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PubMed2006

[Genetics in eating disorders: extending the boundaries of research].

OBJECTIVE: To review the recent literature relevant to genetic research in eating disorders and to discuss unique issues which are crucial for the development of a genetic research project in eating disorders in Brazil. METHOD: A computer literature review was conducted in the Medline database between 1984 and may 2005 with the search terms "eating disorders", "anorexia nervosa", "bulimia nervosa", "binge eating disorder", "family", "twin" and "molecular genetic" studies. RESULTS: Current research findings suggest a substantial influence of genetic factors on the liability to anorexia nervosa and bulimia nervosa. Genetic research with admixed populations should take into consideration sample size, density of genotyping and population stratification. Through admixture mapping it is possible to study the genetic structure of admixed human populations to localize genes that underlie ethnic variation in diseases or traits of interest. CONCLUSIONS: The development of a major collaborative genetics initiative of eating disorders in Brazil and South America would represent a realistic possibility of studying the genetics of eating disorders in the context of inter ethnic groups, and also integrate a new perspective on the biological etiology of eating disorders.

Anorexia Nervosa↗
PubMed2001

Population isolates: their special value for locating genes for bipolar disorder.

OBJECTIVES: Population isolates offer several advantages for those hoping to identify predisposition genes for bipolar disorder (BP). In this review article, the rationale for performing gene mapping studies in this type of population and the results of genetic mapping studies performed to date in population isolates are presented. METHODS: This article begins with a brief review of the concepts involved in mapping genes for BP. The concept of populations that show some degree of historical isolation and their special utility for certain types of gene mapping is presented. Methods of statistical analysis particularly relevant for gene mapping of complex diseases like BP are presented. Finally, several BP gene studies conducted to date in several population isolates are reviewed. RESULTS: Genetic mapping studies of BP have occurred thus far in several isolates or sub-isolates, including the Amish population, Costa Ricans, Finnish, and Canadians (in Quebec), and significant linkage scores have been identified in the latter three isolates. CONCLUSIONS: Possible greater homogeneity and greater consistency of diagnosis are factors that have been cited in several studies of BP done in isolates to date. Another special advantage of working in certain types of population isolate is their appropriateness for using certain types of association or linkage disequilibrium-based approaches at both the genome screening and fine mapping stages. These tests include mapping by linkage disequilibrium analyses, an approach that allows mapping to occur at the population, rather than the pedigree, level.

Bipolar Disorder↗
PubMed2002

[Mapping of fertility-restoring genes with main effects and epistatic effects for CMS-DA in rice].

A test-cross population was established for mapping genes conditioning fertility restoration for dwarf-wild-abortive cytoplasmic male sterility(CMS-DA) in rice. A recombinant inbred line(RIL) population consisting of 210 lines was derived from the cross Xieqingzao B/Miyang 46, in which Xieqingzao B is the maintainer line of CMS-DA Xieqingzao A, and Miyang 46 is the restorer line. Each of the RILs was crossed to Xieqingzao A, and the resulting F1s were used for phenotyping of the spikelet fertility in 1999 and 2000. A linkage map consisting of 129 RFLP and SSLP markers was constructed. QTLs having significant main effects and/or epistatic effects for spikelet fertility were determined with QTLMAPPER 1.0 of mixed linear model. Background genetic variation due to main and epistatic effects of important markers was controlled. Four QTLs having significant main effects for fertility restoration were detected. A major gene qRf-10-2 was located in interval RM258-RZ811 on the long arm of chromosome 10, and QTL qRf-1 displaying a moderate main effect was located in a position close to RG532 on chromosome 1. Two other QTLs were located on chromosome 5 (qRF-5) and the short arm of chromosome 10 (qRf-10-1), in which the main effect of qRf-5 bacame significant only in the absence of qRf-10-2. A significant digenic interaction was detected, which occurred between QTLs qRf-1 and qRf-5. No significant QTL by environmental interactions and epistasis by environmental interactions were detected. Analyses on the gene effects based on markers closest to the Rf genes were made, and multi-locus interactions were implied. The present results were also compared to a previous study on mapping fertility restoration genes in Milyang 46 for wild-abortive CMS Zhenshan 97A, and to other published reports. It was indicated that differences on the genetic control of fertility restoration among different rice populations were mainly attributed to variations on genes with minor main effects and epistatic effects.

