The human apolipoprotein B 3′ hypervariable region: detection of eight new alleles and comparisons of allele frequencies in blacks and whites

We investigated common length polymorphisms in the hypervariable region located 3 to the human gene encoding apolipoprotein B (APOB 3 HVR) as part of the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study. PDAY is a multicenter study of young persons who died of external causes (accident, homicide, and suicide). The APOB 3 HVR contains multiple copies of AT-rich tandem repeats (15bp) called hypervariable elements (HVE). Using polymerase chain reaction (PCR) to amplify APOB sequences in hepatic DNA samples, we identified 22 different HVR alleles among 232 PDAY cases. In addition to 14 previously identified alleles, we detected 8 new alleles that had not been observed in population surveys. Of these new alleles, 7 were present only in black cases. We also examined distributions of HVR allele frequencies for blacks and whites. The frequency distributions for whites did not differ from those from previous studies of French populations (P=0.3811) and Austrian populations (P= 0.1885). In contrast, the allele frequency distribution for blacks differed from whites (P<0.001). Blacks had higher frequencies of smaller alleles (33 repeats) and larger alleles (37 repeats) than whites. We also sequenced specific HVR alleles to identify differences responsible for size variation. The most frequent alleles were identical in sequence to HVR alleles described in previous studies. However, one allele was not identical in sequence to an equivalent-sized allele from a previous study. In all likelihood, detection of sequence substitutions in the APOB 3 HVR would result in an even greater amount of allelic variability than detected by size differences alone.     

Two-nucleotide codon change in a hemoglobin polymorphism of the Celebes black ape (Macaca nigra)

A hemoglobin polymorphism involving variant -chains was demonstrated in the Celebes black ape, Macaca nigra. Fingerprinting and amino acid analysis of the tryptic peptides from the two chain types have shown that they differ by a single amino acid substitution, between lysine and aspartic acid, which requires a two-nucleotide change in the corresponding codon. Another substitution in the same codon is found as a species difference between the black ape -chain and that of other macaques.     

Deletion of arginine (608) in acid sphingomyelinase is the prevalent mutation among Niemann-Pick disease type B patients from northern Africa

There is a high incidence of Niemann-Pick type B disease in the Maghreb region of North Africa, which includes Morocco, Algeria and Tunisia. A hypothesis that there may well be a common, predominant mutant acid sphingomyelinase allele responsible for the type B phenotype in this population has been tested. A deletion of an arginine codon at amino acid residue 608 was found in one patient. The same mutation was also observed in another of our cases. An original screening procedure using 3end digoxigenin-labeled allele-specific oligonucleotides and chemiluminescent detection was developed and used parallel to the conventional assay with 5-end radiolabeled oligonucleotides. Of the 15 non-related, non-Jewish North African type B patients studied, 12 were homozygous and two compound heterozygous for this deletion (26 R608 alleles/30 mutant alleles). Among type B patients from other geographic regions (France, UK, Italy, Czechoslovakia), this mutation was observed in only one of the 16 alleles studied. Our results indicate that deletion of arginine 608 in the acid sphingomyelinase gene is the highly prevalent mutation underlying Niemann-Pick type B disease in the population of Maghreb. A varying severity of the clinical and enzymatic expression within the non-neuronopathic phenotype has however been observed in patients homozygous for the mutation.     

Evolution ofMHC polymorphism: Extensive sharing of polymorphic sequence motifs between human and bovine DRB alleles

The evolution ofMHC polymorphism has been studied by comparing the amino acid and nucleotide sequences of 14 bovine and 32 humanDRB alleles. The comparison revealed an extensive sharing of polymorphic sequence motifs in the two species. Almost identical sets of residues were found at several highly polymorphic amino acid positions in the putative antigen recognition site. Consequently, certain bovine alleles were found to be more similar to certain human alleles than to other bovine alleles. In contrast, the frequencies of silent nucleotide substitutions were found to be much higher in comparisons between species than within species implying that none of the human or bovine DRB alleles originated before the divergence of these distantly related species. The results suggest that the observed similarity inDRB polymorphism is due to convergent evolution and possibly the sharing of short ancestral sequence motifs. However, the relative role of the latter mechanism is difficult to assess due to the biased base composition in the first domain exon of polymorphic class 11 genes. The frequency of silent substitutions betweenDRB alleles was markedly lower in cattle than in man suggesting that theDRB diversity has evolved more rapidly in the former species.     

