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Evidence for the control of phytolith formation in Cucurbita fruits by the hard rind (Hr) genetic locus: Archaeological and ecological implications.

Many angiosperms, both monocotyledons and dicotyledons, heavily impregnate their vegetative and reproductive organs with solid particles of silicon dioxide (SiO(2)) known as opaline phytoliths. The underlying mechanisms accounting for the formation of phytoliths in plants are poorly understood, however. Using wild and domesticated species in the genus Cucurbita along with their F(1) and F(2) progeny, we have demonstrated that the production of large diagnostic phytoliths in fruit rinds exhibits a one-to-one correspondence to the lignification of these structures. We propose that phytolith formation in Cucurbita fruits is primarily determined by a dominant genetic locus, called hard rind (Hr), previously shown to code for lignin deposition. If true, this evidence represents a demonstration of genetic control over phytolith production in a dicotyledon and provides considerable support to hypotheses that silica phytoliths constitute another important system of mechanical defense in plants. Our research also identifies Hr as another single locus controlling more than one important phenotypic difference between wild and domesticated plants, and establishes rind tissue cell structure and hardness under the effects of Hr as an important determinant of phytolith morphology. When recovered from pre-Columbian archaeological sites, Cucurbita phytoliths represent genetically controlled fossil markers of exploitation and domestication in this important economic genus.

Archaeology↗

Functional analysis of the trypanosomal AAA protein TbVCP with trans-dominant ATP hydrolysis mutants.

TbVCP is a member of the AAA (ATPases Associated with a variety of cellular Activities) family of proteins containing two ATPase domains. Southern analysis indicates TbVCP to have a single-locus, two-copy, genomic organization. One copy, but not both, can be disrupted by targeted gene replacement, suggesting that TbVCP is essential for trypanosome viability. Site-directed mutagenesis of the ATP hydrolysis motifs indicates that the second conserved ATPase domain is essential for TbVCP activity. Constitutive overexpression of TbVCP with a single mutation in the second hydrolysis motif or with mutations in both hydrolysis motifs was not possible. Regulated overexpression of these mutants resulted in cell death as a dominant negative phenotype. In each case cell growth arrested at 24-h post-induction and at all stages of the cell cycle as judged by replication of nuclear and kinetoplast genomes. Onset of growth arrest coincided with the development of severe and characteristic morphological alterations for each mutant. Neither constitutive nor regulated overexpression of wild type TbVCP or the single first hydrolysis domain mutant had any overt effect on cell viability or morphology. However, the distinct phenotype of the double mutant indicates that the first hydrolysis domain, although not essential, does modulate overall TbVCP function. Finally, yeast complementation studies demonstrated that TbVCP can functionally replace the yeast homologue Cdc48p, indicating that protein.protein interactions essential to function have been maintained over great phylogenetic distances.

Adenosine Triphosphatases↗

Loss of heterozygosity and microsatellite instability at the retinoblastoma locus in osteosarcomas.

Studies of osteosarcoma cell lines or frozen tissue have detected loss of heterozygosity (LOH) at the retinoblastoma (RB) locus by Southern blot analysis or restriction fragment length polymorphism. Most archived clinical specimens cannot be analyzed by these techniques. We analyzed formalin-fixed, paraffin-embedded samples from 19 cases of osteosarcoma for molecular changes at the RB locus using polymerase chain reaction amplification of polymorphic short tandem repeat sequences (microsatellite repeats). Four repeat sequences, two within and two flanking the RB gene, were analyzed. Fourteen of 18 informative cases (78%) showed molecular changes at the RB locus. LOH was identified in 13 cases (72%). Unexpectedly, microsatellite instability (MI) was found in eight cases (44%). All of the cases of MI involved alterations of more than one repeat unit, and six of eight were associated with LOH. LOH was identified at three unlinked loci in one case and at a single locus in another Microsatellite analysis of archival tissue yields prevalence rates of LOH comparable to those found by other methods and has the added advantage of showing MI. The ability to use formalin-fixed, paraffin-embedded tissue extends genetic analysis to routinely processed surgical material and may permit molecular confirmation of challenging cases of osteosarcoma.

Bone Neoplasms↗

Analysis of a T-cell tumor-specific breakpoint cluster at human chromosome 14q32.

