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At least 73 records · Page 4Linked to original sources
PubMed2002

Genetic analysis of natural variations in the architecture of Arabidopsis thaliana vegetative leaves.

To ascertain whether intraspecific variability might be a source of information as regards the genetic controls underlying plant leaf morphogenesis, we analyzed variations in the architecture of vegetative leaves in a large sample of Arabidopsis thaliana natural races. A total of 188 accessions from the Arabidopsis Information Service collection were grown and qualitatively classified into 14 phenotypic classes, which were defined according to petiole length, marginal configuration, and overall lamina shape. Accessions displaying extreme and opposite variations in the above-mentioned leaf architectural traits were crossed and their F(2) progeny was found to be not classifiable into discrete phenotypic classes. Furthermore, the leaf trait-based classification was not correlated with estimates on the genetic distances between the accessions being crossed, calculated after determining variations in repeat number at 22 microsatellite loci. Since these results suggested that intraspecific variability in A. thaliana leaf morphology arises from an accumulation of mutations at quantitative trait loci (QTL), we studied a mapping population of recombinant inbred lines (RILs) derived from a Landsberg erecta-0 x Columbia-4 cross. A total of 100 RILs were grown and the third and seventh leaves of 15 individuals from each RIL were collected and morphometrically analyzed. We identified a total of 16 and 13 QTL harboring naturally occurring alleles that contribute to natural variations in the architecture of juvenile and adult leaves, respectively. Our QTL mapping results confirmed the multifactorial nature of the observed natural variations in leaf architecture.

Arabidopsis↗
PubMed2005

Natural variation in Vif: differential impact on APOBEC3G/3F and a potential role in HIV-1 diversification.

The HIV-1 Vif protein counteracts the antiviral activity exhibited by the host cytidine deaminases APOBEC3G and APOBEC3F. Here, we show that defective vif alleles can readily be found in HIV-1 isolates and infected patients. Single residue changes in the Vif protein sequence are sufficient to cause the loss of Vif-induced APOBEC3 neutralization. Interestingly, not all the detected defects lead to a complete inactivation of Vif function since some mutants retained selective neutralizing activity against APOBEC3F but not APOBEC3G or vice versa. Concordantly, independently hypermutated proviruses with distinguishable patterns of G-to-A substitution attributable to cytidine deamination induced by APOBEC3G, APOBEC3F, or both enzymes were present in individuals carrying proviruses with completely or partly defective Vif variants. Natural variation in Vif function may result in selective and partial neutralization of cytidine deaminases and thereby promote viral sequence diversification within HIV-1 infected individuals.

Journal Article↗
PubMed2002

Natural variation in the extent of phosphorylation of bone phosphoproteins as a function of in vivo new bone formation induced by demineralized bone matrix in soft tissue and bony environments.

Implants of allogenic demineralized bone matrix were placed in distinct in vivo environments, i.e. calvarial (bony) and subcutaneous (soft tissue) sites. Detailed analyses of the biochemical components were performed. Quantitative levels of osteopontin (OPN), bone sialoprotein (BSP) and calcium phosphate (Ca-P) deposition within each implant environment varied as a function of new bone formation, and were substantially different in samples from calvarial and subcutaneous sites. Quantification of the extent of phosphorylation of affinity-purified OPN and BSP from such implants indicated that: (i) the number of mols of phosphoserine (P-Ser)/mol of affinity-purified OPN or BSP varied as a function of implant time and bone formation within both implant sites, and (ii) the 'effective P-Ser concentration' provided by the total OPN and BSP within each implant site varied and increased as a function of time, being approx. 5-fold higher for BSP in calvarial compared with subcutaneous implants. Peak levels of mols of P-Ser/mol of BSP coincided with maximum rates of Ca-P deposition in calvarial implants. Levels of OPN phosphorylation from both calvarial and subcutaneous implants also indicated fluctuations as a function of bone formation. Hence the present study, for the first time, provides direct evidence of natural variation in the extent of phosphorylation of both OPN and BSP as a function of time of mineralized tissue formation. Further evaluation of the data provides the first evidence of a direct and linear relationship between the rate of Ca-P deposition and the ratio of P-Ser-BSP/P-Ser-OPN for calvarial implants. Data for subcutaneous implants failed to provide such correlation. Overall, the present work demonstrates that the natural biological progression of the process of biomineralization follows strict criteria consistent with the anatomical location. Biomineralization fails to proceed in the same way in a soft tissue environment.