Allelic variations clustered in the antigen binding sites of HLA-Bw62 molecules

HLA-Bw62 is a serologically defined class I antigen specificity, but we show that it represents a family of five distinct alleles in this study. Five variants of HLA-Bw62 antigens were identified by isoelectric focusing, and sequencing studies revealed that these are a family of closely related alleles differing from one another by one to six amino acid substitutions at eight positions: 63 in the 1 domain and 94, 95, 97, 99, 113, 152, and 156 in the 2 domain. These substitutions are located in the two -helices and two adjacent -strands, and the side chains of most amino acids face into the antigen binding groove. Functional assays using an in vitro generated Epstein-Barr virus (EBV)-specific Bw62-restricted cytotoxic T lymphocyte clone indicated that the minimal structural variations located in the antigen binding sites of the HLA-Bw62 variant molecules could affect the presentation of the nominal EBV antigen. This study revealed that the HLA-Bw62 antigen family consists of at least five closely related alleles, and further demonstrated that these alleles with minimal structural variations might play distinct functional roles in regard to antigen presentation.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M83191–83195.     

Assessment of hybridisation between the endangered Chatham Island black robin (<Emphasis Type="Italic">Petroica traversi</Emphasis>) and the Chatham Island tomtit (<Emphasis Type="Italic">Petroica macrocephala chathamensis</Emphasis>)

Hybridisation between an endangered species and a more common species can facilitate population decline and extinction of the endangered species due to wasted reproductive effort, outbreeding depression and/or swamping of alleles due to widespread or complete admixture. The Chatham Island black robin (Petroica traversi) is an endangered songbird species, which was reduced to only five individuals in 1980. Intensive cross-fostering, whereby black robin offspring were placed into nests of the closely related Chatham Island tomtit (Petroica macrocephala chathamensis) to increase reproductive output, contributed to the rapid recovery of the species within 10 years. Several hybridisation events occurred and although those hybrids were successfully eliminated from the population, concerns remained for the possibility of introgression between the two species that may have gone unnoticed. In this study, we genotyped seven microsatellite loci in both species from the two islands where they coexist, to assess the level of hybridisation and the extent of introgression between the two species. The two species shared no alleles at five of the seven loci genotyped, and cluster analysis, AMOVA and admixture analysis of a total of 174 black robins and 78 Chatham Island tomtits showed no evidence of hybridisation or introgression on either of the two islands where they co-exist. As a result, there is no evidence that black robins are currently in any danger of population decline or extinction through hybridisation with tomtits, although small population size and skewed sex ratio, particularly in the smaller of the two populations, may facilitate future hybridisation events.     

Natural variation of potato <Emphasis Type="Italic">allene oxide synthase 2</Emphasis> causes differential levels of jasmonates and pathogen resistance in <Emphasis Type="Italic">Arabidopsis</Emphasis>

Natural variation of plant pathogen resistance is often quantitative. This type of resistance can be genetically dissected in quantitative resistance loci (QRL). To unravel the molecular basis of QRL in potato (Solanum tuberosum), we employed the model plant Arabidopsis thaliana for functional analysis of natural variants of potato allene oxide synthase 2 (StAOS2). StAOS2 is a candidate gene for QRL on potato chromosome XI against the oömycete Phytophthora infestans causing late blight, and the bacterium Erwinia carotovora ssp. atroseptica causing stem black leg and tuber soft rot, both devastating diseases in potato cultivation. StAOS2 encodes a cytochrome P450 enzyme that is essential for biosynthesis of the defense signaling molecule jasmonic acid. Allele non-specific dsRNAi-mediated silencing of StAOS2 in potato drastically reduced jasmonic acid production and compromised quantitative late blight resistance. Five natural StAOS2 alleles were expressed in the null Arabidopsis aos mutant under control of the Arabidopsis AOS promoter and tested for differential complementation phenotypes. The aos mutant phenotypes evaluated were lack of jasmonates, male sterility and susceptibility to Erwinia carotovora ssp. carotovora. StAOS2 alleles that were associated with increased disease resistance in potato complemented all aos mutant phenotypes better than StAOS2 alleles associated with increased susceptibility. First structure models of ‘quantitative resistant’ versus ‘quantitative susceptible’ StAOS2 alleles suggested potential mechanisms for their differential activity. Our results demonstrate how a candidate gene approach in combination with using the homologous Arabidopsis mutant as functional reporter can help to dissect the molecular basis of complex traits in non model crop plants.     

