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PubMed1999

Segregation analysis of tetra- and pentanucleotide short tandem repeat polymorphisms: deviation from Mendelian expectations.

Short tandem repeat (STR) polymorphisms are powerful tools for linkage studies, chromosome mapping and population analysis. The instability of these microsatellite regions is a prevailing event in several tumors and human genetic diseases and, despite various reports associating instability-related genes and meiosis control, the dynamics of these STR regions in normal cells/individuals has frequently been disregarded. Having previously assayed somatic instability in gastric cancer for some tetra- and pentanucleotide STRs and given the increased application of this type of marker for routine forensic expertise, we report the results of an extensive analysis of segregation in nuclear families of a normal population for the same loci. No mutations were detected in 2374 parent/offspring allelic transfers at TH01, TPO, VWA31/A, MBPB, and CD4 STR loci. Nonsignificant differences were found between gene frequencies of parental and offspring generations. However, the segregation analysis revealed significant deviation from Mendelian expectations for: VWA31/A locus - alleles 19, 17 and 14 and TH01 locus - allele 6. In particular, parental meiosis strongly favored specific allele transmission, depending upon the sex of the offspring. Specific mating types are apparently responsible for most of these abnormal segregations. These results suggest selective factors working either at the gametic or zygotic levels.

Female↗
PubMed2005

Optical imaging of functional organization of V1 and V2 in marmoset visual cortex.

Using optical imaging of intrinsic cortical signals, we examined the functional organization of visual cortical areas V1 and V2 of the marmoset (Callithrix jacchus). Previous studies have reported that adult marmosets do not have ocular dominance columns (ODCs); however, recent studies have called this into question. Using optical imaging methods, we examined whether ODCs could be detected in adult marmosets. We found evidence for functional ODCs in some marmosets but not in others. The activation patterns, when present, were relatively weak and appeared as a mosaic of irregular bands or islands. Consistent with studies in other New World monkeys, these data suggest the presence of ODC variability within the marmoset population. Orientation maps in V1 revealed iso-orientation domains organized in semicontinuous bands oriented orthogonal to the V1/V2 border, a pattern unlike that in Macaque monkey. The presence of directional preference maps in V1 was also suggested. In V2, similar to V2 in Macaque monkeys, stripe-like regions of orientation selectivity overlay the pale cytochrome oxidase regions of V2; zones not selective for orientation overlay the cytochrome thin stripes. However, unlike Macaques, we did not observe clear evidence for orientation maps overlying thick cytochrome oxidase stripes. In sum, our data suggest that significant organizational differences exist between the organization of V1 and V2 in the marmoset and that of Old World primates. Implications for the establishment of functional ocular dominance columns, the coestablishment of multiple featural maps, and cortical magnification factors are discussed.

Animals↗
PubMed1995

The potential of microsatellites for hybridization- and polymerase chain reaction-based DNA fingerprinting of chickpea (Cicer arietinum L.) and related species.

The genetic variability in agronomically important chickpea accessions (Cicer arietinum L.) as detected by single-locus restriction fragment length polymorphism (RFLP) probes, random amplified polymorphic DNA (RAPD) and isoenzyme markers, is rather low. Recently, highly polymorphic microsatellites became the markers of choice for linkage mapping and population studies. We are currently following two main strategies to exploit the variability of microsatellites and adjacent sequences for genetic studies in chickpea. (i) In an approach referred to as oligonucleotide fingerprinting, microsatellite-complementary oligonucleotides were employed as multilocus probes for in-gel hybridization. A total of 38 different probes representing di-, tri- and tetranucleotide repeats were used to analyze variability between and within four accessions of C. arietinum. Hybridization signals were obtained with 35 probes. While the abundance and level of polymorphism of different target sequences varied considerably, distinct, intraspecifically informative banding patterns were obtained with the majority of probes and all restriction enzymes tested. No obvious correlation existed between abundance, fingerprint quality, and sequence characteristics of a particular motif. (ii) In a recently developed strategy called microsatellite primed polymerase chain reaction (MP-PCR), microsatellite-complementary oligonucleotides serve as single PCR primers for genomic DNA templates. We tested the general applicability of MP-PCR by amplifying DNA samples from tomato, chickpea and two related annual Cicer species with a variety of di-, tri- and tetranucleotide repeat primers. Most but not all primers generated distinct fingerprint-like banding patterns after agarose gel electrophoresis and ethidium bromide staining of the amplification products. Since the method proved to be sensitive to reaction conditions in a way similar to RAPD analysis, we increased the PCR specificity by the introduction of a modified "touch-down" protocol. In chickpea, touch-down MP-PCR generated highly reproducible banding patterns which predominantly revealed interspecific polymorphisms. The potential of different microsatellite-based strategies for genome analysis in chickpea is discussed.

