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PubMed1994

Partial sequencing and mapping of clones from two maize cDNA libraries.

As one component of a maize genome project, we report the analysis of a number of randomly selected cDNAs, by a combination of measuring mRNA expression, 'single-pass' sequencing (SPS), and genome mapping. Etiolated seedling (490) and membrane-free polysomal endosperm cDNA clones (576) were evaluated for their transcription levels by hybridizing with a probe prepared from total mRNA and categorized as corresponding to abundantly or rarely expressed mRNAs and as either constitutive or tissue-specific. A total 313 clones from the two libraries were submitted to 'single-pass' sequencing from the presumed 5' end of the mRNA and the nucleotide sequence compared with the GenBank database. About 61% of the clones showed no significant similarities within GenBank, 14% of the clones exhibited a high degree of similarity, while the remaining 25% exhibited a lesser degree of similarity. The chromosomal location of more than 300 clones was determined by RFLP mapping using standard populations. The results demonstrate that a combination of analyses provides synergistic information in eventually deducing the actual function of these types of clones.

Chromosomes↗
PubMed1992

Diversity in tachykinin-like peptides in the insect brain.

When testing a large number of antisera against tachykinins of various vertebrates and one insect (the cockroach Leucophaea maderae) we found three distinct populations of tachykinin-immunoreactive neurons in the blowfly: (1) one recognized by antisera against substance P, (2) another by antisera against the frog peptide kassinin and (3) a third with antisera raised against the cockroach peptide Leucokinin I. As a comparison tests on the cockroach Leucophaea showed that only antisera against neurokinin A (NKA) and leucokinin I gave immunostaining, RIA and immunocytochemical displacement tests demonstrated that the each of the three listed types of antisera was specific for the corresponding antigenic peptide and showed virtually no cross reactivity with the other tachykinin peptides. By immunocytochemistry we have mapped the three populations of tachykinin-immunoreactive neurons in the blowfly CNS. Two constitute unique sets of interneurons that were previously not detected with other antisera, the third, recognized by antisera against substance P, is a subpopulation of the FMRFamide immunoreactive neurons. The leucokinin immunoreactive material in the blowfly seems to be chemically different from that in Leucophaea and also the sets of neurons immunolabeled in the two insect species are to some extent different. The preliminary results presented here indicate the presence of multiple forms of tachykinin-like peptides in the blowfly and that these are distinct from those in the cockroach. From the immunocytochemistry it appears that the insect tachykinins may be involved in a variety of regulatory functions in the CNS and in some cases possibly act as neurohormones.

Amino Acid Sequence↗
PubMedDate not supplied

Recent trends in receptor analysis techniques and instrumentation.

Receptor autoradiography allows visualization of receptor binding sites at the regional or light microscopic level. Receptor autoradiography is a mature methodology, in widespread use. It is also a dynamic and expanding methodology, benefiting constantly from the introduction of new techniques and instrumentation. In particular, receptor autoradiography has taken advantage of image analysis instrumentation to provide efficient spatial mapping of receptor populations and their pharmacological characteristics. A major contribution to the understanding of receptors has come from the recent cloning of the genes coding for many of these receptors. This has allowed the use of in situ hybridization to demonstrate the cells expressing mRNA coding for specific receptor subtypes. The result is that many receptor populations, previously thought to be homogeneous, are shown to be composed of several subtypes. As a consequence, the distribution of many receptors requires re-examination, which is aided by the development of new and more selective ligands. With the incorporation of techniques from molecular biology into receptor autoradiography, the demands upon image analysis instruments have expanded. Over the past decade, densitometric image analysers have attained a high level of sophistication for classical receptor autoradiography. However, to serve the needs of today's receptor laboratory, an image analyser must be equally capable in regional densitometry, in counting and spatial mapping of grain and/or cell locations at the microscopic level, and in analysing electrophoresis gels. Advances in image analysis hardware and software are keeping pace with the requirements of receptor laboratories.

Animals↗
PubMed2001

Autoantigen glycoprotein 70 expression is regulated by a single locus, which acts as a checkpoint for pathogenic anti-glycoprotein 70 autoantibody production and hence for the corresponding development of severe nephritis, in lupus-prone PXSB mice.