Animals↗
PubMed2003

Natural variation of the nef gene in human immunodeficiency virus type 2 infections in Portugal.

Human immunodeficiency virus type 2 (HIV-2) infections cause severe immunodeficiency in humans, although HIV-2 is associated frequently with reduced virulence and pathogenicity compared to HIV-1. Genetic determinants that play a role in HIV pathogenesis are relatively poorly understood but nef has been implicated in inducing a more pathogenic phenotype in vivo. However, relatively little is known about the role of nef in HIV-2 pathogenesis. To address this, the genetic composition of 44 nef alleles from 37 HIV-2-infected individuals in Portugal, encompassing a wide spectrum of disease associations, CD4 counts and virus load, has been assessed. All nef alleles were subtype A, with no evidence of gross deletions, truncations or disruptions in the nef-encoding sequence; all were full-length and intact. HIV-2 long terminal repeat sequences were conserved and also indicated subtype A infections. Detailed analysis of motifs that mediate nef function in HIV-1 and simian immunodeficiency virus, such as CD4 downregulation and putative SH2/SH3 interactions, revealed significant natural variation. In particular, the central P(104)xxPLR motif exhibited wide interpatient variation, ranging from an HIV-1-like tetra-proline structure (PxxP)(3) to a disrupted minimal core motif (P(104)xxQLR). The P(107)-->Q substitution was associated with an asymptomatic phenotype (Fisher's exact test, P=0.026) and low virus loads. These data indicate that discrete differences in the nef gene sequence rather than gross structural changes are more likely to play a role in HIV-2 pathogenesis mediated via specific functional interactions.

Adolescent↗
PubMed2006

The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana.

Light has an important role in modulating seedling growth and flowering time. We show that allelic variation at the PHYTOCHROME C (PHYC) photoreceptor locus affects both traits in natural populations of A. thaliana. Two functionally distinct PHYC haplotype groups are distributed in a latitudinal cline dependent on FRIGIDA, a locus that together with FLOWERING LOCUS C explains a large portion of the variation in A. thaliana flowering time. In a genome-wide scan for association of 65 loci with latitude, there was an excess of significant P values, indicative of population structure. Nevertheless, PHYC was the most strongly associated locus across 163 strains, suggesting that PHYC alleles are under diversifying selection in A. thaliana. Our work, together with previous findings, suggests that photoreceptor genes are major agents of natural variation in plant flowering and growth response.

Arabidopsis↗
PubMed2004

Unused natural variation can lift yield barriers in plant breeding.

Natural biodiversity is an underexploited sustainable resource that can enrich the genetic basis of cultivated plants with novel alleles that improve productivity and adaptation. We evaluated the progress in breeding for increased tomato (Solanum lycopersicum) yield using genotypes carrying a pyramid of three independent yield-promoting genomic regions introduced from the drought-tolerant green-fruited wild species Solanum pennellii. Yield of hybrids parented by the pyramided genotypes was more than 50% higher than that of a control market leader variety under both wet and dry field conditions that received 10% of the irrigation water. This demonstration of the breaking of agricultural yield barriers provides the rationale for implementing similar strategies for other agricultural organisms that are important for global food security.

Analysis of Variance↗
PubMed1995

Estimation of arachidonic acid synthesis in full term neonates using natural variation of 13C content.

