independent of body size and obesity. Design: Cross-sectional cohort. Setting: Landspitali, The National University Hospital, Iceland. Participants: One hundred forty patients (87.1% male) from the Icelandic Sleep Apnea Cohort who had both calibrated frontal and profile craniofacial photographs and upper airway MRI. Mean ± standard deviation age 56.1 ± 10.4 y, body mass index 33.5 ± 5.05 kg/m2, with on-average severe OSA (apnea-hypopnea index 45.4 ± 19.7 h-1). Interventions: N/A. Measurements and Results: Relationships between surface facial dimensions (photos) and facial bony dimensions and upper airway soft-tissue volumes (MRI) was assessed using canonical correlation analysis. Photo and MRI craniofacial datasets related in four significant canonical correlations, primarily driven by measurements of (1) maxillary-mandibular relationship (r = 0.8, P < 0.0001), (2) lower face height (r = 0.76, P < 0.0001), (3) mandibular length (r = 0.67, P < 0.0001), and (4) tongue volume (r = 0.52, P = 0.01). Correlations 1, 2, and 3 were unchanged when controlled for weight and neck and waist circumference. However, tongue volume was no longer significant, suggesting facial dimensions relate to tongue volume as a result of obesity. Conclusions: Significant associations were found between craniofacial variable sets from facial photography and MRI. This study confirms that facial photographic phenotype reflects underlying aspects of craniofacial skeletal abnormalities associated with OSA. Therefore, facial photographic phenotyping may be a useful tool to assess intermediate phenotypes for OSA, particularly in large-scale studies. Citation: Sutherland K, Schwab RJ, Maislin G, Lee RW, Benedikstdsottir B, Pack AI, Gislason T, Juliusson S, Cistulli PA. Facial phenotyping by quantitative photography reflects craniofacial morphology measured on magnetic resonance imaging in icelandic sleep apnea patients. SLEEP 2014;37(5):959-968. PMID:24790275

Sutherland, Kate; Schwab, Richard J.; Maislin, Greg; Lee, Richard W.W.; Benedikstdsottir, Bryndis; Pack, Allan I.; Gislason, Thorarinn; Juliusson, Sigurdur; Cistulli, Peter A.

2014-01-01

142

Both allelic variation and expression of nuclear and cytoplasmic transcripts of Hsr-omega are closely associated with thermal phenotype in Drosophila  

PubMed Central

Inducible heat shock genes are considered a major component of the molecular mechanisms that confer cellular protection against a variety of environmental stresses, in particular high temperature extremes. We have tested the association between expression of the heat shock RNA gene hsr-omega and thermoresistance by generating thermoresistant lines of Drosophila melanogaster after application of two distinct regimes of laboratory selection. One set of lines was selected for resistance to knockdown by heat stress and the other was similarly selected but before selection a mild heat exposure known to increase resistance (heat hardening) was applied. A cross between resistant and susceptible lines confirmed our earlier observation that increased thermal tolerance cosegregates with allelic variation in the hsr-omega gene. This cosegregating variation is attributed largely to two haplotype groups. Using quantitative reverse transcription–PCR, we find evidence for divergent phenotypic responses in the two selection regimes, involving both structural and regulatory changes in hsr-omega. Lines selected after hardening showed increased levels of the cytoplasmic transcript but decreased levels of the nuclear transcript. Lines selected without hardening showed decreased levels of the cytoplasmic transcript. The allelic frequency changes at hsr-omega could not by themselves account for the altered transcription patterns. Our results support the idea that the functional RNA molecules transcribed from hsr-omega are an important and polymorphic regulatory component of an insect thermoresistance phenotype. PMID:9482901

McKechnie, Stephen W.; Halford, Michael M.; McColl, Gawain; Hoffmann, Ary A.

1998-01-01

143

Phenotypic variation in a significant spore character in Kudoa (Myxosporea: Multivalvulida) species infecting brain tissue.  

PubMed

Some Kudoa species display variations in the number of polar capsules in spores within an individual pseudocyst. Nonetheless, there is usually a dominant morphotype which forms a significant element of diagnosis. In 2007, a Kudoa isolate from whiting (spores with 5 (dominant) or 6 (minor) polar capsules) was characterized by Burger et al. (2007) as being 100% identical in SSU rDNA to Kudoa yasunagai (spores with 7 polar capsules) from a halibut, despite its obvious morphological differences. The authors hypothesized that either SSU rDNA had reached its level of resolution or that the genetic identity revealed conspecificity. To further investigate these hypotheses, SSU and LSU rDNA sequence data were coupled with principal components, correlation, and regression analyses of morphometric data from different kudoid isolates that infect brain tissue to determine the relationships between spore morphotypes and different kudoid isolates. The trends in morphometrics between the spores of particular isolates were so similar that it was concluded that the molecular results did indicate conspecificity rather than SSU reaching its level of resolution. This phenotypic influence on a significant diagnostic character within the Kudoidae has a major impact on the diagnosis of this, and potentially other, pathogenic species. PMID:20546639

Burger, Mieke A A; Adlard, Robert D

2010-10-01

144

Genetic and Epigenetic Mechanisms for Gene Expression and Phenotypic Variation in Plant Polyploids  

PubMed Central

Polyploidy, or whole-genome duplication (WGD), is an important genomic feature for all eukaryotes, especially many plants and some animals. The common occurrence of polyploidy suggests an evolutionary advantage of having multiple sets of genetic material for adaptive evolution. However, increased gene and genome dosages in autopolyploids (duplications of a single genome) and allopolyploids (combinations of two or more divergent genomes) often cause genome instabilities, chromosome imbalances, regulatory incompatibilities, and reproductive failures. Therefore, new allopolyploids must establish a compatible relationship between alien cytoplasm and nuclei and between two divergent genomes, leading to rapid changes in genome structure, gene expression, and developmental traits such as fertility, inbreeding, apomixis, flowering time, and hybrid vigor. Although the underlying mechanisms for these changes are poorly understood, some themes are emerging. There is compelling evidence that changes in DNA sequence, cis- and trans-acting effects, chromatin modifications, RNA-mediated pathways, and regulatory networks modulate differential expression of homoeologous genes and phenotypic variation that may facilitate adaptive evolution in polyploid plants and domestication in crops. PMID:17280525

Chen, Z. Jeffrey

2007-01-01

145

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

146

Acroscyphodysplasia as a phenotypic variation of pseudohypoparathyroidism and acrodysostosis type 2.  

PubMed

Acroscyphodysplasia (OMIM250215) is a distinctive form of metaphyseal dysplasia characterized by the distal femoral and proximal tibial epiphyses embedded in cup-shaped, large metaphyses known as metaphyseal scypho ("scypho" = cup) deformity. It is also associated with severe growth retardation and brachydactyly. The underlying molecular mechanism of acroscyphodysplasia has not yet been elucidated, although scypho-deformity of the knee has been reported in three patients with acrodysostosis due to a mutation in the PDE4D gene. We report on the clinical, radiological, and molecular findings of five female patients with acroscyphodysplasia; two were diagnosed as pseudohypoparathyroidism (PHP) or Albright hereditary osteodystropy, and the other three as acrodysostosis. They all had radiological findings consistent with severe metaphyseal scypho-deformity and brachydactyly. Heterozygous mutations were identified in the PHP patients consisting of one novel (p.Q19X) and one recurrent (p.R231C) mutation of the GNAS gene, as well as, in the acrodysostosis patients consisting of two novel mutations (p.T224I and p.I333T) of the PDE4D gene. We conclude that metaphyseal acroscyphodysplasia is a phenotypic variation of PHP or acrodysostosis caused by either a GNAS or PDE4D mutation, respectively. PMID:25044890

Mitsui, Toshikatsu; Kim, Ok-Hwa; Hall, Christine M; Offiah, Amaka; Johnson, Diana; Jin, Dong-Kyu; Toh, Teck-Hock; Soneda, Shun; Keino, Dai; Matsubayashi, Shohei; Ishii, Tomohiro; Nishimura, Gen; Hasegawa, Tomonobu

2014-10-01

147

Natural Variation in CDC28 Underlies Morphological Phenotypes in an Environmental Yeast Isolate  

PubMed Central

Morphological differences among individuals in a species represent one of the most striking aspects of biology, and a primary aim of modern genetics is to uncover the molecular basis of morphological variation. In a survey of meiosis phenotypes among environmental isolates of Saccharomyces cerevisiae, we observed an unusual arrangement of meiotic spores within the spore sac in a strain from Ivory Coast, West Africa. We mined population genomic data to identify CDC28 as the major genetic determinant of meiotic and budding cell shape behaviors in this strain. Molecular genetic methods confirmed the role of the Ivory Coast variant of CDC28 in the arrangement of spores after meiosis, in the shape of budding cells in rich medium and in the morphology of filamentous growth during nitrogen limitation. Our results shed new light on the role of CDC28 in yeast cell division, and our work suggests that with the growing availability of genomic data sets in many systems, a priori prediction of functional variants will become an increasingly powerful strategy in molecular genetics. PMID:21527779

Lee, Hana N.; Magwene, Paul M.; Brem, Rachel B.

2011-01-01

148

Artificial neural networks for linkage analysis of quantitative gene expression phenotypes and evaluation of gene × gene interactions  

PubMed Central

Background Using single-nucleotide polymorphism (SNP) genotypes and selected gene expression phenotypes from 14 CEPH (Centre d'Etude du Polymorphisme Humain) pedigrees provided for Genetic Analysis Workshop 15 (GAW15), we analyzed quantitative traits with artificial neural networks (ANNs). Our goals were to identify individual linkage signals and examine gene × gene interactions. First, we used classical multipoint methods to identify phenotypes having nominal linkage evidence at two or more loci. ANNs were then applied to sib-pair identity-by-descent (IBD) allele sharing across the genome as input variables and squared trait sums and differences for the sib pairs as output variables. The weights of the trained networks were analyzed to assess the linkage evidence at each locus as well as potential interactions between them. Results Loci identified by classical linkage analysis could also be identified by our ANN analysis. However some ANN results were noisy, and our attempts to use cross-validated training to avoid overtraining and thereby improve results were only partially successful. Potential interactions between loci with high-ranked weight measures were also evaluated, with the resulting patterns suggesting existence of both synergistic and antagonistic effects between loci. Conclusion Our results suggest that ANNs can serve as a useful method to analyze quantitative traits and are a potential tool for detecting gene × gene interactions. However, for the approach implemented here, optimizing the ANNs and obtaining stable results remains challenging. PMID:18466546

Liu, Ying; Duan, Weimin; Paschall, Justin; Saccone, Nancy L

2007-01-01

149

Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes.  

PubMed

Inter-individual differences in gene expression are likely to account for an important fraction of phenotypic differences, including susceptibility to common disorders. Recent studies have shown extensive variation in gene expression levels in humans and other organisms, and that a fraction of this variation is under genetic control. We investigated the patterns of gene expression variation in a 25 Mb region of human chromosome 21, which has been associated with many Down syndrome (DS) phenotypes. Taqman real-time PCR was used to measure expression variation of 41 genes in lymphoblastoid cells of 40 unrelated individuals. For 25 genes found to be differentially expressed, additional analysis was performed in 10 CEPH families to determine heritabilities and map loci harboring regulatory variation. Seventy-six percent of the differentially expressed genes had significant heritabilities, and genomewide linkage analysis led to the identification of significant eQTLs for nine genes. Most eQTLs were in trans, with the best result (P=7.46 x 10(-8)) obtained for TMEM1 on chromosome 12q24.33. A cis-eQTL identified for CCT8 was validated by performing an association study in 60 individuals from the HapMap project. SNP rs965951 located within CCT8 was found to be significantly associated with its expression levels (P=2.5 x 10(-5)) confirming cis-regulatory variation. The results of our study provide a representative view of expression variation of chromosome 21 genes, identify loci involved in their regulation and suggest that genes, for which expression differences are significantly larger than 1.5-fold in control samples, are unlikely to be involved in DS-phenotypes present in all affected individuals. PMID:16251198

Deutsch, Samuel; Lyle, Robert; Dermitzakis, Emmanouil T; Attar, Homa; Subrahmanyan, Lakshman; Gehrig, Corinne; Parand, Leila; Gagnebin, Maryline; Rougemont, Jacques; Jongeneel, C Victor; Antonarakis, Stylianos E

2005-12-01

150

Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila melanogaster  

PubMed Central

Predicting organismal phenotypes from genotype data is important for plant and animal breeding, medicine, and evolutionary biology. Genomic-based phenotype prediction has been applied for single-nucleotide polymorphism (SNP) genotyping platforms, but not using complete genome sequences. Here, we report genomic prediction for starvation stress resistance and startle response in Drosophila melanogaster, using ?2.5 million SNPs determined by sequencing the Drosophila Genetic Reference Panel population of inbred lines. We constructed a genomic relationship matrix from the SNP data and used it in a genomic best linear unbiased prediction (GBLUP) model. We assessed predictive ability as the correlation between predicted genetic values and observed phenotypes by cross-validation, and found a predictive ability of 0.239±0.008 (0.230±0.012) for starvation resistance (startle response). The predictive ability of BayesB, a Bayesian method with internal SNP selection, was not greater than GBLUP. Selection of the 5% SNPs with either the highest absolute effect or variance explained did not improve predictive ability. Predictive ability decreased only when fewer than 150,000 SNPs were used to construct the genomic relationship matrix. We hypothesize that predictive power in this population stems from the SNP–based modeling of the subtle relationship structure caused by long-range linkage disequilibrium and not from population structure or SNPs in linkage disequilibrium with causal variants. We discuss the implications of these results for genomic prediction in other organisms. PMID:22570636

Ober, Ulrike; Ayroles, Julien F.; Stone, Eric A.; Richards, Stephen; Zhu, Dianhui; Gibbs, Richard A.; Stricker, Christian; Gianola, Daniel; Schlather, Martin; Mackay, Trudy F. C.; Simianer, Henner

2012-01-01

151

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

152

Phenotypic variation in sexually and asexually recruited individuals of the Baltic Sea endemic macroalga Fucus radicans: in the field and after growth in a common-garden  

PubMed Central

Background Most species of brown macroalgae recruit exclusively sexually. However, Fucus radicans, a dominant species in the northern Baltic Sea, recruits new attached thalli both sexually and asexually. The level of asexual recruitment varies among populations from complete sexual recruitment to almost (> 90%) monoclonal populations. If phenotypic traits have substantial inherited variation, low levels of sexual activity will decrease population variation in these traits, which may affect function and resilience of the species. We assessed the level of inherited variation in nine phenotypic traits by comparing variation within and among three monoclonal groups and one group of unique multilocus genotypes (MLGs) sampled in the wild. Results Of the nine phenotypic traits, recovery after freezing, recovery after desiccation, and phlorotannin content showed substantial inherited variation, that is, phenotypic variation in these traits were to a large extend genetically determined. In contrast, variation in six other phenotypic traits (growth rate, palatability to isopod grazers, thallus width, distance between dichotomies, water content after desiccation and photochemical yield under ambient conditions) did not show significant signals of genetic variation at the power of analyses used in the study. Averaged over all nine traits, phenotypic variation within monoclonal groups was only 68% of the variation within the group of different MLGs showing that genotype diversity does affect the overall level of phenotypic variation in this species. Conclusions Our result indicates that, in general, phenotypic diversity in populations of Fucus radicans increases with increased multilocus genotype (MLG) diversity, but effects are specific for individual traits. In the light of Fucus radicans being a foundation species of the northern Baltic Sea, we propose that increased MLG diversity (leading to increased trait variation) will promote ecosystem function and resilience in areas where F. radicans is common, but this suggestion needs experimental support. PMID:22356775

2012-01-01

153

Predator-Induced Phenotypic Plasticity in Larval Newts: Trade-Offs, Selection, and Variation in Nature  

Microsoft Academic Search

Phenotypic plasticity has important ecological consequences because the strengths of species interactions can change with the behavior and morphology of interacting individuals. Evolutionary studies of plasticity can predict conditions under which shifts in phenotypes will occur and, therefore, may modify species interactions. We studied evo- lutionary mechanisms maintaining an induced response to predators in Triturus newt larvae, which are among

Josh Van Buskirk; Benedikt R. Schmidt

2000-01-01

154

Phenotypic variation within a fenugreek ( Trigonella foenum-graecum L.) germplasm collection. I. Description of the collection  

Microsoft Academic Search

Fenugreek (Trigonella foenum-graecum L.) is a minor crop in Australia with potential for seed, forage and green manuring, with most production based on an unnamed\\u000a cultivar (A150000). A germplasm collection of 205 fenugreek accessions was evaluated in the field in south-eastern Australia\\u000a for a range of phenotypic traits. There was significant variation exhibited for all traits including growth habit, flowering

K. M. McCormick; R. M. Norton; H. A. Eagles

2009-01-01

155

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

156

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

157

Alpha 2 HS glycoprotein phenotypes and quantitative hormone and bone measures in postmenopausal women  

Microsoft Academic Search

Summary  It has been suggested that inherited traits play a role in the development of osteoporosis by providing a background for the\\u000a modulation of gene expression. In this study, we examine the influence of the different alleles of alpha2-HS glycoprotein (AHSG), a protein of the bone matrix, on quantitative estrogens, estrone and estradiol, and bone measures,\\u000a bone area and density. Estrogens

June E. Eichner; Christopher A. Friedrich; Jane A. Cauley; Mohammad I. Kamboh; James P. Gutai; Lewis H. Kuller; Robert E. Ferrell

1990-01-01

158

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

159

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

160

Quantitative estimation of Holocene surface salinity variation in the Black Sea using dinoflagellate cyst process length  

E-print Network

of Environmental Sciences, University of Liverpool, Liverpool L69 7ZT, UK c Institute for East China Sea ResearchQuantitative estimation of Holocene surface salinity variation in the Black Sea using (ECSER), 1-14, Bunkyo-machi, Nagasaki 852-8521, Japan d Geological Survey Canada Atlantic, Dartmouth

Pedersen, Tom

161

Effect of chromosome constitution variations on the expression of Turner phenotype.  

PubMed

Turner syndrome (TS) is a chronic disease related to haploinsufficiency of genes that are normally expressed in both X chromosomes in patients with female phenotype that is associated with a wide range of somatic malformations. We made detailed cytogenetic and clinical analysis of 65 patients with TS from the region of Recife, Brazil, to determine the effects of different chromosome constitutions on expression of the TS phenotype. Overall, patients with X-monosomy exhibited a tendency to have more severe phenotypes with higher morbidity, showing its importance in TS prognosis. Additionally, we found rare genetic and phenotypic abnormalities associated with this syndrome. To the best of our knowledge, this is the first case of 45,X,t(11;12)(q22;q22) described as a TS karyotype. Turner patients usually have normal intelligence; however, moderate to severe levels of mental retardation were found in 5 TS cases, which is considerate a very uncommon feature in this syndrome. PMID:23546984

Bispo, A V S; Dos Santos, L O; Burégio-Frota, P; Galdino, M B; Duarte, A R; Leal, G F; Araújo, J; Gomes, B; Soares-Ventura, E M; Muniz, M T C; Santos, N

2013-01-01

162

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

163

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

164

Quantitative-Trait Loci on Chromosomes 1, 2, 3, 4, 8, 9, 11, 12, and 18 Control Variation in Levels of T and B Lymphocyte Subpopulations  

PubMed Central

Lymphocyte subpopulation levels are used for prognosis and monitoring of a variety of human diseases, especially those with an infectious etiology. As a primary step to defining the major gene variation underlying these phenotypes, we conducted the first whole-genome screen for quantitative variation in lymphocyte count, CD4 T cell, CD8 T cell, B cell, and natural killer cell numbers, as well as CD4:CD8 ratio. The screen was performed in 15 of the CEPH families that form the main human genome genetic project mapping resource. Quantitative-trait loci (QTLs) that account for significant proportions of the phenotypic variance of lymphocyte subpopulations were detected on chromosomes 1, 2, 3, 4, 8, 9, 11, 12, and 18. The most significant QTL found was for CD4 levels on chromosome 8 (empirical P=.00005). Two regions of chromosome 4 showed significant linkage to CD4:CD8 ratio (empirical P=.00007 and P=.003). A QTL for the highly correlated measures of CD4 and CD19 levels colocalized at 18q21 (both P=.003). Similarly, a shared region of chromosome 1 was linked to CD8 and CD19 levels (P=.0001 and P=.002, respectively). Several of the identified chromosome regions are likely to harbor polymorphic candidate genes responsible for these important human phenotypes. Their discovery has important implications for understanding the generation of the immune repertoire and understanding immune-system homeostasis. More generally, these data show the power of an integrated human gene–mapping approach for heritable molecular phenotypes, using large pedigrees that have been extensively genotyped. PMID:11951176

Hall, M. A.; Norman, P. J.; Thiel, B.; Tiwari, H.; Peiffer, A.; Vaughan, R. W.; Prescott, S.; Leppert, M.; Schork, N. J.; Lanchbury, J. S.

2002-01-01

165

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

166

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

USGS Publications Warehouse

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. Published 2011. This article is a US Government work and is in the public domain in the USA.

Letcher, B.H.; Coombs, J.A.; Nislow, K.H.

