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At least 217 records · Page 12Linked to original sources
PubMed2004

Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root.

Mutant analysis has been tremendously successful in deciphering the genetics of plant development. However, less is known about the molecular basis of morphological variation within species, which is caused by naturally occurring alleles. In this study, we succeeded in isolating a novel regulator of root growth by exploiting natural genetic variation in the model plant Arabidopsis. Quantitative trait locus analysis of a cross between isogenized accessions revealed that a single locus is responsible for approximately 80% of the variance of the observed difference in root length. This gene, named BREVIS RADIX (BRX), controls the extent of cell proliferation and elongation in the growth zone of the root tip. We isolated BRX by positional cloning. BRX is a member of a small group of highly conserved genes, the BRX gene family, which is only found in multicellular plants. Analyses of Arabidopsis single and double mutants suggest that BRX is the only gene of this family with a role in root development. The BRX protein is nuclear localized and activates transcription in a heterologous yeast system, indicating that BRX family proteins represent a novel class of transcription factors. Thus, we have identified a novel regulatory factor controlling quantitative aspects of root growth.

Amino Acid Sequence↗
PubMed2006

A quantitative trait locus analysis of natural genetic variation for Drosophila melanogaster oxidative stress survival.

Little is known about natural genetic variation for survival under oxidative stress conditions or whether genetic variation for oxidative stress survival is associated with that for life-history traits. We have investigated survival in a high-oxygen environment at 2 adult densities using a set of recombinant inbred lines (RILs) isolated from a natural population of Drosophila melanogaster. Female and male oxidative stress survival was highly correlated. Quantitative trait loci (QTLs) for oxidative stress survival were identified on both autosomes. These QTLs were sometimes sex or density specific but were most often not. QTLs were identified that colocalize to the same region of the genome as longevity in other studies using the same set of RILs. We also determined early-age egg production and found QTLs for this trait, but there was no support for an association between oxidative stress survival and egg production.

Age Factors↗
PubMed2005

Mutations and natural genetic variation in the courtship song of Drosophila.

All Drosophila species have a courtship repertoire by which a male stimulates a female to mate with him. In many species, males vibrate their wings to produce courtship song, an element of courtship that plays an important role in female choice. Each species has a unique courtship song, with the major differences among species songs being in timing and/or structure. Analysis of genetic mutations has revealed 17 genes that affect courtship song in Drosophila melanogaster. Most of the genes were first identified as affecting another trait and were subsequently shown to affect song. Quantitative genetic studies have demonstrated a polygenetic additive genetic architecture for many song traits. Few candidate genes, identified through the classical genetic approach, coincide with the regions implicated as affecting natural variation. With many new tools in genetic analysis and the multiple Drosophila genome projects currently underway, the ability to relate mutational and quantitative analyses will improve.

Animals↗
PubMed2024

Evolution of homologous recombination rates across bacteria.

Bacteria are nonsexual organisms but are capable of exchanging DNA at diverse degrees through homologous recombination. Intriguingly, the rates of recombination vary immensely across lineages where some species have been described as purely clonal and others as "quasi-sexual." However, estimating recombination rates has proven a difficult endeavor and estimates often vary substantially across studies. It is unclear whether these variations reflect natural variations across populations or are due to differences in methodologies. Consequently, the impact of recombination on bacterial evolution has not been extensively evaluated and the evolution of recombination rate-as a trait-remains to be accurately described. Here, we developed an approach based on Approximate Bayesian Computation that integrates multiple signals of recombination to estimate recombination rates. We inferred the rate of recombination of 162 bacterial species and one archaeon and tested the robustness of our approach. Our results confirm that recombination rates vary drastically across bacteria; however, we found that recombination rate-as a trait-is conserved in several lineages but evolves rapidly in others. Although some traits are thought to be associated with recombination rate (e.g., GC-content), we found no clear association between genomic or phenotypic traits and recombination rate. Overall, our results provide an overview of recombination rate, its evolution, and its impact on bacterial evolution.

