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Functional Variation (functional + variation)
Selected AbstractsFunctional variation in a disease resistance gene in populations of Arabidopsis thalianaMOLECULAR ECOLOGY, Issue 22 2008T. H. JORGENSEN Abstract Analyses of functional genetic diversity in natural populations may provide important new insights into gene function and are necessary to understand the evolutionary processes maintaining diversity itself. The importance of including diversity within and between local populations in such studies is often ignored although many of the processes affecting genetic diversity act on this scale. Here we examine the molecular diversity in RPW8 (Recognition of Powdery Mildew), a gene conferring broad-spectrum resistance to powdery mildews in Arabidopsis thaliana stock-center accessions. Our eight UK study populations of the weedy A. thaliana were from locations judged to be subject to a minimum of anthropogenic disturbance and potentially long established. The majority of populations comprised considerable variation both in disease phenotype and RPW8 genotype. Although resistant individuals shared a major RPW8 genotype, no single allele was uniquely associated with resistance. It is concluded that RPW8 is an essential component of resistance to powdery mildews in A. thaliana, but not the only genetic factor involved in this process. No signature of selection was detected at RPW8 with a microsatellite multilocus test using an empirical null model. Unlike many previous studies of this model plant species, we found high levels of genetic diversity and relatively low differentiation (FST = 0.31) between populations at 14 microsatellite markers. This is judged to be due to our sampling being aimed at potentially long established populations and highlights the importance of population choice for studies of genetic diversity within this species. [source] Functional variation of neck muscles and their relation to feeding style in Tyrannosauridae and other large theropod dinosaursTHE ANATOMICAL RECORD : ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Issue 8 2007Eric Snively Abstract Reconstructed neck muscles of large theropod dinosaurs suggest influences on feeding style that paralleled variation in skull mechanics. In all examined theropods, the head dorsiflexor m. transversospinalis capitis probably filled in the posterior dorsal concavity of the neck, for a more crocodilian- than avian-like profile in this region. The tyrannosaurine tyrannosaurids Daspletosaurus and Tyrannosaurus had relatively larger moment arms for lateroflexion by m. longissimus capitis superficialis and m. complexus than albertosaurine tyrannosaurids, and longer dorsiflexive moment arms for m. complexus. Areas of dorsiflexor origination are significantly larger relative to neck length in adult Tyrannosaurus rex than in other tyrannosaurids, suggesting relatively large muscle cross-sections and forces. Tyrannosaurids were not particularly specialized for neck ventroflexion. In contrast, the hypothesis that Allosaurus co-opted m. longissimus capitis superficialis for ventroflexion is strongly corroborated. Ceratosaurus had robust insertions for the ventroflexors m. longissimus capitis profundus and m. rectus capitis ventralis. Neck muscle morphology is consistent with puncture-and-pull and powerful shake feeding in tyrannosaurids, relatively rapid strikes in Allosaurus and Ceratosaurus, and ventroflexive augmentation of weaker jaw muscle forces in the nontyrannosaurids. Anat Rec, 290:934,957, 2007. © 2007 Wiley-Liss, Inc. [source] INTEGRATING EVOLUTIONARY AND FUNCTIONAL APPROACHES TO INFER ADAPTATION AT SPECIFIC LOCIEVOLUTION, Issue 9 2010Jay F. Storz Inferences about adaptation at specific loci are often exclusively based on the static analysis of DNA sequence variation. Ideally, population-genetic evidence for positive selection serves as a stepping-off point for experimental studies to elucidate the functional significance of the putatively adaptive variation. We argue that inferences about adaptation at specific loci are best achieved by integrating the indirect, retrospective insights provided by population-genetic analyses with the more direct, mechanistic insights provided by functional experiments. Integrative studies of adaptive genetic variation may sometimes be motivated by experimental insights into molecular function, which then provide the impetus to perform population genetic tests to evaluate whether the functional variation is of adaptive significance. In other cases, studies may be initiated by genome scans of DNA variation to identify candidate loci for recent adaptation. Results of such analyses can then motivate experimental efforts to test whether the identified candidate loci do in fact contribute