Chromosome Mapping↗
PubMed1998

A composite genetic map of the parasitoid wasp Trichogramma brassicae based on RAPD markers.

Three linkage maps of the genome of the microhymenopteran Trichogramma brassicae were constructed from the analysis of segregation of random amplified polymorphic DNA markers in three F2 populations. These populations were composed of the haploid male progeny of several virgin F1 females, which resulted from the breeding of four parental lines that were nearly fixed for different random amplified polymorphic DNA markers and that were polymorphic for longevity and fecundity characters. As the order of markers common to the three mapping populations was found to be well conserved, a composite linkage map was constructed. Eighty-four markers were organized into five linkage groups and two pairs. The mean interval between two markers was 17.7 cM, and the map spanned 1330 cM.

Animals↗
PubMed2004

High-resolution fine mapping and fluorescence in situ hybridization analysis of sun, a locus controlling tomato fruit shape, reveals a region of the tomato genome prone to DNA rearrangements.

The locus sun on the short arm of tomato chromosome 7 controls morphology of the fruit. Alleles from wild relatives impart a round shape, while alleles from certain cultivated varieties impart an oval shape typical of roma-type tomatoes. We fine mapped the locus in two populations and investigated the genome organization of the region spanning and flanking sun. The first high-resolution genetic map of the sun locus was constructed using a nearly isogenic F(2) population derived from a cross between Lycopersicon pennellii introgression line IL7-4 and L. esculentum cv Sun1642. The mapping combined with results from pachytene FISH experiments demonstrated that the top of chromosome 7 is inverted in L. pennellii accession LA716. sun was located close to the chromosomal breakpoint and within the inversion, thereby precluding map-based cloning of the gene using this population. The fruit-shape locus was subsequently fine mapped in a population derived from a cross between L. esculentum Sun1642 and L. pimpinellifolium LA1589. Chromosome walking using clones identified from several large genomic insert libraries resulted in two noncontiguous contigs flanking sun. Fiber-FISH analysis showed that distance between the two contigs measured 68 kb in L. esculentum Sun1642 and 38 kb in L. pimpinellifolium LA1589, respectively. The sun locus mapped between the two contigs, suggesting that allelic variation at this locus may be due to an insertion/deletion event. The results demonstrate that sun is located in a highly dynamic region of the tomato genome.

Chromosome Mapping↗
PubMed1995

GABAA receptor subunits have differential distributions in the rat retina: in situ hybridization and immunohistochemistry.

The distributions of nine different subunits of the gamma-aminobutyric acidA (GABAA) receptor (alpha 1, alpha 2, alpha 3, alpha 5; beta 1, beta 2, beta 3; gamma 2; delta) were investigated in the rat retina using immunocytochemistry and in situ hybridization. With the exception of the alpha 5 subunit, all subunits could be localized. Each subunit was expressed in characteristic strata within the inner plexiform layer (IPL). Some subunits (e.g., gamma 2) showed a ubiquitous distribution, while others (e.g., delta) were restricted to narrow sublayers. Double labeling experiments using different combinations of the subunit-specific antibodies revealed colocalizations of subunits within individual neurons. Additionally, GABAA receptor subunits were mapped to distinct populations of retinal neurons by coapplication of defined immunocytochemical markers and subunit-specific antibodies. Cholinergic amacrine cells were found to express the alpha 2, beta 1, beta 2/3 and delta subunits, while dopaminergic amacrine cells express the alpha 2, alpha 3 and gamma 2 subunits. Dissociated rod bipolar cells express the alpha 1 and gamma 2 subunits. In summary, this study provides evidence for the existence of multiple GABAA receptor subtypes in the retina. The distinct stratification pattern of the subunits in the IPL suggests that different functional circuits involve specific subtypes of GABAA receptors.

Animals↗
PubMed2004

Rapid triple-labeling method combining in situ hybridization and double immunocytochemistry.