Bacteria↗
PubMed2006

Escherichia coli TolA tolerates multiple amino-acid substitutions as revealed by screening randomized variants for membrane integrity and phage receptor function.

Escherichia coli TolA is a cytoplasmic membrane protein required for outer membrane integrity and the translocation of F-specific filamentous (Ff) bacteriophage DNA. Both phage infection and membrane integrity depend on several TolA interactions, e.g. those of the TolA C-terminal domain (TolAIII). Membrane integrity involves interaction with two host proteins and phage translocation requires direct interaction with the N-terminal domain (N1) of Ff phage protein g3p. Although cocrystallization of TolAIII and N1g3p has identified several contact points, it is still uncertain which residues are selectively involved in the different TolA functions. Thus, four different limited substitution libraries of TolA were created, targeting contacts at positions 415-420. These libraries were introduced into the tolA strain K17DE3tolA/F(+) and several variants, containing complementing, multiple amino-acid substitutions, were identified. However, most randomized variants did not complement the tolA strain K17DE3tolA/F(+). The TolA variants that restored sensitivity to phage infection displayed a considerable sequence variation, while the few variants that restored tolerance to detergent were from the same library. A comparison of the generated residue variation and natural variation, suggests that structural dependence overrides contact residue dependence. Thus, library screening can be efficient in identifying TolA variants with different functionally associated characteristics.

Amino Acid Sequence↗
PubMed1992

A comprehensive study of genic variation in natural populations of Drosophila melanogaster. V. Structural-functional constraints on protein molecules and enzymes and the levels and patterns of variation among genes.

Ever since isozyme-allozyme polymorphisms were detected there has been an incessant effort to relate the amount of observed protein variation to various aspects of molecular structure and function. Structural-functional constraints can limit the amount of overall genic variation, and the observed variation can be due to neutral mutation and random genetic drift, mutation-selection balance, or balancing selection. The present analysis of structural-functional constraints on gene-enzyme variation in natural populations of Drosophila melanogaster shows that while both subunit size and substrate group show significant effects on number of alleles and mean heterozygosity, only substrate group affects population structure significantly. Subunit structure (monomer vs. multimer), IUB enzyme class (e.g., transferase, lyase), and tolerance of null alleles showed no significant effect on level or pattern of variation. While partly interdependent, these results suggest that efforts should be made to distinguish between constraints arising from molecular structure and physiological function.

Animals↗
PubMed2004

Genetic variation in natural honeybee populations, Apis mellifera capensis.

Genetic variation in honeybee, Apis mellifera, populations can be considerably influenced by breeding and commercial introductions, especially in areas with abundant beekeeping. However, in southern Africa apiculture is based on the capture of wild swarms, and queen rearing is virtually absent. Moreover, the introduction of European subspecies constantly failed in the Cape region. We therefore hypothesize a low human impact on genetic variation in populations of Cape honeybees, Apis mellifera capensis. A novel solution to studying genetic variation in honeybee populations based on thelytokous worker reproduction is applied to test this hypothesis. Environmental effects on metrical morphological characters of the phenotype are separated to obtain a genetic residual component. The genetic residuals are then re-calculated as coefficients of genetic variation. Characters measured included hair length on the abdomen, width and length of wax plate, and three wing angles. The data show for the first time that genetic variation in Cape honeybee populations is independent of beekeeping density and probably reflects naturally occurring processes such as gene flow due to topographic and climatic variation on a microscale.

Animals↗
PubMed1972

Enzyme variability in the Drosophila willistoni group. IV. Genic variation in natural populations of Drosophila willistoni.