2011-01-01

167

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

PubMed Central

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

2011-01-01

168

Feeding preferences and host associations of specialist marine herbivores align with quantitative variation in seaweed secondary metabolites  

Microsoft Academic Search

Consequences of congeneric quantitative variation in secondary metabolites of seaweeds on diet specificity and host association in specialist marine her- bivores have received little attention. We investigated quantitative variation in caulerpenyne and oxytoxin 1 in 7 species of green seaweeds from the genus Caulerpa, along with the feeding preferences and host associations of 4 co-occurring sacoglossan molluscs. C. taxifolia and

Finn A. Baumgartner; Cherie A. Motti; Rocky de Nys; Nicholas A. Paul

2009-01-01

169

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

170

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

171

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

NASA Astrophysics Data System (ADS)

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; Zeng, Yingzhi; Huang, Zuohua

2014-09-01

172

Fleece variation in alpaca (Vicugna pacos): a two-locus model for the Suri/Huacaya phenotype  

PubMed Central

Background Genetic improvement of fibre-producing animal species has often induced transition from double coated to single coated fleece, accompanied by dramatic changes in skin follicles and hair composition, likely implying variation at multiple loci. Huacaya, the more common fleece phenotype in alpaca (Vicugna pacos), is characterized by a thick dense coat growing perpendicularly from the body, whereas the alternative rare and more prized single-coated Suri phenotype is distinguished by long silky fibre that grows parallel to the body and hangs in separate, distinctive pencil locks. A single-locus genetic model has been proposed for the Suri-Huacaya phenotype, where Huacaya is recessive. Results Two reciprocal experimental test-crosses (Suri × Huacaya) were carried out, involving a total of 17 unrelated males and 149 unrelated females. An additional dataset of 587 offspring of Suri × Suri crosses was analyzed. Segregation ratios, population genotype frequencies, and/or recombination fraction under different genetic models were estimated by maximum likelihood. The single locus model for the Suri/Huacaya phenotype was rejected. In addition, we present two unexpected observations: 1) a large proportion (about 3/4) of the Suri animals are segregating (with at least one Huacaya offspring), even in breeding conditions where the Huacaya trait would have been almost eliminated; 2) a model with two different values of the segregation ratio fit the data significantly better than a model with a single parameter. Conclusions The data support a genetic model in which two linked loci must simultaneously be homozygous for recessive alleles in order to produce the Huacaya phenotype. The estimated recombination rate between these loci was 0.099 (95% C.L. = 0.029-0.204). Our genetic analysis may be useful for other species whose breeding system produces mainly half-sib families. PMID:20646304

2010-01-01

173

Transcriptional analysis of a Photorhabdus sp. variant reveals transcriptional control of phenotypic variation and multifactorial pathogenicity in insects.  

PubMed

Photorhabdus luminescens lives in a mutualistic association with entomopathogenic nematodes and is pathogenic for insects. Variants of Photorhabdus frequently arise irreversibly and are studied because they have altered phenotypic traits that are potentially important for the host interaction. VAR* is a colonial and phenotypic variant displaying delayed pathogenicity when directly injected into the insect, Spodoptera littoralis. In this study, we evaluated the role of transcriptomic modulation in determining the phenotypic variation and delayed pathogenicity of VAR* with respect to the corresponding wild-type form, TT01?. A P. luminescens microarray identified 148 genes as differentially transcribed between VAR* and TT01?. The net regulator status of VAR* was found to be significantly modified. We also observed in VAR* a decrease in the transcription of genes supporting certain phenotypic traits, such as pigmentation, crystalline inclusion, antibiosis, and protease and lipase activities. Three genes encoding insecticidal toxins (pit and pirB) or putative insecticidal toxins (xnp2) were less transcribed in VAR* than in the TT01?. The overexpression of these genes was not sufficient to restore the virulence of VAR* to the levels of ??01?, which suggests that the lower virulence of VAR* does not result from impaired toxemia in insects. Three loci involved in oxidative stress responses (sodA, katE, and the hca operon) were found to be downregulated in VAR*. This is consistent with the greater sensitivity of VAR* to H(2)O(2) and may account for the impaired bacteremia in the hemolymph of S. littoralis larvae observed with VAR*. In conclusion, we demonstrate here that some phenotypic traits of VAR* are regulated transcriptionally and highlight the multifactorial nature of pathogenicity in insects. PMID:21131515

Lanois, A; Pages, S; Bourot, S; Canoy, A-S; Givaudan, A; Gaudriault, S

2011-02-01

174

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

175

Clonal expansion of the Pseudogymnoascus destructans genotype in North America is accompanied by significant variation in phenotypic expression.  

PubMed

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

176

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

177

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

178

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...

179

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

180

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

181

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

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

Mapping quantitative trait loci controlling variation in forage quality traits in barley  

Microsoft Academic Search

Barley forage quality has a direct relationship to animal performance, but forage quality traits are often neglected or not\\u000a accessible to the plant breeders. Doubled haploid lines (145) from the cross Steptoe × Morex were grown in 2 years of trails\\u000a under irrigated conditions to evaluate the variation in forage quality characteristics, identify quantitative trait loci (QTL)\\u000a for these traits and determine if

Lisa Surber; Hussein Abdel-Haleem; Jack Martin; Pat Hensleigh; Dennis Cash; Jan Bowman; Tom Blake

2011-01-01

184

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

185

Phenotypic variation in exopolysaccharide production in the marine, aerobic nitrogen-fixing unicellular cyanobacterium Cyanothece sp  

Microsoft Academic Search

The aerobic nitrogen-fixing cyanobacterium, Cyanothece sp. BH68K produces non-mucoid variants defective in exopolysaccharide (EPS) production at a high frequency. The EPS-producing wild-type colonies (EPS+) have a characteristic smooth and shiny appearance which allows them to be easily distinguished from the EPS- variants. When grown on agar plates lacking a source of combined nitrogen, the EPS- variants exhibited a yellow phenotype

K. J. Reddy; B. W. Soper; J. Tang; R. L. Bradley

1996-01-01

186

Phenotypic variation in Actinobacillus actionmycetemcomitans during laboratory growth: implications for virulence  

Microsoft Academic Search

This study examined alteration of specific virulence traits associated with phenotypic changes seen when a low-passage disease-associated and well maintained parent strain of Actinobacillus actinomycetemcomitans was compared to a laboratory-grown spontaneous variantlmutant. Clinical isolates of A. actinomycetemcomitans recovered from periodontitis patients typically grow as rough, adherent colonies on primary culture but undergo transformation to smooth, non-adherent colonies following repeated passage

Daniel H. Fine; David Furgang; Helen C. Schreiner; Paul Goncharoff; J. Charlesworth; G. Ghazwan; P. Fitzgerald-Bocarsly; D. H. Figurski

1999-01-01

187

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

188

Relative importance of genetic, ontogenetic, induction, and seasonal variation in producing a multivariate defense phenotype in a foundation tree species.  

PubMed

Plant adaptations for defense against herbivory vary both among species and among genotypes. Moreover, numerous forms of within-plant variation in defense, including ontogeny, induction, and seasonal gradients, allow plants to avoid expending resources on defense when herbivores are absent. We used an 18-year-old cottonwood common garden composed of Populus fremontii, Populus angustifolia, and their naturally occurring F(1) hybrids (collectively referred to as "cross types") to quantify and compare the relative influences of three hierarchical levels of variation (between cross types, among genotypes, and within individual genotypes) on univariate and multivariate phytochemical defense traits. Within genotypes, we evaluated ontogeny, induction (following cottonwood leaf beetle herbivory), and seasonal variation. We compared the effect sizes of each of these sources of variation on the plant defense phenotype. Three major patterns emerged. First, we observed significant differences in concentrations of defense phytochemicals among cross types, and/or among genotypes within cross types. Second, we found significant genetic variation for within-plant differences in phytochemical defenses: (a) based on ontogeny, levels of constitutive phenolic glycosides were nearly three times greater in the mature zone than in the juvenile zone within one cottonwood cross type, but did not significantly differ within another cross type; (b) induced levels of condensed tannins increased up to 65 % following herbivore damage within one cottonwood cross type, but were not significantly altered in another cross type; and (c) concentrations of condensed tannins tended to increase across the season, but did not do so across all cross types. Third, our estimates of effect size demonstrate that the magnitude of within-plant variation in a phytochemical defense can rival the magnitude of differences in defense among genotypes and/or cross types. We conclude that, in cottonwood and likely other plant species, multiple forms of within-individual variation have the potential to substantially influence ecological and evolutionary processes. PMID:22652923

Holeski, Liza M; Hillstrom, Michael L; Whitham, Thomas G; Lindroth, Richard L

2012-11-01

189

Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin/TOR and associated phenotypes in Drosophila melanogaster  

PubMed Central

Background A molecular process based genotype-to-phenotype map will ultimately enable us to predict how genetic variation among individuals results in phenotypic alterations. Building such a map is, however, far from straightforward. It requires understanding how molecular variation re-shapes developmental and metabolic networks, and how the functional state of these networks modifies phenotypes in genotype specific way. We focus on the latter problem by describing genetic variation in transcript levels of genes in the InR/TOR pathway among 72 Drosophila melanogaster genotypes. Results We observe tight co-variance in transcript levels of genes not known to influence each other through direct transcriptional control. We summarize transcriptome variation with factor analyses, and observe strong co-variance of gene expression within the dFOXO-branch and within the TOR-branch of the pathway. Finally, we investigate whether major axes of transcriptome variation shape phenotypes expected to be influenced through the InR/TOR pathway. We find limited evidence that transcript levels of individual upstream genes in the InR/TOR pathway predict fly phenotypes in expected ways. However, there is no evidence that these effects are mediated through the major axes of downstream transcriptome variation. Conclusion In summary, our results question the assertion of the 'sparse' nature of genetic networks, while validating and extending candidate gene approaches in the analyses of complex traits. PMID:19317915

Nuzhdin, Sergey V; Brisson, Jennifer A; Pickering, Andrew; Wayne, Marta L; Harshman, Lawrence G; McIntyre, Lauren M

2009-01-01

190

Genetic and phenotypic variations of inherited retinal diseases in dogs: the power of within- and across-breed studies  

PubMed Central

Considerable clinical and molecular variations have been known in retinal blinding diseases in man and also in dogs. Different forms of retinal diseases occur in specific breed(s) caused by mutations segregating within each isolated breeding population. While molecular studies to find genes and mutations underlying retinal diseases in dogs have benefited largely from the phenotypic and genetic uniformity within a breed, within- and across-breed variations have often played a key role in elucidating the molecular basis. The increasing knowledge of phenotypic, allelic, and genetic heterogeneities in canine retinal degeneration has shown that the overall picture is rather more complicated than initially thought. Over the past 20 years, various approaches have been developed and tested to search for genes and mutations underlying genetic traits in dogs, depending on the availability of genetic tools and sample resources. Candidate gene, linkage analysis, and genome-wide association studies have so far identified 24 mutations in 18 genes underlying retinal diseases in at least 58 dog breeds. Many of these genes have been associated with retinal diseases in humans, thus providing opportunities to study the role in pathogenesis and in normal vision. Application in therapeutic interventions such as gene therapy has proven successful initially in a naturally occurring dog model followed by trials in human patients. Other genes whose human homologs have not been associated with retinal diseases are potential candidates to explain equivalent human diseases and contribute to the understanding of their function in vision. PMID:22065099

Acland, Gregory M.

2014-01-01

191

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

192

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

193

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

194

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

195

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

196

Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness.  

PubMed

Background Lactococcus lactis is industrially employed to manufacture various fermented dairy products. The most cost-effective method for the preservation of L. lactis starter cultures is spray drying, but during this process cultures encounter heat and oxidative stress, typically resulting in low survival rates. However, viability of starter cultures is essential for their adequate contribution to milk fermentation, supporting the ambition to better understand and improve their robustness phenotypes.ResultsThis study describes a transcriptome-phenotype matching approach in which the starter L. lactis MG1363 was fermented under a variety of conditions that differed in the levels of oxygen and/or salt, as well as the fermentation pH and temperature. Samples derived from these fermentations in the exponential phase of bacterial growth were analyzed by full-genome transcriptomics and the assessment of heat and oxidative stress phenotypes. Variations in the fermentation conditions resulted in up to 1000-fold differences in survival during heat and oxidative stress. More specifically, aeration during fermentation induced protection against heat stress, whereas a relatively high fermentation temperature resulted in enhanced robustness towards oxidative stress. Concomitantly, oxygen levels and fermentation temperature induced differential expression of markedly more genes when compared with the other fermentation parameters. Correlation analysis of robustness phenotypes and gene expression levels revealed transcriptome signatures for oxidative and/or heat stress survival, including the metC-cysK operon involved in methionine and cysteine metabolism. To validate this transcriptome-phenotype association we grew L. lactis MG1363 in the absence of cysteine which led to enhanced robustness towards oxidative stress.ConclusionsOverall, we demonstrated the importance of careful selection of fermentation parameters prior to industrial processing of starter cultures. Furthermore, established stress genes as well as novel genes were associated with robustness towards heat and/or oxidative stress. Assessment of the expression levels of this group of genes could function as an indicator for enhanced selection of fermentation parameters resulting in improved robustness during spray drying. The increased robustness after growth without cysteine appeared to confirm the role of expression of the metC-cysK operon as an indicator of robustness and suggests that sulfur amino acid metabolism plays a pivotal role in oxidative stress survival. PMID:25366036

Dijkstra, Annereinou R; Alkema, Wynand; Starrenburg, Marjo; Hugenholtz, Jeroen; van Hijum, Sacha; Bron, Peter A

2014-11-01

197

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

198

A Comparison of Isozyme and Quantitative Genetic Variation in Pinus contorta ssp. latifolia by FsT  

Microsoft Academic Search

We employed Fstatistics 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 (&) for six quantitative traits were compared with the overall estimate of the differentiation (fir) from 19 isozymes that tested neutral to examine whether similar evolutionary

Rong-Cai Yang; Francis C. Yeh; Alvin D. Yanchukt

199

Litter Size Variation in Hypothalamic Gene Expression Determines Adult Metabolic Phenotype in Brandt's Voles (Lasiopodomys brandtii)  

PubMed Central

Background Early postnatal environments may have long-term and potentially irreversible consequences on hypothalamic neurons involved in energy homeostasis. Litter size is an important life history trait and negatively correlated with milk intake in small mammals, and thus has been regarded as a naturally varying feature of the early developmental environment. Here we investigated the long-term effects of litter size on metabolic phenotype and hypothalamic neuropeptide mRNA expression involved in the regulation of energy homeostasis, using the offspring reared from large (10–12) and small (3–4) litter sizes, of Brandt's voles (Lasiopodomys brandtii), a rodent species from Inner Mongolia grassland in China. Methodology/Principal Findings Hypothalamic leptin signaling and neuropeptides were measured by Real-Time PCR. We showed that offspring reared from small litters were heavier at weaning and also in adulthood than offspring from large litters, accompanied by increased food intake during development. There were no significant differences in serum leptin levels or leptin receptor (OB-Rb) mRNA in the hypothalamus at weaning or in adulthood, however, hypothalamic suppressor of cytokine signaling 3 (SOCS3) mRNA in adulthood increased in small litters compared to that in large litters. As a result, the agouti-related peptide (AgRP) mRNA increased in the offspring from small litters. Conclusions/Significance These findings support our hypothesis that natural litter size has a permanent effect on offspring metabolic phenotype and hypothalamic neuropeptide expression, and suggest central leptin resistance and the resultant increase in AgRP expression may be a fundamental mechanism underlying hyperphagia and the increased risk of overweight in pups of small litters. Thus, we conclude that litter size may be an important and central determinant of metabolic fitness in adulthood. PMID:21637839

Zhang, Xue-Ying; Zhang, Qiang; Wang, De-Hua

2011-01-01

200

Colour and size variation in Junonia villida (Lepidoptera, Nymphalidae): subspecies or phenotypic plasticity?  

Microsoft Academic Search

Colour pattern and size variation in the widespread Indo-Pacific Meadow Argus butterfly, Junonia villida (Fabricius, 1787), are reviewed based largely on examination of c. 1500 museum specimens from across its entire geographical range. Including villida, 14 available species-group names for this taxon are documented. The butterfly is recorded from some 200 islands or island groups. Larvae are reported to feed

R. I. VANE-WRIGHT; W. JOHN TENNENT

2011-01-01

201

Strategy for minimizing between-study variation of large-scale phenotypic experiments using multivariate analysis.  

PubMed

We have developed a multistep strategy that integrates data from several large-scale experiments that suffer from systematic between-experiment variation. This strategy removes such variation that would otherwise mask differences of interest. It was applied to the evaluation of wood chemical analysis of 736 hybrid aspen trees: wild-type controls and transgenic trees potentially involved in wood formation. The trees were grown in four different greenhouse experiments imposing significant variation between experiments. Pyrolysis coupled to gas chromatography/mass spectrometry (Py-GC/MS) was used as a high throughput-screening platform for fingerprinting of wood chemotype. Our proposed strategy includes quality control, outlier detection, gene specific classification, and consensus analysis. The orthogonal projections to latent structures discriminant analysis (OPLS-DA) method was used to generate the consensus chemotype profiles for each transgenic line. These were thereafter compiled to generate a global dataset. Multivariate analysis and cluster analysis techniques revealed a drastic reduction in between-experiment variation that enabled a global analysis of all transgenic lines from the four independent experiments. Information from in-depth analysis of specific transgenic lines and independent peak identification validated our proposed strategy. PMID:22978754

Pinto, Rui C; Gerber, Lorenz; Eliasson, Mattias; Sundberg, Björn; Trygg, Johan

2012-10-16

202

Genetic variation and phenotypic plasticity in a trophically polymorphic population of pumpkinseed sunfish ( Lepomis gibbosus )  

Microsoft Academic Search

Summary Adaptive variation can exist at a variety of scales in biological systems, including among species, among local populations of a single species and among individuals within a single population. Trophic or resource polymorphisms in fishes are a good example of the lowest level of this hierarchy. In lakes without bluegill sunfish (Lepomis macrochirus), pumpkinseed sunfish (Lepomis gibbosus) can be

Beren W. Robinson; David Sloan Wilson

1996-01-01

203

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

E-print Network

and between species. Examples of intraspecific color variation in rodents include the canyon mouse (Peromyscus crinitus), the deer mouse (Peromyscus maniculatus), the oldfield mouse (Peromyscus polionotus), Botta (Sumner, 1921; Dice and Blossom, 1937), studies in Peromyscus have clearly demonstrated that owls

Hoekstra, Hopi E.

204

One quantitative trait locus for intra- and interspecific variation in a sex pheromone.  

PubMed

Even though premating isolation is hypothesized to be a major driving force in speciation, its genetic basis is poorly known. In the noctuid moth Heliothis subflexa, one group of sex pheromone components, the acetates, emitted by the female, plays a crucial isolating role in preventing interspecific matings to males of the closely related Heliothis virescens, in which females do not produce acetates and males are repelled by them. We previously found intraspecific variation in acetates in H. subflexa: females in eastern North America contain significantly more acetates than females in Western Mexico. Here we describe the persistence of this intraspecific variation in laboratory-reared strains and the identification of one major quantitative trait locus (QTL), explaining 40% of the variance in acetate amounts. We homologized this intraspecific QTL to our previously identified interspecific QTL using restriction-associated DNA (RAD) tags. We found that a major intraspecific QTL overlaps with one of the two major interspecific QTL. To identify candidate genes underlying the acetate variation, we investigated a number of gene families with known or suspected acetyl- or acyltransferase activity. The most likely candidate genes did not map to our QTL, so that we currently hypothesize that a transcription factor underlies this QTL. Finding a single, large QTL that impacts variation in pheromone blends between and within species is, to our knowledge, the first such example for traits that have been demonstrated to affect premating isolation. PMID:23294019

Groot, A T; Staudacher, H; Barthel, A; Inglis, O; Schöfl, G; Santangelo, R G; Gebauer-Jung, S; Vogel, H; Emerson, J; Schal, C; Heckel, D G; Gould, F

2013-02-01

205

Phenotypic variation and host interactions of Xenorhabdus bovienii SS-2004, the entomopathogenic symbiont of Steinernema jollieti nematodes  

PubMed Central

Summary Xenorhabdus bovienii (SS-2004) bacteria reside in the intestine of the infective-juvenile (IJ) stage of the entomopathogenic nematode, Steinernema jollieti. The recent sequencing of the X. bovienii genome facilitates its use as a model to understand host-symbiont interactions. To provide a biological foundation for such studies, we characterized X. bovienii in vitro and host-interaction phenotypes. Within the nematode host X. bovienii was contained within a membrane bound envelope that also enclosed the nematode-derived intravesicular structure. S. jollieti nematodes cultivated on mixed lawns of X. bovienii expressing green or DsRed fluorescent proteins were predominantly colonized by one or the other strain, suggesting the colonizing population is founded by a few cells. X. bovienii exhibits phenotypic variation between orange-pigmented primary form and cream-pigmented secondary form. Each form can colonize IJ nematodes when cultured in vitro on agar. However, IJs did not develop or emerge from Galleria mellonella insects infected with secondary form. Unlike primary-form infected insects that were soft and flexible, secondary-form infected insects retained a rigid exoskeleton structure. X. bovienii primary and secondary form isolates are virulent toward Manduca sexta and several other insects. However, primary form stocks present attenuated virulence, suggesting that X. bovienii, like X. nematophila may undergo virulence modulation. PMID:22151385

Sugar, Darby R.; Murfin, Kristen E.; Chaston, John M.; Andersen, Aaron W.; Richards, Gregory R.; deLéon, Limaris; Baum, James A.; Clinton, William P.; Forst, Steven; Goldman, Barry S.; Krasomil-Osterfeld, Karina C.; Slater, Steven; Stock, S. Patricia; Goodrich-Blair, Heidi

2011-01-01

206

DNA hypermethylation and X chromosome inactivation are major determinants of phenotypic variation in women heterozygous for G6PD mutations.  