A new, rapid method is described for combining in situ hybridization and immunocytochemistry to define cell populations and to map three-dimensional movements of groups of labeled cells within developing chick embryos. The method allows fluorescently labeled cells to be followed in living embryos and subsequently detected as a permanent reaction product for detailed three-dimensional analysis by immunocytochemistry in histological serial sections. Cell identity can be ascertained using a specific riboprobe and in situ hybridization. With this approach, the movements of two groups of cells can be mapped simultaneously (using two different fluorescent trackers and, subsequently, two different chromogens for immunocytochemistry) to analyze relative movements within an embryo, and when combined with in situ hybridization with a specific riboprobe for cell identity, allows fate mapping studies to be conducted using molecular criteria, rather than solely at morphological/positional criteria. The improved method enables the investigator to extract substantially more information from individual embryos, maximizing the results obtained from labor-intensive fate mapping studies.

Animals↗
PubMed1995

Calbindin-D28k-containing neurons in the human hypothalamus: relationship to dopaminergic neurons.

Calbindin-D28k is a calcium-binding protein that protects nerve cells from degeneration. It is located in the midbrain dopaminergic neurons that are relatively invulnerable to degeneration in Parkinson's disease. Because the hypothalamic dopaminergic neurons do not degenerate in Parkinson's disease, the present study sought to determine whether these neurons also contain calbindin-D28k. Using immunocytochemical staining with antibodies against calbindin-D28k and tyrosine hydroxylase, and computer imaging techniques, the distributions of calbindin-D28k and tyrosine hydroxylase-containing neurons were mapped. Both neuronal populations were present throughout the rostral-caudal extent of the hypothalamus. However, only in the periventricular region, at the preoptic and anterior hypothalamic levels, was there an overlap in the two cellular distributions. Using the presence of neuromelanin pigment as a marker for dopaminergic neurons, approximately 30% of the dopaminergic neurons contain calbindin-D28k in the periventricular region. These data indicate that a sub-population of hypothalamic dopaminergic neurons contain calbindin-D28k. This finding is discussed in terms of why hypothalamic dopaminergic neurons are resistant to degeneration in Parkinson's disease.

Adult↗
PubMed2002

Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice ( Oryza sativa L.).

Four multiplex panels of fluorescent-labeled rice microsatellite markers were designed to survey allelic diversity at a total of 27 simple sequence repeat loci. Automated fragment detection, size calling and binning were used to identify the microsatellite alleles. The panels were tested on 72 accessions representing the diversity of ecotypes and isozyme groups in cultivated rice ( Oryza sativa L.). Genetic diversity was evaluated by estimating the distribution and range of allele sizes, as well as the polymorphism information content (PIC), for each microsatellite locus. The multiplex panels were shown to be useful for fingerprinting and for clustering rice varieties, and genetic associations determined in this analysis agreed well with previous isozyme- and RFLP-based studies of these genotypes. Because of the wide cross-section of germplasm represented, we expect that the allele size-ranges reported here are close to the maximum for cultivated rice. In the future, panels of microsatellites from each rice chromosome will be made to facilitate the mapping of segregating populations and the identification of genes and QTLs underlying traits of interest.

Journal Article↗
PubMed2002

High-resolution genetic map of Nb, a gene that confers hypersensitive resistance to potato virus X in Solanum tuberosum.

Nb is a single dominant gene in potato that confers hypersensitive resistance to potato virus X (PVX) isolates from strain groups 1 and 2. Genetic and molecular analyses showed that Nb is located on the upper arm of chromosome V and forms part of a cluster of resistance genes encoding specificities to many different pathogens. We describe the genetical localisation of molecular markers tightly linked to the Nb locus and the development PCR-based markers suitable for isolation of the Nb resistance gene by positional cloning. A bulked segregant approach was applied to identify polymorphic AFLP markers tightly linked to the Nb locus. These markers were mapped in a population of segregating S1 progeny (1,300 plants) from a self-pollinated potato cultivar, Pentland Ivory. From this analysis, Nb was placed in an interval of 0.76 cM, flanked by the AFLP markers GM339 and GM637. Recombinant PVX strains carrying different combinations of avirulence genes were used in biological assays to show that Nb was also present in potato cv. Cara but was masked by the extreme PVX resistance conferred by the Rx gene. PCR-based screening of a Cara genomic BAC library with markers closest to the Nb locus identified a new marker tightly linked to Nb.

