Identification of four allelic variants of the dog<Emphasis Type="Italic"> IGHA</Emphasis> gene

Multiple IgA subclasses have been identified in humans, primates and lagomorphs, whereas in mice, cattle and dogs only a single subclass has been identified. The two human subclasses (IgA₁ and IgA₂) are defined by a difference in the length of the hinge region of the chains between the CH₁ and CH₂ domains. The single IgA subclass so far identified in dogs has an -chain hinge region with a predicted amino-acid sequence similar to that of the human ₁ chain. Allelic variants that differ in the coding sequence of the hinge region have been identified in mice and pigs. In order to investigate whether allelic variants are present in dogs, a portion of the IGHA gene from eight individual dogs was cloned and sequenced. Four sequence variants were identified, and these differed in the coding region of their hinge. A major difference between the variants was the presence of a base polymorphism in the splice acceptor site for the second exon, which resulted in shortening of the hinge in two of the variants. Individuals expressed one or two of the variants identified, suggesting they may be heterozygous or homozygous. Further work is required to determine the effect of the variation on the biological activity of dog IgA and any relationship to susceptibility to mucosal disease.Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AY576788–AY576795     

Population genetics of Drosophila ananassae: inversion polymorphism and body size in Indian geographical populations

Twelve Indian natural populations of Drosophila ananassae, a cosmopolitan and domestic species, were sampled and laboratory populations (mass cultures) were established from naturally impregnated females. These populations were maintained in the laboratory for some generations and were analysed chromosomally to know the frequency of different inversions. The chromosomal analysis revealed the presence of three cosmopolitan inversions. The data on the whole show that there are significant differences in the frequencies of different chromosome arrangements in these populations. Body size (wing length and thorax length) was measured in both sexes (50 females and 50 males), in all the 12 geographical populations of D. ananassae. There are statistically significant differences in wing length as well as in thorax length of both sexes among different geographical populations. Five geographical strains were crossed reciprocally and body size (wing length and thorax length) was measured in F₁ and F₂ progeny. The comparison of body size (both traits) between mid‐parent, F₁ and F₂ shows that there is an increase in body size in F₁ and F₂ progeny as compared with parents. Thus, there is no break down of heterosis in F₂, which suggests absence of coadaptation in geographical populations of D. ananassae. Scaling test statistical analysis showed additive, dominance and epistatic effects in certain crosses involving geographical strains of D. ananassae. Correlation between chromosome arrangement frequency and body size has also been tested and significant negative correlation has been found between 2L – ST chromosome arrangement and male thorax.     

Multiplex genotyping and allele frequency estimation in pooled DNAs using non-gel capillary electrophoresis

We present a novel approach of single-nucleotide polymorphism (SNP) analysis in which allele-specific oligonucleotide hybridization is followed by non-gel capillary electrophoresis (ASOH-NGCE) in conjunction with laser-induced fluorescence (LIF). This allows rapid multiplex allelotyping and allele frequency estimation. This method, based on site separation of the hybridization duplexes, retains the simplicity and specificity of ASOH and the homogeneous feature of NGCE with poly(N,N-dimethylacrylamide) (PDMA) as a sieving medium. ASOH-NGCE can be applied to multiplex SNP loci genotyping with excellent separation of hybridization mixtures. Average relative standard deviations (RSDs) were low for within-day (1.10%) and between-day (2.41%) reproducibility. Moreover, the allele frequencies in pooled DNAs were accurately determined from peak areas and equilibrium dissociation constants. Our method was highly sensitive in detecting alleles with frequency as low as 1% and in distinguishing allele frequencies differing by 1% between pools. The average value of differences between real and estimated frequencies (accuracy) was only 0.004.     