to functional variation in some fitness-related phenotype. Functional studies can provide corroborative evidence for positive selection at particular loci, and can potentially reveal specific molecular mechanisms of adaptation. [source] Growth properties of 16 non-pioneer rain forest tree species differing in sapling architectureJOURNAL OF ECOLOGY, Issue 5 2009Masahiro Aiba Summary 1.,Sapling architecture may be an important determinant of performance traits, such as light interception and height growth, but few studies have examined the direct relationship between sapling architecture and growth properties. To study this relationship and the potential for strategic diversification, we analysed the growth properties in saplings of 16 Bornean tree species that differ in architecture. 2.,Annual net production significantly differed amongst species and was positively correlated with total above-ground dry mass, total leaf area and crown area. In contrast, the net assimilation rate was weakly but negatively correlated with these architectural traits. The net assimilation rate was virtually independent of leaf size and specific leaf area. Relationships between sapling architecture and relative growth rate in mass were weak. 3.,The relative growth rate in height did not significantly differ amongst species, although their total dry mass, a proxy for extension cost, varied fourfold across species for a given sapling height. This is because the proportional increase in net production with total dry mass, which is based on a larger total leaf area and larger crown area, cancelled out the higher extension cost. All architectural traits, including leaf size and specific leaf area, failed to predict height growth rate. 4.,Synthesis. Relative growth rates in both mass and height were relatively independent of sapling architecture. Of the architectural traits, leaf size, specific leaf area and stem diameter were poor predictors of growth properties, even though they were considered functionally important. These results clearly reject the classic hypothesis that architectural variation leads to a trade-off between height growth and light interception, at least for the species that are under shaded conditions. However, functional variation ranging from species with high net production and low net assimilation rates (in saplings of equal height) to species with the opposite traits, which was accompanied by architectural variation in total dry mass and related size factors, may be important for the coexistence of these tree species. The possibility that small total dry mass may be advantageous in height growth under well-lit conditions should be examined in future studies. [source] Fitness differences associated with Pgi SNP genotypes in the Glanville fritillary butterfly (Melitaea cinxia)JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 2 2009L. ORSINI Abstract Allozyme variation at the phosphoglucose isomerase (PGI) locus in the Glanville fritillary butterfly (Melitaea cinxia) is associated with variation in flight metabolic rate, dispersal rate, fecundity and local population growth rate. To map allozyme to DNA variation and to survey putative functional variation in genomic DNA, we cloned the coding sequence of Pgi and identified nonsynonymous variable sites that determine the most common allozyme alleles. We show that these single-nucleotide polymorphisms (SNPs) exhibit significant excess of heterozygotes in field-collected population samples as well as in laboratory crosses. This is in contrast to previous results for the same species in which other allozymes and SNPs were in Hardy,Weinberg equilibrium or exhibited an excess of homozygotes. Our results suggest that viability selection favours Pgi heterozygotes. Although this is consistent with direct overdominance at Pgi, we cannot exclude the possibility that heterozygote advantage is caused by the presence of one or more deleterious alleles at linked loci. [source] Fish mitochondrial genomics: sequence, inheritance and functional variationJOURNAL OF FISH BIOLOGY, Issue 2 2008K. H. Brown Mitochondrial genomic research currently primarily focuses on the analysis and understanding of how mitochondrial mutations produce detrimental phenotypes in humans. Reasons for this focus on negative impacts include the large number of human diseases that are known to result from specific mitochondrial genomes, and the long held belief that mitochondria change only through the accumulation of mutations due to its clonal, maternal inheritance. Recent studies are beginning to challenge these preconceptions and have shown that mitochondrial genomes can have significant positive impacts. Although the number of studies using fishes as models in mitochondrial research is limited, many fish model species provide