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PubMed1997

Sex ratios: are there natural variations within the human population?

OBJECTIVE: To investigate on a population basis the suggestion that certain factors naturally alter the odds of having a boy or a girl, and that some women are predisposed towards having children of one particular gender. DESIGN: Routine data analysis. POPULATION: Routinely collected data on singleton infants born in Scotland from 1975 to 1988, linked so that births (live and still) to the same mother could be identified. The analyses relate to 549,048 first to fifth order births occurring to 330,088 women whose records were complete from the first delivery onwards. MAIN OUTCOME MEASURES: Gender of infant. RESULTS: Of 549,048 births, 51.4% were male. Apart from random variation, the sex ratio of 1.06 remained constant at all birth orders (P = 0.18). The probability of a male infant appeared unrelated to the genders of the preceding siblings (P > 0.20 in second to fifth deliveries), and there was no evidence of variation with maternal age (P = 0.31), maternal height (P = 0.69), paternal social class (P = 0.12), maternal social class (P = 0.57), year of delivery (P = 0.84) or season of birth (P = 0.41). Whilst mothers whose children were all the same gender were more likely to continue childbearing than those with children of different genders, there was no evidence that those with daughters were more likely to continue than those with sons. CONCLUSIONS: The suggestion that some women have a natural predisposition towards having children of a particular gender is not supported by these data. On a population basis there is no evidence to suggest that gender determination is anything other than a chance process.

Birth Order↗
PubMed2001

Natural variation in light sensitivity of Arabidopsis.

Because plants depend on light for growth, their development and physiology must suit the particular light environment. Plants native to different environments show heritable, apparently adaptive, changes in their response to light. As a first step in unraveling the genetic and molecular basis of these naturally occurring differences, we have characterized intraspecific variation in a light-dependent developmental process-seedling emergence. We examined 141 Arabidopsis thaliana accessions for their response to four light conditions, two hormone conditions and darkness. There was significant variation in all conditions, confirming that Arabidopsis is a rich source of natural genetic diversity. Hierarchical clustering revealed that some accessions had response patterns similar to known photoreceptor mutants, suggesting changes in specific signaling pathways. We found that the unusual far-red response of the Lm-2 accession is due to a single amino-acid change in the phytochrome A (PHYA) protein. This change stabilizes the light-labile PHYA protein in light and causes a 100-fold shift in the threshold for far-red light sensitivity. Purified recombinant Lm-2 PHYA also shows subtle photochemical differences and has a reduced capacity for autophosphorylation. These biochemical changes contrast with previously characterized natural alleles in loci controlling plant development, which result in altered gene expression or loss of gene function.

Arabidopsis↗
PubMed2000

Natural variation in immune responsiveness, with special reference to immunodeficiency and promoter polymorphism in class II MHC genes.

This review deals with natural selection operating on heterozygotes as a key factor controlling (a) the frequency of immunodeficiencies, and (b) promoter polymorphism in MHC class II genes. The known difference in frequency distribution of X-linked and autosomal deficiencies lend support to this possibility, and suggest that the frequency of neonatal defect may rise as old-established equlibria between entry and exit of deleterious mutations change. MHC class II gene promoters differ in their capacity to favor Th1 (or reciprocally Th2) responses, thus suggesting that promoter polymorphism is sustained by the greater flexibility in response that this confers on heterozygotes.

Animals↗
PubMed2000

Natural variation in the essential oil content of Melaleuca alternifolia Cheel (Myrtaceae).

The composition and yield of oil in 615 trees representing the natural populations of Melaleuca alternifolia, or tea tree, was investigated. A sixth distinct oil chemotype was identified. Of the six chemotypes, one chemotype is dominated by terpinen-4-ol, one by 1,8-cineole, one by terpinolene and the remaining three chemotypes are all dominated by 1,8-cineole and differ in either terpinen-4-ol or terpinolene content. Whilst most chemotypes are present throughout the distribution range, a definite correspondence of oil types with geographic location was found. Terpinen-4-ol types predominate in and around the Bungawalbin basin in the Casino area of northern New South Wales (NSW), high 1,8-cineole types predominate toward the southern end of the distribution around Grafton and terpinolene types predominate in southern Queensland. Preliminary formulae have been developed to allow comparisons of oil data obtained by steam distillation with a static headspace gas chromatography method.

