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PubMed1990

Chromosomal rearrangements associated with morphological mutants provide a means for genetic variation of Candida albicans.

At frequencies as high as 1.4%, the pathogenic yeast Candida albicans spontaneously gave rise to morphological mutants exhibiting more than 20 different types of abnormal colonies; approximately two-thirds of the mutants were stable, while the other one-third were unstable and produced mixtures of different colonial forms at very high rates. Abnormal electrophoretic karyotypes were observed for all of the 14 mutants that were examined, indicating that they were associated with different types of single and multiple gross chromosomal rearrangements. Because C. albicans is asexual and does not go through a meiotic cycle, we suggest that the high frequency of chromosomal rearrangements provides a means for genetic variation in this organism.

Candida albicans↗
PubMed2002

Genetic variation of Trigonobalanus verticillata, a primitive species of Fagaceae, in Malaysia revealed by chloroplast sequences and AFLP markers.

The genetic variation of Trigonobalanus verticillata, the most recently described genus of Fagaceae, was studied using chloroplast DNA sequences and AFLP fingerprinting. This species has a restricted distribution that is known to include seven localities in tropical lower montane forests in Malaysia and Indonesia. A total of 75 individuals were collected from Bario, Kinabalu, and Fraser's Hill in Malaysia. The sequences of rbcL, matK, and three non-coding regions (atpB-rbcL spacer, trnL intron, and trnL-trnF spacer) were determined for 19 individuals from these populations. We found a total of 30 nucleotide substitutions and four length variations, which allowed identification of three haplotypes characterizing each population. No substitutions were detected within populations, while the tandem repeats in the trnL -trnF spacer had a variable repeat number of a 20-bp motif only in Kinabalu. The differentiation of the populations inferred from the cpDNA molecular clock calibrated with paleontological data was estimated to be 8.3 MYA between Bario and Kinabalu, and 16.7 MYA between Fraser's Hill and the other populations. In AFLP analysis, four selective primer pairs yielded a total of 431 loci, of which 340 (78.9%) were polymorphic. The results showed relatively high gene diversity (H(S) = 0.153 and H(T) = 0.198) and nucleotide diversity (pi(S) = 0.0132 and pi(T) = 0.0168) both within and among the populations. Although the cpDNA data suggest that little or no gene flow occurred between the populations via seeds, the fixation index estimated from AFLP data (F(ST) = 0.153 and N(ST) = 0.214) implies that some gene flow occurs between populations, possibly through pollen transfer.

Chloroplasts↗
PubMed2006

Segregation of natural and experimental gastrointestinal nematode infection in F2 progeny of susceptible Suffolk and resistant Gulf Coast Native sheep and its usefulness in assessment of genetic variation.

Gastrointestinal nematode parasitism is a concern to small ruminants worldwide. Productivity has been compromised because such nematodes, particularly Haemonchus contortus, have developed resistance to available anthelmintics. Some sheep breeds and lines within breeds are relatively resistant to infection, a trait that may be useful for developing control strategies. Suffolk sheep, which are susceptible to infection, were crossed with Gulf Coast Native sheep, which are more resistant to infection, to produce F1 progeny. F1 rams were bred to F1 ewes which produced 227 F2 offspring. These F2 offspring were evaluated for variability in infection levels, based on fecal egg count (FEC) and blood packed cell volume (PCV), under two natural infection conditions (one at weaning and another after a summer grazing period) and one experimental infection. The range of both FEC and PCV was large for all three infection periods with annual variation. Overall, the range for the three infection periods, respectively, were 167-149,933, 0-31,400 and 17-114,667 eggs per gram (EPG) of feces and 8.7-37.0%, 7.3-33.0% and 8.3-36.0%. This segregation of infection is what would be expected of F(2) progeny from susceptible and resistant parent breeds. Heritabilities of FEC and PCV for the three infection periods, respectively, were 0.15, 0.29 and 0.12, and 0.11, 0.22 and 0.12. Based on segregation of infection, larger heritabilities and maternal environment effects that declined after weaning, the summer natural infection was probably the best model for assessing genetic variation.