excellent opportunity for furthering the understanding of mitochondrial genomes, their interactions with the nuclear genome, the potential for understanding the mechanisms of how functional variation effects organisms and how selection for positive functional variation effects population variation. [source] Association of Markers in the 3, Region of the GluR5 Kainate Receptor Subunit Gene to Alcohol DependenceALCOHOLISM, Issue 5 2009Henry R. Kranzler Background:, Glutamate neurotransmission plays an important role in a variety of alcohol-related phenomena, including alcohol self-administration by both animals and humans. Because the risk for alcohol dependence (AD) is genetically influenced, genes encoding glutamate receptors are candidates to contribute to the risk for AD. We examined the role of variation in the 3, region of GRIK1, the gene that encodes the GluR5 receptor subunit of the kainic acid glutamate receptor, on risk for AD. We focused specifically on this gene because topiramate, a glutamate modulator that binds to the GluR5 subunit, has shown robust efficacy in the treatment of AD. Methods:, We genotyped 7 single nucleotide polymorphisms (SNPs) in the 3,-half of GRIK1, which includes 3 differentially spliced exons, in a sample of EA control subjects (n = 507) and subjects with AD (n = 1,057). Results:, We found nominally significant evidence of association to AD for 3 SNPs (rs2832407 in intron 9, rs2186305 in intron 17, and rs2832387 in the 3,UTR). Empirical p -value estimation revealed that only rs2832407 was significantly associated to phenotype (p = 0.043). Discussion:, These findings provide support for the hypothesis that variation in the 3, portion of the gene encoding the GluR5 kainate receptor subunit contributes to the risk for AD. Further research is needed to ascertain whether this SNP is itself functional or whether the association reflects linkage disequilibrium with functional variation elsewhere in the gene and whether this SNP moderates topiramate's effects in the treatment of AD. [source] Contribution of functional variation in the IL13 gene to allergy, hay fever and asthma in the NSHD longitudinal 1946 birth cohortALLERGY, Issue 8 2009S. Black Background:, Genetic variants of the two adjacent genes, IL13 and IL4 have frequently been reported as being associated with susceptibility to atopy and asthma, both in adults and children, and some studies also suggest association with lung function and chronic obstructive pulmonary disease. Methods:, In this study, we examined for the first time the effect of these variants in 2918 adults in a longitudinal birth cohort, the British National Survey of Health and Development, where there are extensive life style, developmental and environmental data. We examine two IL13 single nucleotide polymorphisms (SNPs) IL13 rs20541 (R110Q) and rs1800925 (,1024C>T) and one IL4 SNP, rs2070874 (,33C>T) with likely function. Results:, We show that IL13 rs20541 and rs1800925 are each significantly associated with self-reported asthma and allergy, and that this association is not confounded by any of the known developmental and environmental risk factors for asthma and atopy, including in particular place of birth. IL13 rs20541 does however act as a confounder for the IL13 rs1800925 associations, meaning that there is no statistical support for rs1800925 having an independent effect. There is nevertheless evidence for interaction between smoking and rs1800925, with allergy as outcome. None of the SNPs showed association with measures of lung function, nor any interaction with the effect of smoking on lung function. Conclusion:, In a longitudinal population cohort we have established a role for polymorphism of IL13 in determining susceptibility to both atopy and asthma. [source] Small genetic differences between ericoid mycorrhizal fungi affect nitrogen uptake by VacciniumNEW PHYTOLOGIST, Issue 3 2009Gwen-Aëlle Grelet Summary ,,Ericoid mycorrhizal fungi have been shown to differ in their pattern of nitrogen (N) use in pure culture. Here, we investigate whether this functional variation is maintained in symbiosis using three ascomycetes from a clade not previously shown to include ericoid mycorrhizal taxa. ,,Vaccinium macrocarpon and Vaccinium vitis-idaea were inoculated with three fungal strains known to form coils in Vaccinium roots, which differed in their patterns of N use in liquid culture. 