Journal Article↗
PubMed2002

Comparative genetic analysis of quantitative traits in sunflower ( Helianthus annuus L.) 1. QTL involved in resistance to Sclerotinia sclerotiorum and Diaporthe helianthi.

Sclerotinia sclerotiorum and Diaporthe helianthi are important pathogens of sunflower ( Helianthus annuus L.). Two hundred and twenty F2-F3 families were developed from an intraspecific cross between two inbred sunflower lines XRQ and PSC8. Using this segregating population a genetic map of 19 linkage groups with 290 molecular markers covering 2,318 cM was constructed. Disease resistances were measured in field experiments during 3 years (1998, 1999 and 2000) for phomopsis and 2 years for S. sclerotiorum (1997 and 1999). QTL were detected using the interval mapping method at a LOD threshold of 3. A total of 15 QTL for each pathogen resistance were detected across several linkage groups, confirming the polygenic nature of the resistances. These QTL explained from 7 to 41% of the phenotypic variability. The QTL for phomopsis resistance, in the 3 years of tests, mapped in the same region, and this was also true for some forms of S. sclerotiorum resistance in the 2 years of tests. On linkage group 8, QTL affecting resistance to both S. sclerotiorum and D. helianthi mycelium extension on leaves colocalised, suggesting a common component in the mechanism of resistance for these two pathogens. The colocalisation of QTL and breeding for resistance to S. sclerotiorum and to D. helianthi by pyramiding QTL in sunflower are discussed.

Journal Article↗
PubMed2003

Two inbred rat strains that differ substantially in hip fragility.

One approach to identifying the genetic influences on skeletal phenotypes involves the creation and genetic mapping of a population of the second filial (F2) offspring derived from a cross of two inbred strains of rodents. The two inbred strains should be chosen based upon a large difference in the phenotype of interest, e.g., bone fragility. We found previously that considerable variation exists in fragility phenotypes among inbred strains of rats, and the phenotypic variation was site specific. In particular, two inbred rat strains, Copenhagen 2331 (COP) and Dark Agouti (DA), were found to differ significantly in femoral neck geometry and strength. The aim of this study was to further characterize hip fragility in COP and DA rats at 6 months of age using peripheral quantitative computed tomography (pQCT), microcomputed tomography (mCT), and biomechanical tests. COP rats had a significantly wider femoral head (P = 0.04) and neck (P = 0.007), significantly larger bone area and cortical bone area in femoral neck (P = 0.03 and P = 0.02, respectively), significantly greater total bone mineral content (BMC) and cortical BMC in femoral neck (P = 0.01 and P = 0.001, respectively), and 65% greater femoral neck cross-sectional moment of inertia (P = 0.02), as compared with DA rats. As a result, COP rats had 22% higher ultimate force (Fu), 68% higher ultimate displacement (du), and 81% higher work to failure (U) than DA rats in the femoral neck biomechanical test (P = 0.04, P = 0.01, and P = 0.02, respectively). The biomechanical properties for the femoral midshaft and lumbar vertebrae were virtually the same in the two rat strains, suggesting a hip-specific genetic effect on bone strength. These data indicate that significant phenotypic variation at the femoral neck site exists between these two inbred strains, and COP rats appear to have genes that specifically enhance the femoral neck structural properties and strength. Therefore these two inbred strains, COP with DA, may facilitate effective genetic studies of hip fragility.

Animals↗
PubMed1999

A molecular marker that segregates with sorghum leaf blight resistance in one cross is maternally inherited in another.