Possible Polyphyletic Origin of Major Histocompatibility Complex Class I Chain-Related Gene A (MICA) Alleles

Phylogenetic relationships among 23 nonhuman primate (NHP) major histocompatibility complex class I chain-related gene (MIC) sequences, 54 confirmed human MICA alleles, and 16 human MICE alleles were constructed with methods of sequence analysis. Topology of the phylogenetic tree showed separation between NHP MICs and human MICs. For human MICs, the topology indicated monophyly for the MICB alleles, while MICA alleles were separated into two lineages, LI and LII. Of these, LI MICA alleles shared a common ancestry with gorilla (Ggo) MIC. One conservative amino acid difference and two nonconservative amino acid differences in the 3 domain were found between the MICA lineages. The nonconservative amino acid differences might imply structural and functional differences. Transmembrane (TM) trinucleotide-repeat variants were found to be specific to the MICA lineages such as A4, A9, and A10 to LI and A5 to LII. Variants such as A5.1 and A6 were commonly found in both MICA lineages. Based on these analyses, we postulate a polyphyletic origin for MICA alleles and their division into two lineages, LI and LII. As such, there would be 30 alleles in LI and 24 alleles in LII, thereby reducing the current level of polymorphism that exists, based on a presumed monophyletic origin. The lower degree of polymorphism in MICA would then be in line with the rest of the human major histocompatibility complex nonclassical class I genes.     

The eighth component of human complement: molecular basis of C8A (C81) polymorphism

Using an exon-specific polymerase chain reaction (PCR) followed by direct DNA sequence analysis we have analyzed the polymorphism of the -chain of the eighth component of human complement (C8) at the DNA level. We found that two common alleles, C8A^*A and C8A^*B, are characterized by the substitution of a single amino acid (Gln to Lys), which is caused by a point mutation of a single nucleotide (C to A) in exon 3 at position 187 of the mature C8 cDNA sequence. Based on this mutation, an allele-specific PCR was designed detecting the two alleles of C8A. We applied this method to type the C8A polymorphism using DNA samples from a Chinese Han population. The comparison with the data of protein typing of the same samples proved that the described method is efficient and reliable for the identification of C8A genotypes and may be valuable for further application in population studies and forensic science.     

Phenylketonuria: detection of a frequent haplotype 4 allele mutation

Summary By sequence analysis of 94 phenylketonuria (PKU) alleles using polymerase chain reaction (PCR) based techniques, we identified a G to A transition in exon 5 of the human phenylalanine hydroxylase gene. This base substitution predicts an Arg¹⁵⁸Glu¹⁵⁸ amino acid exchange and is strongly associated with the mutant haplotype 4 PKU allele.     

Indications for a dimeric structure of an acid phosphatase in the lamprey (Petromyzon fluviatilis L.)

A likely genetic variation in the acid phosphatases from lamprey kidneys is described. Separations with starch gel electrophoresis have given eight different types, three with one zone of acid phosphatase activity and five with three zones. The molecular weights of these different isoenzymes were determined by gel filtration to be between 81,300 and 87,200. This is compared with existing data in the literature for other acid phosphatases. The most likely interpretation for the described variation is a one-locus, homodimeric enzyme system with four different alleles present in the population investigated.     

The immunoglobulin κ locus: polymorphism and haplotypes of Caucasoid and non-Caucasoid individuals

The immunoglobuline locus has previously been characterized by comparing the restriction patterns of the DNA of 23 Caucasoid individuals and defining various polymorphisms and haplotypes. This study has now been extended to a group of 28 Blacks and another group of 13 individuals of different ethnic origins. The predominant haplotype of the Caucasoid group, called haplotype N, was also found frequently in the other groups. Some of the restriction fragment length polymorphism markers typical of haplotype G, on the other hand, were seen 2–3 times more frequently in the black than in the Caucasoid group. Haplotype 11, which is characterized by the absence of about half of the variable gene segments (V) and which had been observed in 3 out of 46 Caucasoid alleles, has been found twice in the 82 alleles of the two new groups. A number of new polymorphisms was detected and new haplotypes were defined, although the structure of the immunoglobulin locus seems generally to be well conserved among different populations.     

Mate-searching behavior of the black chafer <Emphasis Type="Italic">Holotrichia kiotonensis</Emphasis> (Coleoptera: Scarabaeidae): identification of a sex pheromone,and male orientation behavior controlled by olfactory and visual cues