Neonates need arachidonic acid (AA) for their growing tissues, but it is unknown to what extent they can synthesize AA from dietary linoleic acid (LA). We studied infantile AA synthesis by using different natural 13C amounts in dietary fats. The diets of four infants ages 18 +/- 4 days (mean +/- SD) with newly diagnosed phenylketonuria were changed from breast milk or formula to a phenylalanine-free diet with corn oil as the only fat source. Compared with most dietary fats in Europe derived from C3 plants, corn oil LA has a higher 13C content. We determined the 13C content of LA and AA in 0.25-0.5 ml serum before and for 3-4 days after the diet change with gas chromatography combustion isotope ratio mass spectrometry (GC-IRMS). Baseline delta 13C values were -31.5 +/- 1.1% (mean +/- SD) for serum LA and -30.1 +/- 1.2% for AA. The corn oil diet induced changes of delta 13C values over baseline in LA of 8.9 +/- 1.0 on day 1 and 12.7 +/- 0.7 on day 4, respectively. The changes of AA delta 13C values were 0.5 +/- 0.7 and 2.7 +/- 0.7 on days 1 and 4. We conclude that reproducible detection of differences in delta 13C values of fatty acids in small samples of infantile serum, induced by dietary variation of natural 13C amounts, is feasible with GC-IRMS. Since the corn oil diet did not contain AA, the observed change of AA delta 13C shows active endogenous AA synthesis in full-term neonates.(ABSTRACT TRUNCATED AT 250 WORDS)

Arachidonic Acids↗
PubMed2005

The patterns of natural variation in human genes.

Currently, more than 10 million DNA sequence variations have been uncovered in the human genome. The most detailed variation discovery efforts have focused on candidate genes involved in cardiovascular disease or in susceptibilities associated with exposure to environmental agents. Here we provide an overview of natural genetic variation from the literature and in 510 human candidate genes resequenced for variation discovery. The average human gene contains 126 biallelic polymorphisms, 46 of which are common (> or =5% minor allele frequency) and 5 of which are found in coding regions. Using this complete picture of genetic diversity, we explore conservation, signatures of selection, and historical recombination to mine information useful for candidate gene association studies. In general, we find that the patterns of human gene variation suggest that no one approach will be appropriate for genetic association studies across all genes. Therefore, many different approaches may be required to identify the elusive genotypes associated with common human phenotypes.

Algorithms↗
PubMed2004

Top-down approaches to the study of natural variation in complex physiological pathways using the white-footed mouse (Peromyscus leucopus) as a model.

Variation in complex physiological pathways has important effects on human function and medical treatment. Complex pathways involve cells at multiple locations, which serve different functions regulated by many genes and include complex neuroendocrine pathways that regulate physiological function. One of two competing hypotheses regarding the effects of selection on complex pathways predicts that variability should be common within complex pathways. If this hypothesis is correct, then we should expect wide variation in neuroendocrine function to be typical within natural populations. To test this hypothesis, a complex neuroendocrine pathway that regulates photoperiod-dependent changes in fertility in a natural population of white-footed mice (Peromyscus leucopus) was used to test for natural genetic variability in multiple components of the pathway. After testing only six elements in the photoperiod pathway in P. leucopus, genetic variation in the following four of these elements was evident: the circadian clock, melatonin receptor abundance or affinity, sensitivity of the reproductive axis to steroid negative feedback, and gonadotropin-releasing hormone neuronal activity. If this result can be extended to humans, the prediction would be that significant variation at multiple loci in complex neuroendocrine pathways is common among humans, and that variation would exist even in human populations from a common genetic background. This finding could only be drawn from an "exotic" animal model derived from a natural source population, confirming the continuing importance of nontraditional models alongside the standard laboratory species.

Animal Husbandry↗
PubMed2003

A single-nucleotide natural variation (U4 to C4) in an influenza A virus promoter exhibits a large structural change: implications for differential viral RNA synthesis by RNA-dependent RNA polymerase.

The influenza A virus promoter is recognized by the influenza A virus RNA-dependent RNA polymerase, and directs both transcription and replication of the viral RNA genome. Within the sequence of this promoter, flu strains exhibit a natural, unique variation, either a U or a C, at the fourth position from the 3' end. Promoters that contain a C residue (C4 promoter), which are invariably found in genome segments that encode the three RNA polymerase subunits (PB1, PB2 and PA), down-regulate transcription but activate genome replication. Here, we have determined the structure of the C4 promoter by NMR spectroscopy and compared it with the structure of the U4 promoter, which was determined previously. The structure of the internal loop in the C4 promoter is similar to that of the U4 promoter. However, the terminal stem of the C4 promoter is strikingly different from that of the U4 promoter. These structural data suggest that the internal loop is important for polymerase binding to the promoter, and the terminal stem is crucial for differential regulation of transcription and replication.