Journal Article↗
PubMed2006

Natural variation in partial resistance to Pseudomonas syringae is controlled by two major QTLs in Arabidopsis thaliana.

BACKGROUND: Low-level, partial resistance is pre-eminent in natural populations, however, the mechanisms underlying this form of resistance are still poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we used the model pathosystem Pseudomonas syringae pv. tomato DC3000 (Pst) - Arabidopsis thaliana to study the genetic basis of this form of resistance. Phenotypic analysis of a set of Arabidopsis accessions, based on evaluation of in planta pathogen growth revealed extensive quantitative variation for partial resistance to Pst. It allowed choosing a recombinant inbred line (RIL) population derived from a cross between the accessions Bayreuth and Shahdara for quantitative genetic analysis. Experiments performed under two different environmental conditions led to the detection of two major and two minor quantitative trait loci (QTLs) governing partial resistance to Pst and called PRP-Ps1 to PRP-Ps4. The two major QTLs, PRP-Ps1 and PRP-Ps2, were confirmed in near isogenic lines (NILs), following the heterogeneous inbred families (HIFs) strategy. Analysis of marker gene expression using these HIFs indicated a negative correlation between the induced amount of transcripts of SA-dependent genes PR1, ICS and PR5, and the in planta bacterial growth in the HIF segregating at PRP-Ps2 locus, suggesting an implication of PRP-Ps2 in the activation of SA dependent responses. CONCLUSIONS/SIGNIFICANCE: These results show that variation in partial resistance to Pst in Arabidopsis is governed by relatively few loci, and the validation of two major loci opens the way for their fine mapping and their cloning, which will improve our understanding of the molecular mechanisms underlying partial resistance.

Arabidopsis↗
PubMed2004

Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus.

Individual variation in gene expression is important for evolutionary adaptation and susceptibility to diseases and pathologies. In this study, we address the functional importance of this variation by comparing cardiac metabolism to patterns of mRNA expression using microarrays. There is extensive variation in both cardiac metabolism and the expression of metabolic genes among individuals of the teleost fish Fundulus heteroclitus from natural outbred populations raised in a common environment: metabolism differed among individuals by a factor of more than 2, and expression levels of 94% of genes were significantly different (P < 0.01) between individuals in a population. This unexpectedly high variation in metabolic gene expression explains much of the variation in metabolism, suggesting that it is biologically relevant. The patterns of gene expression that are most important in explaining cardiac metabolism differ between groups of individuals. Apparently, the variation in metabolism seems to be related to different patterns of gene expression in the different groups of individuals. The magnitude of differences in gene expression in these groups is not important; large changes in expression have no greater predictive value than small changes. These data suggest that variation in physiological performance is related to the subtle variation in gene expression and that this relationship differs among individuals.

Animals↗
PubMed1993

Catalytic antibody activity elicited by active immunisation. Evidence for natural variation involving preferential stabilization of the transition state.

