HLA alleles and haplotypes in Burmese (Myanmarese) and Karen in Thailand.

This is the first report on human leukocyte antigen (HLA) allele and haplotype frequencies at three class I loci and two class II loci in unrelated healthy individuals from two ethnic groups, 170 Burmese and 200 Karen, originally from Burma (Myanmar), but sampled while residing in Thailand. Overall, the HLA allele and haplotype frequencies detected by polymerase chain reaction sequence-specific primer (PCR-SSP) at five loci (A, B, C, DRB1 and DRQB1) at low resolution showed distinct differences between the Burmese and Karen. In Burmese, five HLA-B*15 haplotypes with different HLA-A and HLA-DR/DQ combinations were detected with three of these not previously reported in other Asian populations. The data are important in the fields of anthropology, transplantation and disease-association studies.

Combining HLA-DR risk alleles and anti-Epstein-Barr virus antibody profiles to stratify multiple sclerosis risk.

BACKGROUND: Risk factors for multiple sclerosis (MS) include human leukocyte antigen (HLA)-DR and Epstein-Barr virus (EBV)-specific antibody responses, including an epitope within EBV nuclear antigen 1 (EBNA-1) that is of recent interest. OBJECTIVE: The objective of this paper is to assess case-control associations between MS risk and anti-EBV antibody levels as well as HLA-DR profiles, gender and age in a population-based cohort. METHODS: Serological responses to EBV were measured in 426 MS patients and 186 healthy controls. HLA-DR typing was performed using sequence-based methods. RESULTS: MS patients had significantly higher levels of antibodies against epitope-specific and polyspecific EBNA-1 and viral capsid antigen (VCA), compared with controls (all p < 10(-15)). In regression analyses, anti-EBNA-1 and anti-VCA antibody levels, protective HLA-DR*04/07/09 alleles and gender (all p < 0.003) contributed independently to a model that classified cases and controls with an odds ratio > 20 (sensitivity 92%, specificity 64%). Notably, the strong influence of high-risk HLA-DR alleles was abrogated after inclusion of EBV serology results. CONCLUSIONS: The ability to discriminate MS cases and controls can be substantially enhanced by including anti-EBV serology as well as HLA-DR risk profiles. These findings support the relevance of EBV-specific immunity in MS pathogenesis, and implicate both HLA-dependent and HLA-independent immune responses against EBNA-1 as prominent disease risk factors.

Polymorphic Alu insertions within the Major Histocompatibility Complex class I genomic region: a brief review.

Most polymorphic Alu insertions (POALINs) belong to a subgroup of the Alu multicopy retrotransposon family of short interspersed nucleotide elements (SINEs) that are categorized as AluYb8 and AluYa5. The number of AluYb8/AluYa5 members (approximately 4,492 copies) is significantly less than the approximately one million fixed Alu copies per human genome. We have studied the presence of POALINs within the Major Histocompatibility Complex (MHC) class I region on the short arm of chromosome 6 (6p21.3) because this region has a high gene density, many genes with immune system functions, large sequence variations and diversity, duplications and redundancy, and a strong association with more than 100 different diseases. Since little is known about POALINs within the MHC genomic region, we undertook to identify some of the members of the AluYb8/AluYa5 subfamily and to study their frequency of distribution and genetic characteristics in different populations. As a result of our comparative genomic analyses, we identified the insertion sites for five POALINs distributed within the MHC class I region. This brief review outlines the locations of the insertions and sequence features of the five MHC POALINs, their single site and haplotype frequencies in different geographic populations, and their association with different HLA class I genes and disease. We show that the MHC POALINs have a potential value as lineage and linkage markers for the study of human population genetics, disease associations, genomic diversity and evolution.

Transition from a hunter-gatherer to a settled lifestyle in the !Kung San: effect on iron, folate, and vitamin B12 nutrition.