Base Sequence↗
PubMed1996

Evaluation of the ALF DNA sequencer for high-speed sizing of short tandem repeat alleles.

DNA typing of short tandem repeat (STR) loci with automated real-time analysis of the fluorescent polymerase chain reaction (PCR) products has given forensic DNA analysis a new dimension. In the present work, the ALF DNA sequencer was evaluated for automated size determination of tetra-nucleotide STRs at high speed. Short gel plates, with a well-to-laser distance of 10 cm, allowed for the analysis of four STR loci (HUMvWF, HUMTH01, D21S11 and HPRT) in one gel lane in less than 75 min. Allele size determination was done with two external allelic ladders for each locus. Lane-to-lane variations were overcome by the inclusion in each lane of two fluorescent PCR products of constant size (123 and 375 bp) that migrated below and above the multiplex of the four STR loci. The accuracy of sizing and allele detection within and between different gels was high (99.89%) for all four STR systems investigated and the gels could be reloaded without a decrease in accuracy of the allele size estimation. This way, the throughput of the system was increased, which is of interest for linkage studies, gene mapping, and population diversity studies.

Alleles↗
PubMed2004

Photoreceptor topography in the duplex retina of the paddlefish (Polyodon spathula).

Retinal whole-mount preparations from the eyes of the North American paddlefish, Polyodon spathula, were examined with a combination of bright field and differential interference contrast microscopy. The entire retina was mapped and population counts of rod and cone photoreceptors were made at regular intervals throughout the retina. The retina is dominated by rods, but a significant percentage (ca. 38%) of the photoreceptors are cones. Mean cone packing density for the entire retina is 6,402+/-1,216 cones/mm2. There is a small (16%) but statistically significant difference between cone packing density in the dorsal retina (6,674+/-1,168 cones/mm2) and the ventral retina (5,745+/-1,076 cones/mm2). There is no region of unusually high cone concentration that might be construed as a fovea or a visual streak. Mean rod packing density for the entire retina is 10,271+/-1,205 rods/mm2. Except in the far periphery, where rods are less numerous, the density of rods is fairly uniform throughout the retina. The data are discussed with regard to paddlefish habitat and behavior.

Analysis of Variance↗
PubMed2006

Population-based analysis of lymphatic mapping and sentinel lymphadenectomy utilization for intermediate thickness melanoma.

BACKGROUND AND OBJECTIVES: Lymphatic mapping and sentinel lymphadenectomy (LM/SL) is the nodal staging procedure of choice for patients with intermediate thickness melanoma. We hypothesize that a significant portion of these patients are not undergoing LM/SL. We explore factors that influence use of LM/SL. METHODS: Analysis was performed of all incident cases of invasive cutaneous melanoma in North Carolina between January 1, 1999 and December 31, 2001. RESULTS: Three thousand four hundred and thirty-six cases of melanoma were reported for 1999-2001. Two hundred and seventy-three cases (8%) were excluded due to metastases. Nine hundred and sixteen cases (29%) were excluded because the T classification was not reported. Of the remaining cases, 1,242 (55%) were intermediate thickness (T2-3); 48% (596/1,242) underwent LM/SL. Subjects >or=60 years old were less likely to receive LM/SL than subjects <60 years (39% vs. 55.4%, P < 0.001). Subjects with head/neck primary tumors were less likely to receive LM/SL than other subjects (33% vs. 51%, P < 0.001). Subjects with T3 tumors were more likely to receive LM/SL than those with T2 tumors (54% vs. 42%, P < 0.001). CONCLUSIONS: Half of all patients with intermediate thickness melanoma in North Carolina do not receive LM/SL. Use of LM/SL varies by patient age and primary tumor site. Further investigation is warranted to explore these differences.

Adult↗
PubMed1995

Identification of two opaque2 modifier loci in quality protein maize.

