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At least 289 records · Page 16Linked to original sources

PubMed2002

Development of microsatellite markers from an ectomycorrhizal fungus, Tricholoma matsutake, by an ISSR-suppression-PCR method.

An inter-simple sequence repeat (ISSR)-suppression-PCR technique established to develop microsatellite markers of plant species was applied to an ectomycorrhizal fungus, Tricholoma matsutake. Six polymorphic SSR markers were developed. All six polymorphic SSR markers were single-locused and co-dominant. Alleles produced by these six single-locused markers ranged from two to nine per locus and the expected heterozygosities were calculated as values from 0.098 to 0.803. The results indicated that the ISSR-suppression-PCR technique was effective and applicable to the development of microsatellite markers from ectomycorrhizal fungi. Furthermore, the six microsatellite loci did not amplify DNA from any other ectomycorrhizal species investigated, except for Tricholoma nauseosum (Swedish matsutake) and Tricholoma fulvocastaneum, suggesting that population genetics and reproduction of T. matsutake could be investigated by the SSR markers developed in the present study.

Basidiomycota↗

PubMed1983

Multiple-locus departures from panmictic equilibrium within and between village gene pools of Amerindian tribes at different stages of agglomeration.

A comparative analysis of departures from multiple-locus Hardy-Weinberg equilibrium is presented for a set of four tribal Indian groups (the Yanomama, Makiritare, Wapishana and Ticuna) from the lowlands of South America. These tribes span a range of agglomeration and acculturation from the most traditional, swidden horticulturalists to frontier townspeople. The small-group social organization typical of traditional horticulturalists leads to substantial departures from tribal panmixia, as manifested by the distribution of multiple-locus genotypes both within and between villages. Within villages, the departures from single-locus Hardy-Weinberg equilibrium are small and nonsignificant, but the departures from gametic equilibrium (independence of loci) are substantial, even for the unlinked loci we have used to characterize these populations. The departures from single-locus homogeneity across villages are also substantial. One of the normal concomitants of increasing acculturation in this setting is an increase in agglomeration. As agglomeration increases, the departures from multiple-locus panmixia decrease, a process that can be very rapid. We discuss both the shifting balance theory of evolution and punctuated evolutionary rates in light of the small group social organization that must have obtained throughout most of human evolution.

Brazil↗

PubMed2003

Heterologous diploid nuclei in the violet root rot fungus, Helicobasidium mompa.

Allelic genes hga1-1 and hga1-2, which encode G protein alpha subunit in the violet root rot fungus, Helicobasidium mompa, were sequenced and characterized. Restriction fragment polymorphism (RFLP) analysis determined that the gene is present as a single locus in the single basidiospore isolates, while strain V169 possessed both alleles of this gene. Therefore, although basidiospore isolates are dikaryon, they are homokaryotic. Field-isolated strain V169, the putative parent strain, is a dikaryotic heterokaryon. Allelic genes hga1-1 and hga1-2 segregated in almost a 1:3 ratio among single basidiospore isolates from the same fruiting body. Moreover, the copy number of hga1-1 was found to be less than that of hga1-2 in the V169 strain. These results suggest that one of the nuclei in the V169 parent strain is homozygous diploid and the other heterozygous diploid. This parent strain produced four homokaryotic and dikaryon basidiospores on each basidium.

Alleles↗

PubMed2001

Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): an overview.

The zebrafish, Danio rerio, has recently become the model system for the genetic analysis of vertebrate development. This paper reviews the advances in zebrafish cytogenetics, obtained through classical and molecular techniques, which will lead to the assignment of specific linkage groups to specific chromosome pairs in the zebrafish genome project. Several chromosome pairs of the 50-chromosome karyotype of D. rerio were differentially stained by classical staining techniques and additional information has been obtained by molecular cytogenetics. Indeed, the analysis of constitutive heterochromatin by C-banding and base-specific fluorochrome staining had suggested a differential composition of peri- and paracentromeric constitutive heterochromatin. The chromosome mapping of distinct AT- and GC-rich zebrafish satellite DNAs by means of PRINS (Primed in situ) and multicolor FISH (Fluorescence in situ Hybridization) has confirmed this hypothesis, which therefore provided the chromosome localization of 10% of the zebrafish genome. The analysis of nucleolus organizer regions (NORs) by silver staining and by FISH with 18S rDNA has also revealed the existence of variable and inactive NORs, in addition to those on the terminal regions of the long arms of the three NOR-bearing chromosome pairs. Other multicopy genes, such as minor ribosomal genes, or multicopy repeats, such as telomere specific sequences, have now been mapped on zebrafish chromosomes. The latest advancement in zebrafish molecular cytogenetics is the chromosome mapping of single locus genes. Single-copy genes from each of the 25 genetic linkage groups are now being mapped on zebrafish chromosomes by using PAC clones.

