Analysis of polymorphism of the hypervariable locus of the apolipoprotein-B gene in populations of the Volga-Ural region

Data on the allelic polymorphism at the hypervariable locus 3' to the apolipoprotein B gene (apo B) in seven Turkic and Finno-Ugric human populations of the Volga-Ural region obtained by means of PCR method are presented. Sixteen allelic variants were distinguished, and the frequency distribution of alleles and genotypes across the populations studied were estimated. Alleles 34 and 36 appeared to be more common (from 13 to 45% in different populations); the calculated heterozygosity indices ranged from 59.3 to 73.4%. Comparison of the data with that on other world populations made it possible to deduce some specific features of the alleles frequency distribution associated with geographic position of the population.     

Allelic polymorphism in the coding region of human T cell receptor V beta 12 gene

Many bilateral distal extension removable partial dentures possess insufficient guidance to control their dislodgement. When such a situation is observed, the tips of retentive clasps must be located in both an occlusogingival and mesiodistal (away from the denture base area) undercut. The specific location can be identified with a dental surveyor that has been adapted to function in two planes. Details of the adaptation process and use of the surveyor are described.     

A HinfI polymorphism in the 5' flanking region of the human VNTR locus D1S80

A restriction fragment length polymorphism (RFLP) characterized by the presence (HinfI+) or absence (HinfI-) of a HinfI site has been found in the 5' flanking region of the VNTR locus D1S80. RFLP-allele frequencies were determined from 82 unrelated individuals: HinfI+ = 0.49, HinfI- = 0.51. The RFLP/VNTR haplotype frequencies show an absolute association between the HinfI+ allele and the VNTR allele of 18 repeat units and an extreme association between the HinfI- allele and the VNTR allele of 24 repeat units. The remaining VNTR alleles associate more randomly with the 2 flanking HinfI alleles.     

Genetic investigations in immigration cases and frequencies of DNA fragments of the VNTR systems D2S44, D5S43, D7S21, D7S22, and D12S11 in Turks

We have included investigations of the DNA polymorphism of variable numbers of tandem repeat (VNTR) regions with restriction fragment length polymorphism (RFLP) in the genetic evaluations in immigrant cases. HinfI-digested DNA was separated by electrophoresis in agarose gels and hybridized with radiolabelled probes detecting the VNTR systems D2S44 (YNH24), D5S43 (MS8), D7S21 (MS31), D7S22 (g3), and D12S11 (MS43a). We used the matching criterion for paternity testing for the parent/child comparisons, i.e. non-match if the intra gel difference exceeded 1.25 mm. A total of 43 immigration cases involving mainly Turks were investigated with DNA technique in parallel with investigations of 10-15 conventional systems. One man was excluded from paternity by both conventional and DNA investigations. Non-exclusion was observed with both conventional and DNA systems in 97 putative mother/child pairs and in 96 putative father/child pairs. In a putative father/child combination with non-exclusion in 18 genetic systems, a single genetic inconsistency ('exclusion') in D7S21 (MS31) was observed. The frequency distributions of HinfI digested DNA fragments of the five VNTR systems in 105 Turks are presented.     

Effective size and polymorphism of linked neutral loci in populations under directional selection

The general theory of the effective size (Ne) for populations under directional selection is extended to cover linkage. Ne is a function of the association between neutral and selected genes generated by finite sampling. This association is reduced by three factors: the recombination rate, the reduction of genetic variance due to drift, and the reduction of genetic variance of the selected genes due to selection. If the genetic size of the genome (L in Morgans) is not extremely small the equation for Ne is [formula, see text] where N is the number of reproductive individuals, C 2 is the genetic variance for fitness scaled by the squared mean fitness, (1 - Z) = Vm/C2 is the rate of reduction of genetic variation per generation and Vm is the mutational input of genetic variation for fitness. The above predictive equation of Ne is valid for the infinitesimal model and for a model of detrimental mutations. The principles of the theory are also applicable to favorable mutation models if there is a continuous flux of advantageous mutations. The predictions are tested by simulation, and the connection with previous results is found and discussed. The reduction of effective size associated with a neutral mutation is progressive over generations until the asymptotic value (the above expression) is reached after a number of generations. The magnitude of the drift process is, therefore, smaller for recent neutral mutations than for old ones. This produces equilibrium values of average heterozygosity and proportion of segregating sites that cannot be formally predicted from the asymptotic Ne, but both parameters can still be predicted by following the drift along the lineage of genes. The spectrum of gene frequencies in a given generation can also be predicted by considering the overlapping of distributions corresponding to mutations that arose in different generations and with different associated effective sizes.     