Animals↗
PubMed1999

Genetic variation in Fitzroya cupressoides (alerce), a threatened South American conifer.

Fitzroya cupressoides (alerce, Cupressaceae) is a large and exceptionally long-lived conifer, endemic to a restricted area of southern Chile and neighbouring areas of Argentina. As a result of its high economic value, the species has been severely exploited for timber, and remnant populations are fragmented and often highly disturbed. The species is thought to have undergone a major range contraction during the last glaciation. In order to assess the extent of genetic variation using DNA markers within and between populations of this species, samples were obtained from throughout the natural range and analysed for random amplified polymorphic DNA (RAPD) variation. Eight 10-mer and three 15-mer primers were used to produce a total of 54 polymorphic bands. Shannon's diversity estimates were calculated to provide an estimate of the degree of variation within each population. Values varied from 0.343 to 0.636 with only the lowest value differing significantly from the others (Spop = 0.547). This indicated that there is a significant degree of variation within each population, and did not provide evidence for genetic 'bottle-neck' effects within the species. A pairwise distance measure calculated from the RAPD data was used as an input for principal coordinate (PCO) and AMOVA analyses. The first three principal coordinates of RAPD distances described 8.3, 5.9 and 5.4% of the total variance, respectively, and a degree of clustering of samples according to their geographical origin was detectable. AMOVA analysis indicated that although most of the variation (85.6%) was found within populations, a significant proportion (P < 0.002) was attributable to differences between populations. An UPGMA dendrogram constructed using phi ST values derived from AMOVA produced a pattern broadly similar to that produced by the PCO, highlighting differences between three main groups of populations within Chile: those from the northern Coastal Range, the southern Coastal Range and Central Depression, and the Andes. Populations from Argentina also emerged as significantly different from those in Chile. These results are interpreted in the context of the postglacial history of the species, and their implications for the development of conservation strategies for Fitzroya are discussed.

Conservation of Natural Resources↗
PubMed2000

Genetic variation in the hepatocyte nuclear factor-3beta gene (HNF3B) does not contribute to maturity-onset diabetes of the young in French Caucasians.

Mutations in genes encoding hepatocyte nuclear factor (HNF) are responsible for three of the five subtypes of maturity-onset diabetes of the young (MODY). This observation and molecular studies indicate that the HNF network is required for normal function of pancreatic beta-cells. This suggests that transcription factors involved in this complex network are candidates for genetic defects in MODY. Because the HNF-3beta gene is implicated in this network, we screened it for mutations in 21 probands of French ancestry with clinical diagnosis of MODY and early-onset type 2 diabetes. All of the five known MODY genes, HNF-4alpha, glucokinase, HNF-1alpha, HNF-1beta, and IPF1, were previously excluded as being the cause of diabetes in these families. By direct sequencing, we identified two transitions, an A-to-G at position -213 and a C-to-T at position -63 in the promoter and exon 1, respectively, of the HNF-3beta gene. A G-to-C transversion at position +32 in the intron 1 and three transitions, C-to-T at position 291, A-to-G at position 837, and G-to-A at position 1188 in the exon 3, resulting in noncoding mutations Ala97Ala, Gly279Gly, and Gln396Gln, respectively, were also identified. The allele frequencies were not significantly different between a control group and MODY probands. Familial segregation studies and linkage analysis showed that genetic variation in the HNF-3beta gene is unlikely to be the cause of early-onset type 2 diabetes in these Caucasian families.

Adult↗
PubMed2006

Implication of SSAT by gene expression and genetic variation in suicide and major depression.