1. The hydrolytic activity of IgG purified from (a) 13 samples of ovine antiserum collected from three animals during a two-year immunisation programme using a phosphate immunogen (comprising the amide conjugate bonded through the carboxy group of 4-nitrophenyl 4-carboxymethylphenyl hydrogen phosphate and amino groups of keyhole-limpet haemocyanin) and (b) a sample of ovine antiserum collected from another animal during an 18-week immunisation programme using an analogous sulphone immunogen (comprising the amide conjugate bonded through the amino group of 4-nitrobenzyl, 4-(4-aminobutoxy)benzyl sulphone and carboxyl groups of keyhole-limpet haemocyanin) were evaluated kinetically by using 4-nitrophenyl 4-(3-aza-2-oxoheptyl)phenyl carbonate and 4-nitrophenyl 4-(2-hydroxyethoxy)phenyl carbonate as substrates. 2. Catalytic activity was found in all 13 samples of anti-phosphate IgG but was absent in the sample of anti-sulphone IgG as well as in all samples of IgG isolated from the serum of non-immunised animals. These findings, taken together with the lack of catalytic activity of the anti-phosphate IgG towards the 2-nitrophenyl 4-(3-aza-2-oxoheptyl)phenyl carbonate, compel the view that the catalytic activity of the anti-phosphate IgG preparation is entirely antibody-mediated and is not due to contaminant hydrolytic enzymes. The fact that catalytic activity was found in all 13 samples of the anti-phosphate IgG provides the first evidence that it is possible, as a routine, to elicit a catalytic antibody response in a host animal via active immunisation. 3. The nature of the, albeit small, variation in the catalytic characteristics of the anti-phosphate IgG (increase in both kcat, the catalytic rate constant calculated as V/2[IgG] and kcat/Km, the apparent second-order rate constant for the overall catalysed conversion of substrate to products, with increase in Km suggests simultaneous improvement in transition state binding and deterioration in substrate binding as predicted from immunogen design and the postulated general mechanistic basis of antibody catalysis. 4. This interpretation is supported by the difference in the values of the dissociation constant Ki for the competitive inhibition by the transition-state analogue 4-methylphenyl 4-nitrophenyl hydrogen phosphate of reactions catalysed by two representative anti-phosphate IgG samples: for the catalysis with Km = 4.5 microM, Ki = 9 nM and for that with Km = 1.3 microM, Ki = 80 nM.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2001

Genetic control of natural variation in Arabidopsis glucosinolate accumulation.

Glucosinolates are biologically active secondary metabolites of the Brassicaceae and related plant families that influence plant/insect interactions. Specific glucosinolates can act as feeding deterrents or stimulants, depending upon the insect species. Hence, natural selection might favor the presence of diverse glucosinolate profiles within a given species. We determined quantitative and qualitative variation in glucosinolates in the leaves and seeds of 39 Arabidopsis ecotypes. We identified 34 different glucosinolates, of which the majority are chain-elongated compounds derived from methionine. Polymorphism at only five loci was sufficient to generate 14 qualitatitvely different leaf glucosinolate profiles. Thus, there appears to be a modular genetic system regulating glucosinolate profiles in Arabidopsis. This system allows the rapid generation of new glucosinolate combinations in response to changing herbivory or other selective pressures. In addition to the qualitative variation in glucosinolate profiles, we found a nearly 20-fold difference in the quantity of total aliphatic glucosinolates and were able to identify a single locus that controls nearly three-quarters of this variation.

Arabidopsis↗
PubMed1980

Natural variation and differential diagnosis of skeletal changes in tuberculosis.

Twenty-six documented cases (17 blacks, 9 whites) of skeletal tuberculosis from the Hamann-Todd Osteological Collection, Cleveland Museum of Natural History, were analyzed for lesion variability and patterns of multiple site involvement. In addition, several documented cases of pathologic conditions (osteomyelitis, vertebral fractures, and malignant bone tumors) that resemble skeletal tuberculosis were photographed and described for use in differential diagnosis. The range of variation of tuberculous lesions was found to be considerable. Thirty-eight percent (10/26) of the cases display skeletal lesions in two or more regions concomitantly. The average number of vertebrae affected, as well as the incidence of multiple bone involvement, were found to be higher in blacks. Certain combinations of skeletal lesions (e.g., spine-rib, spine-rib-sternum, and spine-hip) may be useful in the diagnosis of tuberculosis in dry bone material.

Actinomycosis↗
PubMed2005

Quantitative genetics of natural variation of behavior in Drosophila melanogaster: the possible role of the social environment on creating persistent patterns of group activity.