PubMed

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked incompletely dominant enzyme deficiency that results from G6PD gene mutations. Women heterozygous for G6PD mutations exhibit variation in the loss of enzyme activity but the cause of this phenotypic variation is unclear. We determined DNA methylation and X-inactivation patterns in 71 G6PD-deficient female heterozygotes and 68 G6PD non-deficient controls with the same missense mutations (G6PD Canton c.1376G>T or Kaiping c.1388G>A) to correlate determinants with variable phenotypes. Specific CpG methylations within the G6PD promoter were significantly higher in G6PD-deficient heterozygotes than in controls. Preferential X-inactivation of the G6PD wild-type allele was determined in heterozygotes. The incidence of preferential X-inactivation was 86.2% in the deficient heterozygote group and 31.7% in the non-deficient heterozygote group. A significant negative correlation was observed between X-inactivation ratios of the wild-type allele and G6PD/6-phosphogluconate dehydrogenase (6PGD) ratios in heterozygous G6PD Canton (r=-0.657, p<0.001) or Kaiping (r=-0.668, p<0.001). Multivariate logistic regression indicated that heterozygotes with hypermethylation of specific CpG sites in the G6PD promoter and preferential X-inactivation of the wild-type allele were at risk of enzyme deficiency. PMID:24958328

Wang, Jin; Xiao, Qi-Zhi; Chen, You-Ming; Yi, Sheng; Liu, Dun; Liu, Yan-Hui; Zhang, Cui-Mei; Wei, Xiao-Feng; Zhou, Yu-Qiu; Zhong, Xing-Ming; Zhao, Cun-You; Xiong, Fu; Wei, Xiang-Cai; Xu, Xiang-Min

2014-12-01

207

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

208

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

209

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

210

Sex-specific quantitative trait loci contribute to normal variation in bone structure at the proximal femur in men  

PubMed Central

Bone structure is an important determinant of osteoporotic fracture. In women bone structure is highly heritable and several quantitative trait loci (QTL) have been reported. There are few comparable data in men. This study in men aimed at establishing the heritability of bone structure at the proximal femur, identifying QTL contributing to normal variation in bone structure, and determining which QTL might be sex-specific. Bone structure at the proximal femur was measured in 205 pairs of brothers age 18–61. Heritability was calculated and linkage analysis performed on phenotypes at the proximal femur. Heritability estimates ranged from 0.99 to 0.39. A genome wide scan identified suggestive QTL (LOD>2.2) for femoral shaft width on chromosome 14q (LOD=2.69 at position 99cM), calcar femorale at chromosome 2p (LOD= 3.97 at position 194cM) and at the X chromosome (LOD= 3.01 at position 77cM), femoral neck width on chromosome 5p (LOD=2.28 at position 0 cM), femoral head width on chromosome 11q (LOD=2.30 at position 131 cM) and 15q (LOD=3.11 at position 90 cM), and pelvic axis length on chromosome 4q (LOD= 4.16 at 99cM) and 17q (LOD=2.80 at position 112 cM). Comparison with published data in 437 pairs of premenopausal sisters from the same geographical region suggested that 3 of the 7 autosomal QTL were male-specific. This study demonstrates that bone structure at the proximal femur in healthy men is highly heritable. The occurrence of sex-specific genes in humans for bone structure has important implications for the pathogenesis and treatment of osteoporosis. PMID:16046210

Peacock, Munro; Koller, Daniel L.; Lai, Dongbing; Hui, Siu; Foroud, Tatiana; Econs, Michael J.

2006-01-01

211

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

212

Daily stress reactivity and serotonin transporter gene (5-HTTLPR) variation: internalizing responses to everyday stress as a possible transdiagnostic phenotype  

PubMed Central

Background Recent studies examining the interaction between the 5-HTTLPR locus in the serotonin transporter gene and life stress in predicting depression have yielded equivocal results, leading some researchers to question whether 5-HTTLPR variation indeed regulates depressive responses to stress. Two possible sources of inconsistent data in this literature are imprecise stress assessment methodologies and a restricted focus on depression phenotypes as the outcome of interest, as opposed to transdiagnostic emotional symptoms such as internalizing and externalizing dimensions. The present study aimed to address these critical limitations in prior research by examining how 5-HTTLPR acts in concert with idiographically assessed daily life stress to predict transdiagnostic emotional outcomes. Results One hundred and four healthy young adults genotyped for 5-HTTLPR reported on their life stress exposure and internalizing and externalizing experiences for 14 consecutive days. As hypothesized, daily stress levels were associated with severity of internalizing symptoms, but only for 5-HTTLPR S allele carriers. Additional analyses revealed that these interactive effects of 5-HTTLPR and daily life stress on internalizing symptoms extended to both the distress and fear subdomains of internalizing symptoms. Conclusions Considered together, these results support the validity of the 5-HTTLPR stress sensitivity hypothesis and suggest for the first time that variation at 5-HTTLPR moderates the effects of daily life stress on broadband symptom profiles. PMID:24461074

2014-01-01

213

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

214

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

215

Association between allelic variation due to short tandem repeats in tRNA gene of Entamoeba histolytica and clinical phenotypes of amoebiasis.  

PubMed

Genotypes of Entamoeba histolytica (E. histolytica) may contribute clinical phenotypes of amoebiasis such as amoebic liver abscess (ALA), dysentery and asymptomatic cyst passers state. Hence, we evaluated allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica and clinical phenotypes of amoebiasis. Asymptomatic cyst passers (n=24), patients with dysentery (n=56) and ALA (n=107) were included. Extracted DNA from stool (dysentery, asymptomatic cyst passers) and liver aspirate was amplified using 6 E. histolytica specific tRNA-linked STRs (D-A, A-L, N-K2, R-R, S-Q, and S(TGA)-D) primers. PCR products were subjected to sequencing. Association between allelic variation and clinical phenotypes was analyzed. A total of 9 allelic variations were found in D-A, 8 in A-L, 4 in N-K2, 5 in R-R, 10 in S(TAG)-D and 7 in S-Q loci. A significant association was found between allelic variants and clinical phenotypes of amoebiasis. This study reveals that allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica is associated different clinical outcome of amoebiasis. PMID:24495629

Jaiswal, Virendra; Ghoshal, Ujjala; Mittal, Balraj; Dhole, Tapan N; Ghoshal, Uday C

2014-05-01

216

Two Chinese pedigrees for adenomatous polyposis coli: new mutations at codon 1309 and predisposition to phenotypic variations.  

PubMed

Familial adenomatous polyposis (FAP) is an autosomal dominant inherited disease caused by a mutation in the adenomatous polyposis coli (APC) gene. Some studies have attempted to correlate mutations at codon 1309 with classic FAP (?100 colorectal polyps). We report two Chinese FAP pedigrees with new frameshift mutations at codon 1309, in which affected individuals manifest phenotypic variations. Comprehensive physical examinations were performed for all living individuals and the medical data of deceased patients were collected. Screening of the APC and human mutY homolog (MUTYH) genes for germline mutations was conducted by direct polymerase chain reaction (PCR) sequencing. In two pedigrees, a heterozygous deletion in exon 16 of the APC gene was present in all FAP patients but absent in the unaffected individuals. There were no changes to the MUTYH gene. The first pedigree, with a new frameshift mutation at c.3926_3930 del AAAAG (p. Glu1309Aspfs X4), exhibited obvious differences in the polyp number such that the proband manifested only three colorectal polyps, whereas another patients showed the symptoms of classic FAP. The second pedigree, also traced a new mutation at c.3922_3925 del AAAG (p. Glu1309Argfs X11). Although all of the patients presented with classic polyposis, one of them exhibited a delayed onset of colorectal cancer in his 50s. Two novel mutations at codon 1309 in two Chinese families suffering from FAP could enrich the germline mutation spectrum of the APC gene. Families of individuals might manifest different phenotypes, even with an identical codon 1309 mutation, unlike in previous studies. PMID:24664542

Liao, Dai-Xiang; Li, Bing; Du, Xue-Mei; Yu, Jun-Hui; Chang, Hong; Wu, Zhi-Qiang; Hao, Hao-Jie; Wang, You-Xin; Han, Wei-Dong; Cheng, Shu-Jun; Luo, Cheng-Hua

2014-09-01

217

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

218

Segmental Quantitative MR Imaging Analysis of Diurnal Variation of Water Content in the Lumbar Intervertebral Discs  

PubMed Central

Objective To investigate the changes in water content in the lumbar intervertebral discs by quantitative T2 MR imaging in the morning after bed rest and evening after a diurnal load. Materials and Methods Twenty healthy volunteers were separately examined in the morning after bed rest and in the evening after finishing daily work. T2-mapping images were obtained and analyzed. An equally-sized rectangular region of interest (ROI) was manually placed in both, the anterior and the posterior annulus fibrosus (AF), in the outermost 20% of the disc. Three ROIs were placed in the space defined as the nucleus pulposus (NP). Repeated-measures analysis of variance and paired 2-tailed t tests were used for statistical analysis, with p < 0.05 as significantly different. Results T2 values significantly decreased from morning to evening, in the NP (anterior NP = -13.9 ms; central NP = -17.0 ms; posterior NP = -13.3 ms; all p < 0.001). Meanwhile T2 values significantly increased in the anterior AF (+2.9 ms; p = 0.025) and the posterior AF (+5.9 ms; p < 0.001). T2 values in the posterior AF showed the largest degree of variation among the 5 ROIs, but there was no statistical significance (p = 0.414). Discs with initially low T2 values in the center NP showed a smaller degree of variation in the anterior NP and in the central NP, than in discs with initially high T2 values in the center NP (10.0% vs. 16.1%, p = 0.037; 6.4% vs. 16.1%, p = 0.006, respectively). Conclusion Segmental quantitative T2 MRI provides valuable insights into physiological aspects of normal discs.

Zhu, Tingting; Ai, Tao; Zhang, Wei; Li, Tao

2015-01-01

219

A Geographically Diverse Collection of Schizosaccharomyces pombe Isolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity  

PubMed Central

The fission yeast Schizosaccharomyces pombe has been widely used to study eukaryotic cell biology, but almost all of this work has used derivatives of a single strain. We have studied 81 independent natural isolates and 3 designated laboratory strains of Schizosaccharomyces pombe. Schizosaccharomyces pombe varies significantly in size but shows only limited variation in proliferation in different environments compared with Saccharomyces cerevisiae. Nucleotide diversity, ?, at a near neutral site, the central core of the centromere of chromosome II is approximately 0.7%. Approximately 20% of the isolates showed karyotypic rearrangements as detected by pulsed field gel electrophoresis and filter hybridization analysis. One translocation, found in 6 different isolates, including the type strain, has a geographically widespread distribution and a unique haplotype and may be a marker of an incipient speciation event. All of the other translocations are unique. Exploitation of this karyotypic diversity may cast new light on both the biology of telomeres and centromeres and on isolating mechanisms in single-celled eukaryotes. PMID:22384373

Brown, William R. A.; Liti, Gianni; Rosa, Carlos; James, Steve; Roberts, Ian; Robert, Vincent; Jolly, Neil; Tang, Wen; Baumann, Peter; Green, Carter; Schlegel, Kristina; Young, Jonathan; Hirchaud, Fabienne; Leek, Spencer; Thomas, Geraint; Blomberg, Anders; Warringer, Jonas

2011-01-01

220

COL1A1 Sp1 variation and bone phenotypes in an Italian population  

PubMed Central

Summary Background Osteoporosis is the most common metabolic bone disorder of the elderly, affecting the normal bone turnover with an increased bone resorption and subsequent higher risk of fragility fractures. Collagen type 1 is the most represented protein in bone matrix. A genetic variation (Sp1) in intron 1 of COL1A1 gene has been associated to modulation of expression of the alpha 1 chain of collagen type 1 and it is considered a candidate polymorphism for predisposition to osteoporosis status and fragility fractures. Association studies, in ethnically different populations, are needed to strongly confirm the role of this polymorphism in bone metabolism. Materials and methods We enrolled over 2,000 Italian individuals and studied their bone mineral density (BMD) and fractures in relation to age, sex and body mass index (BMI). Moreover, we analyzed the distribution of Sp1 polymorphism in these individuals and associated it to normal bone status, osteopenic condition or osteoporosis diagnosis, BMD and the presence of low-trauma fractures. Results The most rare ss genotype showed a trend for osteoporosis diagnosis with respect to both normal and osteopenic status. The same genotype resulted to be associated to lower values of BMD both at spine and femur sites. No association was found with fractures. Discussion In conclusion the presence of the homozygote ss genotype seemed to predispose to osteoporosis diagnosis and to be more frequent in subjects with lower spine and femur BMD values. PMID:24133532

Marini, Francesca; Parri, Simone; Masi, Laura; Ciuffi, Simone; Guazzini, Andrea; Fabbri, Sergio; Luzi, Ettore; Cianferotti, Luisella; Brandi, Maria Luisa

2013-01-01

221

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

222

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

223

Quantitative estimation of temperature variations in plantar angiosomes: a study case for diabetic foot.  

PubMed

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

224

Combination of differential growth at two different temperatures with a quantitative real-time polymerase chain reaction to determine temperature-sensitive phenotype of Mycoplasma synoviae.  

PubMed

Mycoplasma synoviae infections result in significant economic losses in the chicken and turkey industries. A commercially available live temperature-sensitive (ts (+)) vaccine strain MS-H has been found to be effective in controlling M. synoviae infections in commercial layer and broiler breeder farms in various countries, including Australia. Detection and differentiation of MS-H from field strains (ts (-)) and from ts (-) MS-H reisolates in vaccinated flocks is vital in routine flock status monitoring. At present microtitration is the only available technique to determine the ts phenotype of M. synoviae. This technique is time consuming and not amenable to automation. In the present study, a quantitative real-time polymerase chain reaction (Q-PCR) was combined with simultaneous culturing of M. synoviae at two different temperatures (33°C and 39.5°C) to determine the ts phenotype of 22 Australian M. synoviae strains/isolates. The M. synoviae type strain WVU-1853 was also included for comparison. A ratio of the copy numbers of the variable lipoprotein haemagglutinin (vlhA) gene at the two temperatures was calculated and a cut-off value was determined and used to delineate the ts phenotype. In all M. synoviae strains/isolates tested in this study, the ts phenotype determined using Q-PCR was in agreement with that determined using conventional microtitration. Combination of Q-PCR with differential growth at two different temperatures is a rapid, reliable and accurate technique that could be used as an effective tool in laboratories actively involved in ts phenotyping of M. synoviae strains/isolates. PMID:23581447

Shahid, Muhammad A; Ghorashi, Seyed A; Agnew-Crumpton, Rebecca; Markham, Philip F; Marenda, Marc S; Noormohammadi, Amir H

2013-04-01

225

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

226

Phenotype variation in two-locus mouse models of Hirschsprung disease: Tissue-specific interaction between Ret and Ednrb  

PubMed Central

Clinical expression of Hirschsprung disease (HSCR) requires the interaction of multiple susceptibility genes. Molecular genetic analyses have revealed that interactions between mutations in the genes encoding the RET receptor tyrosine kinase and the endothelin receptor type B (EDNRB) are central to the genesis of HSCR. We have established two locus noncomplementation assays in mice, using allelic series at Ednrb in the context of Ret kinase-null heterozygotes, to understand the clinical presentation, incomplete penetrance, variation in length of aganglionic segment, and sex bias observed in human HSCR patients. Titration of Ednrb in the presence of half the genetic dose of Ret determines the presentation of an enteric phenotype in these strains, revealing or abrogating a sex bias in disease expression depending on the genotype at Ednrb. RET and EDNRB signaling pathways are also critical for the normal development of other tissues, including the kidneys and neural crest-derived melanocytes. Our data demonstrate that interaction between these genes is restricted to the enteric nervous system and does not affect renal, coat color, and retinal choroid development. PMID:12574515

McCallion, Andrew S.; Stames, Erine; Conlon, Ronald A.; Chakravarti, Aravinda

2003-01-01

227

Quantitative trait loci influencing cholesterol and phospholipid phenotypes map to chromosomes that contain genes regulating blood pressure in the spontaneously hypertensive rat.  

PubMed Central

The frequent coincidence of hypertension and dyslipidemia suggests that related genetic factors might underlie these common risk factors for cardiovascular disease. To investigate whether quantitative trait loci (QTLs) regulating lipid levels map to chromosomes known to contain genes regulating blood pressure, we used a genome scanning approach to map QTLs influencing cholesterol and phospholipid phenotypes in a large set of recombinant inbred strains and in congenic strains derived from the spontaneously hypertensive rat and normotensive Brown-Norway (BN.Lx) rat fed normal and high cholesterol diets. QTLs regulating lipid phenotypes were mapped by scanning the genome with 534 genetic markers. A significant relationship (P < 0.00006) was found between basal HDL2 cholesterol levels and the D19Mit2 marker on chromosome 19. Analysis of congenic strains of spontaneously hypertensive rat indicated that QTLs regulating postdietary lipid phenotypes exist also on chromosomes 8 and 20. Previous studies in the recombinant inbred and congenic strains have demonstrated the presence of blood pressure regulatory genes in corresponding segments of chromosomes 8, 19, and 20. These findings provide support for the hypothesis that blood pressure and certain lipid subfractions can be modulated by linked genes or perhaps even the same genes. PMID:8698878

Bottger, A; van Lith, H A; Kren, V; Krenová, D; Bílá, V; Vorlícek, J; Zídek, V; Musilová, A; Zdobinská, M; Wang, J M; van Zutphen, B F; Kurtz, T W; Pravenec, M

1996-01-01

228

An unbiased method for the quantitation of disease phenotypes using a custom-built macro plugin for the program ImageJ.  

PubMed

Accurate evaluation of disease phenotypes is considered a key step to study plant-microbe interactions, as the rate of host colonization by the pathogenic microbe directly reflects whether the defense response of the plant is compromised. Although several techniques were developed to quantitate the amount of infection, only a few of them are inherently suitable for large disease screens. Here, I describe an unbiased method to quantitate disease phenotypes which manifest themselves by visible symptoms contrasting with the remaining unaffected parts of the host tissue. The method utilizes a macro plugin written for the image processing program "ImageJ" to calculate two values which determine the disease index for a specific treatment. In case the disease symptoms are not clear, a transgenic pathogenic fungus expressing the GUS gene is suitable for high-throughput disease screens, since staining for GUS activity facilitates an easy detection of the blue-stained pathogen. I illustrate the versatility of this method by analyzing a data set from a functional silencing screening experiment in resistant tomato that was inoculated with a GUS-expressing strain of the fungus Cladosporium fulvum. The method calculates a disease index for each silenced plant and thereby provides a basis for the unbiased identification of candidate host genes required for full resistance to this fungus. PMID:22183684

Abd-El-Haliem, Ahmed

2012-01-01

229

A Quantitative Comparison of Human HT-1080 Fibrosarcoma Cells and Primary Human Dermal Fibroblasts Identifies a 3D Migration Mechanism with Properties Unique to the Transformed Phenotype  

PubMed Central

Here, we describe an engineering approach to quantitatively compare migration, morphologies, and adhesion for tumorigenic human fibrosarcoma cells (HT-1080s) and primary human dermal fibroblasts (hDFs) with the aim of identifying distinguishing properties of the transformed phenotype. Relative adhesiveness was quantified using self-assembled monolayer (SAM) arrays and proteolytic 3-dimensional (3D) migration was investigated using matrix metalloproteinase (MMP)-degradable poly(ethylene glycol) (PEG) hydrogels (“synthetic extracellular matrix” or “synthetic ECM”). In synthetic ECM, hDFs were characterized by vinculin-containing features on the tips of protrusions, multipolar morphologies, and organized actomyosin filaments. In contrast, HT-1080s were characterized by diffuse vinculin expression, pronounced ?1-integrin on the tips of protrusions, a cortically-organized F-actin cytoskeleton, and quantitatively more rounded morphologies, decreased adhesiveness, and increased directional motility compared to hDFs. Further, HT-1080s were characterized by contractility-dependent motility, pronounced blebbing, and cortical contraction waves or constriction rings, while quantified 3D motility was similar in matrices with a wide range of biochemical and biophysical properties (including collagen) despite substantial morphological changes. While HT-1080s were distinct from hDFs for each of the 2D and 3D properties investigated, several features were similar to WM239a melanoma cells, including rounded, proteolytic migration modes, cortical F-actin organization, and prominent uropod-like structures enriched with ?1-integrin, F-actin, and melanoma cell adhesion molecule (MCAM/CD146/MUC18). Importantly, many of the features observed for HT-1080s were analogous to cellular changes induced by transformation, including cell rounding, a disorganized F-actin cytoskeleton, altered organization of focal adhesion proteins, and a weakly adherent phenotype. Based on our results, we propose that HT-1080s migrate in synthetic ECM with functional properties that are a direct consequence of their transformed phenotype. PMID:24349113

Schwartz, Michael P.; Rogers, Robert E.; Singh, Samir P.; Lee, Justin Y.; Loveland, Samuel G.; Koepsel, Justin T.; Witze, Eric S.; Montanez-Sauri, Sara I.; Sung, Kyung E.; Tokuda, Emi Y.; Sharma, Yasha; Everhart, Lydia M.; Nguyen, Eric H.; Zaman, Muhammad H.; Beebe, David J.; Ahn, Natalie G.; Murphy, William L.; Anseth, Kristi S.

2013-01-01

230

A quantitative comparison of human HT-1080 fibrosarcoma cells and primary human dermal fibroblasts identifies a 3D migration mechanism with properties unique to the transformed phenotype.  