Cytogenetic abnormalities involving chromosome 14 band q32 are consistently observed in human T-cell tumors. Patients with ataxia-telangiectasia (AT) are especially prone to development of these tumors, which frequently carry either inversion inv(14)(q11;q32) or translocation t(14;14) (q11;q32) chromosomes. We have previously shown that the cytogenetic breakpoints of one t(14;14)(q11;q32) chromosome and two inv(14)(q11;q32) chromosomes in T-cell tumors from AT and non-AT patients join the T-cell receptor alpha chain locus, at chromosome band 14q11, with a region(s) at 14q32 centromeric of the immunoglobulin heavy chain variable region (VH) gene IGHV. We now show that these two inv(14) breakpoints are linked by 2.1 kb of germ-line 14q32 DNA and that the three breakpoints define, by in situ hybridization analysis, a single locus at chromosome band 14q32.1 located about 15-20 million base pairs on the centromeric side of the IGH locus. Sequence analysis of the 14q32.1 breakpoint regions indicates that abnormal recombination does not universally result from mistaken V-D-J joining (D = diversity region; J = joining region). Therefore, we invoke a tumor selection model to describe the role of the 14q32.1 locus in tumor development.

Base Sequence↗

Alternative fitness models with the same allele frequency dynamics.

For any set of one- or two-locus genotypic fitnesses there are alternative sets, usually frequency-dependent and often with quite different biological meanings, that give rise to the same equations for change of allele or haplotype frequencies. Therefore, it is not possible to distinguish among alternative fitness models from allele or haplotype frequency trajectories or equilibrium distributions. For a single locus and for two loci when linkage equilibrium can be assumed, a simple procedure generates some of the alternative fitness sets.

Alleles↗

Utility of canine microsatellites in revealing the relationships of pure bred dogs.

The variability of 19 canine microsatellite loci was examined within and between three pure breeds of dog. Their phylogenetic relationships were estimated by microsatellite and conventional genetic distances which indicated that greyhounds and German shepherds had longer diverse evolutionary histories, whereas Labrador retrievers were established much later. Our three breeds differ mainly in the relative frequencies of alleles at a locus and in distribution of alleles across loci. As a consequence of sampling strategy, greyhounds express significantly lower polymorphism than the other two breeds. However, some highly polymorphic microsatellite loci were common to all three breeds. High exclusion power of such loci made them valuable for parentage testing. Although the exclusion probability at a single locus is relatively low, it increases by every added microsatellite. The six most polymorphic ones sufficed to reach the exclusion probability of 99% in all three breeds tested here. As the majority of pedigree dogs have similar population structures, the data presented can be used to estimate the probability of biological paternity for any dog breed, despite the absence of appropriate population data. Polymorphic canine microsatellites proved to be valuable descriptors of population structure, and evolutionary and filial relationships.

Alleles↗

Characterization and genetic analysis of a lettuce (Lactuca sativa L.) mutant, weary, that exhibits reduced gravitropic response in hypocotyls and inflorescence stems.

A lettuce (Lactuca sativa L.) mutant that exhibits a procumbent growth habit was identified and characterized. In two wild type (WT) genetic backgrounds, segregation patterns revealed that the mutant phenotype was controlled by a recessive allele at a single locus, which was designated weary. Hypocotyls and inflorescence stems of plants homozygous for the weary allele exhibited reduced gravitropic responses compared with WT plants, but roots exhibited normal gravitropism. Microscopic analysis revealed differences in the radial distribution of amyloplasts in hypocotyl and inflorescence stem cells of weary and WT plants. Amyloplasts occurred in a single layer of endodermal cells in WT hypocotyls and inflorescence stems. By contrast, amyloplasts were observed in several layers of cortical cells in weary hypocotyls, and weary inflorescence stem cells lacked amyloplasts entirely. These results are consistent with the proposed role of sedimenting amyloplasts in shoot gravitropism of higher plants. The phenotype associated with the weary mutant is similar to that described for the Arabidopsis mutant sgr1/scr, which is defective in radial patterning and gravitropism.

Flowering Tops↗

A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation.