Base Sequence↗
PubMed1987

Relationship between natural variations in motoneuron number and body size in Xenopus laevis: a test for size matching.

During normal development, tadpoles of Xenopus laevis demonstrate large variations in body size that are carried through metamorphosis. This variation in size exists at the stages when lumbar lateral motor column (L-LMC) motoneurons are produced and when neuronal cell death in this neuron population occurs. Body size, hindlimb size, motoneuron number, and motoneuron size (i.e., neuron nuclear cross-sectional area) were measured in animals from three developmental stages: one prior to significant amounts of cell death, one at the peak rate of cell death, and one after cell death. The hypothesis that neuron population size is matched to peripheral size was tested by using the natural size variation found at each of these stages. The ranges of values for the measurements at the three stages were large. Significant correlations between body size and motoneuron number, as well as between motoneuron number and muscle fiber number, were present after cell death. Since these correlations emerged as cell death reduced neuron numbers, size matching may have occurred and cell death may have adjusted the L-LMC motoneuron population's size to variation in body size. In addition to the correlations between body size and motoneuron number at the end of cell death, neuron numbers before and after cell death were significantly correlated among groups of siblings. The possibility that the number of neurons after cell death was also influenced by differences in the number of L-LMC progenitors is discussed.

Animals↗
PubMed1999

Natural variation of the expression of HLA and endogenous antigen modulates CTL recognition in an in vitro melanoma model.

Increasing attention has been devoted to elucidating the mechanism of lost or decreased expression of MHC or melanoma-associated antigens (MAAs), which may lead to tumor escape from immune recognition. Loss of expression of HLA class I or MAA has, as an undisputed consequence, loss of recognition by HLA class I-restricted cytotoxic T cells (CTLs). However, the relevance of down-regulation remains in question in terms of frequency of occurrence. Moreover the functional significance of epitope down-regulation, defining the relationship between MHC/epitope density and CTL interactions, is a matter of controversy, particularly with regard to whether the noted variability of expression of MHC/epitope occurs within a range likely to affect target recognition by CTLs. In this study, bulk metastatic melanoma cell lines originated from 25 HLA-A*0201 patients were analyzed for expression of HLA-A2 and MAAs. HLA-A2 expression was heterogeneous and correlated with lysis by CTLs. Sensitivity to lysis was also independently affected by the amount of ligand available for binding at concentrations of 0.001 to 1 mM. Natural expression of MAA was variable, independent from the expression of HLA-A*0201, and a significant co-factor determining recognition of melanoma targets. Thus, the naturally occurring variation in the expression of MAA and/or HLA documented by our in vitro results modulates recognition of melanoma targets and may (i) partially explain CTL-target interactions in vitro and (ii) elucidate potential mechanisms for progressive escape of tumor cells from immune recognition in vivo.

Antibodies, Monoclonal↗
PubMed2006

Natural variation in the Pto disease resistance gene within species of wild tomato (Lycopersicon). II. Population genetics of Pto.

Disease resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) in the host species Lycopersicon esculentum, the cultivated tomato, and the closely related L. pimpinellifolium is triggered by the physical interaction between the protein products of the host resistance (R) gene Pto and the pathogen avirulence genes AvrPto and AvrPtoB. Sequence variation at the Pto locus was surveyed in natural populations of seven species of Lycopersicon to test hypotheses of host-parasite coevolution and functional adaptation of the Pto gene. Pto shows significantly higher nonsynonymous polymorphism than 14 other non-R-gene loci in the same samples of Lycopersicon species, while showing no difference in synonymous polymorphism, suggesting that the maintenance of amino acid polymorphism at this locus is mediated by pathogen selection. Also, a larger proportion of ancestral variation is maintained at Pto as compared to these non-R-gene loci. The frequency spectrum of amino acid polymorphisms known to negatively affect Pto function is skewed toward low frequency compared to amino acid polymorphisms that do not affect function or silent polymorphisms. Therefore, the evolution of Pto appears to be influenced by a mixture of both purifying and balancing selection.

Adaptation, Biological↗
PubMed1997

Natural variation and copulatory plug formation in Caenorhabditis elegans.