PubMed

Here, we describe an engineering approach to quantitatively compare migration, morphologies, and adhesion for tumorigenic human fibrosarcoma cells (HT-1080s) and primary human dermal fibroblasts (hDFs) with the aim of identifying distinguishing properties of the transformed phenotype. Relative adhesiveness was quantified using self-assembled monolayer (SAM) arrays and proteolytic 3-dimensional (3D) migration was investigated using matrix metalloproteinase (MMP)-degradable poly(ethylene glycol) (PEG) hydrogels ("synthetic extracellular matrix" or "synthetic ECM"). In synthetic ECM, hDFs were characterized by vinculin-containing features on the tips of protrusions, multipolar morphologies, and organized actomyosin filaments. In contrast, HT-1080s were characterized by diffuse vinculin expression, pronounced ?1-integrin on the tips of protrusions, a cortically-organized F-actin cytoskeleton, and quantitatively more rounded morphologies, decreased adhesiveness, and increased directional motility compared to hDFs. Further, HT-1080s were characterized by contractility-dependent motility, pronounced blebbing, and cortical contraction waves or constriction rings, while quantified 3D motility was similar in matrices with a wide range of biochemical and biophysical properties (including collagen) despite substantial morphological changes. While HT-1080s were distinct from hDFs for each of the 2D and 3D properties investigated, several features were similar to WM239a melanoma cells, including rounded, proteolytic migration modes, cortical F-actin organization, and prominent uropod-like structures enriched with ?1-integrin, F-actin, and melanoma cell adhesion molecule (MCAM/CD146/MUC18). Importantly, many of the features observed for HT-1080s were analogous to cellular changes induced by transformation, including cell rounding, a disorganized F-actin cytoskeleton, altered organization of focal adhesion proteins, and a weakly adherent phenotype. Based on our results, we propose that HT-1080s migrate in synthetic ECM with functional properties that are a direct consequence of their transformed phenotype. PMID:24349113

Schwartz, Michael P; Rogers, Robert E; Singh, Samir P; Lee, Justin Y; Loveland, Samuel G; Koepsel, Justin T; Witze, Eric S; Montanez-Sauri, Sara I; Sung, Kyung E; Tokuda, Emi Y; Sharma, Yasha; Everhart, Lydia M; Nguyen, Eric H; Zaman, Muhammad H; Beebe, David J; Ahn, Natalie G; Murphy, William L; Anseth, Kristi S

2013-01-01

231

Quantitative Susceptibility Mapping of Human Brain Reflects Spatial Variation in Tissue Composition  

PubMed Central

Image phase from gradient echo MRI provides a unique contrast that reflects brain tissue composition variations, such as iron and myelin distribution. Phase imaging is emerging as a powerful tool for the investigation of functional brain anatomy and disease diagnosis. However, the quantitative value of phase is compromised by its nonlocal and orientation dependent properties. There is an increasing need for reliable quantification of magnetic susceptibility, the intrinsic property of tissue. In this study, we developed a novel and accurate susceptibility mapping method that is also phase-wrap insensitive. The proposed susceptibility mapping method utilized two complementary equations: (1) the Fourier relationship of phase and magnetic susceptibility; and (2) the first-order partial derivative of the first equation in the spatial frequency domain. In numerical simulation, this method reconstructed the susceptibility map almost free of streaking artifact. Further, the iterative implementation of this method allowed for high quality reconstruction of susceptibility maps of human brain in vivo. The reconstructed susceptibility map provided excellent contrast of iron-rich deep nuclei and white matter bundles from surrounding tissues. Further, it also revealed anisotropic magnetic susceptibility in brain white matter. Hence, the proposed susceptibility mapping method may provide a powerful tool for the study of brain physiology and pathophysiology. Further elucidation of anisotropic magnetic susceptibility in vivo may allow us to gain more insight into the white matter microarchitectures. PMID:21224002

Li, Wei; Wu, Bing; Liu, Chunlei

2011-01-01

232

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

233

Buschke-Ollendorff syndrome with striking phenotypic variation resulting from a novel c.2203C>T nonsense mutation in LEMD3.  

PubMed

The Buschke-Ollendorff syndrome (BOS) (MIM 166700) is a rare autosomal dominant disorder with highly variable expression that consists of multiple cutaneous elastic nevi and osteopoikilosis. It may exhibit clinical variations, and in some patients either skin or bone lesions may be absent. Recently it has been demonstrated that the heterozygous loss of function in LEMD3 can result in osteopoikilosis, BOS, and melorheostosis. We have studied three generations in a family with BOS with a variable phenotype. The genetic analyses revealed a heterozygous c.2203C>T nonsense mutation at the LEMD3 locus. The mutation induces a change in the 735 arginine codon to a stop codon. This study shows the wide phenotypic variation in BOS and increases the repertory of mutations described to date in LEMD3. PMID:20678097

Yuste-Chaves, Manuela; Cañueto, Javier; Santos-Briz, Ángel; Ciria, Sara; González-Sarmiento, Rogelio; Unamuno, Pablo

2011-01-01

234

Effects of protected fish oil in the diet of periparturient dairy goats on phenotypic variation in blood and milk leukocytes.  

PubMed

The goal of this study was to evaluate the effects of dietary protected fish oil (FO) on phenotypic variation in blood, milk leukocytes, and some productive and metabolic parameters in periparturient dairy goats. About 12 Alpine goats, selected from a larger group of second-parity animals, were fed from 15 days before kidding until the 15th day of lactation with the same basal diet that had been supplemented with either 47 g/head per day of FO or 47 g/head per day hydrogenated palm oil (PO). Dry matter intake, live body weight (LBW), body condition score (BCS), and productive performance were evaluated in 2 weeks after kidding. On days 15, 7, and 2 before kidding and days 2, 7, and 15 after kidding, plasma samples were collected for evaluation of alanine aminotransferase, aspartate aminotransferase, non-esterified fatty acids, glucose, beta-hydroxybutyrate, cholesterol, and urea levels. White blood cell and blood leukocyte subsets were counted in whole blood samples on the kidding day, as well as at 1, 4, and 15 days after kidding. In addition, milk somatic cell count, intramammary infection (IMI), and milk leukocyte subsets were evaluated on days 4 and 15 after kidding. No differences were observed in dry matter intake and BCS, while LBW was higher in FO-fed animals. Milk production and composition, plasma metabolites, and liver enzymes were similar in both experimental groups. Blood CD4 positive cells increased constantly (P = 0.05) in FO-fed group, while CD8 and CD14 cell counts significantly increased 4 days after kidding (P < 0.01). Milk leukocyte subsets showed a significant (P < 0.01) decrease in PO-fed group and a non-significant increase (P = 0.34) in FO-fed group, despite the presence of coagulase negative staphylococci IMI. The results of the productive performance evaluation agreed with those of many other studies, which did not find any significant differences between dairy goats fed diets enriched with FO or PO supplements. The administration of FO to dairy goats in transition appeared to affect the variation in blood leukocytes with a constant increase in CD4- and CD8-positive cells in comparison with a PO fat-supplemented diet. PMID:22444697

Bronzo, V; Puricelli, M; Agazzi, A; Invernizzi, G; Ferroni, M; Moroni, P; Savoini, G

2010-09-01

235

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 Central

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

236

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

237

Structural variation in the Waxy gene and differentiation in foxtail millet [Setaria italica (L.) P. Beauv.]: implications for multiple origins of the waxy phenotype.  

PubMed

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 locus in 79 strains with various waxy phenotypes. We then carried out genomic Southern analysis on 67 strains and identified seven RFLP classes which were designated as types I-VII. RFLP type was correlated with phenotype, such that types I and II corresponded to non-waxy, types III and VI to low-amylose, and types IV, V and VII to waxy phenotypes. The differences between RFLP types could be attributed to insertions in the Waxy gene. Types II and VI were caused by the insertion of a Tourist element into intron 1 and a SINE-like sequence into intron 12, respectively. Types III, IV, V and VII were characterized by the insertion of large sequences into the Waxy gene that may alter the expression of the gene. Thus, multiple, independent insertions in the Waxy gene appear to have caused the loss-of-function waxy phenotypes. Furthermore, the geographical distributions of the three RFLP types associated with the waxy phenotype (types IV, V and VII) were distinct, with type IV being found mainly in Taiwan and Japan, type V in Korea, and type VII in Myanmar. These results indicate a polyphyletic origin for the waxy phenotype in landraces of foxtail millet. PMID:12395195

Fukunaga, K; Kawase, M; Kato, K

2002-10-01

238

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

239

Simulating the yield impacts of organ-level quantitative trait loci associated with drought response in maize: a "gene-to-phenotype" modeling approach.  

PubMed

Under drought, substantial genotype-environment (G x E) interactions impede breeding progress for yield. Identifying genetic controls associated with yield response is confounded by poor genetic correlations across testing environments. Part of this problem is related to our inability to account for the interplay of genetic controls, physiological traits, and environmental conditions throughout the crop cycle. We propose a modeling approach to bridge this "gene-to-phenotype" gap. For maize under drought, we simulated the impact of quantitative trait loci (QTL) controlling two key processes (leaf and silk elongation) that influence crop growth, water use, and grain yield. Substantial G x E interaction for yield was simulated for hypothetical recombinant inbred lines (RILs) across different seasonal patterns of drought. QTL that accelerated leaf elongation caused an increase in crop leaf area and yield in well-watered or preflowering water deficit conditions, but a reduction in yield under terminal stresses (as such "leafy" genotypes prematurely exhausted the water supply). The QTL impact on yield was substantially enhanced by including pleiotropic effects of these QTL on silk elongation and on consequent grain set. The simulations obtained illustrated the difficulty of interpreting the genetic control of yield for genotypes influenced only by the additive effects of QTL associated with leaf and silk growth. The results highlight the potential of integrative simulation modeling for gene-to-phenotype prediction and for exploiting G x E interactions for complex traits such as drought tolerance. PMID:19786622

Chenu, Karine; Chapman, Scott C; Tardieu, François; McLean, Greg; Welcker, Claude; Hammer, Graeme L

2009-12-01

240

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

241

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

242

Variation of quantitative composition of phenolic compounds in rowan (Sorbus aucuparia L.) leaves during the growth season.  

PubMed

The aim of our study was to explore variation peculiarities of qualitative and quantitative composition of phenolic compounds in leaf samples of rowan (Sorbus aucuparia L.) plants growing in natural habitats of Lithuania during their growth season using the HPLC method. In rowan leaf samples, collected during different phenological stages, qualitative and quantitative estimation of neochlorogenic acid, chlorogenic acid, caffeic acid, hyperoside, isoquercitrin, rutin, astragalin, ( - )-epicatechin, procyanidin B1 and procyanidin B2 was performed. Analysis of the qualitative and quantitative composition of phenolic compounds in ethanol extracts of leaf samples of S. aucuparia growing in natural habitats of Lithuania revealed a close relationship between the content of phenolic compounds in S. aucuparia raw plant material and different growth stages. PMID:24697599

Gaivelyte, Kristina; Jakstas, Valdas; Razukas, Almantas; Janulis, Valdimaras

2014-01-01

243

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

244

A Semi-Quantitative Method to Denote Generic Physical Activity Phenotypes from Long-Term Accelerometer Data – The ATLAS Index  

PubMed Central

Background Physical activity is inversely correlated to morbidity and mortality risk. Large cohort studies use wearable accelerometer devices to measure physical activity objectively, providing data potentially relevant to identify different activity patterns and to correlate these to health-related outcome measures. A method to compute relevant characteristics of such data not only with regard to duration and intensity, but also to regularity of activity events, is necessary. The aims of this paper are to propose a new method – the ATLAS index (Activity Types from Long-term Accelerometric Sensor data) – to derive generic measures for distinguishing different characteristic activity phenotypes from accelerometer data, to propose a comprehensive graphical representation, and to conduct a proof-of-concept with long-term measurements from different devices and cohorts. Methods The ATLAS index consists of the three dimensions regularity (reg), duration (dur) and intensity (int) of relevant activity events identified in long-term accelerometer data. It can be regarded as a 3D vector and represented in a 3D cube graph. 12 exemplary data sets of three different cohort studies with 99,467 minutes of data were chosen for concept validation. Results Five archetypical activity types are proposed along with their dimensional characteristics (insufficiently active: low reg, int and dur; busy bee: low dur and int, high reg; cardio-active: medium reg, int and dur, endurance athlete: high reg, int and dur; and weekend warrior: high int and dur, low reg). The data sets are displayed in one common graph, indicating characteristic differences in activity patterns. Conclusion The ATLAS index incorporates the relevant regularity dimension apart from the widely-used measures of duration and intensity. Along with the 3D representation, it allows to compare different activity types in cohort study populations, both visually and computationally using vector distance measures. Further research is necessary to validate the ATLAS index in order to find normative values and group centroids. PMID:23667631

Marschollek, Michael

2013-01-01

245

Quantitative and phenotypic analyses of lymphocyte-monocyte heterokaryons induced by the HIV envelope proteins: Significant loss of lymphoid markers.  

PubMed

Cells infected with the human immunodeficiency virus (HIV) can fuse with CD4(+) cells leading to the formation of multinucleated cells. The presence of multinucleated cells infected with HIV in tissues of patients has been documented, although their cellular composition and role in AIDS pathogenesis is still under study. Here, we present evidence of in vitro heterotypic lymphocyte-monocyte fusion in cocultures of lymphocytic Jurkat T cells expressing the HIV-1 gp120/gp41 glycoproteins (Env) and CD4(+) monocytic THP-1 cells. Using a previously characterized method that involves differential labeling of fusion partners with fluorescent probes and flow cytometry analysis after coculture, up to 20% of double fluorescent cells were detected in 48h. This double fluorescent cell population was produced by heterotypic lymphocyte-monocyte fusion as it was not observed when Jurkat T cells expressing a mutant non-fusogenic Env protein were used. Heterokaryon formation was inhibited by an anti-CD4 monoclonal antibody and the HIV-fusion inhibitor peptide T-20. About 68% of heterokaryons remained alive and non-apoptotic after 2days of coculture. In heterokaryons, CD4 was barely detectable and the expression of the CD3 and CD28 lymphoid markers was greatly reduced, whereas the expression of CD32 and the intracellular antigen CD68, both markers of monocytic cells, remained unchanged. In contrast with unfused T cells, heterokaryons only expressed very low levels of the lymphoid activation marker CD25 following treatment with PMA plus ionomycin. These studies point to the possible generation of lymphocyte-monocyte heterokaryons with a myeloid phenotype during HIV infection, with unknown consequences for AIDS pathogenesis. PMID:21110955

Rivera-Toledo, Evelyn; Huerta, Leonor; Larralde, Carlos; Lamoyi, Edmundo

2011-04-01

246

The effects of qualitative and quantitative variation of aristolochic acids on preference and performance of a  

E-print Network

might ignore qualitative variation in activity. Aristolochic acids are alkaloids characteristic broadly be defined as alkaloids. Alkaloids can further be divided into classes of compounds with similar

Fordyce, James

247

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

248

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

E-print Network

Population substructure and biological differentiation was studied among the Golla, a pastoral caste living in the southern areas of Andhra Pradesh (AP) in India, using 11 anthropometric measurements and 20 quantitative dermatoglyphic variables...

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

2001-04-01

249

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

250

Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species.  

PubMed

Genes involved in the process of memory formation have been studied intensively in model organisms; however, little is known about the mechanisms that are responsible for natural variation in memory dynamics. There is substantial variation in memory retention among closely related species in the parasitic wasp genus Nasonia. After a single olfactory conditioning trial, N. vitripennis consolidates long-term memory that lasts at least 6 days. Memory of the closely related species N. giraulti is present at 24?h but is lost within 2 days after a single trial. The genetic basis of this interspecific difference in memory retention was studied in a backcrossing experiment in which the phenotype of N. giraulti was selected for in the background of N. vitripennis for up to five generations. A genotyping microarray revealed five regions that were retained in wasps with decreased memory retention. Independent introgressions of individual candidate regions were created using linked molecular markers and tested for memory retention. One region on chromosome 1 (spanning ?5.8?cM) and another on chromosome 5 (spanning ?25.6?cM) resulted in decreased memory after 72?h, without affecting 24-h-memory retention. This phenotype was observed in both heterozygous and homozygous individuals. Transcription factor CCAAT/enhancer-binding protein and a dopamine receptor, both with a known function in memory formation, are within these genomic regions and are candidates for the regulation of memory retention. Concluding, this study demonstrates a powerful approach to study variation in memory retention and provides a basis for future research on its genetic basis. PMID:25052416

Hoedjes, K M; Smid, H M; Vet, L E M; Werren, J H

2014-12-01

251

Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species  

PubMed Central

Genes involved in the process of memory formation have been studied intensively in model organisms; however, little is known about the mechanisms that are responsible for natural variation in memory dynamics. There is substantial variation in memory retention among closely related species in the parasitic wasp genus Nasonia. After a single olfactory conditioning trial, N. vitripennis consolidates long-term memory that lasts at least 6 days. Memory of the closely related species N. giraulti is present at 24?h but is lost within 2 days after a single trial. The genetic basis of this interspecific difference in memory retention was studied in a backcrossing experiment in which the phenotype of N. giraulti was selected for in the background of N. vitripennis for up to five generations. A genotyping microarray revealed five regions that were retained in wasps with decreased memory retention. Independent introgressions of individual candidate regions were created using linked molecular markers and tested for memory retention. One region on chromosome 1 (spanning ?5.8?cM) and another on chromosome 5 (spanning ?25.6?cM) resulted in decreased memory after 72?h, without affecting 24-h-memory retention. This phenotype was observed in both heterozygous and homozygous individuals. Transcription factor CCAAT/enhancer-binding protein and a dopamine receptor, both with a known function in memory formation, are within these genomic regions and are candidates for the regulation of memory retention. Concluding, this study demonstrates a powerful approach to study variation in memory retention and provides a basis for future research on its genetic basis. PMID:25052416

Hoedjes, K M; Smid, H M; Vet, L E M; Werren, J H

2014-01-01

252

Variations of ganglioside biosynthetic pathways in the phenotype conversion from myofibroblasts to lipocytes in murine hepatic stellate cell line.  

PubMed

GRX cell line represents hepatic stellate cell and can be transformed from an actively proliferation myofibroblast phenotype into a quiescent fat-storing lipocyte phenotype. Both express the same gangliosides (GM3, GM2, GM1 and GD1a), which are resolved as doublets on HPTLC. Upper/lower band ratio is increased in lipocyte-like cells and the upper band is composed by ceramides with long-chain fatty acids. This study evaluated the contribution of de novo synthesis, sphingosine and Golgi recycling pathways on ganglioside biosynthesis, in both phenotypes. Cells were preincubated with 5 mM beta-chloroalanine (SPT: serine palmitoyltransferase inhibitor) or with 25 muM fumonisin B1 (ceramide synthase inhibitor) and then radiolabeled with [U-(14)C]galactose in the continued presence of inhibitors. Gangliosides were extracted, purified and analyzed by HPTLC. In myofibroblast-like cells, simple gangliosides use the de novo pathway while complex gangliosides are mainly synthesized by recycling pathways. In lipocyte-like cells, de novo pathway has a lesser contribution and this is in agreement with the lower activity of the committed enzyme of sphingolipid synthesis (SPT) detected in this phenotype. SPT mRNA has an identical expression in both phenotypes. It was also observed that gangliosides doublets from myofibroblast-like cells have the same distribution between triton soluble and insoluble fractions (upper band > lower band) while the gangliosides doublets from lipocyte-like cells show an inversion in the insoluble fraction (lower band > upper band) in comparison to soluble fraction. These results indicate that myofibroblast- and lipocyte-like cells have important differences between the glycosphingolipid biosynthetic pathways, which could contribute with the respective glycosphingolipid-enriched membrane microdomain's composition. PMID:17440688

de Aguirres, Aline B; Mello, Paola A; Andrade, Claudia M B; Breier, Ana Carolina; Margis, Rogério; Guaragna, Regina M; Borojevic, Radovan; Guma, Fátima C R; Trindade, Vera M T

2007-09-01

253

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

254

Phenotyping of an in vitro model of ischemic penumbra by iTRAQ-based shotgun quantitative proteomics.  

PubMed

Cerebral ischemia is a major cause of death and long-term disability worldwide. Ischemic penumbra, the electrically silent but metabolically viable perifocal brain tissue, is the target for the much elusive stroke therapy. To characterize the molecular events of the dynamic penumbra, we applied an iTRAQ-based shotgun proteomic approach in an in vitro neuronal model, using the rat B104 neuroblastoma cell line. Various functional and cytometric assays were performed to establish the relevant time-point and conditions for ischemia to recapitulate the pathology of the penumbra. Two replicate iTRAQ experiments identified 1796 and 1566 proteins, respectively (quantitative proteomics for the elucidation of pathophysiology and the discovery of novel therapeutic targets in the field of neuroproteomics. PMID:19916522

Datta, Arnab; Park, Jung Eun; Li, Xin; Zhang, Huoming; Ho, Zhi Shan; Heese, Klaus; Lim, Sai Kiang; Tam, James P; Sze, Siu Kwan

2010-01-01

255

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

256

In Vivo Quantitative Microvasculature Phenotype Imaging of Healthy and Malignant Tissues Using a Fiber-Optic Confocal Laser Microprobe1  

PubMed Central

Real-time in vivo imaging of the microvasculature may help both earlier clinical detection of disease and the understanding of tumor-host interaction at various stages of progression. In vivo confocal and multiphoton microscopy is often hampered by bulky optics setup and has limited access to internal organs. A fiber-optic setup avoids these limitations and offers great user maneuverability. We report here the in vivo validation of a fiber-optic confocal fluorescence microprobe imaging system. In addition, we developed an automated fractal-based image analysis to characterize microvascular morphology based on vessel diameter distribution, density, volume fraction, and fractal dimension from real-time data. The system is optimized for use in the far-red and near-infrared region. The flexible 1.5-mm-diameter fiber-optic bundle and microprobe enable great user maneuverability, with a field of view of 423 x 423 µm and a tissue penetration of up to 15 µm. Lateral and axial resolutions are 3.5 and 15 µm. We show that it is possible to obtain high temporal and spatial resolution images of virtually any abdominal viscera in situ using a far-red blood pool imaging probe. Using an orthotopic model of pancreatic ductal adenocarcinoma, we characterized the tumor surface capillary and demonstrated that the imaging system and analysis can quantitatively differentiate between the normal and tumor surface capillary. This clinically approved fiber-optic system, together with the fractal-based image analysis, can potentially be applied to characterize other tumors in vivo and may be a valuable tool to facilitate their clinical evaluation. PMID:18633456

Lin, Ken Young; Maricevich, Marco; Bardeesy, Nabeel; Weissleder, Ralph; Mahmood, Umar

2008-01-01

257

A Novel Quantitative Approach for Eliminating Sample-To-Sample Variation Using a Hue Saturation Value Analysis Program  

PubMed Central

Objectives As computing technology and image analysis techniques have advanced, the practice of histology has grown from a purely qualitative method to one that is highly quantified. Current image analysis software is imprecise and prone to wide variation due to common artifacts and histological limitations. In order to minimize the impact of these artifacts, a more robust method for quantitative image analysis is required. Methods and Results Here we present a novel image analysis software, based on the hue saturation value color space, to be applied to a wide variety of histological stains and tissue types. By using hue, saturation, and value variables instead of the more common red, green, and blue variables, our software offers some distinct advantages over other commercially available programs. We tested the program by analyzing several common histological stains, performed on tissue sections that ranged from 4 µm to 10 µm in thickness, using both a red green blue color space and a hue saturation value color space. Conclusion We demonstrated that our new software is a simple method for quantitative analysis of histological sections, which is highly robust to variations in section thickness, sectioning artifacts, and stain quality, eliminating sample-to-sample variation. PMID:24595280

McMullen, Eri; Figueiredo, Jose Luiz; Aikawa, Masanori; Aikawa, Elena

2014-01-01

258

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

259

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

260

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

261

Variation in Psychosis Gene ZNF804A Is Associated With a Refined Schizotypy Phenotype but Not Neurocognitive Performance in a Large Young Male Population  

PubMed Central

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.