Identification and strain differentiation of Mycobacterium species on the basis of DNA 16S-23S spacer region polymorphism

Amplification of the region separating the genes coding for the two rRNA species 16S and 23S was performed to identify 56 mycobacterial strains, belonging to eleven species: Mycobacterium tuberculosis, M. avium, M. kansasii, M. gordonae, M. abscessus, M. fortuitum, M. xenopi, M. bovis, M. bovis/BCG, M. africanum and M. intracellulare. Reproducible amplification patterns were obtained with most species with the exception of M. kansasii which showed heterogeneity, confirming the existence of a genetically distinct subspecies within this species. In addition, we used the amplified products as target DNA for restriction endonuclease digestion and RAPD (randomly amplified polymorphic DNA) analysis to compare strains of M. abscessus, M. tuberculosis and M. avium. The discriminatory power of these two typing methods was higher than when whole genomic DNA is used as target. Our results demonstrate that the two-step approach to identification and typing on the basis of the hypervariability of 16S-23S spacer region is reliable, rapid and simple, and consequently could be an epidemiological tool in clinical laboratories.     

A P1-based physical map of the region from D17S776 to D17S78 containing the breast cancer susceptibility gene BRCA1

BRCA1, a breast and ovarian cancer susceptibility locus, has been isolated and maps to 17q21. A physical map of the BRCA1 region which extended from the proximal boundary at D17S776 to the distal boundary at D17S78 was constructed and consists of 51 sequence tagged sites (STSs) from P1 and YAC ends, nine new short-tandem repeat (STR) polymorphic markers, and eight identified genes. The contig, which spans the estimated 2.3 Mb region, contains 29 P1s, 11 YACs, two BACs, and one cosmid. Based on key recombinants in two linked families, BRCA1 was further localized to a region bounded by D17S1321 on the proximal side and D17S1325 on the distal side. Within this estimated 600 kb region, the contig was composed completely of P1s and BACs ordered by STS-content mapping and confirmed by DNA restriction fragment fingerprinting.     

The human dead ringer/bright homolog, DRIL1: cDNA cloning, gene structure, and mapping to D19S886, a marker on 19p13.3 that is strictly linked to the Peutz-Jeghers syndrome

A 2-year trial was conducted to evaluate the cost-effectiveness of heliotherapy for psoriasis. The course and cost of psoriasis of 46 Finnish patients were first closely monitored for 1 year, then the patients received a 4-week supervised heliotherapy treatment in the Canary Islands, Spain, after which they continued to be followed for another year. Heliotherapy dramatically reduced the severity of psoriasis and also seemed to have favourable long-term effects on psoriasis. The mean direct cost of the 4-week heliotherapy for one patient was FIM12,289 (1 Pound = FIM7.0 in 1989). The cost of flights and half-board in Spain formed nearly 60% (FIM7033) of the total cost. In the year preceding heliotherapy, the mean direct annual cost of antipsoriasis therapy was FIM7335 and in the year after FIM5700, a reduction of 22% in annual costs; this change was not statistically significant because there were large variations in costs among patients. The costs of heliotherapy exceeded manyfold the mean monthly cost of conventional psoriasis therapy. There were no overall savings using heliotherapy in those patients suffering mainly from moderately severe psoriasis. Heliotherapy saved costs only in those patients with severe psoriasis that required expensive medication or ward treatment. Although heliotherapy cannot be regarded as an economical treatment for the average patients with psoriasis, it clears psoriasis effectively and is preferred by patients. Thus, heliotherapy constitutes an alternative for patients suffering severe psoriasis.     

Influence of coding region polymorphism on the peripheral expression of a human TCR V beta gene

A number of human TCR V beta gene segments are reported to be polymorphic, with alleles differing by one or a small number of amino acid substitutions. In the absence of detailed structural information regarding the interaction of specific positions in the TCR with Ag or MHC, the significance of such variation is difficult to assess. In this report the relative use of the two common alleles of the human V beta 6.7 gene, 6.7a and 6.7b, which differ by two non-conservative amino acid substitutions, and the use of two common alleles of the V beta 12.2 gene, which differ by only silent substitutions, were measured in PBL derived from individuals heterozygous for these alleles. Equal use of V beta 12.2 alleles was observed, consistent with the inability of selection mechanisms to discriminate between the products of these alleles that are indistinguishable at the amino acid level. However, statistically significant skewing in the use of V beta 6.7 alleles was observed in 15 of 16 individuals studied. Expression levels for each allele ranged from 16 to 84% of the total V beta 6.7 signal in heterozygous individuals, with either the 6.7a or the 6.7b allele predominant in different individuals. Based on segregation studies in families, it seems unlikely that other unidentified polymorphism in the TCR beta locus, such as in the V beta 6.7 promoter, was responsible for the differential allele expression. Family studies provided no evidence for an association between specific HLA haplotypes and V beta 6.7 allele use. These results indicate that even modest allelic variation in human TCR V beta coding regions can have a significant impact on the expression of human V beta genes in the peripheral repertoire.     