Animals↗

PubMed1995

Genetic differentiation among populations of Myopus schisticolor (the wood lemming)--isozyme variation.

To investigate genetic differentiation among populations of the wood lemming Myopus schisticolor (Muridae, Rodentia) isozyme variation in 10 populations from three regions, Fennoscandia, Western and Eastern Siberia, was examined. From 20 loci examined, the two most polymorphic ones, Idh-1 and Pgi-1, were used in the complete survey. The results of hierarchical F-statistics analysis showed significant differentiation among all populations; single locus FPT values agreed well (Idh-1, FPT = 0.20; Pgi-1, FPT = 0.20). However, allele frequencies at each locus demonstrated different patterns of subdivision among populations within regions and between regions. Thus, significant values of F-statistics within (FPR = 0.10) and between (FRT = 0.10) regions were found at Idh-1. Pgi-1 showed no significant differentiation among populations within regions (FPR = 0.01). The subdivision among populations at Pgi-1 was based on differentiation between regions (FRT = 0.19). The lack of differentiation among populations within a geographical region at the Pgi-1 locus is surprising for any rodent species, and the discrepancy between single-locus patterns of subdivision seems likely to result from selection at the Pgi-1 locus.

Animals↗

PubMed1996

On the potential for estimating the effective number of breeders from heterozygote-excess in progeny.

The important parameter of effective population size is rarely estimable directly from demographic data. Indirect estimates of effective population size may be made from genetic data such as temporal variation of allelic frequencies or linkage disequilibrium in cohorts. We suggest here that an indirect estimate of the effective number of breeders might be based on the excess of heterozygosity expected in a cohort of progeny produced by a limited number of males and females. In computer simulations, heterozygote excesses for 30 unlinked loci having various numbers of alleles and allele-frequency profiles were obtained for cohorts produced by samples of breeders drawn form an age-structured population and having known variance in reproductive success and effective number. The 95% confidence limits around the estimate contained the true effective population size in 70 of 72 trials and the Spearman rank correlation of estimated and actual values was 0.991. An estimate based on the heterozygote excess might have certain advantages over the previous estimates, requiring only single-locus and single-cohort data, but the sampling error among individuals and the effect of departures from random union of gametes still need to be explored.

Breeding↗

PubMed1989

Polymerase chain reaction: replication errors and reliability of gene diagnosis.

The impact of replication errors on the reliability of polymerase chain reaction (PCR) data is studied theoretically. Practical applications of our results to RFLP analysis and oligonucleotide probing confirm that for practical purposes replication errors can be neglected if a large number of starting templates (e.g. 100,000) is being used. For single locus analysis in single cells, however, the probability of false diagnosis due to such errors is of the order of 1 percent.

DNA Replication↗

PubMed2004

Gene-gene interaction in folate-related genes and risk of neural tube defects in a UK population.

OBJECTIVE: To investigate the contribution of polymorphic variation in genes involved in the folate-dependent homocysteine pathway in the aetiology of neural tube defects (NTD). DESIGN: Case-control association study. SUBJECTS: A total of 530 individuals from families affected by NTD, 645 maternal controls, and 602 healthy newborn controls from the northern UK. MAIN OUTCOME MEASURES: Seven polymorphisms in six genes coding for proteins in the folate-dependent homocysteine pathway (MTHFR 677C-->T, MTHFR 1298A-->C, MTRR 66A-->G, SHMT 1420C-->T, CbetaS 844ins68, GCPII 1561C-->T, RFC-1 80G-->A). The impact of each polymorphism and the effect of gene-gene interactions (epistasis) upon risk of NTD were assessed using logistic regression analysis. RESULTS: The MTHFR 677C-->T polymorphism was shown to represent a risk factor in NTD cases (CC v CT+TT odds ratio (OR) 2.03 [95% confidence interval (CI) 1.09, 3.79] p = 0.025) and the MTRR 66A-->G polymorphism was shown to exert a protective effect in NTD cases (AA v AG+GG OR 0.31 [95% CI 0.10, 0.94] p = 0.04). When statistical tests for interaction were conducted, three genotype combinations in cases (MTRR/GCPII; MTHFR 677/CbetaS; MTHFR 677/MTRR) and one combination in case mothers (CbetaS/RFC-1) were shown to elevate NTD risk. Maternal-fetal interaction was also detected when offspring carried the MTHFR 677C-->T variant and mothers carried the MTRR 66A-->G variant, resulting in a significantly elevated risk of NTD. CONCLUSION: Both independent genetic effects and gene-gene interaction were observed in relation to NTD risk. Multi-locus rather than single locus analysis might be preferable to gain an accurate assessment of genetic susceptibility to NTD.