2013-01-01

262

Quantitative autism traits in first degree relatives: evidence for the broader autism phenotype in fathers, but not in mothers and siblings.  

PubMed

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 genetic research suggest that the genetic etiology of ASD is different in multiplex and simplex families. We compared 117 unaffected siblings and 276 parents of at least one child with ASD with 280 children and 595 adults from the general population on the presence of QAT using the Social Responsiveness Scale (SRS). Mean SRS scores for siblings, control children, parents and control adults were 25.4, 26.6, 33.7 and 32.9. Fathers of children with ASD showed significantly higher levels of QAT than controls, but siblings and mothers did not. We could not detect a statistically significant difference in SRS scores between relatives from simplex and multiplex families. These results do not support the theory of differential (genetic) etiology in multiplex and simplex families and suggest that a carried genetic risk is generally not expressed phenotypically in most relatives, except in fathers. PMID:21949002

De la Marche, Wouter; Noens, Ilse; Luts, Jan; Scholte, Evert; Van Huffel, Sabine; Steyaert, Jean

2012-05-01

263

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

264

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

265

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

266

Spatial and temporal variation in the kdr allele L1014S in Anopheles gambiae s.s. and phenotypic variability in susceptibility to insecticides in Western Kenya  

PubMed Central

Background Malaria vector control in Africa depends upon effective insecticides in bed nets and indoor residual sprays. This study investigated the extent of insecticide resistance in Anopheles gambiae s.l., Anopheles gambiae s.s. and Anopheles arabiensis in western Kenya where ownership of insecticide-treated bed nets has risen steadily from the late 1990s to 2010. Temporal and spatial variation in the frequency of a knock down resistance (kdr) allele in A. gambiae s.s. was quantified, as was variation in phenotypic resistance among geographic populations of A. gambiae s.l. Methods To investigate temporal variation in kdr frequency, individual specimens of A. gambiae s.s. from two sentinel sites were genotyped using RT-PCR from 1996-2010. Spatial variation in kdr frequency, species composition, and resistance status were investigated in additional populations of A. gambiae s.l. sampled in western Kenya in 2009 and 2010. Specimens were genotyped for kdr as above and identified to species via conventional PCR. Field-collected larvae were reared to adulthood and tested for insecticide resistance using WHO bioassays. Results Anopheles gambiae s.s. showed a dramatic increase in kdr frequency from 1996 - 2010, coincident with the scale up of insecticide-treated nets. By 2009-2010, the kdr L1014S allele was nearly fixed in the A. gambiae s.s. population, but was absent in A. arabiensis. Near Lake Victoria, A. arabiensis was dominant in samples, while at sites north of the lake A. gambiae s.s was more common but declined relative to A. arabiensis from 2009 to 2010. Bioassays demonstrated that A. gambiae s.s. had moderate phenotypic levels of resistance to DDT, permethrin and deltamethrin while A. arabiensis was susceptible to all insecticides tested. Conclusions The kdr L1014S allele has approached fixation in A. gambiae s.s. populations of western Kenya, and these same populations exhibit varying degrees of phenotypic resistance to DDT and pyrethroid insecticides. The near absence of A. gambiae s.s. from populations along the lakeshore and the apparent decline in other populations suggest that insecticide-treated nets remain effective against this mosquito despite the increase in kdr allele frequency. The persistence of A. arabiensis, despite little or no detectable insecticide resistance, is likely due to behavioural traits such as outdoor feeding and/or feeding on non-human hosts by which this species avoids interaction with insecticide-treated nets. PMID:21235783

2011-01-01

267

Common variations in noncoding regions of the human natriuretic peptide receptor A gene have quantitative effects  

PubMed Central

Genetic susceptibility to common conditions, such as essential hypertension and cardiac hypertrophy, is probably determined by various combinations of small quantitative changes in the expression of many genes. NPR1, coding for natriuretic peptide receptor A (NPRA), is a potential candidate, because NPRA mediates natriuretic, diuretic, and vasorelaxing actions of the nariuretic peptides, and because genetically determined quantitative changes in the expression of this gene affect blood pressure and heart weight in a dose-dependent manner in mice. To determine whether there are common quantitative variants in human NPR1, we have sequenced the entire human NPR1 gene and identified 10 polymorphic sites in its non-coding sequence by using DNA from 34 unrelated human individuals. Five of the sites are single nucleotide polymorphisms; the remaining five are length polymorphisms, including a highly variable complex dinucleotide repeat in intron 19. There are three common haplotypes 5’ to this dinucleotide repeat and three 3’ to it, but the 5’ haplotypes and 3’ haplotypes appear to be randomly associated. Transient expression analysis in cultured cells of reporter plasmids with the proximal promoter sequences of NPR1 and its 3’ untranslated regions showed that these polymorphisms have functional effects. We conclude that common NPR1 alleles can alter expression of the gene as much as two-fold and could therefore significantly affect genetic risks for essential hypertension and cardiac hypertrophy in humans. PMID:12483301

Knowles, Joshua W.; Erickson, Laurie M.; Guy, Vanessa K.; Sigel, Carlie S.; Wilder, Jennifer C.

2009-01-01

268

HSP90 AND THE QUANTITATIVE VARIATION OF WING SHAPE IN DROSOPHILA MELANOGASTER  

Microsoft Academic Search

The molecular chaperone protein Hsp90 has been widely discussed as a candidate gene for developmental buffering. We used the methods of geometric morphometrics to analyze its effects on the variation among individuals and fluctuating asymmetry of wing shape in Drosophila melanogaster. Three different experimental approaches were used to reduce Hsp90 activity. In the first experiment, developing larvae were reared in

Vincent Debat; Claire C. Milton; Suzannah Rutherford; Christian Peter Klingenberg; Ary A. Hoffmann

2006-01-01

269

Induced quantitative variation for penicillin titre in clonal populations of Aspergillus nidulans.  

PubMed

The variation in penicillin titre within populations of cultures of Aspergillus nidulans derived from untreated conidia and from conidia treated with ethyl methanesulphonate (EMS), near-ultraviolet light in the presence of 8-methoxypsoralen (8MOP) or N-methyl-N'-nitro-N-nitrosoguanidine (NTG), each at several dose levels, was determined. Both mutagentreated and untreated populations showed a continuous distribution of pencillin titres. The population mean titre of the mutagenized populations was decreased and the range of titres was increased relative to those of the control populations. No differences between sister cultures could be detected in three untreated populations, but nine out of ten populations derived from mutagenized conidia showed significant variation for penicillin titre. In general the magnitude of this induced variation increased with increasing dosage of the mutagen. Comparisons at fixed survival levels indicate that 8MOP mutagenesis is less effective for the induction of variation in penicillin titre than EMS or NTG mutagenesis. A statistical procedure was adopted to classify the survivors as unchanged cultures ('0'), titre-increasing mutants ('+') or titre-decreasing mutants ("-"). The frequency of both '+' and '-' mutants increased following mutagenesis, with NTG being the most active of the three mutagens. Over all treatments, these two mutant classes were recovered with equal frequency. The frequency of "+" mutants was largely independent of mutagen dose, within the ranges used, and moderate treatments (around 10% survival) gave as high or higher frequencies than more extreme doses. All three mutagens, and in particular NTG, produced morphological mutants. These contained an increased frequency of titre-decreasing mutants, but increases in titre appeared to be independent of changes in colony morphology. Estimates based on the observed frequencies of penicillin titre mutants suggest that several hundred genes are potentially capable of affecting this continuous variable. PMID:372487

Simpson, I N; Caten, C E

1979-01-01

270

Phenotypic differentiation in female preference related to geographic variation in male predation risk in the Trinidad guppy ( Poecilia reticulata )  

Microsoft Academic Search

Populations of the Trinidad guppy range from areas with high levels of predation by other species of fish to areas with little or no piscine predation. Previous studies have shown that variation among populations in male coloration can be explained by a balance between female preference for brighter males and natural selection against bright males. High levels of male courtship

Gregory Stoner; Felix Breden

1988-01-01

271

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

272

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

273

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

274

Morphological variation in the freshwater blenny Salaria fluviatilis from Corsican rivers: adaptive divergence, phenotypic plasticity or both?  

PubMed

The first goal of this study was to determine whether morphological variation in the freshwater blenny Salaria fluviatilis results in spatially structured populations distributed around Corsica, France, which would suggest genetically differentiated populations through reproductive isolation by distance. The second goal was to determine whether some morphological traits are related to water velocity, one of the most contrasting habitat characteristics in these rivers, which would suggest an adaptation to local conditions. The results showed that the morphology of S. fluviatilis differed among the three main geographic areas studied in Corsica and that geographically distant populations of S. fluviatilis were less similar morphologically and genetically than close ones. The results also indicated that the morphological differences among populations conformed to functional expectations. Overall, the results suggest that the morphological variation of S. fluviatilis from Corsican rivers is an adaptive response to water velocity and that these populations are in a process of reproductive isolation by distance. PMID:24524151

Magnan, P; Proulx, R; Berrebi, P; Blondel, J; Perret, P; Roché, B

2014-01-01

275

The effect of variation in physical properties of porous bioactive glass on the expression and maintenance of the osteoblastic phenotype  

NASA Astrophysics Data System (ADS)

Revision surgery to replace failed hip implants is a significant health care issue that is expected to escalate as life expectancy increases. A major goal of revision surgery is to reconstruct femoral intramedullary bone-stock loss. To address this problem of bone loss, grafting techniques are widely used. Although fresh autografts remain the optimal material for all forms of surgery seeking to restore structural integrity to the skeleton, it is evident that the supply of such tissue is limited. In recent years, calcium phosphate ceramics have been studied as alternatives to autografts and allografts. The significant limitations associated with the use of biological and synthetic grafts have led to a growing interest in the in vitro synthesis of bone tissue. The approach is to synthesize bone tissue in vitro with the patient's own cells, and use this tissue for the repair of bony defects. Various substrates including metals, polymers, calcium phosphate ceramics and bioactive glasses, have been seeded with osteogenic cells. The selection of bioactive glass in this study is based on the fact that this material has shown an intense beneficial biological effect which has not been reproduced by other biomaterials. Even though the literature provides extensive data on the effect of pore size and porosity on in vivo bone tissue ingrowth into porous materials for joint prosthesis fixation, the data from past studies cannot be applied to the use of bioactive glass as a substrate for the in vitro synthesis of bone tissue. First, unlike the in vivo studies in the literature, this research deals with the growth of bone tissue in vitro. Second, unlike the implants used in past studies, bioactive glass is a degradable and resorbable material. Thus, in order to establish optimal substrate characteristics (porosity and pore size) for bioactive glass, it was important to study these parameters in an in vitro model. We synthesized porous bioactive glass substrates (BG) with varying pore sizes and porosity and determined the effect of substrate properties on the expression and maintenance of the osteoblastic phenotype, using an in vitro culture of osteoblast-like cells. Our data showed that porous bioactive glass substrates support the proliferation and maturation of osteoblast-like cells. Within the conditions of the experiment, we also found that at a given porosity of 44% the pore size of bioactive glass neither directs nor modulates the in vitro expression of the osteoblastic phenotype. On the other hand, at an average pore size of 92 mum, when cultures are maintained for 14 days, cell activity is greatly affected by the substrate porosity. As the porosity increases from 35% to 59%, osteoblast activity is adversely affected. (Abstract shortened by UMI.)

Effah Kaufmann, Elsie Akosua Biraa

276

Genomic Analysis of QTLs and Genes Altering Natural Variation in Stochastic Noise  

Microsoft Academic Search

Quantitative genetic analysis has long been used to study how natural variation of genotype can influence an organism's phenotype. While most studies have focused on genetic determinants of phenotypic average, it is rapidly becoming understood that stochastic noise is genetically determined. However, it is not known how many traits display genetic control of stochastic noise nor how broadly these stochastic

Jose M. Jimenez-Gomez; Jason A. Corwin; Bindu Joseph; Julin N. Maloof; Daniel J. Kliebenstein

2011-01-01

277

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

278

Properties of the phenotypic variants of Pseudomonas aurantiaca and P. fluorescens  

Microsoft Academic Search

Different capacity for phenotypic variation of Pseudomonas aurantiaca and P. fluorescens in populations of cyst-like resting cells (CRC) during their germination on solid media, was shown to be a characteristic\\u000a trait of biodiversity for the dormant forms of these bacteria. This biodiversity manifests itself as qualitative and quantitative\\u000a differences in the spectra and emergence frequency of phenotype variants, obtained by

A. L. Mulyukin; A. N. Kozlova; G. I. El’-Registan

2008-01-01

279

Phenotypic profiling of DPYD variations relevant to 5-fluorouracil sensitivity using real-time cellular analysis and in vitro measurement of enzyme activity  

PubMed Central

In the 45 years since its development, the pyrimidine analog 5-fluorouracil (5-FU) has become an integral component of many cancer treatments, most notably for the management of colorectal cancer. An appreciable fraction of patients who receive 5-FU suffer severe adverse toxicities, which in extreme cases may result in death. Dihydropyrimidine dehydrogenase (DPD, encoded by DPYD) rapidly degrades 85% of administered 5-FU, and as such, limits the amount of drug available for conversion into active metabolites. Clinical studies have suggested that genetic variations in DPYD increase the risk for 5-FU toxicity, however there is not a clear consensus as to which variations are relevant predictors. In the present study, DPYD variants were expressed in mammalian cells, and the enzymatic activity of expressed protein was determined relative to wild type. Relative sensitivity to 5-FU for cells expressing DPYD variations was also measured. The DPYD*2A variant (exon 14 deletion caused by IVS14+1G>A) was confirmed to be catalytically inactive. Compared to wild type, two variants, S534N and C29R, showed significantly higher enzymatic activity. Cells expressing S534N were more resistant to 5-FU mediated toxicity compared to cells expressing wild type DPYD. These findings support the hypothesis that selected DPYD alleles are protective against severe 5-FU toxicity, and, as a consequence, may decrease the effectiveness of 5-FU an anti tumor drug in carriers. Additionally, this study demonstrates a method that may be useful for phenotyping other genetic variations in pharmacologically relevant pathways. PMID:23328581

Offer, Steven M.; Wegner, Natalie J.; Fossum, Croix; Wang, Kangsheng; Diasio, Robert B.

2013-01-01

280

Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory behaviors  

PubMed Central

Most heritable behavioral traits have a complex genetic basis, but few multigenic traits are understood at a molecular level. Here we show that the C. elegans strains N2 and CB4856 have opposite behavioral responses to simultaneous changes in environmental O2 and CO2. We identify two quantitative trait loci (QTL) that affect this trait, and map each QTL to a single-gene polymorphism. One gene, npr-1, encodes a previously described neuropeptide receptor whose high activity in N2 promotes CO2 avoidance. The second gene, glb-5, encodes a neuronal globin domain protein whose high activity in CB4856 modifies behavioral responses to O2 and combined O2/CO2 stimuli. glb-5 acts in O2–sensing neurons to increase O2-evoked calcium signals, implicating globins in sensory signaling. An analysis of wild C. elegans strains indicates that the N2 alleles of npr-1 and glb-5 arose recently in the same strain background, possibly as an adaptation to laboratory conditions. PMID:19285466

McGrath, Patrick T.; Rockman, Matthew V.; Zimmer, Manuel; Jang, Heeun; Macosko, Evan Z; Kruglyak, Leonid; Bargmann, Cornelia I.

2009-01-01

281

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

282

Variations in type III effector repertoires, pathological phenotypes and host range of Xanthomonas citri pv. citri pathotypes.  

PubMed

The mechanisms determining the host range of Xanthomonas are still undeciphered, despite much interest in their potential roles in the evolution and emergence of plant pathogenic bacteria. Xanthomonas citri pv. citri (Xci) is an interesting model of host specialization because of its pathogenic variants: pathotype A strains infect a wide range of Rutaceous species, whereas pathotype A*/A(W) strains have a host range restricted to Mexican lime (Citrus aurantifolia) and alemow (Citrus macrophylla). Based on a collection of 55 strains representative of Xci worldwide diversity assessed by amplified fragment length polymorphism (AFLP), we investigated the distribution of type III effectors (T3Es) in relation to host range. We examined the presence of 66 T3Es from xanthomonads in Xci and identified a repertoire of 28 effectors, 26 of which were shared by all Xci strains, whereas two (xopAG and xopC1) were present only in some A*/A(W) strains. We found that xopAG (=avrGf1) was present in all A(W) strains, but also in three A* strains genetically distant from A(W) , and that all xopAG-containing strains induced the hypersensitive response (HR) on grapefruit and sweet orange. The analysis of xopAD and xopAG suggested horizontal transfer between X.?citri pv. bilvae, another citrus pathogen, and some Xci strains. A strains were genetically less diverse, induced identical phenotypic responses and possessed indistinguishable T3E repertoires. Conversely, A*/A(W) strains exhibited a wider genetic diversity in which clades correlated with geographical origin and T3E repertoire, but not with pathogenicity, according to T3E deletion experiments. Our data outline the importance of taking into account the heterogeneity of Xci?A*/A(W) strains when analysing the mechanisms of host specialization. PMID:23437976

Escalon, Aline; Javegny, Stéphanie; Vernière, Christian; Noël, Laurent D; Vital, Karine; Poussier, Stéphane; Hajri, Ahmed; Boureau, Tristan; Pruvost, Olivier; Arlat, Matthieu; Gagnevin, Lionel

2013-06-01

283

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

284

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

285

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

286

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

287

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

288

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

289

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

290

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

291

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

292

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

293

Classification of Cryptococcus neoformans and yeast-like fungus isolates from pigeon droppings by colony phenotyping and ITS genotyping and their seasonal variations in Korea.  

PubMed

Cryptococcus neoformans (C neoformans) is a frequent cause of invasive fungal disease in immunocompromised human hosts. Ninety-eight samples of pigeon droppings were collected from the pigeon shelters in Seoul, and cultured on birdseed agar (BSA) and Sabouraud dextrose agar (SDA). One hundred yeast-like colonies were selected and identified via phenotype characteristics, such as colony morphology and biochemical characteristics. This was then followed with genotyping via sequencing of the internal transcribed spacer (ITS) region. The colonies were classified into four kinds of colony color types: brown type (BrT), beige type (BeT), pink type (PT), and white type (WT). Numbers of isolated BrT, BeT, PT, and WT colonies were 22 (22%), 30 (30%), 19 (19%), and 39 (39%), respectively. All BrT colonies were identified as C neoformans. BeT were identified as 19 isolates of Cryptococcus laurentii, 10 isolates of Malassezia furfur, and 1 isolate of Cryptococcus uniguttulatus. PT was divided into two colony color types: light-PT (l-PT) and deep-PT (d-PT). Eighteen of l-PT and one of d-PT were identified as Rhodotorula glutinis and Rhodotorula mucilaginosa, respectively. WT were identified as 34 isolates of Cryptococcus guilliermondii, 3 isolates of Cryptococcus zeylanoides, 1 isolate of Cryptococcus sake, and 1 isolate of Stephanoascus ciferrii. Most strains were classified identically with the use of either phenotype or genotyping techniques, but C uniguttulatus and C sake classified by phenotyping were Pseudozyma aphidis and Cryptococcus famata by genotyping. This rapid screening technique of pathogenic yeast-like fungi by only colony characteristics is also expected to be very useful for primary yeast screening. Additionally, we investigated the seasonal variations of C neoformans and other yeast-like fungi from 379 pigeon-dropping samples that were collected from February 2011 to March 2011. We isolated 685 yeast-like fungi from the samples. Almost all C neoformans and yeast-like fungi were isolated in the fall (298 strains, 43.5%) and spring (244 strains, 35.6%). A few yeast-like fungi were isolated in winter (98 strains, 14.3%) and summer (45 strains, 6%). These results would be used as an important indicator related to epidemiology and prevention of pathogenic yeast-like fungi infections transmitted through pigeon droppings. PMID:22545529

Chae, H S; Jang, G E; Kim, N H; Son, H R; Lee, J H; Kim, S H; Park, G N; Jo, H J; Kim, J T; Chang, K S

2012-03-01

294

Karyotypic and phenotypic variations between cell lines established from a primary colorectal tumour and two corresponding metastases from one patient.  