Retroviral envelope glycoprotein gp70 is present in the sera of immunologically normal and autoimmune-prone strains of mice. However, only lupus-prone mice spontaneously develop gp70-anti-gp70 immune complexes (gp70IC), and these have been implicated in the development of nephritis. We investigated the genetic factors that affect the production of both free serum gp70 and gp70IC in the lupus-prone BXSB mouse strain by analyzing (BXSB x (C57BL/10 x BXSB)F(1))- and (C57BL/10 x (C57BL/10 x BXSB)F(1))-backcrossed male mice. Production of gp70 mapped to a single major locus located on chromosome 13 (Bxs6) with a maximum log likelihood of the odds of 36.7 (p = 1.6 x 10(-38)). The level of gp70IC was highly dependent on Bxs6-related gp70 production, and high titer autoantibody production only occurred when serum gp70 levels were greater than a threshold value of approximately 4.0 microg/ml. The subdivision of the (BXSB x (C57BL/10 x BXSB)F(1))-backcrossed mice into those homozygous or heterozygous for Bxs6 enabled a remarkable association to be observed between high levels of gp70IC and severe nephritis in the Bxs6 homozygote population. A further mapping study in these two subgroups identified a previously unrecognized interval associated with the production of autoantibodies.

Animals↗
PubMed2005

Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases.

Sugarcane (Saccharum spp.) is a clonally propagated outcrossing polyploid crop of great importance in tropical agriculture. Up to now, all sugarcane genetic maps had been developed using either full-sib progenies derived from interspecific crosses or from selfing, both approaches not directly adopted in conventional breeding. We have developed a single integrated genetic map using a population derived from a cross between two pre-commercial cultivars ('SP80-180' x 'SP80-4966') using a novel approach based on the simultaneous maximum-likelihood estimation of linkage and linkage phases method specially designed for outcrossing species. From a total of 1,118 single-dose markers (RFLP, SSR and AFLP) identified, 39% derived from a testcross configuration between the parents segregating in a 1:1 fashion, while 61% segregated 3:1, representing heterozygous markers in both parents with the same genotypes. The markers segregating 3:1 were used to establish linkage between the testcross markers. The final map comprised of 357 linked markers, including 57 RFLPs, 64 SSRs and 236 AFLPs that were assigned to 131 co-segregation groups, considering a LOD score of 5, and a recombination fraction of 37.5 cM with map distances estimated by Kosambi function. The co-segregation groups represented a total map length of 2,602.4 cM, with a marker density of 7.3 cM. When the same data were analyzed using JoinMap software, only 217 linked markers were assigned to 98 co-segregation groups, spanning 1,340 cM, with a marker density of 6.2 cM. The maximum-likelihood approach reduced the number of unlinked markers to 761 (68.0%), compared to 901 (80.5%) using JoinMap. All the co-segregation groups obtained using JoinMap were present in the map constructed based on the maximum-likelihood method. Differences on the marker order within the co-segregation groups were observed between the two maps. Based on RFLP and SSR markers, 42 of the 131 co-segregation groups were assembled into 12 putative homology groups. Overall, the simultaneous maximum-likelihood estimation of linkage and linkage phases was more efficient than the method used by JoinMap to generate an integrated genetic map of sugarcane.

Chromosome Mapping↗
PubMed2002

Maximum a posteriori Bayesian estimation of oral cyclosporin pharmacokinetics in patients with stable renal transplants.

OBJECTIVE: To develop a maximum a posteriori probability (MAP) Bayesian estimator for the pharmacokinetics of oral cyclosporin, based on only three timepoints, and evaluate its performance with respect to a full-profile nonlinear regression approach. PATIENTS: 20 adult patients with stable renal transplants given orally administered microemulsified cyclosporin and mycophenolate. METHODS: Cyclosporin was assayed by liquid chromatography-mass spectrometry. Nonlinear regression and MAP Bayesian estimation were performed using a home-made program and a previously designed pharmacokinetic model including an S-shaped absorption profile described by a gamma distribution. OUTCOME MEASURES AND RESULTS: MAP Bayesian estimation using the best limited sampling strategy (before administration, and 1 and 3 hours after administration) was compared with nonlinear regression (taken as the reference method) for the prediction of the different pharmacokinetic parameters and exposure indices. Median relative prediction error was -0.49 and -3.42% for area under the concentration-time curve over the administration interval of 12 hours (AUC12) and estimated peak drug concentration (Cmax), respectively (nonsignificant). Relative precision was 2.00 and 4.32%, and correlation coefficient (r) was 0.985 and 0.955, for AUC12 and Cmax, respectively. CONCLUSION: This paper reports preliminary results in a stable renal transplant patient population, showing that MAP Bayesian estimation can allow accurate prediction of AUC12 and Cmax with only three samples (0, 1 and 3 hours). Although these results require confirmation by further studies in other clinical settings, using other drug combinations, other analytical methods and commercially available pharmacokinetic software, the method seems promising as a tool for the therapeutic drug monitoring of cyclosporin in clinical practice or for exposure-controlled studies.