Case-Control Studies↗

PubMed2000

Replication of linkage of familial combined hyperlipidemia to chromosome 1q with additional heterogeneous effect of apolipoprotein A-I/C-III/A-IV locus. The NHLBI Family Heart Study.

Familial combined hyperlipidemia (FCHL), the most common familial dyslipidemia, is implicated in up to 20% of cases of premature coronary heart disease. Although underlying mutations for FCHL have yet to be identified, several candidate genes/regions have been identified. A positive linkage to chromosome 1q markers has been reported, with the highest lod score of 5.93 occurring at a location between D1S104 and D1S1677. Using the same diagnostic criteria, the Family Heart Study (FHS) has defined 71 FCHL families, comprising 170 cases, for a total of 137 possible affected sibling pairs. The FCHL criteria require elevation in serum low density lipoprotein cholesterol and triglyceride levels within the family, with at least 2 affected first-degree relatives. Markers D1S104 and D1S1677 were typed, and significant allele sharing was found in FCHL sibships (multipoint lod score with use of the model from the Finnish study was 2.52, and multipoint nonparametric score was 2.48; P=0.007), replicating linkage in this chromosome 1 region. In addition, previously reported linkage of FCHL to apolipoprotein A-I/C-III/A-IV has been investigated in FHS families. FHS results revealed positive but nonsignificant allele sharing among FCHL sibships with apolipoprotein A-I/C-III/A-IV by use of marker D11S4127 (nonparametric linkage score 1.11, P=0.13). Two-locus analyses of D1S104 and D11S4127 suggested possible heterogeneity rather than epistasis, with a maximum 2-locus lod score of 3.05. A nonparametric 2-locus analysis revealed significant improvement in the 2-locus versus single-locus scores. Finally, no linkage was found with markers near the lipoprotein lipase gene region.

Alleles↗

PubMed2001

Possibility of paternity testing using RFLP analysis on a very small amount of material.

Paternity testing by DNA analysis was carried out using dental pulpal and chorionic villous tissue from two children respectively, and fresh blood samples obtained from the alleged parents. DNA was extracted spectroscopically from the pulp of an upper wisdom tooth (16 micrograms) and the chorionic villi (53 micrograms). The RFLP method was used for DNA analysis of the parent-child relationships because both of the DNAs extracted had a high molecular weight. Distinct bands were detected with 32P-labelled multi-locus (Myo) and single locus (pYNH24) DNA probes. In the case of the dental specimen all of the bands of the child's DNA were found to be derived from either of the alleged parents, demonstrating a consistent parent-child relationship (the probability of established paternity was 99.86%) whilst in the case of the villous specimen the father-child relationship was denied. This procedure can provide much information using very little material for analysis but where the samples are in a good condition.

Child↗

PubMedDate not supplied

[Stain examination with DNA technology--a retrospective analysis].

The extended possibilities of forensic stain analyses during recent years have mainly resulted from the application of DNA technology. Among the VNTR polymorphisms, one can differentiate between five consecutive generations of systems, i.e. multi locus systems (MLS), single locus systems (SLS), so-called AMPFLP's (amplificable fragment length polymorphisms), short tandem repeats (STR's), micro satellite systems. The routine application in our laboratory lets us distinguish 3 phases: (I) RFLP phase (MLS+SLS); (II) combined application of RFLP-SLS and AMPFLP's; (III) PCR phase (combined application of AMPFLP's and STR's.--Investigations applying conventional blood group systems and RFLP analysis have been cancelled in phase III. Since 1989 328 cases have been investigated. The number of cases per year was doubled in phase III compared to phase I, but the proportion of DNA determination has been increased by app. 800%. Although in phase III the stain material was on average more degraded and quantitatively smaller the application of STR systems was successful in 90% of all cases and therefore much more effective than other systems. Compared to phase I, the probabilities of inclusion were smaller in phase III. Problematic stains were more often investigated. Also, a strategic change has occurred. New standards had to be elaborated, i.e. to the avoidance of contamination, to the critical evaluation of stain composition and to the validation of systems.