Leaf blight-resistant sorghum accession SC326-6 was crossed to the susceptible cultivar BTx623 to analyze the genetic basis for resistance. Field scoring of inoculated F2 progeny revealed that resistance was transmitted as a dominant single-gene trait. By combining the random amplified polymorphic DNA (RAPD) technique with bulked-segregant analysis, it was possible to identify PCR amplification products that segregated with disease response. Primer OPD12 amplified a 323-bp band (D12R) that segregated with resistance. Creation of longer primers, or SCARs (sequence characterized amplified regions) for D12R resulted in the amplification of a single major band of the predicted size from all the resistant F2 progeny and the resistant parent SC326-6, but not from BTx623 or 24 of 29 susceptible F2 progeny. The SCAR primers also amplified a single band with DNA from IS3620C, the female parent in a cross with BTx623 that has been used to produce a recombinant inbred population for RFLP mapping. An equivalent band was amplified from all 137 recombinant inbred progeny, indicating that organelle DNA is the amplification target in this cross.

Base Sequence↗
PubMed2004

Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York city.

Hispanic and African American populations exhibit an increased risk of obesity compared with populations of European origin, a feature that may be related to inherited risk alleles from Native American and West African parental populations. However, a relationship between West African ancestry and obesity-related traits, such as body mass index (BMI), fat mass (FM), and fat-free mass (FFM), and with bone mineral density (BMD) in African American women has only recently been reported. In order to evaluate further the influence of ancestry on body composition phenotypes, we studied a Hispanic population with substantial European, West African, and Native American admixture. We ascertained a sample of Puerto Rican women living in New York ( n=64), for whom we measured BMI and body composition variables, such as FM, FFM, percent body fat, and BMD. Additionally, skin pigmentation was measured as the melanin index by reflectance spectroscopy. We genotyped 35 autosomal ancestry informative markers and estimated population and individual ancestral proportions in terms of European, West African, and Native American contributions to this population. The ancestry proportions corresponding to the three parental populations are: 53.3+/-2.8% European, 29.1+/-2.3% West African, and 17.6+/-2.4% Native American. We detected significant genetic structure in this population with a number of different tests. A highly significant correlation was found between skin pigmentation and individual ancestry ( R(2)=0.597, P<0.001) that was not attributable to differences in socioeconomic status. A significant association was also found between BMD and European admixture ( R(2)=0.065, P=0.042), but no such correlation was evident with BMI or the remaining body composition measurements. We discuss the implications of our findings for the potential use of this Hispanic population for admixture mapping.

Aged↗
PubMed2006

Gene polymorphisms for elucidating the genetic structure of the heavy-metal hyperaccumulating trait in Thlaspi caerulescens and their cross-genera amplification in Brassicaceae.

Genetic polymorphism was investigated in Thlaspi caerulescens J. & C. Presl at 15 gene regions, of which seven have been identified to putatively play a role in heavy-metal tolerance or hyperaccumulation. Single nucleotide and length polymorphisms were assessed at four cleaved amplified polymorphic sequences (CAPS) and 11 simple sequence repeat (microsatellite) loci, respectively. The utility of these loci for genetic studies in T. caerulescens was measured among seven natural populations (135 individuals). Fourteen loci rendered polymorphism, and the number of alleles per locus varied from 2 to 5 and 1 to 27 for CAPS and microsatellites, respectively. Up to 12 alleles per locus were detected in a population. The global observed heterozygosity per population varied between 0.01 and 0.31. Additionally, cross-species/genera amplification of loci was investigated on eight other Brassicaceae (five individuals per population). Overall, 70% of the cross-species/genera amplifications were successful, and among them, more than 40% provided intraspecific polymorphisms within a single population. This indicates that such markers may, as well, allow comparative population genetic or mapping studies between and within several Brassicaceae, particularly for genes involved in traits such as heavy-metal tolerance and/or hyperaccumulation.

Alleles↗
PubMed2006

Mapping and measuring social disparities in premature mortality: the impact of census tract poverty within and across Boston neighborhoods, 1999-2001.