In 1969 a group of hunter-gatherer San were studied (Am J Clin Nutr 1971;24:229-42). Their state of hematological nutrition was excellent with a negligible incidence of iron, folate, or vitamin B12 deficiency. A genetically and linguistically similar San community who have been settled for the past 15 yr were the subjects of the present study. Anemia, due in the main to iron and/or folate deficiency, has become more common. Alcoholism has become rife in both sexes and all age groups. Our findings show that a settled lifestyle has resulted in a significant deterioration in the San's hematological nutrition.

Antifungal synergism. A proposed dosage for corneal storage medium.

Fungal infections from eye bank-preserved corneas have led us to search for antifungal agents that will eliminate yeast and mold in McCarey-Kaufman (MK) medium and concurrently be nontoxic. Amphotericin B, natamycin, nystatin, and clotrimazole were tested in synergistic combinations in vitro against nine yeast and six mold specimens. For average yeast and mold concentrations of 3.4 X 10(4) and 1.36 X 10(4) colony-forming units (CFUs)/mL at 5 degrees C, and 3.36 X 10(4) and 2.3 X 10(3) CFUs/mL at 37 degrees C, respectively, a synergistic combination of all four drugs at one twelfth the minimal fungicidal concentrations proved fungicidal. This synergistic combination did not alter donor human corneal morphology under specular microscopy, nor did it inhibit rabbit corneal endothelial cell division preserved and propagated in antifungal supplemented MK medium. The synergistic drug mixture did prove to be fungicidal when the endothelial cells were challenged with fungal inoculum.

The effects of gestational age and gender on grief after pregnancy loss.

The roles of gestational age and gender in grief reactions following loss of pregnancy were explored. Parents with losses later in pregnancy reported more intense grief than did those whose losses were earlier. Women expressed higher levels of grief than did men six to eight weeks after the loss; however, this difference had decreased by one and two years after the loss.

The distribution of major histocompatibility complex class I polymorphic Alu insertions and their associations with HLA alleles in a Chinese population from Malaysia.

The frequency and association of polymorphic Alu insertions (POALINs) with human leucocyte antigen (HLA) class I genes within the class I genomic region of the major histocompatibility complex (MHC) have been reported previously for three populations: the Australian Caucasian, Japanese and north-eastern Thai populations. Here, we report on the individual insertion frequency of the five POALINs within the MHC class I region, their HLA-A and HLA-B associations, the POALIN haplotype frequencies and the HLA-A/POALIN four-loci haplotype frequencies in the Malaysian Chinese population. The phylogenetic relationship of the four populations based on the five POALIN allele frequencies was also examined. In the Malaysian Chinese population, the POALIN AluyHG was present at the highest frequency (0.560), followed by AluyHJ (0.300), AluyMICB (0.170), AluyTF (0.040) and AluyHF (0.030). The most frequent five-loci POALIN haplotype of the 16 inferred haplotypes was the AluyHG single insertion haplotype at a frequency of 0.489. Strong associations were present between AluyHJ and HLA-A24, HLA-A33 and HLA-A11 and between AluyHG and HLA-A2, HLA-A24 and HLA-A11, and these were reflected by the inferred haplotype frequencies constructed from the combination of the HLA-A locus and the AluyHG, AluyHJ and AluyHF loci. The strongest association of AluyMICB was with the HLA-B54 allele (five of five), whereas the associations with the other 17 HLA-B alleles were weak, moderate or undetermined. Phylogenetic analysis of the five POALIN allele frequencies places the Malaysian Chinese closest to the Japanese and north-eastern Thai populations in the same cluster and separate to the Australian Caucasian population. The MHC POALINs are confirmed in this study to be informative genetic markers in lineage (haplotype) analysis, population genetics and evolutionary relationships, especially in studying the MHC genomic region.

Development of a multilocus sequence typing scheme for intestinal spirochaetes within the genus Brachyspira.