Administration, Oral↗
PubMed1999

Linkage mapping of rat chromosome 5 markers generated from chromosome-specific libraries.

Seventy-six novel microsatellite markers with various simple sequence repeat (SSR) motifs are reported in this paper. They were generated on the basis of non-radioactive library screening procedures from flow-sorted rat Chromosome (Chr) 5-specific DNA, and were mapped in three rat backcross populations. Fifty-four of these markers mapped to Chr 5, while the other 22 mapped to other chromosomes of the rat genome. The marker D3Uwm8 is a new microsatellite marker for the rat syndecan 4 (ryudocan) gene. A genotyping protocol based on agarose gel electrophoresis is also provided in this paper.

Animals↗
PubMed2001

[Microsatellite marker analysis of a soybean recombinant inbred line NJRIKY].

The prerequisite of genomic research such as genetic mapping is construction of a suitable segregating population and its reasonable evaluation before use. A recombinant inbred line (RILs), NJRIKY, was constructed through a cross between Kefeng 1 and Nannong 1138-2. The present study was focused on evaluation of genetic structure of the RILs through the simple sequence repeats (SSRs) analysis. A total number of 138 pairs of SSRs primers covering the whole soybean genome were randomly selected for polymorphic analysis between two parents. 86 pairs of which were polymorphic and polymorphic rate is up to 62.32%. 90 polymorphic loci were found. Further analysis with polymorphic SSRs loci on the sampled lines indicated that not only segregation of most SSRs loci conformed to the ratio of 1:1, but also almost each sampled line tended to homozyge. The distribution of genotypic composition was normal. The population is ideal for genetic mapping and other genomic research.

Microsatellite Repeats↗
PubMed2004

Quantitative trait loci affecting plant regeneration from protoplasts of Brassica oleracea.

Quantitative trait loci (QTLs) controlling the plant-regeneration ability of Brassica oleracea protoplasts were mapped in a population of 128 F(2) plants derived from a cross between the high-responding, rapid-cycling line and a low-responding, broccoli breeding line of B. oleracea. A modified bulked segregant analysis with AFLP markers identified two QTLs for plant regeneration. In a multiple regression analysis, the two QTLs explained 83% of the total genetic variation for regeneration recorded 15 weeks after initial transfer of microcalli to regeneration medium. Both QTLs showed additive effects, and the alleles contributing to the high regeneration frequencies were derived from the high-responding, rapid-cycling line. Using microsatellites with known location, the two QTLs were mapped to linkage groups O2 and O9 on the map published by Sebastian et al. [(2000) Theor Appl Genet 100:75-81] or to chromosomes C8 and C7 on the map published by Saal et al. [(2001) Theor Appl Genet 102:695-699]. QTLs for the early flowering trait of the rapid-cycling parent have previously been mapped to the same two linkage groups. Association between flowering time and regeneration ability was, however, not found in the present material, indicating that plant-regeneration ability can be transferred between cultivars independently of the early flowering trait. The detection of two major QTLs for plant regeneration in B. oleracea may provide the initial step towards the identification of markers suitable for marker-assisted selection of regeneration ability.

Brassica↗
PubMed1996

A retrotransposon-like sequence linked to the S-locus of Nicotiana alata is expressed in styles in response to touch.