Using a set of nine effectively isogenic lines collected from nature in 1998, we observed unperturbed behaviors of mixed-sex groups of Drosophila melanogaster. We repeatedly scanned replicated groups of genetically identical individuals, five females and five males, and recorded the behavior of each individual (i.e., walking, feeding, grooming, flying, courting, mating, fighting, or resting). From these behaviors, we made a composite variable of activity for our quantitative genetic analysis. Genotypes differed in activity, explaining 14.41% of the variation in activity; 8.60% of the variation was explained by a significant genotype x sex interaction, which signifies genetic variation for sexual dimorphism in behavior. Phenotypic plasticity explained 11.13% of the variation in activity. Different genotypes and sexes within genotypes had different rank orders of the component behaviors that contribute to activity. We found no effect of common rearing environment. Instead, differences between replicate groups within genotype accounted for 19.47% variation in activity, and activity was significantly repeatable across scans. This emergent group behavior is likely caused by differences between groups of interacting individuals, even though individuals were genetically identical across groups. Thus, emergent group behavior explained almost as much variation in activity as the combined sources of genetic variation (23.01%), and this is an additional level on which selection could operate: individuals and groups. We discuss how differences among groups could change patterns of additive genetic variation available for evolution. Furthermore, because the behavior of an individual is influenced by conspecifics, genotype interactions between individuals could contribute to indirect selection. Finally, if we consider activity as a syndrome governing all component behaviors with strong genetic correlations among behaviors within an individual, then these component behaviors cannot evolve independently. These results suggest that reductionist approaches of molecular behavior genetics may be incomplete and/or misleading when considering similar phenotypes at the population level or when trying to understand how behaviors evolve.

Analysis of Variance↗
PubMed1999

An epigenetic mutation responsible for natural variation in floral symmetry.

Although there have been many molecular studies of morphological mutants generated in the laboratory, it is unclear how these are related to mutants in natural populations, where the constraints of natural selection and breeding structure are quite different. Here we characterize a naturally occurring mutant of Linaria vulgaris, originally described more than 250 years ago by Linnaeus, in which the fundamental symmetry of the flower is changed from bilateral to radial. We show that the mutant carries a defect in Lcyc, a homologue of the cycloidea gene which controls dorsoventral asymmetry in Antirrhinum. The Lcyc gene is extensively methylated and transcriptionally silent in the mutant. This modification is heritable and co-segregates with the mutant phenotype. Occasionally the mutant reverts phenotypically during somatic development, correlating with demethylation of Lcyc and restoration of gene expression. It is surprising that the first natural morphological mutant to be characterized should trace to methylation, given the rarity of this mutational mechanism in the laboratory. This indicates that epigenetic mutations may play a more significant role in evolution than has hitherto been suspected.

Amino Acid Sequence↗
PubMed2006

Natural variation in MAM within and between populations of Arabidopsis lyrata determines glucosinolate phenotype.

The genetic variation that underlies the glucosinolate phenotype of Arabidopsis lyrata ssp. petraea was investigated between and within populations. A candidate glucosinolate biosynthetic locus (MAM, containing methylthioalkylmalate synthase genes) was mapped in A. lyrata to a location on linkage group 6 corresponding to the homologous location for MAM in A. thaliana. In A. thaliana MAM is responsible for side chain elongation in aliphatic glucosinolates, and the MAM phenotype can be characterized by the ratios of long- to short-chain glucosinolates. A quantitative trait loci (QTL) analysis of glucosinolate ratios in an A. lyrata interpopulation cross found one QTL at MAM. Additional QTL were identified for total indolic glucosinolates and for the ratio of aliphatic to indolic glucosinolates. MAM was then used as the candidate gene for a within-population cosegregation analysis in a natural A. lyrata population from Germany. Extensive variation in microsatellite markers at MAM was found and this variation cosegregated with the same glucosinolate ratios as in the QTL study. The combined results indicate that both between- and within-population genetic variation in the MAM region determines phenotypic variation in glucosinolate side chains in A. lyrata.