The purpose of this study was to evaluate a multilocus sequence typing (MLST) scheme for intestinal spirochaetes of the genus Brachyspira. Eight loci mainly coding for enzymes previously used in multilocus enzyme electrophoresis analysis of Brachyspira species were examined in 66 Brachyspira field isolates and type/reference strains. The isolates and strains were recovered from pigs, birds, dogs and a mouse and originated from seven European countries, the USA and Canada. Forty-six isolates represented recognized Brachyspira species and 20 represented provisionally designated species or isolates that have not been classified. Only two loci gave PCR products for all 66 strains and isolates, but amplicons for seven loci were obtained for 44 of the isolates. Sequences for each locus had a DNA allelic variation of 30-47 and an amino acid allelic variation of 14-47 that gave rise to the same number of sequence and amino acid types (58) for the strains and isolates studied. A population snapshot based on sequence and amino acid types showed a close phylogenetic relationship amongst the porcine isolates from the same geographical regions, and indicated a close evolutionary relationship between isolates recovered from pigs and mallards. A general concordance was obtained between the MLST groupings and classifications based on culture and biochemical tests, 16S rDNA sequence analysis and random amplified polymorphic DNA analysis. This is a first step towards establishing an MLST system for use in identifying Brachyspira species and determining relationships between individual strains and species in the genus.

The association between non-melanoma skin cancer and a young dimorphic Alu element within the major histocompatibility complex class I genomic region.

A non-melanoma skin cancer (NMSC) susceptibility locus within the major histocompatibility complex (MHC) class I region was previously identified telomeric of the HLA-C gene using high-density microsatellite markers. Here, we have extended the previous microsatellite study by using the same DNA samples obtained from 154 NMSC patients and 213 normal controls from the town of Busselton in Western Australia and examined the relationship between five polymorphic Alu insertions (POALINs) within the MHC class I region and their association with NMSC. The genotype distribution of the AluyTF insertion that is located within the NMSC susceptibility region telomeric of the HLA-C gene was significantly increased according to the Fisher's exact test in the NMSC patients, and it was not in Hardy-Weinberg equilibrium in the control group. There was no difference between the cancer patients and controls for the genotypes of the AluyMICB locus within intron 1 of the MICB gene and the other three POALINs (AluyHJ, AluyHG and AluyHF) that are located within the genomic region of the HLA-A, -G and -F gene cluster. The test for significant linkage disequilibrium for 10 pairs of POALIN loci and estimations of two locus POALIN haplotype frequencies also revealed AluyTF differences between the cases and controls. In conclusion, the MHC class I POALIN, AluyTF, that is located within the NMSC susceptibility locus and near the HLA-C gene was strongly associated with NMSC. This finding, using five different polymorphic Alu insertion markers, supports the previous microsatellite association study that one or more genes located in close proximity to the AluyTF insertion has a potential role in NMSC.

Polymorphic Alu insertions and their associations with MHC class I alleles and haplotypes in the northeastern Thais.

Polymorphic Alu insertions (POALINs) are known to contribute to the strong polymorphic nature of the Major Histocompatibility Complex (MHC). Previous population studies on MHC POALINs were limited to only Australian Caucasians and Japanese. Here, we report on the individual insertion frequency of the five POALINs within the MHC class I region, their HLA-A and -B associations, and the three and four locus alpha block POALIN haplotype frequencies in the Northeastern (NE) Thai population. Of the five POALINs, the lowest frequency was 0.018 for AluyHF and the highest frequency was 0.292 for AluyHJ and AluyHG. The strongest positive associations between the POALINs and HLA class I alleles was between AluyMICB and HLA-B*57, AluyHJ and HLA-A*24 and HLA-A*01, and AluyHG and HLA-A*02, supporting previous findings in Caucasians and Japanese. Single POALIN haplotypes were found more frequently than multiple POALIN haplotypes. However, of the seven different POALIN haplotypes within the MHC alpha block, there were only two significant differences between the NE Thais, Caucasians and Japanese. This study confirms that the MHC POALINs are in linkage disequilibrium with HLA-A and -B alleles and that there are significant frequency differences for some of the POALINs when compared between NE Thai, Caucasians and Japanese.