Genetic polymorphism of the 3' VNTR region of the human dopaminergic function gene DAT1 (human dopamine transporter gene) in the Mongolian population

The hypervariable region of the dopamine transporter gene (DAT1) was amplified from samples in the Mongolian population. This region includes a variable number of tandem repeats of a 40-bp core unit in the 3' untranslated region of DAT1. Vandenbergh et al. (1992) reported variability in the number of repeats of this 3' flanking region ranging from 3 to 11 times in white and black populations. We examined polymorphism at the DAT1 locus in 78 native Mongolian subjects. We found alleles with 7 to 13 repeats, which is different from the findings of Vandenbergh et al. (1992). The allele distribution of the Mongolian population is similar to that in the Japanese population, reported previously by Nakatome et al. (1995). Chi-square analysis showed a significant lack of homogeneity between our findings in Mongolian subjects and those reported previously in white and black populations. The DAT1 locus was estimated to have a heterozygosity index of 14.1%, and the polymorphic information content was calculated to be 0.16.     

The murine CYLN2 gene: genomic organization, chromosome localization, and comparison to the human gene that is located within the 7q11.23 Williams syndrome critical region

Several agents that act through G-protein-coupled receptors and also stimulate phosphoinositide-specific phospholipase C (PI-PLC), including angiotensin II, vasopressin, norepinephrine, and prostaglandin (PG) F2alpha, activated the ERK1 (p44mapk) and ERK2 (p42mapk) members of the mitogen-activated protein (MAP) kinase family in primary cultures of rat hepatocytes, measured as phosphorylation of myelin basic protein (MBP) by a partially purified enzyme, immunoblotting, and in-gel assays. All these agonists induced a peak activation (two to threefold increase in MBP-phosphorylation) at 3-5 min, followed by a brief decrease, and then a sustained elevation or a second increase of the MAP kinase activity that lasted for several hours. Although all the above agents also stimulated PI-PLC, implicating a Gq-dependent pathway, the elevations of the concentration of inositol (1,4,5)-trisphosphate did not correlate well with the MAP kinase activity. Furthermore, pretreatment of the cells with pertussis toxin markedly reduced the MAP kinase activation by angiotensin II, vasopressin, norepinephrine, or PGF2alpha. In addition, hepatocytes pretreated with pertussis toxin showed a diminished MAP kinase response to epidermal growth factor (EGF). The results indicate that agonists acting via G-protein-coupled receptors have the ability to induce sustained activation of MAP kinase in hepatocytes, and suggest that Gi-dependent mechanisms are required for full activation of the MAP kinase signal transduction pathway by G-protein-coupled receptors as well as the EGF receptor.     

Allelic polymorphism and site-specific recombination in the opc locus of Neisseria meningitidis

The opc gene is widespread in epidemic and endemic Neisseria meningitidis, but most strains of certain epidemic clones (ET-37 complex, Cluster A4) and a few random endemic isolates lack an opc gene. Four percent of the 1148 bp that contain opc plus the surrounding intergenic region was polymorphic (18 alleles), and many of the alleles contained a 230 bp insertion at a fixed location in the intergenic region. The presence or absence of the insertion reflects site-specific recombination. The alleles are stably inherited within clonal groupings for up to at least 50 years, with rare cases of horizontal genetic exchange. Most statistical methods indicated significant intragenic recombination events within this dataset.     