Genetic modifiers of opaque2 convert the soft, starchy endosperm of opaque2 maize mutants to a hard, vitreous phenotype, while maintaining the enhanced lysine content of the grain. Genetic analysis of F2 segregating seeds from crosses of opaque2 by modified opaque2 genotypes indicated that the modifiers are complex traits that act codominantly. We developed two different segregating F2 populations and mapped the modifier loci by restriction fragment length polymorphism (RFLP) analysis. A relationship was found between formation of vitreous endosperm and the locus encoding the gamma-zein storage protein, which maps near the centromere of chromosome 7. Endosperm modification was consistently associated with the presence of two rather than one gamma-zein gene at this locus. A second modifier locus was mapped near the telomere of chromosome 7L.

Alleles↗
PubMed1995

Characterization of cDNA clones containing CCA trinucleotide repeats derived from human brain.

Expansion mutation is the cause of eight neuropsychiatric disorders. Thus far each disease is the result of expansion of a C-G rich trinucleotide repeat that is polymorphic for length in the general population. We now report the identification of seven novel cDNA clones with CCA or equivalent trinucleotide repeats obtained by screening a human frontal cortex cDNA library. The repeat lengths of two clones, CCA11 (linked to D20S101, expressed in human brain as a 3.2 kb message) and CCA38 (linked to D5S404), are highly polymorphic in a normal human population. CCA54, mapped to chromosome 19, appears to correspond to a portion of the human gene encoding the alpha 1 subunit of a P-type calcium channel. Expansion mutations at these loci should be considered as possible candidates in evaluating the genetic etiologies of diseases linked to chromosomes 5, 19, and 20.

Base Sequence↗
PubMed2006

Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers.

The archipelago of Indonesia has a long history of rice production across a broad range of rice-growing environments resulting in a diverse array of local Indonesian rice varieties. Although some have been incorporated into modern breeding programs, the vast majority of these landraces remain untapped. To better understand this rich source of genetic diversity we have characterized 330 rice accessions, including 246 Indonesian landraces and 63 Indonesian improved cultivars, using 30 fluorescently-labeled microsatellite markers. The landraces were selected across 21 provinces and include representatives of the classical subpopulations of cere, bulu, and gundil rices. A total of 394 alleles were detected at the 30 simple sequence repeat loci, with an average number of 13 alleles per locus across all accessions, and an average polymorphism information content value of 0.66. Genetic diversity analysis characterized the Indonesian landraces as 68% indica and 32% tropical japonica, with an indica gene diversity of 0.53 and a tropical japonica gene diversity of 0.56, and a Fst of 0.38 between the two groups. All of the improved varieties sampled were indica, and had an average gene diversity of 0.46. A set of high quality Indonesian varieties, including Rojolele, formed a separate cluster within the tropical japonicas. This germplasm presents a valuable source of diversity for future breeding and association mapping efforts.

Chromosomes, Plant↗
PubMed2002

Evidence of gene conversion events between paralogous sequences produced by tetraploidization in Salmoninae fish.

We investigated the occurrence of gene conversions between paralogous sequences of Salmoninae derived from ancestral tetraploidization and their effect on the evolutionary history of DNA sequences. A microsatellite with long flanking regions (750 bp) including both coding and noncoding sequences was analyzed. Microsatellite size polymorphism was used to detect the alleles of both paralogous counterparts and infer linkage arrangement between loci. DNA sequencing of seven Salmoninae species revealed that paralogous sequences were highly differentiated within species, especially for noncoding regions. Ten gene conversion events between paralogous sequences were inferred. While these events appears to have homogenized regions of otherwise highly differential paralogous sequences, they amplified the differentiation among orthologous sequences. Their effects were larger on coding than on noncoding regions. As a consequence, noncoding sequences grouped by orthologous lineages in phylogenetic trees, whereas coding regions grouped by taxa. Based upon these results, we present a model showing how gene conversion events may also result in the PCR amplification of nonorthologous sequences in different taxa, with obvious complications for phylogenetic inferences, comparative mapping, and population genetic studies.

Animals↗
PubMed1989

A skin test survey of valley fever in Tijuana, Mexico.

Results of a study of the prevalence of valley fever among 1128 residents of Tijuana, Baja California are presented. Children from primary and middle schools (n = 497) and adults from technical institutes and maquiladoras (assembly plants) were tested for reaction to both spherulin and coccidioidin during 1985-1986, and they completed a questionnaire containing 23 variables on their socio-environment. Place of residence was mapped. The population sampled is largely middle class. Discriminant analysis indicates the distribution of positive cases is not clustered, nor can it be correlated with geomorphic factors such as mesa tops, canyons, or valley bottoms.