HLA-A, B and C polymorphisms in three major populations living in South Africa.

The HLA class I antigen gene and haplotype frequencies of three major population groups living in the Transvaal province of South Africa were determined. The HLA-A, B and C antigens were tested in 877 South African Negroids, 381 Coloured and 771 Caucasoids. Differences in gene and haplotype frequencies between the various populations were observed. HLA-A11 appears with a low frequency in the Negroids (gf = 0.004) and the Caucasoids revealed an absence of HLA-Bw70. The frequencies of the HLA antigens in the Coloured population were generally intermediate between those of the other two groups. The most frequent haplotypes were A3, B7; A30, B8 and A2, B58 in the Caucasoids, Negroids and Coloured respectively. Genetic distance analysis reveals that Negroids and Caucasoids are distinct groups and the Coloured occupy an intermediate position.

A genetic profile of the South African Ashkenazi Jewish population.

The South African Ashkenazi Jewish population is described in terms of the prevailing frequencies of the genes at 25 red cell enzyme and serum protein loci and 4 placental enzyme loci. Variation was encountered in 23 of these systems. The Tay-Sachs allele which occurs at polymorphic frequencies in Ashkenazi populations was found at a frequency of 0.022, which suggests that approximately 1 baby with Tay-Sachs disease could be expected out of every 2,000 born in this community should preventive measures not be taken. The atypical serum pseudocholinesterase cholinesterase allele was encountered at a relatively low frequency and instances of scoline apnoea would be expected to occur only during approximately 1 out of every 10,000 surgical operations performed. A single case of glucose-6-phosphate dehydrogenase deficiency was discovered during the survey. In general, the allele frequencies in the systems studied do not differ radically from those of Ashkenazi populations living in other parts of the world. In accordance with other Ashkenazi populations, the frequencies of certain alleles in our samples provide support for the belief that the Ashkenazim have their origin in the Middle East.

Gentamicin sulfate attachment and release from anodized Ti-6A1-4V orthopedic materials.

A novel method has been developed to attach, retain, and release antibiotics from titanium based materials. This technique consists of forming porous surface coatings by anodizing and using the surface chemical properties of the oxide coatings to attach antibiotics. Coatings with pores in the size range 0.1-0.5 micron have been formed in acid solutions. The attachment and retainment of gentamicin sulfate, a cationic antibiotic, to the coatings has been investigated using microbiological methods. In vitro test results have shown that the duration of antimicrobial activity on the surface of anodized materials is dependent on the porosity and isoelectric point of the coatings. Using microporous oxide coatings formed in phosphoric acid solutions, it has been found that antimicrobial activity could be retained for more than 2 weeks.

Alpha-1-antitrypsin variation in Southern Africa.

Eleven Southern African populations were shown to be polymorphic at the alpha 1-antitrypsin locus. A 'new' electrophoretically detectable alpha 1-antitrypsin variant (PiWsan) which has a lower isoelectric point than does PiM, was found in the Bantu-speaking Negro and San populations. PiWsan appears to be functionally normal as judged by quantitative and qualitative studies.

Ciprofloxacin attachment to porous-coated titanium surfaces.

A simple and effective method for attaching ciprofloxacin HCl salt to the surface of porous-coated titanium based orthopedic materials was developed. The method utilizes the electrophoretic migration of both fine ciprofloxacin HCl particles and ciprofloxacin ions to deposit the antibiotic salt on a positively biased surface. The quantity of antibiotic deposited can be easily and effectively controlled by varying the time of deposition and applied voltage. In vitro tests have indicated that the antimicrobial activity of the treated surfaces is retained for a period of 5 days. The method allows a significant amount of antibiotic to be deposited and could theoretically be used to deliver antibiotics to the tissues surrounding prosthetic devices in order to prevent postoperative infections.