Blood Grouping and Crossmatching↗

PubMed1997

Identification and characterization of microsatellites in Norway spruce (Picea abies K.).

Norway spruce (Picea abies) genomic libraries were screened for presence of dinucleotide AC/GT and AG/CT microsatellites (or simple sequence repeats). On average, one (AG)n microsatellite every 194 kb and one (AC)n microsatellite every 406 kb were found. Forty-six positive clones were sequenced and primers flanking 24 AG microsatellites and 12 AC microsatellites diesigned. Only seven (20%) of them produced the expected single-locus polymorphic pattern when used to amplify Norway spruce DNAs. The other primer pairs gave either multiple bands or bad amplification, or a single monomorphic fragment. Such a small proportion of successful primer pairs was attributed to the high level of complexity of the Norway spruce genome. Dot blot analysis of the clones showed that many of them contained repetitive DNA and that those giving the single-locus polymorphic patterns usually corresponded to single-copy sequences. A family of repetitive DNA that contained AG repeats was identified and was present in about 40,000 copies per haploid genome. Simple Mendelian inheritance was observed for all the polymorphisms tested. The average number of alleles was 13, ranging from 6 to 22, and the expected heterozygosity was 0.79 when seven microsatellites were used to genotype a panel of 18 trees representing different populations. Compared with isozymes, microsatellites are about five times more informative and could provide an extremely valuable source of markers for genome mapping and genetic diversity studies.

Alleles↗

PubMed2004

Epistasis in quantitative trait locus linkage analysis: interaction or main effect?

This paper explores a two-locus variance components model of quantitative trait locus (QTL) linkage for sib-pairs that incorporates epistasis. For a range of epistatic models the expected variance components and noncentrality parameter per sib-pair can be calculated, to indicate the power to detect epistasis. In QTL linkage analysis, additive and epistatic effects are in fact partially confounded; as a result, variance components under incorrect submodels can be distorted, with two main implications. First, the analysis of a single locus can in fact detect a QTL that has no main effect but interacts epistatically with another (unmeasured) locus. That is, single-locus approaches do not necessarily preclude the detection of purely epistatically interacting loci. Second, because the nonepistatic variance component estimates in submodels can partially absorb epistatic variance when it is not explicitly modeled, power to formally detect epistasis is low.

Alleles↗

PubMed1992

Sequence analysis of members of the human Ig VH4 gene family derived from a single VH locus. Identification of novel germ-line members.

We have generated a mouse x human heterohybridoma that contains a single copy of chromosome 14 and, thus, a haploid set of Ig VH genes. This cell line was used to investigate the germ-line content and nucleotide sequences of members of the VH4 gene family in a polymerase chain reaction-based approach. The analysis of 58 full-length sequences revealed the presence of 12 different germ-line VH4 genes, each of which is potentially functional. These germ-line VH4 genes were compared with the nucleotide sequences of published VH4 genes. Three VH4 genes were 100% identical to previously published sequences and belong to a group of VH4 genes that are strongly conserved and highly prevalent in the human population. Three VH4 genes in our collection displayed greater than 99.3% sequence identity with reported germ-line VH4 sequences and likely represent allelic counterparts of these genes. Six genes displayed less than 97.2% sequence identity with published VH4 genes and were identified as novel members of the human VH4 gene family or more distantly related alleles of known VH4 genes. Collectively, these data suggest that, overall, the human VH4 gene family may be more diverse than hitherto assumed, whereas a number of individual members are nonpolymorphic and extremely well conserved.

Amino Acid Sequence↗

PubMed2001

Murine lupus genetics: lessons learned.

Recent reverse genetic studies in murine lupus have taught us the following lessons: (1) Lupus is extremely polygenic; (2) A single locus may be associated with many different phenotypes; (3) What appears to be a single locus may turn out to be a cluster of loci; (4) Different loci facilitate different immunologic steps leading to lupus; (5) Epistatic interactions between loci may engender novel autoimmune phenotypes; (6) Whereas some loci may be pathogenic, others may confer disease resistance; (7) Whereas the expression of some loci is sex-dependent, the expression of others clearly is not; (8) Two or more loci may have an impact on the same phenotype; (9) Lupus susceptibility loci appear to co-cluster with other autoimmunity susceptibility loci; (10) Lupus genes are likely to be polymorphic alleles with subtle impacts, rather than outright mutations with extreme functions. In contrast, forward genetic studies have revealed that molecules that impact apoptosis, the clearance of apoptotic cells, B-cell or T-cell function, and end-organ pathology can all potentially contribute to lupus. Collectively, the loci and genes identified by these two different approaches factorize into a few distinct pathways leading to lupus. Delineating the molecular mediators of these distinct checkpoints is the challenge that lies ahead.