指间区纹的遗传学研究Ⅱ.指间区纹的镶嵌显性遗传

10 1个核心家庭的指间区纹分布状况经分析发现Ⅲ、Ⅳ区 ,左右手控制花纹的基因都是等位的。Ⅲ、Ⅳ区是等位的不同基因的镶嵌显性遗传。一个基因同时控制左右手对应区 ,不同基因表达的左右对称度不一。复等位基因中有 6种是完全显性的 ,另发现一种不完全显性。这是指区间区纹的主基因 ,还极少地存在着一种隐性的Ⅲ区纹基因。在随机人群中计算出了这些基因的频率。这一遗传模型可有亲子鉴定佐证等应用。     

Use of Chou-Fasman amino acid conformational parameters to analyze the organization of the genetic code and to construct protein genealogies

Summary Chou-Fasman parameters, measuring preferences of each amino acid for different conformational regions in proteins, were used to obtain an amino acid difference index of conformational parameter distance (CPD) values. CPD values were found to be significantly lower for amino acid exchanges representing in the genetic code transitions of purines, GA than for exchanges representing either transitions of pyrimidines, CU, or transversions of purines and pyrimidines. Inasmuch as the distribution of CPD values in these non GA exchanges resembles that obtained for amino acid pairs with double or triple base differences in their underlying codons, we conclude that the genetic code was not particularly designed to minimize effects of mutation on protein conformation. That natural selection minimizes these changes, however, was shown by tabulating results obtained by the maximum parsimony method for eight protein genealogies with a total occurrence of 4574 base substitutions. At the beginning position of the codons GA transitions were in very great excess over other base substitutions, and, conversely, CU transitions were deficient. At the middle position of the codons only fast evolving proteins showed an excess of GA transitions, as though selection mainly preserved conformation in these proteins while weeding out mutations affecting chemical properties of functional sites in slow evolving proteins. In both fast and slow evolving proteins the net direction of transitions and transversions was found to be from G beginning codons to non-G beginning codons resulting in more commonly occurring amino acids, especially alanine with its generalized conformational properties, being replaced at suitable sites by amino acids with more specialized conformational and chemical properties. Historical circumstances pertaining to the origin of the genetic code and the nature of primordial proteins could account for such directional changes leading to increases in the functional density of proteins.In order to further explore the course of protein evolution, a modified parsimony algorithm was developed for constructing protein genealogies on the basis of minimum CPD length. The algorithm's ability to judge with finer discrimination that in protein evolution certain pathways of amino acid substitution should occur more readily than others was considered a potential advantage over strict maximum parsimony. In developing this CPD algorithm, the path of minimum CPD length through intermediate amino acids allowed by the genetic code for each pair of amino acids was determined. It was found that amino acid exchanges representing two base changes have a considerably lower average CPD value per base substitution than the amino acid exchanges representing single base changes. Amino acid exchanges representing three base changes have yet a further marked reduction in CPD per base change. This shows how extreme constraining effects of stabilizing selection can be circumvented, for by way of intermediate amino acids almost any amino acid can ultimately be substituted for another without damage to an evolving protein's conformation during the process.     

Prevalence of C282Y and H63D mutations in the haemochromatosis (HFE) gene in Tunisian population

The studies of the HFE mutations: H63D and C282Y in North African populations have revealed the extreme rarity or even the absence of the C282Y mutation. We have examined 1140 chromosomes (570 Tunisian people) for the presence of the two HFE mutations by PCR-RFLP analysis. We have found that the allele frequencies are, respectively, 15.17% (+/-2.1%) for the H63D and 0.09% (+/-0.17%) for the C282Y. These results are consistent with the worldwide spread of the H63D mutation and the north European restriction of the C282Y. This study will be completed by determining whether homozygote trait for H63D and associated risk factors (beta thalassémia) can lead to iron overload in Tunisia.     