Phophoglucomutase first locus polymorphism as revealed by isoelectric focusing in Southern Africa.

Eleven Southern African populations (representing European, Asian and Negroid populations) have been typed for the first locus phosphoglucomutase (PGM1) using isoelectric focusing (pH range 5.0-8.0) in acrylamide gels. The gene frequencies of the four common alleles at this locus in these populations were compared to those found previously in European and Negroid populations. Marked differences in gene frequencies were observed: Negroes have a lower PGM1(2-) compared with Caucasoids due to a lower PGM1(2-) frequency, Indians a relatively high PGM1(2) due to a higher frequency of the PGM1(2+) allele. The Afrikaans and Ashkenazim do not differ appreciably from their European counterparts. The appearances of the rarer PGM1(6) and PGM1(7) alleles on isoelectric focusing are described and some kinetic properties examined. The PGM2(2-1), or 'Atkinson' phenotype, can also be detected with this technique.

Retrograde ejaculation and pregnancy. A case report.

A patient with retrograde ejaculation following a transurethral resection of the prostate was able to father a child using spermatozoa recovered from the bladder. The method of recovery of these spermatozoa is described.

Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli.

A run of 11 adenine or thymine residues at the 5' end of an out-of-frame lacZ gene causes a high level of beta-galactosidase expression in E. coli. This effect was not observed for a run of guanine residues. Reverse transcription of mRNA isolated from E. coli containing the run of 11 A's reveals heterogeneity of transcript length while reverse transcription of mRNA isolated from S. cerevisiae containing the same gene shows no heterogeneity. Protein sequencing of the beta-galactosidase molecules derived from the out-of-frame construct containing a run of adenines reveals the addition of a lysine at the run. A new method was developed where messages small enough to allow resolution of single nucleotide differences on an acrylamide gel are electrophoresed, electroblotted onto nylon and probed. This confirmed the reverse transcription results and showed that additional residues can be added to transcripts derived from DNA containing 10 or 11 thymine residues. A mechanism for slippage is discussed where the A-U rich RNA-DNA hybrid can denature during elongation and rehybridize in an offset position, causing the addition of extra residues to the transcript.

Serogenetic and haematological studies on the Kgalagadi of Botswana.

A sample of Kgalagadi, Negro speakers of a Sotho/Tswana Bantu language, inhabitants of Botswana, have been investigated for variation in 27 gene-marker systems and for haematological status and the presence of intestinal parasites. They have been found to show indications of genetic affinity both to the other Sotho/Tswana and to the Mbanderu divisions of the Herero, a Bantu-speaking Negro people of Namibia. The latter affinity appears the closer. Although the historical connection between the peoples seems unlikely on cultural and oral-historical grounds, it is not impossible, given the shallow depth of the oral history of the Herero and the consequent doubts about the antiquity of their present cultural system. Nothing in the genetic profile of the Kgalagadi contradicts the claim that they represent a very early, and perhaps the first, wave of Negro immigration into southern Africa. They have been investigated for intestinal parasites and haematological status as well. They appear to be haematologically healthy, and to possess only the narrow range of parasites previously found in the Kalahari Desert, apart from one subject in whom Hymenolepis nana (Dwarf tapeworm) was found.

Sero-genetic studies on the Ambo of Namibia.

The Ambo are the largest population group of Namibia/South West Africa and consist of seven geographical and sociopolitical entities speaking different dialects of a common language. Nearly 600 individuals representing all the dialect groups were tested for 23 sero-genetic systems: the results reveal no evidence of significant San admixture and unusual alleles suggest an affinity with the Herero which confirms oral traditions of a common origin. Genetic distance measurements indicate that the Dama may also have a connection with these peoples and it is probable that most of the Bantu-speaking Negroes of Namibia/South West Africa come from the same stock.