Localization of the hemochromatosis gene close to D6S105

The hemochromatosis (HC) gene is known to be linked to HLA-A (6p21.3); however, its precise location has been difficult to determine because of a lack of additional highly polymorphic markers for this region. The recent identification of short tandem repeat sequences (microsatellites) has now provided this area with a number of markers with similar polymorphic index to the HLA serological polymorphisms. Using four microsatellites--D6S105, D6S109, D6S89, and F13A--together with the HLA class I loci HLA-A and HLA-B in 13 large pedigrees clearly segregating for HC, we have been able to refine the location of the HC gene. We identified no recombination between HC and HLA-A or D6S105, and two-point analyses placed the HC gene within one centimorgan (cM) of HLA-A and D6S105 (HLA-A maximum of the lod score [Zmax] of 9.90 at recombination fraction [theta] of 0.0, and D6S105 Zmax of 8.26 at theta of 0.0). The markers HLA-B, D6S109, D6S89, and F13A were separated from the HC locus by recombination, defining the centromeric and telomeric limits for the HC gene as HLA-B and D6S109, respectively. A multipoint map constructed using HLA-B, HLA-A, and D6S109 indicates that the HC gene is located in a region less than 1 cM proximal to HLA-A and less than 1 cM telomeric of HLA-A. These pedigree data indicate an association between HC and specific alleles at HLA-A and D6S105 (i.e., HLA-A3 and D6S105 allele 8).(ABSTRACT TRUNCATED AT 250 WORDS)     

Linkage of the NKG2 and CD94 receptor genes to D12S77 in the human natural killer gene complex

Rapid advances in modern gene seeking techniques and the sequence data evolving from related genome research should provide both new targets for drug discovery and new insights into risk factors for many neurological and psychiatric disorders. Coupled with the high speed synthetic capabilities available in many companies, high-throughput screening is identifying potential novel drug candidates at extraordinary rates. This enables the drug discoverer to be more precise in the biological specificity of drugs taken to human trials thereby reducing the potential side-effect profile of clinical candidates. The ability to create large libraries of compounds also allows researchers to focus on metabolism and pharmacokinetics at an earlier stage in the drug development process to minimize drug-drug interactions via common sites of metabolism and optimize duration of action for particular indications. An emerging bottleneck in psychopharmacological drug discovery is the relative paucity of preclinical behavioral models predictive of clinical efficacy and the need to carry out early clinical trials to demonstrate therapeutic utility. However, through the use of recently developed chip technology, coupled with data bases of information about single nucleotide polymorphisms in potential candidate genes or risk factors for psychiatric disorders, it should be possible in the near future to stratify clinical populations genetically for inclusion in specific drug treatment trials. The ultimate goal of this research is to obtain homogeneous populations for trials and to predict risk before the phenotype of the disorder is manifest.     

ECK, a human EPH-related gene, maps to 1p36.1, a common region of alteration in human cancers

Mouse eck, a member of the EPH gene family, has been mapped to mouse chromosome 4. The syntenic relationship between this chromosome and human chromosome 1 suggests that the human ECK gene maps to the distal short arm of human chromosome 1 (1p). Since this region is frequently deleted or altered in certain tumors of neuroectodermal origin, it is important to define the specific chromosomal localization of the human ECK gene. PCR screening of a rodent-human somatic cell hybrid panel by ECK-specific primers showed that ECK is indeed localized to human chromosome 1. Additional PCR screening of a regional screening panel for chromosome 1p indicated that ECK is localized to 1p36, distal to FUCA1. Furthermore, fluorescence in situ hybridization analysis with an ECK-specific P1 clone showed that ECK maps proximal to genetic marker D1S228. Taken together, the data suggest that ECK maps to 1p36.1, a region that is frequently deleted in neuroblastoma, melanoma, and other neuroectodermal tumors.     

The isolation of eukaryotic ribosomal proteins. The purification and characterization of the 40 S ribosomal subunit proteins S2, S3, S4, S5, S6, S7, S8, S9, S13, S23/S24, S27, and S28

The proteins of the small subunit of rat liver ribosomes were separated into five groups by stepwise elution from carboxymethylcellulose with LiCl at pH 6.5 (Collatz, E., Lin, A., St?ffler, G., Tsurugi, K., and Wool, I.G., (1976) J. Biol. Chem. 251, 1808-1816). From the several groups, 12 proteins (S2,S3, S4, S5, S6, S7, S8, S9, S13, S23/S24, S27, and S28) wereisolated by ion exchange chromatography on carboxymethylcellulose, by chromatography on sulfopropyl-Sephadex, and by gel filtration through Sephadex G-75. The amount of protein obtained varied from 1 to 9 mg depending on the number of steps required for the preparation; several proteins had no detectable contamination and the impurities in the others were no greater than 9%. The molecular weight of the proteins was estimated by polyazrylamide gel electrophoresis in sodium dodecyl sulfate; the amino acid composition was determined.