Recent advances in genome research have accelerated the process of locating candidate genes and the variable sites within them and have simplified the task of genotype measurement. The development of statistical and computational strategies to utilize information on hundreds -- soon thousands -- of variable loci to investigate the relationships between genome variation and phenotypic variation has not kept pace, particularly for quantitative traits that do not follow simple Mendelian patterns of inheritance. We present here the combinatorial partitioning method (CPM) that examines multiple genes, each containing multiple variable loci, to identify partitions of multilocus genotypes that predict interindividual variation in quantitative trait levels. We illustrate this method with an application to plasma triglyceride levels collected on 188 males, ages 20--60 yr, ascertained without regard to health status, from Rochester, Minnesota. Genotype information included measurements at 18 diallelic loci in six coronary heart disease--candidate susceptibility gene regions: APOA1--C3--A4, APOB, APOE, LDLR, LPL, and PON1. To illustrate the CPM, we evaluated all possible partitions of two-locus genotypes into two to nine partitions (approximately 10(6) evaluations). We found that many combinations of loci are involved in sets of genotypic partitions that predict triglyceride variability and that the most predictive sets show nonadditivity. These results suggest that traditional methods of building multilocus models that rely on statistically significant marginal, single-locus effects, may fail to identify combinations of loci that best predict trait variability. The CPM offers a strategy for exploring the high-dimensional genotype state space so as to predict the quantitative trait variation in the population at large that does not require the conditioning of the analysis on a prespecified genetic model.

Adult↗

Linkage of late-onset Fuchs corneal dystrophy to a novel locus at 13pTel-13q12.13.

PURPOSE: To identify the gene locus underlying the inheritance of late-onset Fuchs corneal dystrophy (FCD) in a large white kindred. METHODS: Genotypes of small tandem repeat polymorphisms were obtained from 17 affected and 3 unaffected family members, followed by genetic linkage analysis. RESULTS: In this family, classic late-onset FCD appeared to be inherited as a single, dominant Mendelian trait. In two exceptional sibships, however, children aged 10 and 13 years had FCD. In each sibship, both parents were found to be affected, opening the possibility that this unusually early age of onset was the result of homozygosity for an FCD mutation. Genotype results, however, were not consistent with consanguinity of the parents, who appear to have independent cases of FCD. A whole-genome linkage scan mapped FCD to a single locus at 13pTel-13q12.13, with significant two-point LOD scores of 3.91 at D13S1236 and 3.80 at D13S1304. The 26.4-Mb disease interval contains the chromosome 13 nucleolus organizer (RNR1), the centromere, and 44 annotated protein-encoding genes. So far, exons of 10 of these genes have been screened, but no mutations have been found. CONCLUSIONS: FCD1 is the first genetic locus to be identified for late-onset FCD, a common disease of the aging cornea. The exceptional early onset of the disease observed in two children is unusual and might be the result of digenic interaction between FCD1 and an independent late-onset FCD mutation.

Adolescent↗

Evidence for genetic heterogeneity in familial Wilms' tumor.

Wilms' tumor (WT), a childhood kidney cancer, occurs both sporadically and, less frequently, in a familial context. Genetic linkage studies of several large WT families have excluded the one cloned WT gene, WT1, as the locus responsible for familial predisposition. These data demonstrate the existence of a familial predisposition gene distinct from WT1 and, more broadly, imply that the genetic etiology of WT is heterogenous. However, it has been unknown whether the predisposition observed in large WT families is also heterogenous or perhaps is due to mutations at a single locus. Recently, examination of a large French-Canadian WT family has demonstrated genetic linkage to 17q12-q21. We report here the results from a genetic linkage study of six WT pedigrees. Analyses of genotype data from eight loci within the 17q12-q21 region in these families resulted in cumulative lod scores of <-4.0 through the region, thereby excluding linkage. The ability to rule out the 17q region as the site of a predisposition gene in several of these pedigrees individually demonstrates the existence of more than one gene that predisposes to WT in large pedigrees and again emphasizes that the etiology of WT is genetically heterogenous.

Adult↗

Genetic analysis of manic-depressive illness.

Two threshold models, a single locus model, and two combined models are fitted to data on familial incidence of bipolar affective disorder in 194 nuclear families ascertained through a bipolar proband. The relative fit of alternative transmission models is tested by a likelihood ratio chi-square with the degrees of freedom defined by the difference in the number of parameters estimated by each model. All parameters are estimated by the method of maximum likelihood. The simplest threshold model, permitting only a single background familial correlation, is found to provide a statistically poorer fit than any of the alternative models, and may be rejected as a model for the etiology of bipolar affective disorder. The four remaining models are statistically indistinguishable. It is suggested, however, that the involvement of a major locus in the etiology of this disorder deserves further scrutiny since any of the models incorporating a major locus, with or without a multifactorial background, are consistently associated with greater likelihoods than the complex threshold model. It is also noted that diagnostic criteria are critical in the analysis. In the present study, relatives of probands are considered affected if a diagnosis of bipolar or unipolar affective disorder is present. When only bipolar relatives are considered affected, none of the transmission models may be rejected. Finally, the results of these analyses are found to be independent of the ascertainment parameter.