The identification and documentation of health disparities are important functions of public health surveillance. These disparities, typically falling along lines defined by gender, race/ethnicity, and social class, are often made visible in urban settings as geographic disparities in health between neighborhoods. Recognizing that premature mortality is a powerful indicator of disparities in both health status and access to health care that can readily be monitored using routinely available public health surveillance data, we undertook a systematic analysis of spatial variation in premature mortality in Boston (1999-2001) across neighborhoods and sub-neighborhoods in relation to census tract (CT) poverty. Using a multilevel model based framework, we estimated that the incidence of premature mortality was 1.39 times higher (95% credible interval 1.09-1.78) among persons living in the most economically deprived CTs (>/=20% below poverty) compared to those in the least impoverished tracts (<5% below poverty). We present maps of model-based standardized mortality ratios that show substantial within-neighborhood variation in premature mortality and a sizeable decrease in spatial variation after adjustment for CT poverty. Additionally, we present maps of model-based direct standardized rates that can more readily be compared to externally published rates and targets, as well as maps of the population attributable fraction that show that in some of Boston's poorest neighborhoods, the proportion of excess deaths associated with CT poverty reaches 25-30%. We recommend that these methods be incorporated into routine analyses of public health surveillance data to highlight continuing social disparities in premature mortality.

Adolescent↗
PubMed1996

FISH digital imaging microscopy in mosquito genomics.

The yellow fever mosquito, Aedes aegypti, transmits pathogens that affect both humans and livestock, and has been the focus of extensive research to identify genetic loci that may be useful in control strategies. Fluorescence in situ hybridization (FISH) and digital imaging microscopy have provided a rapid mechanism to populate the physical map with probes derived from genetic markers, cDNAs and recombinant genomic libraries. When the physical and genetic linkage maps are aligned, map-based cloning will allow the rapid isolation of target genomic sequences. The strategy of FISH mapping and the results of initial hybridization studies are reviewed here by Martin Ferguson, Susan Brown and Dennis Knudson. An Ae. aegypti-specific genomic database, which collates data from mapping studies, sequences, references and other relevant information, is also discussed.

Journal Article↗
PubMed1996

Neural dynamics in cortex-striatum co-cultures--II. Spatiotemporal characteristics of neuronal activity.

Neural dynamics in organotypic cortex-striatum co-cultures grown for three to six weeks under conditions of dopamine deficiency are described. Single neuron activities were recorded intra- and extracellularly, and spatiotemporal spreading of population activity was mapped using voltage-sensitive dyes. The temporal properties of spike firing were characterized by interspike interval histograms, autocorrelation and crosscorrelation. Cortical pyramidal neurons (n = 40) showed irregular firing with a weak tendency to burst or to oscillate. Crosscorrelations revealed strong near-coincident firing and synaptic interactions. Disinhibition was a notable feature in a strongly firing cortical interneuron. Cortical activity spread in the co-culture, thus inducing an overall, homogeneous depolarization in the striatal part. Striatal cells were divided into principal cells and type I and II secondary cells. Principal cells (n = 40) were similar to those reported previously in vivo. Spiking activity ranged from irregular spiking at very low rates to episodic bursting, with an average burst duration of 1 s. Interspike intervals were single-peaked. Intracellular recordings revealed characteristic, long-lasting subthreshold depolarizations ("enabled state") that were shortened by local muscarinic receptor blockade. During prolonged time periods in the "enabled state", locally applied bicuculline induced strong firing in most principal neurons. Striatal secondary type I neurons (n = 25) showed high spiking rates, single- and double-peaked interval histograms and low-threshold, short-lasting stereotyped bursting activity and occasional rhythmic bursting. The firing of these neurons was increased by bicuculline. Crosscorrelations showed synchronization of these cells with principal cell activity. Secondary type II neurons (n = 15) revealed tonic, irregular firing patterns similar to cortical neurons, except with occasional firing in doublet spikes. We conclude that under conditions of dopamine deficiency in corticostriatal co-cultures (i) the cortex induces the "enabled" state and typical bursting mode in striatal principal neurons; (ii) principal neurons are strongly inhibited during the "enabled" state; (iii) muscarinic activity, presumably from tonically active striatal cholinergic interneurons, stabilizes the "enabled" state; (iv) striatal GABAergic interneurons receives synaptic inhibition and take part in synchronized activity among striatal principal cells. Our results favor the view of the striatum as a lateral inhibition network.

Animals↗