CONTEXT: A large body of evidence suggests that predisposition to suicide, an important public health problem, is mediated to a certain extent by neurobiological factors. OBJECTIVE: To investigate patterns of expression in suicide with and without major depression and to identify new molecular targets that may play a role in the neurobiology of these conditions. DESIGN: Brain gene expression analysis was performed using the Affymetrix HG-U133 chipset in the orbital cortex (Brodmann area [BA] 11), the dorsolateral prefrontal cortex (BA8/9), and motor cortex (BA4). Subsequent studies were carried out in independent samples from adjacent areas to validate positive findings, confirm their relevance at the protein level, and investigate possible effects of genetic variation. SUBJECTS: We investigated 12 psychiatrically normal control subjects and 24 suicide victims, including 16 with and 8 without major depression, in the brain gene expression analysis, validation, and protein studies. The genetic studies included 181 suicide completers and 80 psychiatrically normal controls. All subjects investigated were male and of French Canadian origin. MAIN OUTCOME MEASURES: Gene expression measures from microarray, semiquantitative reverse transcription-polymerase chain reaction, immunohistochemistry, and Western blot analyses. RESULTS: Twenty-six genes were selected because of the consistency of their expression pattern (fold change, >1.3 in either direction [P<or=.01] in at least 2 regions). The spermine/spermidine N(1)-acetyltransferase gene (SSAT) was successfully validated by reverse transcription-polymerase chain reaction, immunohistochemistry, and Western blot analyses. A variant located in the SSAT polyamine-responsive element regulatory region (SSAT342A/C) demonstrated a significant effect of genotype on SSAT brain expression levels (F(1) = 5.34; P = .02). Further investigation of this variant in an independent sample of 181 male suicide completers and 80 male controls showed a higher frequency of the SSAT342C allele among suicide cases (odds ratio, 2.7; 95% confidence interval, 1.4-5.3; P = .005), suggesting that this allele may increase predisposition to suicide. CONCLUSIONS: These data suggest a role for SSAT, the rate-limiting enzyme in the catabolism of polyamines, in suicide and depression and a role for the SSAT342 locus in the regulation of SSAT gene expression.

Acetyltransferases↗
PubMed1994

Genetic variation in the humoral immune response against Vibrio salmonicida and in antibody titre against Vibrio anguillarum and total IgM in Atlantic salmon (Salmo salar).

Total IgM level and antibody titre to Vibrio anguillarum O-antigen after bath-vaccination, and specific antibody response to V. salmonicida O-antigen at three different samplings were analysed in family material of Atlantic salmon (Salmo salar), consisting of 791 fish belonging to 34 maternal full-sib groups within 12 paternal half-sib groups. The fish were immunized twice, and blood samples collected three times. After the third blood sampling, the fish were challenged with V. anguillarum. Medium to low genetic variation was recorded in total IgM and in the antibody titres against V. anguillarum O-antigen and V. salmonicida O-antigen, with heritability estimates of 0.12, 0.18 and from 0.03 to 0.12, respectively. Moderate to high genetic and phenotypic correlations were found between the V. salmonicida O-antigen titres at different samplings. Genetic and phenotypic correlations between the initial titres were moderate to low. The effect of different immune traits, including Aeromonas salmonicida A-layer titres (previously described), on the ability to survive the challenge was examined. The likelihood of surviving the challenge was affected positively by the A. salmonicida A-layer titre at the second sampling, and almost significantly affected by the initial V. anguillarum O-antigen titre. Production traits, such as mean slaughter weight and mean proportion of survivors in a corresponding full-sib material, were obtained in the sea-rearing period. No significant full-sib correlation between immune parameters and production traits was detected.