Biometry↗

Generalization of the extended transmission disequilibrium test to two unlinked disease loci.

The extended transmission disequilibrium test (ETDT) of Sham and Curtis [1995] is a powerful test of the null hypothesis of no linkage between a multi-allelic marker locus and a disease susceptibility locus of unknown location in the presence of association between alleles at the two loci. We propose a generalization of the ETDT to test simultaneously for linkage of markers to two unlinked disease loci. Analysis of the simulated data for Problem 2 would suggest improvements in power to detect linkage to pairs of disease loci over single locus tests. This is as a result of the two locus model taking account of epistasis between the disease loci.

Alleles↗

Retroposition of the AFC family of SINEs (short interspersed repetitive elements) before and during the adaptive radiation of cichlid fishes in Lake Malawi and related inferences about phylogeny.

Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation. To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed repetitive elements) at orthologous loci. We identified six loci at which a SINE sequence had apparently been specifically inserted by retroposition in the common ancestor of all the investigated species of endemic cichlids in Lake Malawi. At another locus, unique sharing of a SINE sequence was evident among all the investigated species of endemic non-Mbuna cichlids with the exception of Rhamphochromis sp. The relationships were in good agreement with those deduced in previous studies with various different markers, demonstrating that the SINE method is useful for the elucidation of phylogenetic relationships among cichlids in Lake Malawi. We also characterized a locus that exhibited transspecies polymorphism with respect to the presence or absence of the SINE sequence among non-Mbuna species. This result suggests that incomplete lineage sorting and/or interspecific hybridization might have occurred or be occurring among the species in this group, which might potentially cause misinterpretation of phylogenetic data, in particular when a single-locus marker, such as a sequence in the mitochondrial DNA, is used for analysis.

Animals↗

Polymorphism at the tetranucleotide repeat locus DYS389 in 10 populations reveals strong geographic clustering.

Several short tandem repeat polymorphism loci at the non-recombining part of the Y chromosome have been described recently and are now widely used for the investigation of the history and the diversity of man. The tetranucleotide repeat polymorphism at the DYS389 locus consists of two repetitive stretches with different numbers of (TCTG)n (TCTA)m repeat units. To study the overall variability of this locus, 768 alleles from males from 10 human populations (two sub-Saharan African, four Caucasoid and four Asian/Amerind populations) were investigated. The alleles found in the populations of different geographic origin exhibited remarkable differences in the number and arrangement of repeats in the two repetitive stretches and up to nine different sequence variants for a single fragment length have been detected. So far 53 different alleles, i.e. haplotypes, have been observed. Analysis of molecular variance (AMOVA) indicates that at least 24.5% of the total genetic variance was found between the populations and that these differences were significant in most pairwise comparisons. We propose a model, in which both founder effects and genetic drift together with single step replication slippage mutations explain the picture of haplotype diversity observed with this single locus.

Alleles↗

A genome-wide search for susceptibility loci to human essential hypertension.

We undertook a systematic search of the entire human genome with the affected sibling-pair model to identify major susceptibility loci to essential hypertension. Affected nuclear families (n=263) were recruited and divided according to definite or probable genetic contribution to hypertension depending on number of hypertensive siblings. The largest nuclear families were first screened with a set of microsatellite markers. Regions on the genome with P<0.05 were tested against the second set of smaller families. An exclusion map was generated to identify regions in which hypertension-causing genes are unlikely to reside. Sibling-pair linkage analysis identified a single locus on chromosome 11q (P<0.004) in the first pass. A second pass with nuclear families that had only affected sibling pairs was, as expected, insufficient to support linkage to 11q. Multipoint exclusion-linkage analysis showed that 3 genetic loci are necessary to explain familial aggregation of essential hypertension. Our preliminary findings suggest that no single region within the human genome contains genes with a major contribution to essential hypertension. We show that the disease is indeed polygenic, with each gene providing a relatively small risk. Our exclusion map will help future investigators to concentrate on areas likely to contain these genes. The region on chromosome 11 is the first to point to a new candidate gene for hypertension that has arisen out of a genome search, but replication of these results at a higher significance is necessary before positional cloning can be justified.