Adolescent↗
PubMed2006

Long-lived memory T lymphocyte responses against SARS coronavirus nucleocapsid protein in SARS-recovered patients.

The nucleocapsid (N) protein is a structural component of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and can induce antibody responses in SARS patients during infection. However, it is not known whether SARS-CoV N protein can induce a long persistence of memory T-cell response in human. In this study, we found that peripheral blood mononuclear cells (PBMCs) from fully recovered SARS individuals rapidly produced IFN-gamma and IL-2 following stimulation with a pool of overlapping peptides that cover the entire N protein sequence. The N-specific IFN-gamma(+)CD4(+) T cells were mainly composed of CD45RA(-)CCR7(+)CD62L(-) cells, whereas IFN-gamma(+)CD8(+) memory T cells were mostly contained within CD45RA(+)CCR7(-)CD62L(-) cell population. Epitope mapping study indicated that a cluster of overlapping peptides located in the C-terminal region (amino acids [aa] 331 to 362) of N protein contained at least two different T-cell epitopes. The results indicated that human memory T-cell responses specific for SARS-CoV N protein could persist for 2 years in the absence of antigen, which would be a valuable for the design of effective vaccines against SARS-CoV and for basic studies of human T-cell memory.

CD4-Positive T-Lymphocytes↗
PubMed2000

Postnatal changes in Fos-like immunoreactivity evoked by hypoxia in the rat brainstem and hypothalamus.

We have recently used Fos expression in adult rats to map neuronal populations activated in the brainstem and hypothalamus during the acute ventilatory response to moderate hypoxia (O(2) 11%). Although present at birth, this response evolves postnatally. The present investigation aimed at a better understanding of these maturational processes by delineating structures that might functionally develop after birth. The developmental pattern Fos expression evoked by hypoxia was analysed in rats aged from 0 to 26 postnatal days. The numbers of Fos positive neurons markedly increased with the age in the medullary areas related to respiratory control during the 2 first postnatal weeks. Thereafter, the response plateaued in the nucleus tractus solitarius and attenuated in the ventral medulla. In the upper brainstem (parabrachial area, central grey) and the hypothalamus (posterior and dorsomedial nuclei, ventral zone), Fos response to hypoxia was absent or weak at birth and increased until late development. The significance of the development of evoked Fos expression in these rostral sites is discussed together with their possible contribution to the maturation of O(2)-sensitive chemoreflex pathways.

Age Factors↗
PubMed2000

Brainstem and hypothalamic areas involved in respiratory chemoreflexes: a Fos study in adult rats.

The adaptation to hypoxia and hypercapnia requires the activation of several anatomical structures along the neuraxis. In this study, using Fos immunoreactivity, we sought to map neuronal populations involved in chemoreflex networks activated during the responses to moderate hypoxia (O(2) 11%), and hypercapnia (CO(2) 5%) in the brainstem and the hypothalamus of the rat. In the medulla, hypoxia elicited marked and significant staining in the nucleus of the solitary tract (NTS), and in parapyramidal neurons located near the ventral surface, whereas hypercapnia evoked significantly c-fos only near the ventral surface in paraolivar neurons. In contrast, within pontine and suprapontine structures, both hypoxia and hypercapnia evoked similarly Fos immunoreactivity in the lateral parabrachialis area, the central grey, the caudal hypothalamus (dorsomedial and posterior hypothalamic nuclei), and in a ventro-lateral hypothalamic area, extending from the rostral limit of the mammillary nuclei to the retrochiasmatic area. More rostrally, labelling was observed in the paraventricular nucleus of the hypothalamus in response to hypercapnia, and in the supraoptic nucleus in response to hypoxia. These results support the hypothesis that chemoreflexes pathways are not only restricted to medulla and pons but also involved mesencephalic and hypothalamic regions. The parabrachialis area and the central grey may be key relays between caudal and ventral hypothalamic neurons, and medullary neurons involved in the response to hypoxia and hypercapnia.

Animals↗
PubMed2002

The tau H1 haplotype is associated with Parkinson's disease in the Norwegian population.