15N was used to trace the uptake of -N, -N and glutamine-N into shoots. ,,15N transfer differed among the three fungal strains, including two that had identical internal transcribed spacer (ITS) sequences, and was quantitatively related to fungal growth in liquid culture at low carbon availability. ,,These results demonstrate that functional differences among closely related ericoid mycorrhizal fungi are maintained in symbiosis with their hosts, and suggest that N transfer to plant shoots in ericoid mycorrhizas is under fungal control. [source] Evaluation of detergents for the soluble expression of ,-helical and ,-barrel-type integral membrane proteins by a preparative scale individual cell-free expression systemFEBS JOURNAL, Issue 23 2005Christian Klammt Cell-free expression has become a highly promising tool for the fast and efficient production of integral membrane proteins. The proteins can be produced as precipitates that solubilize in mild detergents usually without any prior denaturation sttif. Alternatively, membrane proteins can be synthesized in a soluble form by adding detergents to the cell-free system. However, the effects of a representative variety of detergents on the production, solubility and activity of a wider range of membrane proteins upon cell-free expression are currently unknown. We therefore analyzed the cell-free expression of three structurally very different membrane proteins, namely the bacterial ,-helical multidrug transporter, EmrE, the ,-barrel nucleoside transporter, Tsx, and the porcine vasopressin receptor of the eukaryotic superfamily of G-protein coupled receptors. All three membrane proteins could be produced in amounts of several mg per one ml of reaction mixture. In general, the detergent 1-myristoyl-2-hydroxy- sn -glycero-3-[phospho- rac -(1-glycerol)] was found to be most effective for the resolubilization of membrane protein precipitates, while long chain polyoxyethylene-alkyl-ethers proved to be most suitable for the soluble expression of all three types of membrane proteins. The yield of soluble expressed membrane protein remained relatively stable above a certain threshold concentration of the detergents. We report, for the first time, the high-level cell-free expression of a ,-barrel type membrane protein in a functional form. Structural and functional variations of the analyzed membrane proteins are evident that correspond with the mode of expression and that depend on the supplied detergent. [source] Secondary structure and dynamics of micelle bound ,- and ,-synucleinPROTEIN SCIENCE, Issue 5 2006Yoon-hui Sung Abstract We have used solution state NMR spectroscopy to characterize the secondary structure and backbone dynamics of the proteins ,- and ,-synuclein in their detergent micelle-bound conformations. Comparison of the results with those previously obtained for the Parkinson's disease-linked protein ,-synuclein shows that structural differences between the three homologous synuclein family members are directly related to variations in their primary amino acid sequences. An 11-residue deletion in the lipid-binding domain of ,-synuclein leads to the destabilization of an entire segment of the micelle-bound helical structure containing the deletion site. The acidic C-terminal tail region of ,-synuclein, which displays extensive sequence divergence, is more highly disordered than the corresponding regions in the other two family members. The observed structural differences are likely to mediate functional variations between the three proteins, with differences between ,- and ,-synuclein expected to revolve around their lipid interactions, while differences in ,-synuclein function are expected to result from different protein,protein interactions mediated by its unique C-terminal tail. [source] CASE REPORT: Clinical application of mfERG/VEP in assessing superior altitudinal hemifield lossCLINICAL AND EXPERIMENTAL OPTOMETRY, Issue 4 2005Dr Henry Ho-lung Chan PhD FAAO Multifocal ERG (mfERG) and multifocal VEP (mfVEP) have been used widely in the investigation of pathological changes or functional variations in the visual system. Altitudinal hemifield loss is a visual field defect that is usually found in patients with ischaemic optic neuropathy (ION). Anterior ischaemic optic neuropathy (AION) is a complex multi-factorial disease and it is difficult to diagnose according to clinical symptoms and signs alone. AION is believed to be caused by an infarction of the optic nerve due to the occlusion of the posterior ciliary arteries. The current report presents a patient diagnosed with non-arteritic AION. In this report, the mfERG findings did not match the results of the visual field test but those of the mfVEP did. After consideration of the visual electrophysiological and visual field results, the defect arises from neither the retina nor the visual pathway behind the optic chiasma. Hence, the optic nerve is the most likely location of the lesion, causing the superior altitudinal hemi-field loss. This report shows that the mfERG and mfVEP techniques can be used for objective visual field assessment to supplement the conventional visual field testing. [source] | ||||||||||||||||