In the black chafer Holotrichia kiotonensis Brenske (Coleoptera: Scarabaeidae), mating behavior was observed between 1940 and 2010 hours at < 0.1 lx in both the laboratory and the field. In the laboratory, an ether extract of female abdominal glands induced a series of pre-mating behaviors such as short-distance orientation and abdominal bending. When the extract was fractionated by silica gel column chromatography, the active fraction was eluted with 50% ether in hexane and 100% ether. Gas chromatography–mass spectrometry analysis revealed that both active fractions contained anthranilic acid (2-amino-benzoic acid) as a major compound. The amount of this compound was determined to be ca. 600 ng/female by high performance liquid chromatography analysis with a fluorescence detector. In the field, male chafers were observed to land on cotton balls impregnated with 10 mg of authentic anthranilic acid. When a white ball treated with anthranilic acid was placed 2–10 cm away from an untreated black ball, males were observed to land significantly more frequently on the latter. These results suggest that males could recognize white balls below 0.1 lx and landed on black balls. When a treated black ball was placed beside an untreated black ball, more males landed on the former. The difference was significant when the distance between the two lures was 5 or 10 cm, but not significant when it was 2 cm. These observations demonstrated that anthranilic acid was the sex-attractant pheromone for the black chafer H. kiotonensis and that the males located and landed on a pheromone source by using olfaction in conjunction with visual orientation. The importance of visual orientation in this nocturnal species is discussed in comparison with the congeneric diurnal species Holotrichia loochooana loochooana.     

Development of a method for the identification of S alleles in Brassica oleracea based on digestion of PCR-amplified DNA with restriction endonucleases

Summary The development of a technique for the identification of S alleles involved in self-incompatibility in Brassica oleracea which is based on the polymerase chain reaction (PCR) amplification of genomic DNA followed by restriction analysis is described. Primers homologous to conserved regions near to the 5 and 3 ends of the S coding sequence were used to amplify a number of members of the S multigene family. However, by designing a selective primer and using a higher temperature for annealing in the PCR, we were able to amplify certain members from the multigene family preferentially. These were considered to be the S-locus glycoprotein genes (SLG), since the patterns of restriction bands of the PCR products were shown to correspond to those of the SLG where sequence data were available. DNA samples from plants with certain S alleles were found not to amplify efficiently using the selective primers and high annealing temperature. This property, however, could be used as a means of distinguishing plants homozygous for these S alleles, as was demonstrated by an examination of a small F₂ population that was segregating for the S5 and S29 alleles. In the investigation of the F₂ population, it was found that preferential amplification of one of the alleles of the heterozygotes occurred when the consensus primers were used in the PCR. However, by using different primers, homologous to another region of the S sequence, we were able to amplify both alleles of the heterozygotes equally. The genotypes of the plants were determined by restriction analysis of PCR products and agreed with results based on pollen-tube growth tests.     

Inheritance of black sigatoka disease resistance in plantain-banana (Musa spp.) hybrids

Black sigatoka (Mycosphaerella fijiensis Morelet), an airborne fungal leaf-spot disease, is a major constraint to plantain and banana (Musa spp.) production world-wide. Gaining further knowledge of the genetics of host-plant resistance will enhance the development of resistant cultivars, which is considered to be the most appropriate means to achieve stable production. Genetic analysis was conducted on 101 euploid (2x, 3x and 4x) progenies, obtained from crossing two susceptible triploid plantain cultivars with the resistant wild diploid banana Calcutta 4. Segregating progenies, and a susceptible reference plantain cultivar, were evaluated over 2 consecutive years. Three distinct levels of host response to black sigatoka were defined as follows: susceptible (< 8 leaves without spots), less susceptible (8–10) and partially resistant (> 10). Segregation ratios for resistance at the 2x level fitted a genetic model having one major recessive resistance allele (bs ₁) and two independent alleles with additive effects (bsr ₂ and bsr ₃). A similar model explains the results at the 4x level assuming that the favourable resistance alleles have a dosage effect when four copies of them are present in their respective loci (bs _i ⁴ ). The proposed model was further validated by segregation data of S ₁ progenies. Mechanisms of black sigatoka resistance are discussed in relation to the genetic model.     

Cloning and expression of <Emphasis Type="Italic">Perilla frutescens FAD2</Emphasis> gene and polymorphism analysis among cultivars

?12 fatty acid desaturase (FAD2) is a key enzyme for linoleic acid and linolenic acid biosynthesis. Perilla frutescens is a special oil plant species with highest linolenic acid content. In this study, based on RACE, two alleles for one FAD2 gene were isolated from P. frutescens cultivar C2: the 3956 bp PfFAD2a and the 3959 bp PfFAD2b, both with a full-length cDNA of 1526 bp, and both encoding a 382aa basic protein. The alleles have identities of over 98%, and their encoded proteins differ only by substitution of a strongly similar residue. Saccharomyces cerevisiae heterologous expression suggested that PfFAD2a/b both encode a bio-functional FAD2 enzyme. Phylogenetic analyses indicated that PfFAD2 shows the highest homologies to FAD2 genes from dicots such as Boraginaceae and Burseraceae. PfFAD2a/b expressions are mainly restricted to developing seeds. PfFAD2a/b expression in the seedling leaf is upregulated by cold (4 °C) and repressed by heat (42 °C). Each of the eight cultivars contains two alleles for one PfFAD2 and 40 SNP sites are found. One allelic gene in cultivars C1 and P1 is pseudogene because of premature stop codon mutation in 5′ coding region. All other normal PfFAD2 genes/allelic genes encode identical or very similar proteins. PfFAD2a/b expression level in developing seeds also varies among the eight cultivars. This study provides systemic molecular and functional features of PfFAD2 and enables its application in the study of plant fatty acids traits.     