Most of the available natural isolates of the nematode Caenorhabditis elegans have been examined and compared with the standard laboratory wild type (Bristol N2). Molecular markers, in particular transposon restriction fragment length polymorphisms, were used to assign these isolates to 22 different races, for which brood size and spontaneous male frequency were determined. Several distinctive traits were observed in some of these races. One example is mab-23, in a race from Vancouver, which leads to severe distortion of male genitalia and prevents male mating. Another is gro-1, segregating in a Californian race, which is associated with slow growth, heat resistance and longevity. Many races differ from N2 in carrying a dominant allele at the plg-1 locus, causing copulatory plug formation by males. Properties and possible advantages of the plugging trait have been investigated. The dominant plg-1 allele does not lead to increased male mating efficiency, but males from a Stanford race (CB4855), in which the plugging trait was first observed, are much more virile than N2 males. Crosses between N2 and CB4855 indicate that the higher virility is due to multiple factors. Size differences between N2 and CB4855 are associated with factors mapping to LGV and LGX.

Animals↗
PubMed2002

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

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 of clines in South America and Australia. Chromosome substitution revealed the largest effects on chromosome three in both continents, and minor effects on the X and second chromosome. Similarly, QTL analysis of the Australian cline identified QTL with largest effects on the third chromosome, with smaller effects on the second. However, no QTL were found on the X chromosome. We also compared the coincidence of locations of QTL with the locations of five microsatellite loci previously shown to vary clinally in Australia. Permutation tests using both the sum of the LOD scores and the sum distance to nearest QTL peak revealed there were no significant associations between locations of clinal markers and QTL's. The lack of significance may, in part, be due to broad QTL peaks identified in this study. Future studies using higher resolution QTL maps should reveal whether the degree of clinality in microsatellite allele frequencies can be used to identify QTL in traits that vary along an environmental gradient.

Animals↗
PubMed2000

Natural variation in phytochrome signaling.

The phytochromes, photoreceptors sensitive to red and far-red light, are critical for sensing foliage shade, canopy breaks, and neighbor proximity. A combination of molecular genetic, evolutionary, and ecological techniques are being used to understand how phytochromes function in the natural environment. We discuss studies on the adaptive value of phytochrome mediated plasticity, as well as the role that variation in phytochrome expression and function might play in allowing plants to adapt to unique light environments. Continued study of phytochrome signaling variation may reveal how natural selection acts at the molecular level.

Adaptation, Physiological↗
PubMed2004

Genetic basis of natural variation in D. melanogaster antibacterial immunity.

Many genes involved in Drosophila melanogaster innate immune processes have been identified, but whether naturally occurring polymorphism in these genes leads to variation in immune competence among wild flies has not been tested. We report here substantial variability among wild-derived D. melanogaster in the ability to suppress infection by a Gram-negative entomopathogen, Serratia marcescens. Variability in immune competence was significantly associated with nucleotide polymorphism in 16 innate immunity genes, corresponding primarily to pathogen recognition and intracellular signaling loci, and substantial epistasis was detected between intracellular signaling and antimicrobial peptide genes. Variation in these genes, therefore, seems to drive variability in immunocompetence among wild Drosophila.

Alleles↗
PubMed1995

Effect of diet and natural variations in climates on the performance of laying hens.

1. Laying hens raised in 3 natural tropical environments were fed on 2 series of diets with a view to defining the optimum combination of climate and dietary energy. 2. A combination of 3 growing climates, 3 laying climates (temperate, hot dry, hot humid), and 2 dietary energy concentrations (10.03 and 11.70 MJ ME/kg with protein concentrations proportional to energy) were tested for 46 weeks using 432 point-of-lay pullets. 3. Both growing and laying climates significantly affected most traits measured during the laying period. The patterns of egg production showed good persistency in all environments and differences observed reduced with age. 4. The difference between the high and low energy intake reduced at high ambient temperatures. Feeding low energy diets did not affect mean age at first egg, rate of lay or the egg output in the hot dry environment, nor egg weight in either hot dry or hot humid climates. Rather, feeding low energy diets resulted in improved body weight change in all 3 laying environments. 5. The growing climate and diet interacted significantly on body weight change, while highly significant interactions between laying climate and diet occurred on rate of lay, food and energy intake and egg weight during the laying period.

Animals↗