We have identified a family of repetitive sequences in the genome of Nicotiana alata named Tna1 (Transposon of N. alata). The first element we characterised was a genomic clone for the N. alata s6-ribonuclease (S6-RNase), a gene required for self-incompatibility in this species. The DNA sequence of this element resembles the integrase domain of retrotransposons of the gypsy class and is most similar to a retrotransposon from Lilium henryi. A transcript present in N.alata styles (self-incompatibility genotype S6S6) hybridized to Tna1 and accumulated in the style following either pollination or touching. This transcript was cloned from a cDNA library and was encoded by second, partial Tna1 elements. Neither the transcribed sequence nor the original Tna1 element contain an open reading frame or is likely to be able to transpose. The second element was mapped using a population of N.alata plants segregating for alleles of the self-incompatibility locus and is closely linked to the S6-allele. The Tna1 element is present in a number of Nicotiana species and appears to have been active at least twice during the evolution of this genus.

Amino Acid Sequence↗
PubMed2003

Quantitative trait loci that influence the expression of guarding and stinging behaviors of individual honey bees.

This study was conducted to test for the effect of three stinging behaviors QTLs (sting-1, sting-2 and sting-3) on the expression of guarding and stinging behavior of individual honey bees, and to determine if results of defensive behavior QTLs found in studies with Africanized honey bees could be extended to other populations of bees. Samples of guards, stingers, foragers and nurse bees were taken from two backcross colonies derived from a defensive colony and a gentle colony. The genotype of each bee for both types of colonies was determined for two sequence tagged site (STS) markers linked to sting-1 and for another two STSs, one linked to sting-2 and one linked to sting-3. Results showed that sting-1 had an effect on the expression of both stinging and guarding behaviors, sting-2 and sting-3 influenced the expression of guarding behavior. These results indicate that division of labor is influenced by specific QTLs. Results also show that QTLs mapped in a population of Africanized honey bees using colony level phenotypes also influenced the expression of guarding and stinging behavior of individual bees of other populations.

Aggression↗
PubMed2003

Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC.

Detailed knowledge of linkage disequilibrium (LD) is regarded as a prerequisite for population-based disease gene mapping. Variable patterns across the human genome are now recognized, both between regions and populations. Here, we demonstrate that LD may also vary within a genomic region in a haplotype-specific manner. In 864 Caucasian unrelated individuals, we describe haplotype-specific LD patterns across the human MHC by the construction of gene-specific allelic haplotypes at 25 loci between HLA-A and Tapasin. Strong and extensive LD is found across both common and rare haplotypes, suggesting that haplotype structure is influenced by factors other than genetic drift, including both selection and differential haplotype recombination. Knowledge of haplotype-specific LD in the HLA may explain the apparent discrepant data from previous studies of global LD, help delineate key areas in mapping HLA-associated diseases and, together with recombination data, provide valuable information about a population's demographic history and the selective pressures operating on it.

Alleles↗
PubMed2005

Cosmopolitan linkage disequilibrium maps.

Linkage maps have been invaluable for the positional cloning of many genes involved in severe human diseases. Standard genetic linkage maps have been constructed for this purpose from the Centre d'Etude du Polymorphisme Humain and other panels, and have been widely used. Now that attention has shifted towards identifying genes predisposing to common disorders using linkage disequilibrium (LD) and maps of single nucleotide polymorphisms (SNPs), it is of interest to consider a standard LD map which is somewhat analogous to the corresponding map for linkage. We have constructed and evaluated a cosmopolitan LD map by combining samples from a small number of populations using published data from a 10-megabase region on chromosome 20. In support of a pilot study, which examined a number of small genomic regions with a lower density of markers, we have found that a cosmopolitan map, which serves all populations when appropriately scaled, recovers 91 to 95 per cent of the information within population-specific maps. Recombination hot spots appear to have a dominant role in shaping patterns of LD. The success of the cosmopolitan map might be attributed to the co-localisation of hot spots in all populations. Although there must be finer scale differences between populations due to other processes (mutation, drift, selection), the results suggest that a whole-genome standard LD map would indeed be a useful resource for disease gene mapping.

Chromosome Mapping↗
PubMed2006

Construction of a genetic linkage map of Thlaspi caerulescens and quantitative trait loci analysis of zinc accumulation.