PubMed

In an attempt to characterise the mode of dissemination of colorectal carcinoma cells in host tissues, we established in vitro 3 human cancer cell lines isolated from a single patient: ALT-I from a primary colorectal tumour, ALT-F from the corresponding hepatic metastasis, and ALT-G from the lymphatic metastasis. The three cell lines exhibit variations in morphology, karyotype, antigens expression, anchorage-independent cell growth and tumorigenicity in nude mice related to their origin. Studies of the biological properties of these cell lines showed that the ALT tumour cells maintain, in vitro, some biochemical expressions, morphological properties and cytogenetic characteristics largely described for colon carcinoma in vivo. Significant increases of carcinoembryonic and CA19.9 antigens expressions were noted in the primary tumour cells as well as in the comparative metastatic ones. The karyotypes shared structural rearrangements and chromosome losses frequently described in fresh colorectal cancers, and revealed increasing alterations from the primary to the hepatic and lymph node tumours. Although the metastatic potential of the ALT cell lines was not demonstrated in the present paper, significant differences in the tumorigenic properties between the primary and the corresponding metastatic tumour cells were evident using in vitro and in vivo investigations. The present data support the hypothesis that, in our model, the hepatic metastasis might occur before or independently of the proximal lymph node metastasis originating from the colorectal carcinoma. PMID:7960578

Grégoire, M; Blottière, H M; Muleris, M; Douillard, J Y; Meflah, K

1993-01-01

295

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

296

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

297

Bone Mineral Density Variation in Men is influenced by Sex-Specific and Non Sex-Specific Quantitative Trait Loci  

PubMed Central

Introduction A major predictor of age-related osteoporotic fracture is peak areal bone mineral density (aBMD) which is a highly heritable trait. However, few linkage and association studies have been performed in men to identify the genes contributing to normal variation in aBMD. The aim of this study was to perform a genome wide scan in healthy men to identify quantitative trait loci (QTL) that were significantly linked to aBMD and to test whether any of these might be sex-specific. Methods aBMD at the spine and hip were measured in 515 pairs of brothers, aged 18-61 (405 white pairs, 110 black pairs). Linkage analysis in the brother sample was compared with results in a previously published sample of 774 sister pairs to identify sex-specific quantitative trait loci (QTL). Results A genome wide scan identified significant QTL (LOD>3.6) for aBMD on chromosomes 4q21 (hip), 7q34 (spine), 14q32 (hip), 19p13 (hip), 21q21 (hip), and 22q13 (hip). Analysis suggested that the QTL on chromosome 7q34, 14q32, and 21q21 were male-specific whereas the others were not sex-specific. Conclusions This study demonstrates that six QTL were significantly linked with aBMD in men. One was linked to spine and five were linked to hip. When compared to published data in women from the same geographical region, the QTL on chromosomes 7, 14 and 21 were male-specific. The occurrence of sex-specific genes in humans for aBMD has important implications for the pathogenesis and treatment of osteoporosis. PMID:19427925

Peacock, Munro; Koller, Daniel L.; Lai, Dongbing; Hui, Siu; Foroud, Tatiana; Econs, Michael J.

2009-01-01

298

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

299

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

300

Next Generation Quantitative Genetics in Plants  

PubMed Central

Most characteristics in living organisms show continuous variation, which suggests that they are controlled by multiple genes. Quantitative trait loci (QTL) analysis can identify the genes underlying continuous traits by establishing associations between genetic markers and observed phenotypic variation in a segregating population. The new high-throughput sequencing (HTS) technologies greatly facilitate QTL analysis by providing genetic markers at genome-wide resolution in any species without previous knowledge of its genome. In addition HTS serves to quantify molecular phenotypes, which aids to identify the loci responsible for QTLs and to understand the mechanisms underlying diversity. The constant improvements in price, experimental protocols, computational pipelines, and statistical frameworks are making feasible the use of HTS for any research group interested in quantitative genetics. In this review I discuss the application of HTS for molecular marker discovery, population genotyping, and expression profiling in QTL analysis. PMID:22645550

Jiménez-Gómez, José M.

2011-01-01

301

The Distribution and ‘In Vivo’ Phase Variation Status of Haemoglobin Receptors in Invasive Meningococcal Serogroup B Disease: Genotypic and Phenotypic Analysis  

PubMed Central

Two haemoglobin-binding proteins, HmbR and HpuAB, contribute to iron acquisition by Neisseria meningitidis. These receptors are subject to high frequency, reversible switches in gene expression - phase variation (PV) - due to mutations in homopolymeric (poly-G) repeats present in the open reading frame. The distribution and PV state of these receptors was assessed for a representative collection of isolates from invasive meningococcal disease patients of England, Wales and Northern Ireland. Most of the major clonal complexes had only the HmbR receptor whilst the recently expanding ST-275-centred cluster of the ST-269 clonal complex had both receptors. At least one of the receptors was in an ‘ON’ configuration in 76.3% of the isolates, a finding that was largely consistent with phenotypic analyses. As PV status may change during isolation and culture of meningococci, a PCR-based protocol was utilised to confirm the expression status of the receptors within contemporaneously acquired clinical specimens (blood/cerebrospinal fluid) from the respective patients. The expression state was confirmed for all isolate/specimen pairs with <15 tract repeats indicating that the PV status of these receptors is stable during isolation. This study therefore establishes a protocol for determining in vivo PV status to aid in determining the contributions of phase variable genes to invasive meningococcal disease. Furthermore, the results of the study support a putative but non-essential role of the meningococcal haemoglobin receptors as virulence factors whilst further highlighting their vaccine candidacy. PMID:24098814

Lucidarme, Jay; Findlow, Jamie; Chan, Hannah; Feavers, Ian M.; Gray, Stephen J.; Kaczmarski, Edward B.; Parkhill, Julian; Bai, Xilian; Borrow, Ray; Bayliss, Christopher D.

2013-01-01

302

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

303

A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene  

Microsoft Academic Search

In nature, genetic variation usually takes the form of a continuous phenotypic range rather than discrete classes. The genetic variation underlying quantitative traits results from the segregation of numerous interacting quantitative trait loci (QTLs), whose expression is modified by the environment. To uncover the molecular basis of this variation, we characterized a QTL (Brix9-2-5) derived from the green-fruited tomato species

Eyal Fridman; Tzili Pleban; Dani Zamir

2000-01-01

304

Physiological Integration and Phenotypic Variation  

E-print Network

Speaker: Lynn "Marty" Martin, PhD Assistant Professor Department of Integrative Biology, University. Martin is interested in how animals endure and thrive in their natu- ral environments. His research

Arnold, Jonathan

305

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement.  

PubMed

More accurate and precise phenotyping strategies are necessary to empower high-resolution linkage mapping and genome-wide association studies and for training genomic selection models in plant improvement. Within this framework, the objective of modern phenotyping is to increase the accuracy, precision and throughput of phenotypic estimation at all levels of biological organization while reducing costs and minimizing labor through automation, remote sensing, improved data integration and experimental design. Much like the efforts to optimize genotyping during the 1980s and 1990s, designing effective phenotyping initiatives today requires multi-faceted collaborations between biologists, computer scientists, statisticians and engineers. Robust phenotyping systems are needed to characterize the full suite of genetic factors that contribute to quantitative phenotypic variation across cells, organs and tissues, developmental stages, years, environments, species and research programs. Next-generation phenotyping generates significantly more data than previously and requires novel data management, access and storage systems, increased use of ontologies to facilitate data integration, and new statistical tools for enhancing experimental design and extracting biologically meaningful signal from environmental and experimental noise. To ensure relevance, the implementation of efficient and informative phenotyping experiments also requires familiarity with diverse germplasm resources, population structures, and target populations of environments. Today, phenotyping is quickly emerging as the major operational bottleneck limiting the power of genetic analysis and genomic prediction. The challenge for the next generation of quantitative geneticists and plant breeders is not only to understand the genetic basis of complex trait variation, but also to use that knowledge to efficiently synthesize twenty-first century crop varieties. PMID:23471459

Cobb, Joshua N; Declerck, Genevieve; Greenberg, Anthony; Clark, Randy; McCouch, Susan

2013-04-01

306

Quantitative developmental genetic analysis reveals that the ancestral dipteran wing vein prepattern is conserved in Drosophila melanogaster  

Microsoft Academic Search

Quantitative complementation tests provide a quick test of the hypothesis that a particular gene contributes to segregating\\u000a phenotypic variation. A set of wild-type alleles is assayed for variation in their ability to complement the degree of dominance\\u000a of the quantitative effect of a loss of function allele. Analysis of 15 loci known to be involved in wing patterning in Drosophila

Arnar Palsson; Greg Gibson

2000-01-01

307

A quantitative genetic and epigenetic model of complex traits  

PubMed Central

Background Despite our increasing recognition of the mechanisms that specify and propagate epigenetic states of gene expression, the pattern of how epigenetic modifications contribute to the overall genetic variation of a phenotypic trait remains largely elusive. Results We construct a quantitative model to explore the effect of epigenetic modifications that occur at specific rates on the genome. This model, derived from, but beyond, the traditional quantitative genetic theory that is founded on Mendel’s laws, allows questions concerning the prevalence and importance of epigenetic variation to be incorporated and addressed. Conclusions It provides a new avenue for bringing chromatin inheritance into the realm of complex traits, facilitating our understanding of the means by which phenotypic variation is generated. PMID:23102025

2012-01-01

308

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

309

Population sub-structure and patterns of quantitative variation among the Gollas of Southern Andhra Pradesh, India  

E-print Network

Population substructure and biological differentiation was studied among the Golla, a pastoral caste living in the southern areas of Andhra Pradesh (AP) in India, using 11 anthropometric measurements and 20 quantitative dermatoglyphic variables...

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

2001-08-01

310

Assessment of the Quantitative Ability of AdvanSure TB/NTM Real-Time PCR in Respiratory Specimens by Comparison with Phenotypic Methods  

PubMed Central

Accurate quantification of mycobacterial load is important to evaluate disease severity and to monitor the course of treatment in tuberculosis (TB). We evaluated the quantitative capability of the AdvanSure TB/NTM real-time PCR kit (LG Life Science, Korea) to determine the cycle threshold (Ct) for mycobacterial burden. We retrospectively analyzed data from 108 patients whose respiratory specimens (sputums and bronchoalveolar lavage fluids) were positive for Mycobacterium tuberculosis complex (85 culture-positive and 23 culture-negative specimens). We compared Ct values with grades of acid-fast bacilli (AFB) staining, semi-quantitative colony count on solid medium, and time to positivity (TTP) in liquid and solid media. We also investigated the cutoff Ct value for predicting stain-positive status. Ct value showed significant reverse correlation with AFB staining grade (rs=-0.635, P<0.01). Ct value significantly decreased as the semi-quantitative counts on the solid medium increased (P<0.001), and the mean Ct value of each of the groups 1+, 2+, 3+, and 4+ were 29.0, 30.0, 27.1, and 25.5, respectively. A weak correlation between Ct value and TTP in liquid and solid media was observed (rs=0.468 and 0.365, respectively). A cutoff Ct value of <33.2 best predicted stain positivity, with a sensitivity of 95.0% and a specificity of 32.0%. Our findings suggest the potential use of AdvanSure TB/NTM real-time PCR kit for quantitatively determining bacterial burden, albeit with some enhancements. PMID:24422196

Lee, Hyeyoung; Park, Kang Gyun; Lee, Gundong; Park, Joonhong; Park, Yong-Gyu

2014-01-01

311

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

312

Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates anxiety in mice  

Microsoft Academic Search

Here we present a strategy to determine the genetic basis of variance in complex phenotypes that arise from natural, as opposed to induced, genetic variation in mice. We show that a commercially available strain of outbred mice, MF1, can be treated as an ultrafine mosaic of standard inbred strains and accordingly used to dissect a known quantitative trait locus influencing

Binnaz Yalcin; Saffron A G Willis-Owen; Jan Fullerton; Anjela Meesaq; Robert M Deacon; J Nicholas P Rawlins; Richard R Copley; Andrew P Morris; Jonathan Flint; Richard Mott

2004-01-01

313

The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information  

Microsoft Academic Search

The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease. The MP Ontology supports different levels and richness of phenotypic knowledge and flexible annotations to individual genotypes. It continues to develop dynamically via collaborative input from research groups, mutagenesis

Cynthia L Smith; Carroll-Ann W Goldsmith; Janan T Eppig

2004-01-01

314

Epistasis and Quantitative Traits: Using Model Organisms to Study Gene-Gene Interactions  

PubMed Central

Summary The role of epistasis in the genetic architecture of quantitative traits is controversial, despite the biological plausibility that non-linear molecular interactions underpin the genotype-phenotype map. This controversy arises because most genetic variation for quantitative traits is additive. However, additive variance is consistent with pervasive epistatic gene action. Here, I discuss experimental designs to detect the contribution of epistasis to quantitative trait phenotypes in model organisms. These studies indicate that epistatic gene action is common, and that additivity can be an emergent property of underlying genetic interaction networks. Epistasis causes hidden quantitative genetic variation in natural populations and could be responsible for the small additive effects, missing heritability and lack of replication typically observed for human complex traits. PMID:24296533

Mackay, Trudy F. C.

2014-01-01

315

High-dimensional and large-scale phenotyping of yeast mutants  

PubMed Central

One of the most powerful techniques for attributing functions to genes in uni- and multicellular organisms is comprehensive analysis of mutant traits. In this study, systematic and quantitative analyses of mutant traits are achieved in the budding yeast Saccharomyces cerevisiae by investigating morphological phenotypes. Analysis of fluorescent microscopic images of triple-stained cells makes it possible to treat morphological variations as quantitative traits. Deletion of nearly half of the yeast genes not essential for growth affects these morphological traits. Similar morphological phenotypes are caused by deletions of functionally related genes, enabling a functional assignment of a locus to a specific cellular pathway. The high-dimensional phenotypic analysis of defined yeast mutant strains provides another step toward attributing gene function to all of the genes in the yeast genome. PMID:16365294

Ohya, Yoshikazu; Sese, Jun; Yukawa, Masashi; Sano, Fumi; Nakatani, Yoichiro; Saito, Taro L.; Saka, Ayaka; Fukuda, Tomoyuki; Ishihara, Satoru; Oka, Satomi; Suzuki, Genjiro; Watanabe, Machika; Hirata, Aiko; Ohtani, Miwaka; Sawai, Hiroshi; Fraysse, Nicolas; Latgé, Jean-Paul; François, Jean M.; Aebi, Markus; Tanaka, Seiji; Muramatsu, Sachiko; Araki, Hiroyuki; Sonoike, Kintake; Nogami, Satoru; Morishita, Shinichi

2005-01-01

316

Does natural selection alter genetic architecture? An evaluation of quantitative genetic variation among populations of Allonemobiussocius and A. fasciatus  

Microsoft Academic Search

To make long-term predictions using present quantitative genetic theory it is necessary to assume that the genetic variance-covariance matrix (G) remains constant or at least changes by a constant fraction. In this paper we examine the stability of the genetic architecture of two traits known to be subject to natural selection; femur length and ovipositor length in two species of

Roff; Mousseau

1999-01-01

317

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

318

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

319

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

320

Gain-of-function phenotypes of many CLAVATA3/ESR genes, including four new family members, correlate with tandem variations in the conserved CLAVATA3/ESR domain.  

PubMed

Secreted peptide ligands are known to play key roles in the regulation of plant growth, development, and environmental responses. However, phenotypes for surprisingly few such genes have been identified via loss-of-function mutant screens. To begin to understand the processes regulated by the CLAVATA3 (CLV3)/ESR (CLE) ligand gene family, we took a systems approach to gene identification and gain-of-function phenotype screens in transgenic plants. We identified four new CLE family members in the Arabidopsis (Arabidopsis thaliana) genome sequence and determined their relative transcript levels in various organs. Overexpression of CLV3 and the 17 CLE genes we tested resulted in premature mortality and/or developmental timing delays in transgenic Arabidopsis plants. Overexpression of 10 CLE genes and the CLV3 positive control resulted in arrest of growth from the shoot apical meristem (SAM). Overexpression of nearly all the CLE genes and CLV3 resulted in either inhibition or stimulation of root growth. CLE4 expression reversed the SAM proliferation phenotype of a clv3 mutant to one of SAM arrest. Dwarf plants resulted from overexpression of five CLE genes. Overexpression of new family members CLE42 and CLE44 resulted in distinctive shrub-like dwarf plants lacking apical dominance. Our results indicate the capacity for functional redundancy of many of the CLE ligands. Additionally, overexpression phenotypes of various CLE family members suggest roles in organ size regulation, apical dominance, and root growth. Similarities among overexpression phenotypes of many CLE genes correlate with similarities in their CLE domain sequences, suggesting that the CLE domain is responsible for interaction with cognate receptors. PMID:16489133

Strabala, Timothy J; O'donnell, Philip J; Smit, Anne-Marie; Ampomah-Dwamena, Charles; Martin, E Jane; Netzler, Natalie; Nieuwenhuizen, Niels J; Quinn, Brian D; Foote, Humphrey C C; Hudson, Keith R

2006-04-01

321

No Genetic Diversity at Molecular Markers and Strong Phenotypic Plasticity in Populations of Ranunculus nodiflorus, an Endangered Plant Species in France  

PubMed Central

Background and Aims Although conservation biology has long focused on population dynamics and genetics, phenotypic plasticity is likely to play a significant role in population viability. Here, an investigation is made into the relative contribution of genetic diversity and phenotypic plasticity to the phenotypic variation in natural populations of Ranunculus nodiflorus, a rare annual plant inhabiting temporary puddles in the Fontainebleau forest (Paris region, France) and exhibiting metapopulation dynamics. Methods The genetic diversity and phenotypic plasticity of quantitative traits (morphological and fitness components) were measured in five populations, using a combination of field measurements, common garden experiments and genotyping at microsatellite loci. Key Results It is shown that populations exhibit almost undetectable genetic diversity at molecular markers, and that the variation in quantitative traits observed among populations is due to a high level of phenotypic plasticity. Despite the lack of genetic diversity, the natural population of R. nodiflorus exhibits large population sizes and does not appear threatened by extinction; this may be attributable to large phenotypic plasticity, enabling the production of numerous seeds under a wide range of environmental conditions. Conclusions Efficient conservation of the populations can only be based on habitat management, to favour the maintenance of microenvironmental variation and the resulting strong phenotypic plasticity. In contrast, classical actions aiming to improve genetic diversity are useless in the present case. PMID:17468109

Noel, Florence; Machon, Nathalie; Porcher, Emmanuelle

2007-01-01

322

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

323

Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another.  

PubMed

A large recombinant inbred population of soybean has been characterized for 220 restriction fragment-length polymorphism (RFLP) markers. Values for agronomic traits also have been measured. Quantitative trait loci (QTL) for height, yield, and maturity were located by their linkage to RFLP markers. QTL controlling large amounts of trait variation were analyzed for the dependence of trait variation on particular alleles at a second locus by comparing cumulative distributions of the trait for each genotype (four genotypes per pair of loci). Interesting pairs of loci were analyzed statistically with maximum likelihood and Monte Carlo comparison of additive and epistatic models. For each locus affecting height, variation was conditional upon the presence of a particular allele at a second unlinked locus that itself explained little or no trait variation. The results show that interactions between QTL are frequent and control large effects. Interactions distinguished between different QTL in a single linkage group and between QTL that affect different traits closely linked to one RFLP marker--i.e., distinguished between pleiotropy and closely linked genes. The implications for the evolution of inbreeding plants and for the construction of agronomic breeding strategies are discussed. PMID:7753859

Lark, K G; Chase, K; Adler, F; Mansur, L M; Orf, J H

1995-05-01

324

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

325

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

326

Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).  

PubMed

Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed. PMID:23251515

Parnmen, Sittiporn; Lücking, Robert; Lumbsch, H Thorsten

2012-01-01

327

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

328

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

329

A Colony Multiplex Quantitative PCR-Based 3S3DBC Method and Variations of It for Screening DNA Libraries  

PubMed Central

A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After describing pooling strategies and issues that should be considered in DNA library screening, here we report an efficient colony multiplex quantitative PCR-based 3-step, 3-dimension, and binary-code (3S3DBC) method we used to screen genes from a planarian genomic DNA fosmid library. This method requires only 3 rounds of PCR reactions and only around 6 hours to distinguish one or more desired clones from a large DNA library. According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements. PMID:25646755

An, Yang; Toyoda, Atsushi; Zhao, Chen; Fujiyama, Asao; Agata, Kiyokazu

2015-01-01

330

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.

331

Asthma phenotypes  

Microsoft Academic Search

The many roads leading to the syndrome of asthma have proven to be intricately interconnected. The chronic inflammation of\\u000a asthma is characterized by airway hyperreactivity and variable reversibility. Past classification systems relied on assessment\\u000a of daily impairment and the distinction between intrinsic (nonallergic) and extrinsic (allergic). With more precise asthma\\u000a phenotypes, association studies likely will have greater significance. In addition,

Steve Handoyo; Lanny J. Rosenwasser

2009-01-01

332

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

333

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

334

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

335

Genetic and environmental components of phenotypic variation in immune response and body size of a colonial bird, Delichon urbica (the house martin)  

Microsoft Academic Search

Directional selection for parasite resistance is often intense in highly social host species. Using a partial cross-fostering experiment we studied environmental and genetic variation in immune response and morphology in a highly colonial bird species, the house martin (Delichon urbica). We manipulated intensity of infestation of house martin nests by the haematophagous parasitic house martin bug Oeciacus hirundinis either by

Philippe Christe; Anders Pape Møller; Nicola Saino; Florentino de Lope

2000-01-01

336

Genet. Res., Camb. (2000), 76, pp. 295304. With 2 figures. Printed in the United Kingdom # 2000 Cambridge University Press 295 Maintenance of genetic variation in phenotypic plasticity  

E-print Network

Noach et al. (1996) in a Drosophila melanogaster population from Tanzania, and Karan et al. (1999.dejong!bio.uu.nl melanogaster population from southern France, found significant GME interaction for wing length. The study on Drosophila to test the theory. In seven of eight pair-wise comparisons genetic variation in reaction norm

Gavrilets, Sergey

337

Quantitative and qualitative variation of fat in model vanilla custard desserts: effects on sensory properties and consumer acceptance.  