Arabidopsis↗
PubMed2003

Natural variation in populations of persistently colonizing bacteria affect human host cell phenotype.

The highly diverse bacterium Helicobacter pylori, which persistently colonizes the human stomach, provides models to study the role of genome plasticity in host adaptation. Within H. pylori populations from 2 colonized individuals, intragenomic recombination between cagA DNA repeat sequences leads to deletion or duplication of tyrosine phosphorylation sites in the CagA protein, which is injected by a type IV secretion system into host cells. Experimental coculture of gastric epithelial cells with the strains containing these naturally occurring CagA phosphorylation site variants induced markedly divergent host cell morphologic responses. Mutants were constructed in which a phosphorylation site was either added or deleted in the expressed CagA protein; coculture studies confirmed that the naturally occurring differences in CagA phosphorylation are responsible for the observed phenotypic variation. These findings indicate that within an individual host, intragenomic recombination between H. pylori repetitive DNA produces strain variants differing in their signals to host cells.

Amino Acid Sequence↗
PubMed2003

Natural variation of copper, zinc, cadmium and selenium concentrations in Bembicium nanum and their potential use as a biomonitor of trace metals.

Copper, zinc, cadmium and selenium were measured in the gastropod mollusc Bembicium nanum at two uncontaminated locations, Jervis Bay and Rosedale, NSW, to determine natural variability of metals associated with gender, mass, shore position and temporal variability. Trace metals were also measured in B. nanum at three industrialised locations to determine the accumulation of trace metals in contaminated environments.Copper, zinc, cadmium and selenium concentrations were not significantly different between male and female B. nanum. No significant relationships were found between zinc, cadmium and selenium concentrations and mass. There was a significant relationship between copper concentration and mass but only 19% of the variation was explained by mass. Generally inherent variability within samples had a greater influence than gender or variations in mass on trace metal concentrations. No trend was found in cadmium and selenium concentrations with variation in shoreline position. Copper and zinc concentrations increased further away from the low tide mark, with a decrease in metal concentrations at the furthest site from the water. Variability in metal concentrations is attributable to variations in food source, food availability and different immersion times.Copper, zinc, cadmium and selenium concentrations varied over a 12-month period. Copper, cadmium and selenium were taken up and lost over time, as metal body burden followed the same trend as metal concentrations. Zinc concentrations were influenced by mass. Copper and cadmium concentrations fluctuated throughout the 12-month period but with no clear seasonal trends. Selenium concentrations peaked in spring (October), with concentrations remaining uniform over the other months. These differences in mean concentrations between months were most likely due to inherent trace metal variability associated with differences in food availability and changes in metabolic rates associated with changes in temperature during the study period. Measurement of trace metals in B. nanum at contaminated sites showed that B. nanum accumulates metals in response to contamination.B. nanum meets most of the requirements to be a biomonitor of trace metal contamination as they are abundant, sedentary, easy to identify, provide sufficient tissue for analysis, tolerate high concentrations of pollutants and they accumulate trace metals in response to contamination. However, as trace metal concentration can vary with mass, shoreline position and temporally, care must be taken to collect individual organisms with similar mass from similar shoreline positions and times.

Animals↗
PubMedDate not supplied

Phenomenon of life span instability in Drosophila melanogaster: II. Change in rhythm of natural variations of life span after single exposure to gamma-irradiation.

The dynamics of life span (LS) have been studied in successive generations of postirradiation and control groups of Drosophila melanogaster, strain D-32, after a single exposure to Co60 gamma-quantum irradiation. It has been shown using mathematical procedures that in all postirradiation generations, with one exception, survival curves retain their canonical shape. This is indicative of the unchangeable nature of LS distribution. The mean LS of the progeny of irradiated parents either coincides with control values or can be higher or lower. Moreover, single irradiation results in an altered time-scanning of LS variations in successive generations as compared with controls. The possible origin of LS instability is discussed.