Animals↗
PubMed2004

A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

Recent studies have identified a small number of genomic rearrangements that occur frequently in the general population. Bioinformatics tools are now available for systematic genome-wide surveys of higher-order structures predisposing to such common variations in genomic architecture. Segmental duplications (SDs) constitute up to 5 per cent of the genome and play an important role in generating additional rearrangements and in disease aetiology. We conducted a genome-wide database search for a form of SD, palindromic segmental duplications (PSDs), which consist of paired, inverted duplications, and which predispose to inversions, duplications and deletions. The survey was complemented by a search for SDs in tandem orientation (TSDs) that can mediate duplications and deletions but not inversions. We found more than 230 distinct loci with higher-order genomic structure that can mediate genomic variation, of these about 180 contained a PSD. A number of these sites were previously identified as harbouring common inversions or as being associated with specific genomic diseases characterised by duplication, deletions or inversions. Most of the regions, however, were previously unidentified; their characterisation should identify further common rearrangements and may indicate localisations for additional genomic disorders. The widespread distribution of complex chromosomal architecture suggests a potentially high degree of plasticity of the human genome and could uncover another level of genetic variation within human populations.

Chromosomes, Human↗
PubMed2006

Genetic variation in the Vibrio vulnificus group 1 capsular polysaccharide operon.

Vibrio vulnificus produces human disease associated with raw-oyster consumption or wound infections, but fatalities are limited to persons with chronic underlying illness. Capsular polysaccharide (CPS) is required for virulence, and CPS expression correlates with opaque (Op) colonies that show "phase variation" to avirulent translucent (Tr) phenotypes with reduced CPS. The results discussed here confirmed homology of a V. vulnificus CPS locus to the group 1 CPS operon in Escherichia coli. However, two distinct V. vulnificus genotypes or alleles were associated with the operon, and they diverged at sequences encoding hypothetical proteins and also at unique, intergenic repetitive DNA elements. Phase variation was examined under conditions that promoted high-frequency transition of Op to Tr forms. Recovery of Tr isolates in these experiments showed multiple genotypes, which were designated TR1, TR2, and TR3: CPS operons of TR1 isolates were identical to the Op parent, and cells remained phase variable but expressed reduced CPS. TR2 and TR3 showed deletion mutations in one (wzb) or multiple genes, respectively, and deletion mutants were acapsular and locked in the Tr phase. Complementation in trans restored the Op phenotype in strains with the wzb deletion mutation. Allelic variation in repetitive elements determined the locations, rates, and extents of deletion mutations. Thus, different mechanisms are responsible for reversible phase variation in CPS expression versus genetic deletions in the CPS operon of V. vulnificus. Repetitive-element-mediated deletion mutations were highly conserved within the species and are likely to promote survival in estuarine environments.

Alleles↗
PubMed1981

Genetic variation in the quantitative levels of an NADP (H)-binding protein (FX) in human erythrocytes.

FX is a red cell NADP(H)-binding protein that has been well defined biochemically and immunologically but whose function is still unknown. Preliminary data indicated that the levels of this protein are significantly increased in hemizygotes, heterozygotes, and homozygotes for the G6PD Mediterranean mutant, thus raising the question of whether or not the individual variation in FX levels is more or less directly influenced by X-linked genes. The present study, based on a large series of population and family data collected in Sardinia, confirms unequivocally the above mentioned interaction, but shows at the same time that the variances in FX levels "between sibships" are 2-3 times larger than those "within sibships," when the analysis is done separately for the G6PD-normal or the G6PD-deficient sibs. From the comparison of the interclass and intraclass correlation coefficients, it appears that about 60% of the total variation of FX is of genetic origin. Moreover, the FX levels of children, analyzed in a pairwise manner, were found to be more positively correlated with those of their fathers (r = 0.39) than with those of their maternal grandfathers (0.20). This latter finding obviously favors the conclusion that "autosomal" rather than "X-linked" genes are involved in the determination of the FX levels.

Adult↗
PubMed2003

Genetic variations in the interleukin-12/interleukin-23 receptor (beta1) chain, and implications for IL-12 and IL-23 receptor structure and function.