We describe allelic variation at 28 gene loci in natural populations of D. willistoni. Seventy samples were studied from localities extending from Mexico and Florida, through Central America, the West Indies, and tropical South America, down to South Brazil. At least several hundred, and often several thousand, genomes were sampled for each locus. We have discovered a great deal of genetic variation. On the average, 58% loci are polymorphic in a given population. (A locus is considered polymorphic when the frequency of the most common allele is no greater than 0.95). An individual fly is heterozygous, on the average, at 18.4% loci.-Concerning the pattern of the variation, the most remarkable finding is the similarity of the configuration of allelic frequencies from locality to locality throughout the distribution of the species. Our observations support the conclusion that balancing natural selection is the major factor responsible for the considerable genetic variation observed in D. willistoni.

Alleles↗
PubMed1989

Sources and nature of variation in DNA analysis of follicular thyroid adenoma.

We investigated the sources and nature of variation that may occur in the DNA analysis of thyroid adenomas from cytological and histological samples. Imprints and smears gave identical results. However, the nuclear area was higher in smears where the optical density of the nuclei was lower. In measuring imprints, the interactive selection of nuclei was preferred to the automatic, because the risk of measuring nuclear fragments or undesired objects was thus avoided. The reproducibility and the variation of the DNA measurements depended on the degree of observer training in quantitative pathology, the method of field selection, and the type of instrumentation. Biological variation in the spatial distribution of nuclei with different ploidy values in some adenomas seemed to hide the influence of section thickness on measurements. Our data seem to suggest that it is best to apply a constant section thickness and 5 micron sections seem acceptable.

Adenoma↗
PubMed2001

Genetic and molecular dissection of naturally occurring variation.

Recent progress in plant genome analysis has made it possible to examine the naturally occurring allelic variation underlying complex traits. Many studies have described the genetic mapping of quantitative trait loci for several kinds of complex phenotypic traits. Some researchers have taken up the challenge of performing the molecular cloning of genes at these loci, and examples of cloning have recently been reported. Naturally occurring allelic variation could be a new resource for the functional analysis of plant genes.

Alleles↗
PubMed1999

Spatial variations in natural background radiation: absorbed dose rates in air in Colorado.

Large and small-scale spatial variations in natural ambient background radiation dose rates in Colorado were investigated at 1,150 specific locations with particular attention to 40 of the more populated areas along the Front Range of the Rocky Mountains. Total dose rates (including cosmic and terrestrial components) in Front Range communities below 2,000 m elevation averaged 135 nGy h(-1). Terrestrial dose rates had a coefficient of variation of 17%. Communities above 2,000 m had a mean total dose rate of 196 nGy h(-1), and a terrestrial dose rate coefficient of variation of 17%. Across all Front Range communities, the coefficient of variation for terrestrial dose rates was 22%. Within individual communities, coefficient of variation values for terrestrial dose rates ranged from 3 to 21%. Smaller-scale spatial variability (to within a few meters) was relatively small (coefficient of variation values generally ranged from 3 to 7%). A significant linear relationship (r2 = 0.83) between the size of area surveyed (km2) and coefficient of variation value for terrestrial dose rates was found. West of the Continental Divide, the terrestrial component accounted for roughly 60% of total measured dose rates, while east of the Continental Divide, where enriched granitic source rocks and associated soils are prevalent, the terrestrial component generally accounted for two-thirds or more of total dose rates.

Air Pollutants, Radioactive↗
PubMed1996

Functional consequences of natural sequence variation in the activation domain of HIV-1 Rev.

Initial infection with an attenuated form of human immunodeficiency virus type 1 (HIV-1) may give rise to some of the rare asymptomatic infections that have been observed. Recently, data have been presented suggesting that a persistent mutation in the essential activation domain of the HIV-1 Rev regulatory protein might have contributed to the maintenance of the asymptomatic state in one individual. Here, we have used a range of assays for in vivo Rev function to examine whether natural sequence variation in the normally highly conserved Rev activation domain can indeed affect Rev function. Analysis of five distinct natural sequence variants of the Rev domain demonstrated that each produced a two- to fourfold drop in Rev function when compared to the consensus activation domain sequence A sixth sequence, reported for the MN isolate of HIV-1, proved entirely inactive. However, resequencing of this region of the MN genome revealed that this isolate actually encodes a consensus Rev activation domain. Overall, these data reveal that even natural sequence variation in the essential Rev activation domain can result in significantly reduced Rev function and suggest that isolates containing such sequence variation are likely to replicate less effectively.