Animals↗
PubMed1997

Natural variation in a Drosophila clock gene and temperature compensation.

The threonine-glycine (Thr-Gly) encoding repeat within the clock gene period of Drosophila melanogaster is polymorphic in length. The two major variants (Thr-Gly)17 and (Thr-Gly)20 are distributed as a highly significant latitudinal cline in Europe and North Africa. Thr-Gly length variation from both wild-caught and transgenic individuals is related to the flies' ability to maintain a circadian period at different temperatures. This phenomenon provides a selective explanation for the geographical distribution of Thr-Gly lengths and gives a rare glimpse of the interplay between molecular polymorphism, behavior, population biology, and natural selection.

Alleles↗
PubMed2005

Natural variation in toxicity of wheat: potential for selection of nontoxic varieties for celiac disease patients.

BACKGROUND & AIMS: Celiac disease (CD) is an intestinal disorder caused by T-cell responses to peptides derived from the gluten proteins present in wheat. Such peptides have been found both in the gliadin and glutenin proteins in gluten. The only cure for CD is a lifelong gluten-free diet. It is unknown, however, if all wheat varieties are equally harmful for patients. We investigated whether wheat varieties exist with a natural low number of T-cell-stimulatory epitopes. METHODS: Gluten proteins present in public databases were analyzed for the presence of T-cell-stimulatory sequences. In addition, wheat accessions from diploid (AA, SS/BB, and DD genomes), tetraploid (AABB), and hexaploid (AABBDD) Triticum species were tested for the presence of T-cell-stimulatory epitopes in gliadins and glutenins by both T-cell and monoclonal antibody-based assays. RESULTS: The database analysis readily identified gluten proteins that lack 1 or more of the known T-cell-stimulatory sequences. Moreover, both the T-cell- and antibody-based assays showed that a large variation exists in the amount of T-cell-stimulatory peptides present in the wheat accessions. CONCLUSIONS: Sufficient genetic variation is present to endeavor the selection of wheat accessions that contain low amounts of T-cell-stimulatory sequences. Such materials may be used to select and breed wheat varieties suitable for consumption by CD patients, contributing to a well-balanced diet and an increase in their quality of life. Such varieties also may be useful for disease prevention in individuals at risk.

Celiac Disease↗
PubMed1997

Artificial mutations and natural variations in the CD46 molecules from human and monkey cells define regions important for measles virus binding.

CD46 was previously shown to be a primate-specific receptor for the Edmonston strain of measles virus. This receptor consists of four short consensus regions (SCR1 to SCR4) which normally function in complement regulation. Measles virus has recently been shown to interact with SCR1 and SCR2. In this study, receptors on different types of monkey erythrocytes were employed as "natural mutant proteins" to further define the virus binding regions of CD46. Erythrocytes from African green monkeys and rhesus macaques hemagglutinate in the presence of measles virus, while baboon erythrocytes were the least efficient of the Old World monkey cells used in these assays. Subsequent studies demonstrated that the SCR2 domain of baboon CD46 contained an Arg-to-Gln mutation at amino acid position 103 which accounted for reduced hemagglutination activity. Surprisingly, none of the New World monkey erythrocytes hemagglutinated in the presence of virus. Sequencing of cDNAs derived from the lymphocytes of these New World monkeys and analysis of their erythrocytes with SCR1-specific polyclonal antibodies indicated that the SCR1 domain was deleted in these cells. Additional experiments, which used 35 different site-specific mutations inserted into CD46, were performed to complement the preceding studies. The effects of these artificial mutations were documented with a convenient binding assay using insect cells expressing the measles virus hemagglutinin. Mutations which mimicked the change found in baboon CD46 or another which deleted the SCR2 glycosylation site reduced binding substantially. Another mutation which altered GluArg to AlaAla at positions 58 and 59, totally abolished binding. Finally, the epitopes for two monoclonal antibodies which inhibit measles virus attachment were mapped to the same regions implicated by mutagenesis.

Amino Acid Sequence↗