Cell-mediated immunity (CMI) plays an essential role in human host defense against intracellular bacteria. Type-1 cytokines, particularly gamma interferon (IFN-gamma), interleukin-12 (IL-12), and IL-23, the major cytokines that regulate IFN-gamma production, are essential in CMI. This is illustrated by patients with unusual severe infections caused by poorly pathogenic mycobacteria and Salmonella species, in whom genetic deficiencies have been identified in several key genes in the type-1 cytokine pathway, including IL12RB1, the gene encoding the beta1 chain of the IL-12 and IL-23 receptors. Several mutations in IL12RB1 with deleterious effects on human IL-12R function have been identified, including nonsense and missense mutations. In addition, a number of coding IL12RB1 polymorphisms have been reported. In order to gain more insight into the effect that IL12RB1 mutations and genetic variations can have on IL-12Rbeta1 function, three approaches have been followed. First, we determined the degree of conservation at the variant amino acid positions in IL-12Rbeta1 between different species, using known deleterious mutations, known variations in IL-12Rbeta1, as well as novel coding variations that we have identified at position S74R and R156H. Second, we analyzed the potential impact of these amino acid variations on the three-dimensional structure of the IL-12Rbeta1 protein. Third, we analyzed the putative functions of different IL-12Rbeta1 domains, partly based on their homology with gp130, and analyzed the possible effects of the above amino acid variations on the function of these domains. Based on these analyses, we propose an integrated model of IL-12Rbeta1 structure and function. This significantly enhances our molecular understanding of the human IL-12 and IL-23 systems.

Alternative Splicing↗
PubMed1996

Genetic variation in the strongly canalized sex pheromone communication system of the European corn borer, Ostrinia nubilalis Hübner (Lepidoptera; Pyralidae).

The major difference in pheromone production between the so-called E and Z strains of the European corn borer Ostrinia nubilalis is controlled by two alleles at a single autosomal locus. E-strain females produce an (E)-11-tetradecenyl acetate pheromone with 1-3% of the Z isomer, whereas Z-strain females produce the opposite blend. In laboratory-reared insects we found that F1 females produced, on average, a 71:29 E/Z ratio, but the distribution was clearly bimodal. The variability in pheromone blend produced by heterozygous females could be explained by the existence of two different alleles in the Z strain which in combination with the E-strain allele for the major production locus cause the production of a component mixture either high or low in the F isomer. In addition, evidence was found for an independently inherited factor, existing in the E strain, with a dominant effect on the amount of E isomer produced by females homozygous for Z-alleles at the major production locus. Thus, the low variability normally found in the pheromone mixture produced by O. nubilalis and other moth females may, by canalization, hide a considerable amount of underlying genetic variation.

Animals↗
PubMed2001

Genetic variation in pure lines and crosses of large-bodied turkey lines. 2. Carcass traits and body shape.

An experimental line (F) of turkeys was reciprocally crossed with sire lines (designated A and B) from each of two commercial breeders in order to study the inheritance of carcass traits and body shape. The birds were weighed and killed at 17 wk of age, and various measurements of muscling, leg bones, and body shape were made. Additive genetic variation, as indicated by line differences, was an important source of variation in most traits. The only traits that did not exhibit a line difference in any comparison were weight of the drumstick muscles, tarsometatarsal width, keel length, and Body Depth 2 (body depth at a point 2.54 cm anterior to the posterior end of the keel). Heterosis of live BW was greater in males than in females. Heterosis in the weight of the pectoralis major and p. minor muscles were similar to those of live BW, but heterosis in the weight of the leg muscles were higher than that of live BW. The average heterosis for bone measurements (length of the femur, tarsometatarsal, and tibiotarsal bones and tarsometatarsal width) was very low and ranged from -0.3 to 1.4%. For measurements of body shape [keel length, Body Depth 1 (body depth measured at the cranial process of the keel), Body Depth 2, ratio of Body Depth 1 to Body Depth 2, length, width, and height of the body cavity, and body cavity volume index), heterosis was low and the average ranged from -2.7 to 2.6%. Based on an analysis of both sexes combined, the commercial sire lines differed in BW, weights of the p. minor and drumstick muscles, weights of the tarsometatarsal, femur, and tibiotarsal bones, lengths of the tarsometatarsal and femur bones, and various measurements of body shape (Body Depth 1, body depth ratio, body cavity length and height, and body cavity volume index). Relative to the commercial sire lines, the F line was smaller, had less breast and leg muscling, and, in general, larger leg bones when sexes were combined. The carcass of the F line was deeper than that of the commercial sire lines when measured at the cranial process of the keel but not at 2.54 cm anterior to the posterior portion of the keel. Body cavity height and body cavity volume index were larger in the F line than in the commercial sire lines.