Amino Acid Sequence↗
PubMed2001

Naturally occurring variations in maternal behavior in the rat are associated with differences in estrogen-inducible central oxytocin receptors.

Naturally occurring variations in maternal licking/grooming influence neural development and are transmitted from mother to female offspring. We found that the induction of maternal behavior in virgin females through constant exposure to pups (pup sensitization) was significantly shorter in the offspring of High compared with Low licking/grooming mothers, suggesting differences in maternal responsivity. In randomly selected females screened for individual differences in maternal responsivity and subsequently mated, there was a significant and negative correlation (r = -0.73) between the latency to exhibit maternal behavior in the pup sensitization paradigm and the frequency of pup licking/grooming during lactation. Females that were more maternally responsive to pups and that showed increased levels of pup licking/grooming also showed significantly higher oxytocin receptor levels in the medial preoptic area, the lateral septum, the central nucleus (n.) of the amygdala, the paraventricular n. of the hypothalamus, and the bed n. of the stria terminalis. Intracerebroventricular administration of an oxytocin receptor antagonist to mothers on postpartum day 3 completely eliminated the differences in pup licking/grooming, suggesting that differences in oxytocin receptor levels are functionally related to maternal behavior. Finally, estrogen treatment of virgin females significantly increased oxytocin receptor binding in the medial preoptic area and lateral septum of female offspring of High, but not Low, licking/grooming mothers. These findings suggest that maternal licking/grooming influences the development of estrogen sensitivity in brain regions that regulate maternal behavior, providing a potential mechanism for the intergenerational transmission of individual differences in maternal behavior.

Animals↗
PubMed2003

The role of abiotic factors and pesticide levels on enzymatic activity in the freshwater mussel Anodonta cygnea at three different exposure sites.

Natural variation in abiotic factors, such as temperature and pH, probably influence the activity of enzymes used as potential biomarkers in bivalve mollusks to assess environmental contamination in the field. Changes in levels of an enzymatic biomarker may thus merely reflect natural variation in the annual physiological cycle of a species rather than exposure to contaminants. To investigate this issue, we documented the relationship between pesticide levels in water and three different enzymatic biomarkers over 1 year in enclosed populations of the freshwater unionid mussel Anodonta cygnea at three different sites of exposure. We considered the natural variation in temperature, pH and dissolved oxygen over the year and across the different sites as a potential correlate of enzymatic activity to disentangle the relative contribution of abiotic factors and pesticide levels. Pesticide levels varied among the three sites and over the course of the year. Catalase (CAT) and acetylcholinesterase activity (AChE) varied as a function of abiotic factors but showed no relation to pesticide levels. Glutathione S-transferase (GST) activity was also related to abiotic factors but also decreased with increases in total pesticide levels. The lack of activity induction or inhibition by pesticides and the natural variation in abiotic factors among sites and across time limits the use of CAT and AChE to assess environmental contamination in this species.

Acetylcholinesterase↗
PubMed1994

Naturally occurring variation in bristle number and DNA polymorphisms at the scabrous locus of Drosophila melanogaster.

The association between quantitative genetic variation in bristle number and molecular variation at a candidate neurogenic locus, scabrous, was examined in Drosophila melanogaster. Approximately 32 percent of the genetic variation in abdominal bristle number (21 percent for sternopleural bristle number) among 47 second chromosomes from a natural population was correlated with DNA sequence polymorphisms at this locus. Several polymorphic sites associated with large phenotypic effects occurred at intermediate frequency. Quantitative genetic variation in natural populations caused by alleles that have large effects at a few loci and that segregate at intermediate frequencies conflicts with the classical infinitesimal model of the genetic basis of quantitative variation.