PubMed

The effects of variation in fat content (0.1% to 15.8%) and type of fat, using different types of milk, dairy cream, or vegetable fat cream, on sensory characteristics and consumer acceptance of starch-based vanilla model custards were studied. Descriptive analysis with trained panelists and consumer testing with untrained assessors were applied. Descriptive data were related to hedonic data using principal component analysis to determine drivers of liking and disliking. Results demonstrated an increasing effect of fat concerning visual and oral thickness, creamy flavor, and fat-related texture properties, as well as a decreasing effect concerning yellow color and surface shine. A lack of fat caused moderate intensities in pudding-like flavor attributes and an intensive jelly texture. Adding a vegetable fat cream led to lower intensities in attributes yellow color, cooked flavor, thick, and jelly texture, whereas intensities in vegetable fat flavor and fat-related texture properties increased. All consumers favored custards with medium fat contents, being high in pudding-like and vegetable fat flavor as well as in fat-related texture attributes. Nonfat custards were rejected due to jelly texture and moderate intensities in pudding-flavor attributes. High-fat samples were liked by some consumers, but their high intensities in thickness, white color, and creamy flavor also drove disliking for others. PMID:23772708

Tomaschunas, Maja; Köhn, Ehrhard; Bennwitz, Petra; Hinrichs, Jörg; Busch-Stockfisch, Mechthild

2013-06-01

338

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

339

Levels of genetic polymorphism: marker loci versus quantitative traits.  

PubMed Central

Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variation within and among species has been documented most extensively using allozyme electrophoresis. This reveals wide differences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for allozymes can be used to infer patterns of genetic variation in quantitative traits depends on the forces generating and maintaining variability. Allozyme variation is probably not strictly neutral but, nevertheless, heterozygosity is expected to be influenced by population size and genetic distance will be affected by time since divergence. The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. It is a better predictor of general phenotypic divergence and of postzygotic isolation between populations or species, but is only weakly correlated with prezygotic isolation. Studies of grasshopper and planthopper mating signal variation and assortative mating illustrate how these characters evolve independently of general genetic and morphological variation. The role of such traits in prezygotic isolation, and hence speciation, means that they will contribute significantly to the diversity of levels of genetic variation within and among species. PMID:9533123

Butlin, R K; Tregenza, T

1998-01-01

340

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

341

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

342

Phenotypic divergence of the common toad (Bufo bufo) along an altitudinal gradient: evidence for local adaptation.  

PubMed

Variation in the environment can induce different patterns of genetic and phenotypic differentiation among populations. Both neutral processes and selection can influence phenotypic differentiation. Altitudinal phenotypic variation is of particular interest in disentangling the interplay between neutral processes and selection in the dynamics of local adaptation processes but remains little explored. We conducted a common garden experiment to study the phenotypic divergence in larval life-history traits among nine populations of the common toad (Bufo bufo) along an altitudinal gradient in France. We further used correlation among population pairwise estimates of quantitative trait (QST) and neutral genetic divergence (FST from neutral microsatellite markers), as well as altitudinal difference, to estimate the relative role of divergent selection and neutral genetic processes in phenotypic divergence. We provided evidence for a neutral genetic differentiation resulting from both isolation by distance and difference in altitude. We found evidence for phenotypic divergence along the altitudinal gradient (faster development, lower growth rate and smaller metamorphic size). The correlation between pairwise QSTs-FSTs and altitude differences suggested that this phenotypic differentiation was most likely driven by altitude-mediated selection rather than by neutral genetic processes. Moreover, we found different divergence patterns for larval traits, suggesting that different selective agents may act on these traits and/or selection on one trait may constrain the evolution on another through genetic correlation. Our study highlighted the need to design more integrative studies on the common toad to unravel the underlying processes of phenotypic divergence and its selective agents in the context of environmental clines. PMID:25074572

Luquet, E; Léna, J-P; Miaud, C; Plénet, S

2015-01-01

343

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

344

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

345

Quantitative genetics of pigmentation development in 2 populations of the common garter snake, Thamnophis sirtalis.  

PubMed

The evolutionary importance of ontogenetic change has been noted since Darwin. However, most analyses of phenotypic evolution focus on single landmark ages. Here, we present an inheritance study that quantifies genetic variation in pigmentation across early-age (i.e., birth to 180 days) development in 2 populations of the common garter snake, Thamnophis sirtalis. The populations are phenotypically distinct and geographically isolated (Manitoba, CA and Northern California, USA). There were highly significant differences between populations for the developmental trajectory of mean pigmentation, with the Manitoba population exhibiting a mean pigmentation level that increased across ontogeny, whereas the California population exhibited mean pigmentation that was invariant across ontogeny. Subsequent quantitative genetic analyses revealed heritable variation at all ages in Manitoba but low levels of phenotypic and genetic variation in California at all ages. A quantitative genetic decomposition of the longitudinal genetic variance-covariance matrix for the age-specific pigmentation phenotypes in the Manitoba population revealed 2 primary orthogonal axes that explained most ( approximately 100%) of the pigmentation variation across ontogeny. The primary axis, explaining 93% of the genetic variation, is an axis of genetic variation whose principal value loadings change from positive to negative across development, suggesting that the most rapid evolutionary response to selection on pigmentation variation will occur in the direction characterized by a tradeoff in early-age versus late-age pigmentation phenotypes. Pigmentation is known to be ecologically important and subject to rapid evolution under selection. Our study shows that significant differences exist between these 2 populations for their capacity to respond to selection on pigmentation which is not only influenced by the population of origin but also by the developmental process. We suggest that developmental timing may be a potential explanatory mechanism for the difference between the populations. PMID:20453034

Westphal, Michael F; Morgan, Theodore J

2010-01-01

346

Genetic analysis of genome-wide variation in human gene expression  

PubMed Central

Natural variation in gene expression is extensive in humans and other organisms, and variation in the baseline expression level of many genes has a heritable component. To localize the genetic determinants of these quantitative traits (expression phenotypes) in humans, we used microarrays to measure gene expression levels and performed genome-wide linkage analysis for expression levels of 3,554 genes in 14 large families. For approximately 1,000 expression phenotypes, there was significant evidence of linkage to specific chromosomal regions. Both cis- and trans-acting loci regulate variation in the expression levels of genes, although most act in trans. Many gene expression phenotypes are influenced by several genetic determinants. Furthermore, we found hotspots of transcriptional regulation where significant evidence of linkage for several expression phenotypes (up to 31) coincides, and expression levels of many genes that share the same regulatory region are significantly correlated. The combination of microarray techniques for phenotyping and linkage analysis for quantitative traits allows the genetic mapping of determinants that contribute to variation in human gene expression. PMID:15269782

Morley, Michael; Molony, Cliona M.; Weber, Teresa M.; Devlin, James L.; Ewens, Kathryn G.; Spielman, Richard S.; Cheung, Vivian G.

2010-01-01

347

Phenotypic variation resulting from a deficiency of epidermal growth factor receptor in mice is caused by extensive genetic heterogeneity that can be genetically and molecularly partitioned.  

PubMed Central

The timing of lethality caused by homozygosity for a null allele of the epidermal growth factor receptor (Egfrtm1Mag) in mice is strongly dependent on genetic background. Initial attempts to genetically map background modifiers using Swiss-derived, outbred CD-1 mice were unsuccessful. To investigate the genetic architecture contributing to survival of Egfrtm1Mag homozygous embryos, the genetic variability segregating within the outbred population was partitioned by surveying viability of Egfrtm1Mag mutants using intercrosses between 129S6/SvEvTAC-Egfrtm1Mag and nine Swiss-derived, inbred strains: ALR/LtJ, ALS/LtJ, APN, APS, ICR/HaRos, NOD/LtJ, NON/LtJ, SJL/J, and SWR/J. The observations showed that these strains support varying levels of survival of Egfrtm1Mag homozygous embryos, suggesting that genetic heterogeneity within the CD-1 stock contributed to the original lack of Egfrtm1Mag modifier detection. Similar to the Swiss-derived intercrosses, nine congenic strains, derived from 129S6/SvEvTAC, AKR/J, APN, BALB/cJ, BTBR-T+ tf/tf, C3H/HeJ, C57BL/6J, DBA/2J, and FVB/NJ inbred backgrounds, also supported varying levels of survival of Egfrtm1Mag mutants. By intercrossing the congenic lines to create hybrid F1 embryos, different genetic backgrounds were found to have complementary modifiers. Analysis of the congenic lines argues against heterosis of outbred backgrounds contributing to Egfrtm1Mag phenotypic variability. A detailed analysis of the crosses suggests that modifiers function at three distinct stages of development. One class of modifiers supports survival of Egfrtm1Mag homozygous embryos to mid-gestation, another class supports development through the mid-gestation transition from yolk-sac to placental-derived nutrient sources, and a third class supports survival through later stages of gestation. Data from microarray analysis using RNA from wild-type and Egfrtm1Mag mutant placentas support the existence of extensive genetic heterogeneity and suggest that it can be molecularly partitioned. This method should be generally useful to partition heterogeneity contributing to other complex traits. PMID:15342520

Strunk, Karen E; Amann, Vicky; Threadgill, David W

2004-01-01

348

Extensive cross-environment fitness variation lies along few axes of genetic variation in the model alga, Chlamydomonas reinhardtii.  

PubMed

Variation is essential to ecological and evolutionary dynamics, but genetic variation of quantitative traits may be concentrated in a limited number of dimensions, constraining ecoevolutionary dynamics. We describe high-dimension variation in natural accessions of the model alga, Chlamydomonas reinhardtii, and test the hypothesis that extensive fitness variation across 30 environments is constrained to a small number of axes. We used high-throughput phenotyping to investigate morphological, fitness, and genotype × environment (G × E) variation in 18 natural C. reinhardtii accessions in 30 environments. The organismal phenotypes of cell cycle, cell size, and phototactic behavior exhibited substantial genetic variation between lines, and we found up to 74-fold fitness variation across accessions and environments. Approximately 47% of the extensive G × E variation is accounted for by the first two principal components (PCs) of the G-matrix corresponding to covariation in metals response, nitrogen availability, or salt and nutrient response. The natural variation of C. reinhardtii accessions supports the hypothesis that, despite abundant genetic variation across single environments, the species' adaptive response should be constrained along few major axes of selection. These results highlight the utility of natural accessions for integrating ecoevolutionary and genetic research. PMID:25264298

Malcom, Jacob W; Hernandez, Kyle M; Likos, Raquel; Wayne, Tierney; Leibold, Mathew A; Juenger, Thomas E

2015-01-01

349

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

350

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

351

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

352

Sex differences in grey seal diet reflect seasonal variation in foraging behaviour and reproductive expenditure: evidence from quantitative fatty acid signature analysis.  

PubMed

1. Intraspecific variation in diet can be an important component of a species niche breadth. We tested the hypothesis that sex differences in seasonal foraging behaviour and energy storage of sexually size dimorphic grey seals Halichoerus grypus (Fabrisius 1971) are reflected in differences in the diet and niche breadth. Diet composition was estimated for 496 adult (226 males, 270 females) and 91 juvenile (46 males/45 females; all 6 months old) grey seals sampled between 1993 and 2000 using quantitative fatty acid signature analysis. Niche breadth and overlap were estimated using the Shannon-Weaver diversity index (H') and the Morisita-Horn index (C(H)), respectively. 2. Sand lance Ammodytes dubius (Reinhardt 1837) and redfish Sebastes sp. (Cuvier 1829) accounted for a high proportion of the diet in both sexes and age groups. However, the diets of adult males were significantly more diverse across all seasons (H': males 0.36 +/- 0.007 vs. females 0.28 +/- 0.007) and less energy dense in spring (male 5.3 +/- 0.07 kJ g(-1) vs. females 5.6 +/- 0.09 kJ g(-1)) than those of adult females. 3. Season and sex explained most of the observed variation in adult diets, but there were significant sex-season interactions. These differences were most evident during the post-breeding (spring) foraging period when energy acquisition is important to female recovery of nutrient stores needed to support pregnancy. Females selected fewer and higher quality prey species in spring than males. 4. There were no sex differences in the diets of juvenile grey seals. Although many of the species overlapped with those eaten by adults, juvenile niche breadth (H': 0.41 +/- 0.014, n = 91) was significantly broader than that of adults (H': 0.30 +/- 0.011, n = 115). Juvenile diets were also of lower energy density (5.3 +/- 0.04 kJ g(-1)) than those of adults (5.6 +/- 0.09 kJ g(-1)), suggesting less selectivity in these young and relatively naïve predators. 5. Sex-specific seasonal changes in diet correspond to seasonal changes in diving behaviour and rate of body energy accumulation of adult males and females. Sex-specific reproductive requirements appear to be a primary factor generating the intraspecific variation in the seasonal foraging ecology of this large marine carnivore. However, sex differences in the breadth and energy content of diets also suggest the influence of body-size dimorphism as a factor shaping the diet of this species. PMID:17439466

Beck, Carrie A; Iverson, Sara J; Bowen, W Don; Blanchard, Wade

2007-05-01

353

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 characteristic xenobiotic metabolic profile was observed for CNS responders, which revealed higher urinary levels of pyruvate isonicotinylhydrazone and ?-glucosyl isonicotinylhydrazide and lower levels of acetylisoniazid compared to CNS non-responders. This suggested that the capacity for acetylation of INH was lower in CNS responders, leading to increased metabolism via conjugation with pyruvate and glucose. In addition, the endogenous metabolic profile of CNS responders revealed higher urinary levels of lactate and glucose, in comparison to CNS non-responders. Pharmacometabonomic analysis of the pre-dose ¹H NMR urinary spectra identified a metabolic signature that correlated with the development of INH-induced adverse CNS effects and may represent a means of predicting adverse events and acetylation capacity when challenged with high dose INH. Given the widespread use of INH for the treatment of tuberculosis, this pharmacometabonomic screening approach may have translational potential for patient stratification to minimize adverse events. PMID:22873827

Cunningham, Katharine; Claus, Sandrine P; Lindon, John C; Holmes, Elaine; Everett, Jeremy R; Nicholson, Jeremy K; Coen, Muireann

2012-09-01

354

Phenotypic Plasticity in the Interactions and Evolution of Species  

Microsoft Academic Search

When individuals of two species interact, they can adjust their phenotypes in response to their respective partner, be they antagonists or mutualists. The reciprocal phenotypic change between individuals of interacting species can reflect an evolutionary response to spatial and temporal variation in species interactions and ecologically result in the structuring of food chains. The evolution of adaptive phenotypic plasticity has

Anurag A. Agrawal

2001-01-01

355

Quantitative trait loci affecting starvation resistance in Drosophila melanogaster.  

PubMed Central

The ability to withstand periods of scarce food resources is an important fitness trait. Starvation resistance is a quantitative trait controlled by multiple interacting genes and exhibits considerable genetic variation in natural populations. This genetic variation could be maintained in the face of strong selection due to a trade-off in resource allocation between reproductive activity and individual survival. Knowledge of the genes affecting starvation tolerance and the subset of genes that affect variation in starvation resistance in natural populations would enable us to evaluate this hypothesis from a quantitative genetic perspective. We screened 933 co-isogenic P-element insertion lines to identify candidate genes affecting starvation tolerance. A total of 383 P-element insertions induced highly significant and often sex-specific mutational variance in starvation resistance. We also used deficiency complementation mapping followed by complementation to mutations to identify 12 genes contributing to variation in starvation resistance between two wild-type strains. The genes we identified are involved in oogenesis, metabolism, and feeding behaviors, indicating a possible link to reproduction and survival. However, we also found genes with cell fate specification and cell proliferation phenotypes, which implies that resource allocation during development and at the cellular level may also influence the phenotypic response to starvation. PMID:15126400

Harbison, Susan T; Yamamoto, Akihiko H; Fanara, Juan J; Norga, Koenraad K; Mackay, Trudy F C

2004-01-01

356

Automated, computerized, feature-based phenotype analysis of slit lamp images of the mouse lens.  

PubMed

Longitudinal studies of a variety of transgenic mouse models for lens development can create substantial challenges in database management and analysis. We report a novel, automated, feature-based informatics approach to screening lens phenotypes in a large database of slit lamp images. Digital slit lamp images of normal and abnormal lenses in eyes of wild type (wt), SC1 null and SPARC null transgenic mice were recorded for quantitative evaluation of their structural phenotype. The images were processed to improve the contrast of structural features that corresponded to rings of opacity and fluctuations in scattering intensity in the lenses. Measurable attributes were assigned to the features in the lens images and given as an output vector of 46 dimensions. Characteristic patterns were correlated with the structural phenotype of each mutant and wt lens and a statistical fit for each phenotype was defined. The genotype was identified correctly in nearly 85% of the slit lamp images on the basis of an automated computer analysis of the lens structural phenotype. The automated computer algorithm has the potential to evaluate a large database of slit lamp images and distinguish mouse genotypes on the basis of lens phenotypes objectively using a neural network analysis of the structural features observed in the slit lamp images. The neural network approach is a promising technology for objective evaluation of genotype/phenotype relationships based on structural features and light scattering in lenses. Further improvements in the automated method can be expected to simplify and increase the accuracy and efficiency of the feature based analysis of structural phenotypes linked to genetic variation. PMID:18304532

Yuen, Jenny; Li, Yi; Shapiro, Linda G; Clark, John I; Arnett, Ernest; Sage, E Helene; Brinkley, James F

2008-04-01

357

Automated, Computerized, Feature-Based Phenotype Analysis of Slit Lamp Images of the Mouse Lens  

PubMed Central

Longitudinal studies of a variety of transgenic mouse models for lens development can create substantial challenges in database management and analysis. We report a novel, automated, feature-based informatics approach to screening lens phenotypes in a large database of slit lamp images. Digital slit lamp images of normal and abnormal lenses in eyes of wild type (wt), SC1 null and SPARC null transgenic mice were recorded for quantitative evaluation of their structural phenotype. The images were processed to improve the contrast of structural features that corresponded to rings of opacity and fluctuations in scattering intensity in the lenses. Measurable attributes were assigned to the features in the lens images and given as an output vector of 46 dimensions. Characteristic patterns correlated with the structural phenotype of each mutant and wt lens and a statistical fit for each phenotype was defined. The genotype was identified correctly in nearly 85% of the slit lamp images on the basis of an automated computer analysis of the lens structural phenotype. The automated computer algorithm has the potential to evaluate a large database of slit lamp images and distinguish mouse genotypes on the basis of lens phenotypes objectively using a neural network analysis of the structural features observed in the slit lamp images. The neural network approach is a promising technology for objective evaluation of genotype/phenotype relationships based on structural features and light scattering in lenses. Further improvements in the automated method can be expected to simplify and increase the accuracy and efficiency of the feature based analysis of structural phenotypes linked to genetic variation. PMID:18304532

Yuen, Jenny; Li, Yi; Shapiro, Linda G.; Clark, John I.; Arnett, Ernest; Sage, E. Helene; Brinkley, James F.

2008-01-01

358

Quantitative Epigenetics Through Epigenomic Perturbation of Isogenic Lines  

PubMed Central

Interindividual differences in chromatin states at a locus (epialleles) can result in gene expression changes that are sometimes transmitted across generations. In this way, they can contribute to heritable phenotypic variation in natural and experimental populations independent of DNA sequence. Recent molecular evidence shows that epialleles often display high levels of transgenerational instability. This property gives rise to a dynamic dimension in phenotypic inheritance. To be able to incorporate these non-Mendelian features into quantitative genetic models, it is necessary to study the induction and the transgenerational behavior of epialleles in controlled settings. Here we outline a general experimental approach for achieving this using crosses of epigenomically perturbed isogenic lines in mammalian and plant species. We develop a theoretical description of such crosses and model the relationship between epiallelic instability, recombination, parent-of-origin effects, as well as transgressive segregation and their joint impact on phenotypic variation across generations. In the limiting case of fully stable epialleles our approach reduces to the classical theory of experimental line crosses and thus illustrates a fundamental continuity between genetic and epigenetic inheritance. We consider data from a panel of Arabidopsis epigenetic recombinant inbred lines and explore estimates of the number of quantitative trait loci for plant height that resulted from a manipulation of DNA methylation levels in one of the two isogenic founder strains. PMID:21385727

Johannes, Frank; Colomé-Tatché, Maria

2011-01-01

359

Evolution of molecular phenotypes under stabilizing selection  

NASA Astrophysics Data System (ADS)

Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes.

Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

2013-01-01

360

Quantitative PCR Reveals Strong Spatial and Temporal Variation of the Wasting Disease Pathogen, Labyrinthula zosterae in Northern European Eelgrass (Zostera marina) Beds  

PubMed Central

Seagrass beds are the foundation species of functionally important coastal ecosystems worldwide. The world’s largest losses of the widespread seagrass Zostera marina (eelgrass) have been reported as a consequence of wasting disease, an infection with the endophytic protist Labyrinthula zosterae. During one of the most extended epidemics in the marine realm, ?90% of East and Western Atlantic eelgrass beds died-off between 1932 and 1934. Today, small outbreaks continue to be reported, but the current extent of L. zosterae in European meadows is completely unknown. In this study we quantify the abundance and prevalence of the wasting disease pathogen among 19 Z. marina populations in northern European coastal waters, using quantitative PCR (QPCR) with primers targeting a species specific portion of the internally transcribed spacer (ITS1) of L. zosterae. Spatially, we found marked variation among sites with abundances varying between 0 and 126 cells mg?1 Z. marina dry weight (mean: 5.7 L. zosterae cells mg?1 Z. marina dry weight ±1.9 SE) and prevalences ranged from 0–88.9%. Temporarily, abundances varied between 0 and 271 cells mg?1 Z. marina dry weight (mean: 8.5±2.6 SE), while prevalences ranged from zero in winter and early spring to 96% in summer. Field concentrations accessed via bulk DNA extraction and subsequent QPCR correlated well with prevalence data estimated via isolation and cultivation from live plant tissue. L. zosterae was not only detectable in black lesions, a sign of Labyrinthula-induced necrosis, but also occurred in green, apparently healthy tissue. We conclude that L. zosterae infection is common (84% infected populations) in (northern) European eelgrass populations with highest abundances during the summer months. In the light of global climate change and increasing rate of marine diseases our data provide a baseline for further studies on the causes of pathogenic outbreaks of L. zosterae. PMID:23658711

Bockelmann, Anna-Christina; Tams, Verena; Ploog, Jana; Schubert, Philipp R.; Reusch, Thorsten B. H.

2013-01-01

361

Male fertility versus sterility, cytotype, and DNA quantitative variation in seed production in diploid and tetraploid sea lavenders (Limonium sp., Plumbaginaceae) reveal diversity in reproduction modes.  

PubMed

The genus Limonium Miller, a complex taxonomic group, comprises annuals and perennials that can produce sexual and/or asexual seeds (apomixis). In this study, we used diverse cytogenetic and cytometric approaches to analyze male sporogenesis and gametogenesis for characterizing male reproductive output on seed production in Limonium ovalifolium and Limonium multiflorum. We showed here that the first species is mostly composed of diploid cytotypes with 2n = 16 chromosomes and the latter species by tetraploid cytotypes with 2n = 32, 34, 35, 36 chromosomes and had a genome roughly twice as big as the former one. In both species, euploid and aneuploid cytotypes with large metacentric chromosomes having decondensed interstitial sites were found within and among populations, possibly involved in chromosomal reconstructions. L. ovalifolium diploids showed regular meiosis resulting in normal tetrads, while diverse chromosome pairing and segregation irregularities leading to the formation of abnormal meiotic products are found in balanced and non-balanced L. multiflorum tetraploids. Before anther dehiscence, the characteristic unicellular, bicellular, or tricellular pollen grains showing the typical Limonium micro- or macro-reticulate exine ornamentation patterns were observed in L. ovalifolium using scanning electron microscopy. Most of these grains were viable and able to produce pollen tubes in vitro. In both balanced and unbalanced L. multiflorum tetraploids, microspores only developed until the "ring-vacuolate stage" with a collapsed morphology without the typical exine patterns, pointing to a sporophytic defect. These microspores were unviable and therefore never germinated in vitro. L. ovalifolium individuals presented larger pollen grains than those of L. multiflorum, indicating that pollen size and ploidy levels are not correlated in the Limonium system. Cytohistological studies in mature seeds from both species revealed that an embryo and a residual endosperm were present in each seed. Flow cytometric seed screens using such mature seeds showed quantitative variations in seeds ploidy level. It is concluded that male function seems to play an important role in the reproduction modes of Limonium diploids and tetraploids. PMID:23086613

Róis, Ana Sofia; Teixeira, Generosa; Sharbel, Timothy F; Fuchs, Jörg; Martins, Sérgio; Espírito-Santo, Dalila; Caperta, Ana D

2012-12-01

362

Phenotypic response of Lycopersicon chilense to water deficit  

Microsoft Academic Search

ABSTRACT Environmental-induced phenotypic variation in plants is often considered to be a functional response that maximizes fitness in heterogeneousenvironments. Lycopersicon chilense, a tomato species endemic to Atacama Desert, shows altitudinal phenotypics variations in their natural environments, which could be due to different soil water availabilities. It is hypothesized that (a) seeds coming from populations of different environments, cultivated in the

CARLOS MALDONADO; FRANCISCO A SQUEO; ERIC IBACACHE

2003-01-01

363

The phenotypic variance within plastic traits under migration-mutation-selection balance.  

PubMed

How phenotypic variances of quantitative traits are influenced by the heterogeneity in environment is an important problem in evolutionary biology. In this study, both genetic and environmental variances in a plastic trait under migration-mutation-stabilizing selection are investigated. For this, a linear reaction norm is used to approximate the mapping from genotype to phenotype, and a population of clonal inheritance is assumed to live in a habitat consisting of many patches in which environmental conditions vary among patches and generations. The life cycle is assumed to be selection-reproduction-mutation-migration. Analysis shows that phenotypic plasticity is adaptive if correlations between the optimal phenotype and environment have become established in both space and/or time, and it is thus possible to maintain environmental variance (V(E)) in the plastic trait. Under the special situation of no mutation but maximum migration such that separate patches form an effective single-site habitat, the genotype that maximizes the geometric mean fitness will come to fixation and thus genetic variance (V(G)) cannot be maintained. With mutation and/or restricted migration, V(G) can be maintained and it increases with mutation rate but decreases with migration rate; whereas VE is little affected by them. Temporal variation in environmental quality increases V(G) while its spatial variance decreases V(G). Variation in environmental conditions may decrease the environmental variance in the plastic trait. PMID:16892964

Zhang, Xu-Sheng

2006-06-01

364

Three monthly coral Sr\\/Ca records from the Chagos Archipelago covering the period of 1950–1995 A.D.: reproducibility and implications for quantitative reconstructions of sea surface temperature variations  

Microsoft Academic Search

In order to assess the fidelity of coral Sr\\/Ca for quantitative reconstructions of sea surface temperature variations, we\\u000a have generated three monthly Sr\\/Ca time series from Porites corals from the lagoon of Peros Banhos (71°E, 5°S, Chagos Archipelago). We find that all three coral Sr\\/Ca time series are\\u000a well correlated with instrumental records of sea surface temperature (SST) and air

Miriam Pfeiffer; Wolf-Christian Dullo; Jens Zinke; Dieter Garbe-Schönberg

2009-01-01

365

Phenotypes of chronic obstructive pulmonary disease.  

PubMed

The current clinical classification of smoking-related lung disease fails to take into account the heterogeneity of chronic obstructive pulmonary disease (COPD). With an increased understanding of pathophysiologic variation, COPD now clearly represents a spectrum of overlapping diseases with important extrapulmonary consequences. A "phenotype" describes the outward physical manifestations of a particular disease, and compromises anything that is part of the observable structure, function or behavior of an individual. Such phenotypic distinctions in COPD include: frequent exacerbator, pulmonary cachectic, rapid decliner, airways hyperresponsiveness, impaired exercise tolerance, and emphysema versus airways disease. These variable manifestations, each with unique prognostic, clinical and physiologic ramifications, represent distinct phenotypes within COPD. While all of these phenotypes have smoking as a common risk factor, the other risk factors that determine these phenotypes remain poorly understood. An individual smoker has variable expression of each phenotype and there is mounting evidence that COPD phenotypes have different clinical outcomes. These phenotypes can be broadly classified into one of three groups: clinical, physiologic and radiographic. This review presents the evidence for the spectrum of COPD phenotypes with a focused discussion on the pathophysiologic, epidemiologic and clinical significance of each subtype. PMID:18027163

Friedlander, Adam L; Lynch, David; Dyar, Liesel A; Bowler, Russell P

2007-12-01

366

Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality1[W][OA  

PubMed Central

Recent advances in -omics technologies such as transcriptomics, metabolomics, and proteomics along with genotypic profiling have permitted dissection of the genetics of complex traits represented by molecular phenotypes in nonmodel species. To identify the genetic factors underlying variation in primary metabolism in potato (Solanum tuberosum), we have profiled primary metabolite content in a diploid potato mapping population, derived from crosses between S. tuberosum and wild relatives, using gas chromatography-time of flight-mass spectrometry. In total, 139 polar metabolites were detected, of which we identified metabolite quantitative trait loci for approximately 72% of the detected compounds. In order to obtain an insight into the relationships between metabolic traits and classical phenotypic traits, we also analyzed statistical associations between them. The combined analysis of genetic information through quantitative trait locus coincidence and the application of statistical learning methods provide information on putative indicators associated with the alterations in metabolic networks that affect complex phenotypic traits. PMID:22223596

Carreno-Quintero, Natalia; Acharjee, Animesh; Maliepaard, Chris; Bachem, Christian W.B.; Mumm, Roland; Bouwmeester, Harro; Visser, Richard G.F.; Keurentjes, Joost J.B.

2012-01-01

367

Variation and Genetic Control of Protein Abundance in Humans  

PubMed Central

Gene expression differs among both individuals and populations and is thought to be a major determinant of phenotypic variation. Although variation and genetic loci responsible for RNA expression levels have been analyzed extensively in human populations1–5, our knowledge is limited regarding the differences in human protein abundance and their genetic basis. Variation in mRNA expression is not a perfect surrogate for protein expression because the latter is influenced by a battery of post-transcriptional regulatory mechanisms, and, empirically, the correlation between protein and mRNA levels is generally modest6,7. Here we used isobaric tandem mass tag (TMT)-based quantitative mass spectrometry to determine relative protein levels of 5953 genes in lymphoblastoid cell lines (LCLs) from 95 diverse individuals genotyped in the HapMap Project8,9. We found that protein levels are heritable molecular phenotypes that exhibit considerable variation between individuals, populations, and sexes. Levels of specific sets of proteins involved in the same biological process co-vary among individuals, indicating that these processes are tightly regulated at the protein level. We identified cis-pQTLs (protein quantitative trait loci), including variants not detected by previous transcriptome studies. This study demonstrates the feasibility of high throughput human proteome quantification which, when integrated with DNA variation and transcriptome information, adds a new dimension to the characterization of gene expression regulation. PMID:23676674

Wu, Linfeng; Candille, Sophie I; Choi, Yoonha; Xie, Dan; Li-Pook-Than, Jennifer; Tang, Hua; Snyder, Michael

2013-01-01

368

Genetic and Environmental Contributions to Variation in Baboon Cranial Morphology  

PubMed Central

The development, function, and integration of morphological characteristics are all hypothesized to influence the utility of traits for phylogenetic reconstruction by affecting the way in which morphological characteristics evolve. We use a baboon model to test the hypotheses about phenotypic and quantitative genetic variation of traits in the cranium that bear on a phenotype’s propensity to evolve. We test the hypotheses that: 1) individual traits in different functionally and developmentally defined regions of the cranium are differentially environmentally, genetically, and phenotypically variable; 2) genetic covariance with other traits constrains traits in one region of the cranium more than those in others; 3) and regions of the cranium subject to different levels of mechanical strain differ in the magnitude of variation in individual traits. We find that the levels of environmental and genetic variation in individual traits are randomly distributed across regions of the cranium rather than being structured by developmental origin or degree of exposure to strain. Individual traits in the cranial vault tend to be more constrained by covariance with other traits than those in other regions. Traits in regions subject to high degrees of strain during mastication are not any more variable at any level than other traits. If these results are generalizable to other populations, they indicate that there is no reason to suppose that individual traits from any one part of the cranium are intrinsically less useful for reconstructing patterns of evolution than those from any other part. PMID:20623673

Roseman, Charles C.; Willmore, Katherine E.; Rogers, Jeffrey; Hildebolt, Charles; Sadler, Brooke E.; Richtsmeier, Joan T.; Cheverud, James M.

2011-01-01

369

Metabolomic phenotyping of a cloned pig model  

PubMed Central

Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5) was for the first time elucidated by nuclear magnetic resonance (NMR)-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n = 6) by multivariate data analysis, which revealed differences in the metabolic phenotypes. Plasma lactate was higher for cloned vs control pigs, while multiple metabolites were altered in the bile. However a lower inter-individual variability for cloned pigs compared with control pigs could not be established. Conclusions From the present study we conclude that cloned and normal outbred pigs are phenotypically different. However, it cannot be concluded that the use of cloned animals will reduce the inter-individual variation in intervention studies, though this is based on a limited number of animals. PMID:21859467

2011-01-01

370

Propagation of genetic variation in gene regulatory networks  

NASA Astrophysics Data System (ADS)

A future quantitative genetics theory should link genetic variation to phenotypic variation in a causally cohesive way based on how genes actually work and interact. We provide a theoretical framework for predicting and understanding the manifestation of genetic variation in haploid and diploid regulatory networks with arbitrary feedback structures and intra-locus and inter-locus functional dependencies. Using results from network and graph theory, we define propagation functions describing how genetic variation in a locus is propagated through the network, and show how their derivatives are related to the network’s feedback structure. Similarly, feedback functions describe the effect of genotypic variation of a locus on itself, either directly or mediated by the network. A simple sign rule relates the sign of the derivative of the feedback function of any locus to the feedback loops involving that particular locus. We show that the sign of the phenotypically manifested interaction between alleles at a diploid locus is equal to the sign of the dominant feedback loop involving that particular locus, in accordance with recent results for a single locus system. Our results provide tools by which one can use observable equilibrium concentrations of gene products to disclose structural properties of the network architecture. Our work is a step towards a theory capable of explaining the pleiotropy and epistasis features of genetic variation in complex regulatory networks as functions of regulatory anatomy and functional location of the genetic variation.

Plahte, Erik; Gjuvsland, Arne B.; Omholt, Stig W.

2013-08-01

371

An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution  

Microsoft Academic Search

Studies of the evolution of development characterize the way in which gene regulatory dynamics during ontogeny constructs and channels phenotypic variation. These studies have identified a number of evolutionary regularities: (1) phenotypes occupy only a small subspace of possible phenotypes, (2) the influence of mutation is not uniform and is often canalized, and (3) a great deal of morphological variation

Elhanan Borenstein; David C. Krakauer

2008-01-01

372

Endocrine correlates of alternative phenotypes in the white-throated sparrow ( Zonotrichia albicollis)  

Microsoft Academic Search

Many vertebrate species exhibit alternative phenotypes (or morphs), in which one sex displays phenotypic variation equal to or greater than the variation between the sexes. Males in such species typically display differences in reproductive strategies and morphology. Steroid hormones such as testosterone are known modulators of reproductive behavior and morphology and therefore are obvious candidates for the mediation of phenotypic

L. H. Spinney; G. E. Bentley; M. Hau

2006-01-01

373

A common, non-optimal phenotypic endpoint in experimental adaptations of bacteriophage lysis time  

E-print Network

Background: Optimality models of evolution, which ignore genetic details and focus on natural selection, are widely used but sometimes criticized as oversimplifications. Their utility for quantitatively predicting phenotypic ...

Heineman, Richard H.

374

Hairy?s Inheritance: Investigating Variation, Selection, and Evolution with Wisconsin Fast Plants  

NSDL National Science Digital Library

In this investigation, learners will gather their own evidence to explain how environmental pressures (selection for hairiness) and inheritance can effect phenotypic variation over time. As learners observe two or more generations of Wisconsin Fast Plants, learners observe carefully and track quantitatively the average number of hairs on the first true leaf margin of Rapid-cycling Brassica rapa (Fast Plants). As the generations of plants grow, students will make observations that will serve as evidence to support or refute their explanations about the observed patterns in the inheritance of the hairy trait.-This pdf file contains considerable background information about Brassicas and the relationship among phenotype, genotype, and environment.

Lauffer, Daniel W.

375

High-throughput hyperdimensional vertebrate phenotyping.  

PubMed

Most gene mutations and biologically active molecules cause complex responses in animals that cannot be predicted by cell culture models. Yet animal studies remain too slow and their analyses are often limited to only a few readouts. Here we demonstrate high-throughput optical projection tomography with micrometre resolution and hyperdimensional screening of entire vertebrates in tens of seconds using a simple fluidic system. Hundreds of independent morphological features and complex phenotypes are automatically captured in three dimensions with unprecedented speed and detail in semitransparent zebrafish larvae. By clustering quantitative phenotypic signatures, we can detect and classify even subtle alterations in many biological processes simultaneously. We term our approach hyperdimensional in vivo phenotyping. To illustrate the power of hyperdimensional in vivo phenotyping, we have analysed the effects of several classes of teratogens on cartilage formation using 200 independent morphological measurements, and identified similarities and differences that correlate well with their known mechanisms of actions in mammals. PMID:23403568

Pardo-Martin, Carlos; Allalou, Amin; Medina, Jaime; Eimon, Peter M; Wählby, Carolina; Fatih Yanik, Mehmet

2013-01-01

376

Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network  

PubMed Central

Despite recent improvements in molecular techniques, biological knowledge remains incomplete. Any theorizing about living systems is therefore necessarily based on the use of heterogeneous and partial information. Much current research has focused successfully on the qualitative behaviors of macromolecular networks. Nonetheless, it is not capable of taking into account available quantitative information such as time-series protein concentration variations. The present work proposes a probabilistic modeling framework that integrates both kinds of information. Average case analysis methods are used in combination with Markov chains to link qualitative information about transcriptional regulations to quantitative information about protein concentrations. The approach is illustrated by modeling the carbon starvation response in Escherichia coli. It accurately predicts the quantitative time-series evolution of several protein concentrations using only knowledge of discrete gene interactions and a small number of quantitative observations on a single protein concentration. From this, the modeling technique also derives a ranking of interactions with respect to their importance during the experiment considered. Such a classification is confirmed by the literature. Therefore, our method is principally novel in that it allows (i) a hybrid model that integrates both qualitative discrete model and quantities to be built, even using a small amount of quantitative information, (ii) new quantitative predictions to be derived, (iii) the robustness and relevance of interactions with respect to phenotypic criteria to be precisely quantified, and (iv) the key features of the model to be extracted that can be used as a guidance to design future experiments. PMID:21935350

Bourdon, Jérémie; Eveillard, Damien; Siegel, Anne

2011-01-01

377

Epigenetic correlates of plant phenotypic plasticity: DNA methylation differs between prickly and  

E-print Network

Epigenetic correlates of plant phenotypic plasticity: DNA methylation differs between prickly that epigenetic variation caused by changes in DNA methylation are related to phenotypic plasticity plasticity and epigenetic changes in plants, and also contribute to the crystallization of the consensus

Herrera, Carlos M.

378

Statistical models for trisomic phenotypes  

SciTech Connect

Certain genetic disorders are rare in the general population but more common in individuals with specific trisomies, which suggests that the genes involved in the etiology of these disorders may be located on the trisomic chromosome. As with all aneuploid syndromes, however, a considerable degree of variation exists within each phenotype so that any given trait is present only among a subset of the trisomic population. We have previously presented a simple gene-dosage model to explain this phenotypic variation and developed a strategy to map genes for such traits. The mapping strategy does not depend on the simple model but works in theory under any model that predicts that affected individuals have an increased likelihood of disomic homozygosity at the trait locus. This paper explores the robustness of our mapping method by investigating what kinds of models give an expected increase in disomic homozygosity. We describe a number of basic statistical models for trisomic phenotypes. Some of these are logical extensions of standard models for disomic phenotypes, and some are more specific to trisomy. Where possible, we discuss genetic mechanisms applicable to each model. We investigate which models and which parameter values give an expected increase in disomic homozygosity in individuals with the trait. Finally, we determine the sample sizes required to identify the increased disomic homozygosity under each model. Most of the models we explore yield detectable increases in disomic homozygosity for some reasonable range of parameter values, usually corresponding to smaller trait frequencies. It therefore appears that our mapping method should be effective for a wide variety of moderately infrequent traits, even though the exact mode of inheritance is unlikely to be known. 21 refs., 8 figs., 1 tab.

Lamb, N.E.; Sherman, S.L.; Feingold, E. [Emory Univ., Atlanta, GA (United States)

1996-01-01

379

IL10 Gene Polymorphisms Are Associated With Asthma Phenotypes in Children  

PubMed Central

IL10 is an anti-inflammatory cytokine that has been found to have lower production in macrophages and mononuclear cells from asthmatics. Since reduced IL10 levels may influence the severity of asthma phenotypes, we examined IL10 single-nucleotide polymorphisms (SNPs) for association with asthma severity and allergy phenotypes as quantitative traits. Utilizing DNA samples from 518 Caucasian asthmatic children from the Childhood Asthma Management Program (CAMP) and their parents, we genotyped six IL10 SNPs: 3 in the promoter, 2 in introns, and one in the 3? UTR. Using family-based association tests, each SNP was tested for association with asthma and allergy phenotypes individually. Population-based association analysis was performed with each SNP locus, the promoter haplotypes and the 6-loci haplotypes. The 3? UTR SNP was significantly associated with FEV1 as a percent of predicted (FEV1PP) (P=0.0002) in both the family and population analyses. The promoter haplotype GCC was positively associated with IgE levels and FEV1PP (P=0.007 and 0.012, respectively). The promoter haplotype ATA was negatively associated with lnPC20 and FEV1PP (P=0.008 and 0.043, respectively). Polymorphisms in IL10 are associated with asthma phenotypes in this cohort. Further studies of variation in the IL10 gene may help elucidate the mechanism of asthma development in children. PMID:14748015

Lyon, Helen; Lange, Christoph; Lake, Stephen; Silverman, Edwin K.; Randolph, Adrienne G.; Kwiatkowski, David; Raby, Benjamin A.; Lazarus, Ross; Weiland, Katy M.; Laird, Nan; Weiss, Scott T.

2013-01-01

380

Factors That Contribute to Assay Variation in Quantitative Analysis of Sex Steroid Hormones Using Liquid and Gas Chromatography-Mass Spectrometry  

ERIC Educational Resources Information Center

The list of physiological events in which sex steroids play a role continues to increase. To decipher the roles that sex steroids play in any condition requires high quality cohorts of samples and assays that provide highly accurate quantitative measures. Liquid and gas chromatography coupled with mass spectrometry (LC-MS and GC-MS) have…

Xu, Xia; Veenstra, Timothy D.

2012-01-01