Zinc (Zn) hyperaccumulation seems to be a constitutive species-level trait in Thlaspi caerulescens. When compared under conditions of equal Zn availability, considerable variation in the degree of hyperaccumulation is observed among accessions originating from different soil types. This variation offers an excellent opportunity for further dissection of the genetics of this trait. A T. caerulescens intraspecific cross was made between a plant from a nonmetallicolous accession [Lellingen (LE)], characterized by relatively high Zn accumulation, and a plant from a calamine accession [La Calamine (LC)], characterized by relatively low Zn accumulation. Zinc accumulation in roots and shoots segregated in the F3 population. This population was used to construct an LE/LC amplified fragment length polymorphism (AFLP)-based genetic linkage map and to map quantitative trait loci (QTL) for Zn accumulation. Two QTL were identified for root Zn accumulation, with the trait-enhancing alleles being derived from each of the parents, and explaining 21.7 and 16.6% of the phenotypic variation observed in the mapping population. Future development of more markers, based on Arabidopsis orthologous genes localized in the QTL regions, will allow fine-mapping and map-based cloning of the genes underlying the QTL.

Chromosome Mapping↗
PubMedDate not supplied

Mapping the SF-12 to the EuroQol EQ-5D Index in a national US sample.

BACKGROUND: Preference scores for the Medical Outcomes Study (MOS) SF-12 would enable its use in cost-effectiveness analyses. Previous mapping studies of MOS instruments top reference-based instruments have not examined performance in national samples. PARTICIPANTS: 15,000 adults in the 2000 Medical Expenditure Panel Survey annual survey including the SF-12 and EQ-5D Index. METHODS: Regression of the EQ-5D Index scores onto the physical and mental component summary scores of the SF-12, testing 2nd-4th degree polynomial and spline models, including and excluding sociodemographics. RESULTS: A 2nd degree polynomial model explained 63% of the variance in EQ-5D scores, with robust internal and external validation. More complex mod-els explained minimally additional variance. Compared with EQ-5D valuations, prediction models overestimated the lowest health states (6% of the population). CONCLUSIONS: The mapped SF-12 yields usable preference-scaled scores, with some caution for the lowest health states.

Adult↗
PubMed2001

Highly optimized tolerance in epidemic models incorporating local optimization and regrowth.

In the context of a coupled map model of population dynamics, which includes the rapid spread of fatal epidemics, we investigate the consequences of two new features in highly optimized tolerance (HOT), a mechanism which describes how complexity arises in systems which are optimized for robust performance in the presence of a harsh external environment. Specifically, we (1) contrast global and local optimization criteria and (2) investigate the effects of time dependent regrowth. We find that both local and global optimization lead to HOT states, which may differ in their specific layouts, but share many qualitative features. Time dependent regrowth leads to HOT states which deviate from the optimal configurations in the corresponding static models in order to protect the system from slow (or impossible) regrowth which follows the largest losses and extinctions. While the associated map can exhibit complex, chaotic solutions, HOT states are confined to relatively simple dynamical regimes.

Journal Article↗
PubMed2003

Localization of a susceptibility gene for type 2 diabetes to chromosome 5q34-q35.2.

We report a genomewide linkage study of type 2 diabetes (T2D [MIM 125853]) in the Icelandic population. A list of type 2 diabetics was cross-matched with a computerized genealogical database clustering 763 type 2 diabetics into 227 families. The diabetic patients and their relatives were genotyped with 906 microsatellite markers. A nonparametric multipoint linkage analysis yielded linkage to 5q34-q35.2 (LOD = 2.90, P=1.29 x 10(-4)) in all diabetics. Since obesity, here defined as body mass index (BMI) > or =30 kg/m(2), is a key risk factor for the development of T2D, we studied the data either independently of BMI or by stratifying the patient group as obese (BMI > or =30) or nonobese (BMI <30). A nonparametric multipoint linkage analysis yielded linkage to 5q34-q35.2 (LOD = 3.64, P=2.12 x (10)-5) in the nonobese diabetics. No linkage was observed in this region for the obese diabetics. Linkage analysis conditioning on maternal transmission to the nonobese diabetics resulted in a LOD score of 3.48 (P=3.12 x 10(-5)) in the same region, whereas conditioning on paternal transmission led to a substantial drop in the LOD score. Finally, we observed potential interactions between the 5q locus and two T2D susceptibility loci, previously mapped in other populations.

Aged↗