Alleles↗
PubMed1976

Darwin's finches: population variation and natural selection.

Van Valen's model, which relates morphological variation to ecological variation in an adaptive scheme, was investigated with individually marked and measured Darwin's finches on two adjacent Galápagos islands, Santa Cruz and Daphne Major. Results show that environmental heterogeneity is correlated with large continuous, morphological variation: variation in bill dimensions of Geospiza fortis is greater on Santa Cruz than on Daphne, as is environmental heterogeneity. Within populations of this species, different phenotypes distribute themselves in different habitat patches, select foods of different sizes and hardness, and exploit them with efficiencies that are phenotype- (bill size) dependent. These data constitute indirect evidence that natural selection has a controlling influence over the level of phenotypic variation exhibited by a population. Further evidence is that phenotypes did not survive equally well during the study period; on Daphne island G. fortis was apparently subjected to directional selection on bill tip length and G. scandens to normalizing selection on body weight and bill depth. Other factors which may have contributed to the establishment of a difference in variation between Santa Cruz and Daphne populations are the founder effect, genetic drift, and assortative mating. Annual climatic unpredictability is considered a source of environmental heterogeneity which, through its effect upon food supply, favors large morphological variation. It is predicted that species of large individual size are more influenced by this than are small species, and consequently exhibit greater size-corrected variation. The prediction is tested with data from six Geospiza species, and found to be correct.

Adaptation, Biological↗
PubMed2005

Influence of naturally occurring variations in maternal care on prepulse inhibition of acoustic startle and the medial prefrontal cortical dopamine response to stress in adult rats.

In rats, naturally occurring variations in maternal care contribute to the development of individual differences in the behavioral and neuroendocrine responses to stress during adulthood. The dopamine (DA) projection to the medial prefrontal cortex (mPFC) plays an important role in mediating stress responsivity and is thought to be involved also in regulating sensorimotor gating. In the present study, we compared prepulse inhibition (PPI) of acoustic startle as well as the left and right mPFC DA stress responses in the adult offspring of high- and low-licking/grooming (LG) dams. Our data indicate that the offspring of low-LG animals are impaired on measures of PPI compared with high-LG animals. We also observed in low-LG animals a significant blunting of the mPFC DA stress responses that was lateralized to the right hemisphere, whereas in high-LG animals, the left and right mPFC DA stress responses were equally attenuated. Although mPFC levels of DA transporter did not differ between the two groups of animals, mPFC levels of catechol-O-methyl transferase immunoreactivity of low-LG animals were significantly lower than those of high-LG animals. These data provide evidence that variations in maternal care can lead to lasting changes in mPFC DA responsivity to stress and suggest the possibility that such changes in mesocorticolimbic DA function can also lead to deficits in sensorimotor gating.

Acoustic Stimulation↗
PubMed1986

Seasonal changes in some plasma hormones in pigeons: diurnal variation under natural photoperiods with constant or seasonally changing ambient temperature.

The diurnal variations of several plasma hormones and free fatty acids (FFA) were studied during periods in summer and winter for pigeons reared either outdoors or indoors. The latter were subjected to constant temperature and naturally varying photoperiods. A significant seasonal variation in the mean daily levels of triiodothyronine (T3), thyroxine (T4), corticosterone (B), lutropin (LH) and FFA was seen in the outdoor birds and in the T4 and B levels of indoor birds. The diurnal variation of hormone levels was generally more pronounced in winter in both groups. Cold ambient temperature significantly decreased the plasma LH level and potentiated the increasing effect of short photoperiod on plasma B level. Diurnal variation of plasma FFA level seems to be under the control of photoperiod, without any effects due to the ambient temperature. No significant correlation was found between FFA and GH concentrations.

Acclimatization↗