Aged↗

Polyploid and multilocus extensions of the Wahlund inequality.

Wahlund's inequality informally states that if a structured and an unstructured population have the same allele frequencies at a locus, the structured population contains more homozygotes. We show that this inequality holds generally for ploidy level P, that is, the structured population has more P-polyhomozygotes. Further, for M randomly chosen loci (M >or= 2), the structured population is also expected to contain more M-multihomozygotes than an unstructured population with the same single-locus homozygosities. The extended inequalities suggest multilocus identity coefficients analogous to F(ST). Using microsatellite genotypes from human populations, we demonstrate that the multilocus Wahlund inequality can explain a positive bias in "identity-in-state excess".

Chromosome Mapping↗

Linkage of butterfly mate preference and wing color preference cue at the genomic location of wingless.

Sexual isolation is a critical form of reproductive isolation in the early stages of animal speciation, yet little is known about the genetic basis of divergent mate preferences and preference cues in young species. Heliconius butterflies, well known for their diversity of wing color patterns, mate assortatively as a result of divergence in male preference for wing patterns. Here we show that the specific cue used by Heliconius cydno and Heliconius pachinus males to recognize conspecific females is the color of patches on the wings. In addition, male mate preference segregates with forewing color in hybrids, indicating a genetic association between the loci responsible for preference and preference cue. Quantitative trait locus mapping places a preference locus coincident with the locus that determines forewing color, which itself is perfectly linked to the wing patterning candidate gene, wingless. Furthermore, yellow-colored males of the polymorphic race H. cydno alithea prefer to court yellow females, indicating that wing color and color preference are controlled by loci that are located in an inversion or are pleiotropic effects of a single locus. Tight genetic associations between preference and preference cue, although rare, make divergence and speciation particularly likely because the effects of natural and sexual selection on one trait are transferred to the other, leading to the coordinated evolution of mate recognition. This effect of linkage on divergence is especially important in Heliconius because differentiation of wing color patterns in the genus has been driven and maintained by natural selection for Müllerian mimicry.

Animals↗

Vanillin (3-methoxy-4-hydroxybenzaldehyde) inhibits mutation induced by hydrogen peroxide, N-methyl-N-nitrosoguanidine and mitomycin C but not (137)Cs gamma-radiation at the CD59 locus in human-hamster hybrid A(L) cells.

We have investigated the ability of the naturally occurring plant essence vanillin (3-methoxy-4-hydroxybenzaldehyde) to inhibit mutation at the CD59 locus on human chromosome 11 by hydrogen peroxide, N-methyl-N-nitrosoguanidine, mitomycin C and (137)Cs gamma-radiation in human-hamster hybrid A(L) cells. Previous studies using vanillin have suggested that it can inhibit chromosome aberrations induced by hydrogen peroxide and mitomycin C, as well as inhibiting X-ray- and UV-induced mutations at the hprt locus. Other studies with vanillin have shown that it can increase both the toxicity and mutagenicity of ethyl methane sulfonate and increase the induction of sister chromatid exchange by mitomycin C and a variety of other mutagens. The increased sensitivity of the A(L) assay, which is due in part to its ability to detect both small (single locus) and large (multilocus) genetic damage, allows us to measure the effect of vanillin at low doses of mutagen. Vanillin is shown, in these studies, to inhibit mutation induced by hydrogen peroxide, N-methyl-N-nitrosoguanidine and mitomycin C, as well as to enhance the toxicity of these agents. Vanillin had no effect on either toxicity or mutation induced by (137)Cs gamma-radiation. The vanillin-induced potentiation of H(2)O(2) toxicity is shown not to involve inhibition of catalase or glutathione peroxidase. These results show that vanillin is able to inhibit mutation at the CD59 locus and modify toxicity in a mutagen-specific manner. Possible mechanisms to explain the action of vanillin include inhibition of a DNA repair process that leads to the death of potential mutants or enhancement of DNA repair pathways that protect from mutation but create lethal DNA lesions during the repair process.

Animals↗