Eleven novel microsatellite markers for the Chinese alligator (Alligator sinensis)

Chinese alligator (Alligator sinensis) is a critically endangered species endemic to China. In this study, we developed 11 novel microsatellite loci for this rare species and applied them to examine genetic variation of indigenous alligators from Changxing Nature Reserve and America-born Chinese alligators. The 11 polymorphic microsatellites presented a total of 31 alleles among 57 individuals scored, yielding an average of 2.82 alleles per locus. One allele was unique to the American population but four private alleles were detected in the Changxing population. The average expected and observed heterozygosities were 0.400 and 0.482 for the Changxing alligators and 0.520 and 0.621 for the America-born individuals, respectively. These microsatellite markers would be useful tools in the genetic examination of this endangered species.     

Intron III-Specific Markers for Screening of β-amylase Alleles in Barley Cultivars

In modern malting barley breeding it is important to increase the level of -amylase activity level in barley. The aim of this study was to investigate if a PCR method for screening -amy1 alleles can be used as an indicator for -amylase activity level in barley. Activity was assayed from 24 cultivars, 7 lines, and a Hordeum spontaneum PI 296897 strain grown in the same field. The -amy1 alleles were identified by amplifying the intron III-specific region of the gene using PCR. No new alleles were detected in addition to the three alleles found earlier: cv Adorra-like, cv Haruna Nijo-like and PI 296897-like -amy1 allele. Samples were grouped according to the nature of their -amy1 locus and enzyme activities were compared between the groups. Cultivars carrying a cv Haruna Nijo-like -amy1 allele had 1.3 times and lines carrying a PI 296897-like -amy1 allele had 2.1 times higher -amylase activity than cultivars carrying a cv Adorra-like -amy1 allele. The mean activities are significantly different in the allele groups (Kruskal–Wallis: for protein H= 11.54, P< 0.01; for meal H= 12.74, P< 0.01). PCR fragments can be used as allele specific markers to predict the level of -amylase activity in breeding when such variation of the intron III is concerned.     

Distribution of the CD4 Alleles in Sus scrofa Demonstrates the Genetic Profiles of Western Breeds and Miniature Pigs

Widely used antipig CD4 monoclonal antibodies (mAbs) fail to recognize CD4 alleles characteristic of miniature pig lines such as the National Institutes of Health (NIH) miniature pigs and microminipigs. We surveyed polymorphisms in the coding sequence of the porcine CD4 gene among Western and Oriental pig breeds and Japanese wild boars and investigated their distribution. Of the 13 alleles that we identified among the 47 animals, 2 in group I and 3 in group II were found exclusively in Western breed pigs. Group IV alleles, which included mAb-nonbinding alleles, were found frequently in Oriental breed pigs, suggesting that the mAb-nonbinding allele arose from the gene pool of Oriental pigs. Group IV alleles were also found in Duroc and Large White pigs, suggesting genetic inflow from Oriental pig breeds into Western breeds. Comparison of the CD4 sequences of species in Cetartiodactyla suggested that the group IV alleles in Sus scrofa occurred before the divergence of this species from the other artiodactyls. The different antibody specificities of the various CD4 alleles may facilitate the discrimination of T-cell populations in transplantation studies using miniature pigs. The significance of the preservation of CD4 polymorphisms to immune function in pigs warrants further investigation.     

Genetic variation of European beech (Fagus sylvatica L.) along an altitudinal transect at Mount Vogelsberg in Hesse, Germany

Allelic and genotypic variation at 13 different enzyme loci of autochthonous European beech (Fagus sylvatica L.) was investigated in six 110-160-year-old stands growing at elevations between 150 and 660 m above sea level on the western slope of mount Vogelsberg in central Germany. The highest elevated population showed the highest number of effective alleles (Ne), the highest total heterozygosity (He) and the highest population differentiation deltaT. Also, the genotype SKD-A2A3 of shikimate dehydrogenase was significantly more frequent at the two highest elevated stands (P = 11%) than at the three lowest elevated stands (P = 1%). Further differences in genotype frequencies between 11 of 15 stand pairs were elevation independent.