Biochemical composition of maize (Zea mays L.) pollen

Summary Pollen grains containing either the Wx, wx, Su ₁, su ₁, Sh ₂ or sh ₂ alleles were stored at 0, 1, 2, 3, 4 and 5 days at 2 °C. After each storage period, a portion of pollen from each genotype was analyzed for free amino acid content. Over all genotypes, storage significantly altered the content of all 16 amino acids measured. With increasing storage, a relatively consistent increase in aspartic acid, isoleucine, leucine, phenylalanine, ethanolanine, aminobutyric acid, NH₃ and lysine was found. A relatively consistent decrease in glutamic acid, proline, glycine and alanine occurred with increasing storage. No consistent response to storage was obtained with threonine-serine, valine, histidine and the unknown. Apparently, storage or stage of viability loss has a pronounced effect on amino acid metabolism in maize pollen grains. The experiment was designed so that comparisons free of genetic background effects could be made between alleles at each locus. Significant allele X storage interactions at each locus were found as follows: at the waxy locus, aspartic acid, glycine, alanine and ethanolanine; at the sugary locus, aspartic acid, alanine, ethanolanine and aminobutyric acid; and at the shrunken locus, aspartic acid, alanine, valine, leucine and ethanolanine. Amino acid metabolism is apparently influenced by the action of the alleles at these loci. The differences between the loci in the amino acids affected indicate the different areas of amino acid metabolism are influenced by each locus.Journal Series Paper No. 4425, Florida Agricultural Experiment Station.     

Examination of the Role of DNA Polymerase Proofreading in the Mutator Effect of Miscoding tRNAs

We previously described Escherichia coli mutator tRNAs that insert glycine in place of aspartic acid and postulated that the elevated mutation rate results from generating a mutator polymerase. We suggested that the proofreading subunit of polymerase III, , is a likely target for the aspartic acid-to-glycine change that leads to a lowered fidelity of replication, since the altered subunits resulting from this substitution (approximately 1% of the time) are sufficient to create a mutator effect, based on several observations of mutD alleles. In the present work, we extended the study of specific mutD alleles and constructed 16 altered mutD genes by replacing each aspartic acid codon, in series, with a glycine codon in the dnaQ gene that encodes . We show that three of these genes confer a strong mutator effect. We have also looked for new mutator tRNAs and have found one: a glycine tRNA that inserts glycine at histidine codons. We then replaced each of the seven histidine codons in the mutD gene with glycine codons and found that in two cases, a strong mutator phenotype results. These findings are consistent with the subunit playing a major role in the mutator effect of misreading tRNAs.     

Inheritance of high oleic acid content in the seed oil of soybean mutant M23

A mutant line, M23, of soybean [Glycine max (L.) Merr.] was found to have two fold increases in oleic acid content in the seed oil compared with the original variety, Bay. Our objective was to determine the inheritance of the high oleic acid content in this mutant. Reciprocal crosses were made between M23 and Bay. There were no maternal and cytoplasmic effects for oleic acid content. The F₁ seeds and F₁ plants were significantly different from either parents or the midparent value, indicating partial dominance of oleic acid content in these crosses. The oleic acid content segregated in the F₂ seeds and F₂ plants in a trimodal pattern with normal, intermediate and high classes, satisfactorily fitting a 121 ratio. The seeds of a backcross between M23 and F₁ segregated into intermediate and high classes in a ratio of 11. These results indicated that oleic acid content was controlled by two alleles at a single locus with a partial dominant effect. Thus, the allele in M23 was designated ol and the genotypes of M23 and Bay were determined to be olol and 0l0l, respectively. The oleic acid contents of the F₂ seeds and F₂ plants were inversely related with the linoleic acid content which segregated in a trimodal pattern with normal, intermediate and low classes in a 121 ratio. Thus, it was assumed that the low linoleic acid content in M23 was also controlled by the ol alleles. Because a diet with high oleic acid content reduces the content of low density lipoprotein cholesterol in blood plasma, the mutant allele, ol, would be useful in improving soybean cultivars for high oleic acid content.