Animals↗
PubMed1980

Genetic variation among hepatitis B and related viruses.

Hepatitis B virus (HBV) of man has several characteristics that distinguish it from viruses of other groups. These include its ultrastructure, viral DNA size and structure, a virion DNA polymerase which repairs a single-stranded region in the viral DNA, liver tropism, character of persistent infection, and association with hepatitis and hepatocellular carcinoma. Recently three other viruses have been found in other animal species that appear to share these characteristics although the viruses are not identical. HBV, Woodchuck hepatitis virus (WHV), ground squirrel hepatitis virus (GSHV), and duck hepatitis virus (DHV) appear to be members of a new virus group that might be designated the Hepadna virus group. Genetic variation among hepatitis B viruses includes the antigenic variation in the surface antigen (HBsAg) which constitutes the known HBsAg subtypes. There is also frequent variation in DNA base sequence among HBVs isolated from different patients.

Animals↗
PubMed1998

Genetic variation within the Hereford breed of cattle.

Genetic differentiation among Hereford populations from Britain, Ireland, Sweden, Canada and New Zealand together with six other beef breeds was assessed using blood type polymorphisms. Changes in the genetic structure of the British Hereford population over time were also examined. Loci surveyed were seven red cell antigen systems (A, B, C, F, L, S, Z), and two serum protein loci (transferrin and albumin). Within group variation was measured by the average expected heterozygosity, and between group relationships by genetic distance. There was significant genetic differentiation among Hereford populations from different countries. Differences between Hereford groups, however, were not as large as differences between breeds. There were also significance differences among British herds. The proportion of Canadian genes in the British 'hybrid' population was estimated to have increased from 0.42 (+/- 0.34) in the 1970s to 0.98 (+/- 0.11) in the 1990s. Canadian Hereford groups were found to be less heterozygous than other groups, and replacement of the British population with Canadian animals may lead to loss of variation. Breeding strategies that preserve original native genes in British Hereford populations should be considered by commercial breeders, in order to prevent the long-term loss of genetic variation within the breed.

Alleles↗
PubMed2003

Diabetes duration may modify the association between genetic variation in the glycoprotein Ia subunit of the platelet collagen receptor and risk of severe diabetic retinopathy: a working hypothesis.

Genetic factors appear to contribute to the severity and progression of diabetic retinopathy. We assessed the associations of the C807T and Glu505Lys variants of the glycoprotein Ia (alpha(2) integrin) subunit of the platelet/endothelial collagen receptor and risk of retinopathy in a population-based survey of 288 diabetic patients in one Swedish community. Neither variant was associated with retinopathy risk overall. However, the 807T variant was associated with increased risk of severe retinopathy, and the association was modified by diabetes duration. Among patients with diabetes of longer duration (>/=25 years), the 807T variant was strongly associated with risk of severe retinopathy (odds ratio 7.49, 95% confidence interval 1.75 to 32.1). There was no association between the 807T variant and risk of severe retinopathy among patients with diabetes duration <25 years. The Lys505 variant of glycoprotein Ia was associated with an odds ratio for severe retinopathy of 1.88 (95% confidence interval 0.83 to 4.24). Overall, there was a significant interaction between glycoprotein Ia genotype and duration of diabetes on the risk of retinopathy (P-value for interaction = 0.019). These results suggest the hypothesis that genetic variation of platelet glycoprotein Ia may play a particularly important role during the advanced stages of diabetic retinopathy.

Adult↗