We investigated the association of Parkinson's disease (PD) with tau gene H1 haplotypes in the Norwegian population. In a sample of 96 unrelated PD cases and 68 control subjects, we observed an increased risk of PD for persons with the tau H1 haplotype (odds ratio=5.52; 95% confidence interval: 2.64-11.10; P=2.17x10(-6)). Findings provide evidence that tau participates in the PD pathogenic process and demonstrate the value of isolated populations in mapping complex traits.

Adult↗
PubMed2001

Two-locus identity probabilities and identity disequilibrium in a partially selfing subdivided population.

Measures of association of genes at different loci (linkage disequilibrium) are widely used to determine whether the structure of natural populations is clonal or not, to map genes from population data, or to test for the homogeneity of response of molecular markers to background selection, for example. However, the usual definitions of parameters for gametic associations may not be suitable for all these purposes. In this paper, we derive the recursion equations for one- and two-locus identity probabilities in an infinite island model. We study the role of drift, gene flow, partial selfing and mutation model on the expected association of genes across loci. We define the 'within-subpopulation identity disequilibrium' as the difference between the joint two-locus probability of identity in state and the expected product of one-locus identity probabilities. We evaluate this parameter as a function of recombination rate, effective size, gene flow and selfing rate. Within-subpopulation identity disequilibrium attains maximum values for intermediate immigration rates, whatever the selfing rate. Moreover, identity disequilibrium may be very small, even for high selfing rates. We discuss the implications of these findings for the analysis of data from natural populations.

Alleles↗
PubMed2002

Transitions in self-reported musculoskeletal pain and interference with activities among newspaper workers.

Active surveillance of symptoms and disability due to musculoskeletal disorders (MSD) in working populations can map individual transitions in symptom intensity or disability level. Using repeat surveys, this study examined if aetiological risk factors for new symptoms or disability, measured by interference with activities, were similar to prognostic risk factors for subsequent outcomes of symptoms and disability. This paper reports on 379 Toronto newspaper workers who completed questionnaires in 1996 and 1997. Questions on pain/discomfort during the last year, episode frequency and duration formed the basis for constructing three mutually exclusive symptom levels: noncases (Level 1); mild cases (Level 2); and more severe or frequent pain cases (Level 3). A similar construction of overall interference levels was based on the frequency with which musculoskeletal pain/discomfort interfered with daily, recreational, social and family activities, or ability to do one's job during the previous 12 months. The last was also examined as work interference alone. Levels of symptoms were cross-tabulated by overall and work interference at the two time points and Markov models of transitions between states were formulated. Results indicate that period prevalence of symptoms and overall interference increased between phases, though only significantly for symptoms (Levels 2 and 3, 65.7-70.7%, p = 0.04), while work interference was unchanged (17.9-17.0%). Equivalent proportions of workers improved as worsened in symptoms (21.1 and 22.4%, respectively), overall interference (16.7 and 17.8%), and work interference (7.4 and 6.6%). The only significant predictor for those without work interference at time one was job tenure, which was protective against work interference (Odds Ratio (OR) 1.06, 95% Confidence Interval (CI) 1.01-1.12). Among those who had more severe/frequent symptoms at time one, lack of improvement over time was predicted by longer job tenure (OR = 0.92 per year, CI: 0.87-0.97), greater psychological demands of work (OR = 0.65 per point, CI: 0.51-0.84) and marginally by greater upper extremity disability score. At time one, women with work interference were more likely to have persistent interference at time two (OR = 7.22, CI: 1.57-33.20). Suggestive findings included opposite effects of social support at work: reduced risk of development of new symptoms but increased risk of persistence at the highest symptom level.

Activities of Daily Living↗
PubMed2006

A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep.

Texel sheep are renowned for their exceptional meatiness. To identify the genes underlying this economically important feature, we performed a whole-genome scan in a Romanov x Texel F2 population. We mapped a quantitative trait locus with a major effect on muscle mass to chromosome 2 and subsequently fine-mapped it to a chromosome interval encompassing the myostatin (GDF8) gene. We herein demonstrate that the GDF8 allele of Texel sheep is characterized by a G to A transition in the 3' UTR that creates a target site for mir1 and mir206, microRNAs (miRNAs) that are highly expressed in skeletal muscle. This causes translational inhibition of the myostatin gene and hence contributes to the muscular hypertrophy of Texel sheep. Analysis of SNP databases for humans and mice demonstrates that mutations creating or destroying putative miRNA target sites are abundant and might be important effectors of phenotypic variation.

Animals↗