Animals↗

PubMed2001

Random amplified polymorphic DNA diversity of marginal and central populations in Pinus contorta subsp. latifolia.

Fifteen populations of lodgepole pine (Pinus contorta subsp. latifolia) were surveyed for diversity across 52 random amplified polymorphic DNAs (RAPDs). The objective was to compare single-locus and multilocus structures in four marginal, three intermediate, and eight central populations. Single-locus estimates indicated average observed and expected heterozygosity to be 0.19 and 0.17, respectively. When these estimates were split into population categories, a clear trend of increasing diversity was detected in the direction of marginal to central populations. F-statistics indicated an excess of heterozygotes, with F(IS) ranging from -0.08 for marginal populations to -0.15 for central populations and averaging -0.12 over 15 populations. The estimates of F(ST) decreased towards the margins of the species range, indicating increased population differentiation. Forty-nine of 52 RAPDs tested neutral in the Ewens-Watterson analysis. Multilocus analysis showed significant two-locus and high-order gametic disequilibria in all 15 populations. The most prominent components of the two-locus analysis were the variance of disequilibrium (VD, 46.2%) and the multilocus Wahlund effect (31.9%). This high value for VD indicated that founder effects could explain much of the observed multilocus associations. When analyzed by population categories, the VD showed a decreasing trend indicating that variation due to founder effects was more prominent in marginal populations. The two-locus Wahlund effect (WC) that is characteristic of strong population subdivision was highest in the central populations. This indicated significant levels of gene flow between populations with different allelic combinations.

DNA Primers↗

PubMed1993

Organizational differences between cytoplasmic male sterile and male fertile Brassica mitochondrial genomes are confined to a single transposed locus.

Comparison of the physical maps of male fertile (cam) and male sterile (pol) mitochondrial genomes of Brassica napus indicates that structural differences between the two mtDNAs are confined to a region immediately upstream of the atp6 gene. Relative to cam mtDNA, pol mtDNA possesses a 4.5 kb segment at this locus that includes a chimeric gene that is cotranscribed with atp6 and lacks an approximately 1kb region located upstream of the cam atp6 gene. The 4.5 kb pol segment is present and similarly organized in the mitochondrial genome of the common nap B.napus cytoplasm; however, the nap and pol DNA regions flanking this segment are different and the nap sequences are not expressed. The 4.5 kb CMS-associated pol segment has thus apparently undergone transposition during the evolution of the nap and pol cytoplasms and has been lost in the cam genome subsequent to the pol-cam divergence. This 4.5 kb segment comprises the single DNA region that is expressed differently in fertile, pol CMS and fertility restored pol cytoplasm plants. The finding that this locus is part of the single mtDNA region organized differently in the fertile and male sterile mitochondrial genomes provides strong support for the view that it specifies the pol CMS trait.

Adenosine Triphosphatases↗

PubMed1972

Study of four new kindreds with inherited thyroxine-binding globulin abnormalities. Possible mutations of a single gene locus.

Five families with inherited thyroxine-binding globulin (TBG) abnormalities were studied. On the basis of serum thyroxine (T(4))- binding capacity of TBG in affected males, three family types were identified: TBG deficiency, low TBG, and high TBG capacity. In all families evidence for X-linked inheritance was obtained and in one family all criteria establishing this mode of inheritance were met. Only females were heterozygous, exhibiting values intermediate between affected males and normals. Overlap in heterozygotes was most commonly encountered in families with low TBG. QUANTITATIVE VARIATION IN THE SERUM CONCENTRATION OF FUNCTIONALLY NORMAL TBG WAS DEMONSTRATED BY: (a) failure of serum from TBG-deficient subjects to react with anti-TBG antibodies; (b) normal kinetics of T(4) and triiodothyronine-binding to TBG in sera from subjects with low TBG and high TBG capacity; (c) concordance of estimates of TBG concentration by T(4) saturation and by immunological methods; and (d) normal rate of heat inactivation of TBG. No abnormalities in serum transport of cortisol, testosterone, aldosterone, or thyroxine bound to prealbumin could be detected. These observations suggest that all the TBG abnormalities thus far observed reflect mutations at a single X-linked locus involved in the control of TBG synthesis.

Adolescent↗