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D S Dunn

Publications and source records attributed to D S Dunn.

At least 19 recordsLinked to original sources
PubMed2006

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.

Aged↗
PubMed2005

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.

Alu Elements↗
PubMed2005

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.

Chromosome Mapping↗
PubMed2003

Association of MHC dimorphic Alu insertions with HLA class I and MIC genes in Japanese HLA-B48 haplotypes.

A large proportion of Japanese with the HLA-B48 allele have a MICA gene deletion associated with a MICB null allele within the class I region of the Major Histocompatibility Complex (MHC). Here, we report for the first time a novel positive association between the presence of a polymorphic Alu insertion, AluyMICB, within the first intron of the MICB gene and the MICAdel/MICBnull/HLA-B48 haplotype for five of six well-characterized Japanese cell-lines. The AluyMICB insertion was found to be present at a frequency of 0.242 in 86 Japanese tissue donors and in four of the five individuals with the HLA-B48 allele. The AluyMICB insertion was also associated with at least three different MICB alleles, *0102, *0107N and *0105, and three different HLA-B alleles, B13, B48 and B57, respectively, in the seven Workshop cell-lines (the 4th Asia-Oceania Histocompatibility Workshop, and the 10th International Histocompatibility Workshop) and the six Japanese cell-lines that were selected for this study. Based on the analysis of associations between different polymorphic markers within the beta block, the MICB*0102 allele was inferred to be the ancestral form of the MICB*0105 and MICB*0107N alleles. The AluyMICB polymorphism can now be used to further investigate its relationship with other MICB alleles and consequently their origins. In addition, we have examined the absence and presence of three other polymorphic Alu markers distributed within the alpha block of the class I region of the HLA-B48/AluyMICB haplotype. We conclude that the extended HLA-B haplotypes are best defined by considering multiple genomic sites including the four polymorphic Alu insertions described in this study.

Alu Elements↗
PubMed2001

Genomic and phylogenetic analysis of the human CD1 and HLA class I multicopy genes.

The human CD1 proteins belong to a lipid-glycolipid antigen-presenting gene family and are related in structure and function to the MHC class I molecules. Previous mapping and DNA hybridization studies have shown that five linked genes located within a cluster on human chromosome 1q22-23 encode the CD1 protein family. We have analyzed the complete genomic sequence of the human CD1 gene cluster and found that the five active genes are distributed over 175,600 nucleotides and separated by four expanded intervening genomic regions (IGRs) ranging in length between 20 and 68 kb. The IGRs are composed mostly of retroelements including five full-length L1 PA sequences and various pseudogenes. Some L1 sequences have acted as receptors for other subtypes or families of retroelements. Alu molecular clocks that have evolved during primate history are found distributed within the HLA class I duplicated segments (duplicons) but not within the duplicons of CD1. Phylogeny of the alpha3 domain of the class I-like superfamily of proteins shows that the CD1 cluster is well separated from HLA class I by a number of superfamily members including MIC (PERB11), HFE, Zn-alpha2-GP, FcRn, and MR1. Phylogenetically, the human CD1 sequences are interspersed by CD1 sequences from other mammalian species, whereas the human HLA class I sequences cluster together and are separated from the other mammalian sequences. Genomic and phylogenetic analyses support the view that the human CD1 gene copies were duplicated prior to the evolution of primates and the bulk of the HLA class I genes found in humans. In contrast to the HLA class I genomic structure, the human CD1 duplicons are smaller in size, they lack Alu clocks, and they are interrupted by IGRs at least 4 to 14 times longer than the CD1 genes themselves. The IGRs seem to have been created as "buffer zones" to protect the CD1 genes from disruption by transposable elements.

Antigens, CD1↗
PubMed2000

Coevolution of HLA-B and PERB11.1 (MICA): significance of independent triplet expansion within the transmembrane region of PERB11.1 (MICA).

Several highly polymorphic sequences are present in the beta block of the MHC, especially HLA-B, HLA-C, PERB11.1 (MICA), and PERB11.2 (MICB). It is now apparent that the polymorphism of PERB11.1 is of the same order as that of HLA-A, -B, and -C and it has been suggested that PERB11 could explain some of the disease associations previously attributed to HLA-B. Phylogenetic analysis of PERB11 alpha-domain sequences demonstrates relationships with HLA-B cross-reactive serogroups. In contrast, the transmembrane polymorphisms do not appear to be associated with either PERB11 or HLA-B. These data indicate that PERB11 and HLA-B have evolved in concert from their common ancestors and that the transmembrane polymorphisms have arisen independently and more recently. MHC disease associations will need to be reviewed in the light of mechanisms such as receptor binding and signaling.

Base Sequence↗
PubMed1995

Psychological measures: reliability in the assessment of stroke patients.

OBJECTIVE: To determine whether acute stroke patients can give reliable responses to standardized psychological measures. DESIGN: Survey design with retrospective review of Neurobehavioral Cognitive Status Examination (NCSE) scores. SETTING: A rehabilitation hospital in Philadelphia. PATIENTS: 106 consecutive admissions to stroke services at a rehabilitation hospital were evaluated according to the following inclusion criteria: Patients at least 65 years of age, English speaking, having a documented history of cerebrovascular accident (CVA), possession of receptive speech comprehension, and the ability to maintain attention adequate for participation in the study interview. Of the 47 eligible for participation, 10 patients refused participation and 13 were discharged before the interview could be completed. Thus 24 patients were interviewed, with one patient unable to complete the second half of the interview. MAIN OUTCOME MEASURES: In phase 1, the patient's performance on a structured interview (including the Multidimensional Health Locus of Control Scales (MHLC), Life Orientation Test (LOT), and Center for Epidemiological Studies Depression Scale (CES-D) scales) produced a Total Reliability Score, indicating the overall reliability of the patient's responses. In phase 2, NCSE scores were examined (retrospectively) for their ability to predict the patient's Total Reliability Score on the structured interview. RESULTS: Using Total Reliability Scores, 9 patients were categorized as "passing," 9 were categorized as "uncertain," and 5 were categorized as "failing" the interview. The NCSE was predictive for individuals who had a very low likelihood of being able to respond consistently. The NCSE failed to identify which individuals would respond in a reliable fashion. CONCLUSIONS: It is both possible and important to assess response reliability when using psychological measures soon after stroke. Future research will need to document other potential predictors of interview performance, including combinations of NCSE subscales.

Aged↗
PubMed1994

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.

Biocompatible Materials↗
PubMed1993

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.

Alloys↗
PubMed1991

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.

Abortion, Spontaneous↗
PubMed1990

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.

Adenine↗
PubMed1990

In quest of the tyrosinase-positive oculocutaneous albinism gene.

The gene which causes tyrosinase-positive oculocutaneous albinism (ty-pos OCA) is not known. Forty-seven Bantu-speaking Negroid families with ty-pos OCA were studied in an attempt to find linkage to the gene. Fifteen 'classical' and seven DNA polymorphisms were used in the search for linkage. Close linkage was excluded for the Rh, Gc and beta-globin loci. There is no suggestion of linkage to MNS, ABO, PGM1, 6PGD, ACP1, GPX1, GLO1, GPT1, PEP A, Tf, alpha 1-AT, Hp, DQA, DXA and three arbitrary restriction fragment length polymorphisms (RFLPs). There is a slightly positive lod score for pAW101 (D14S1) (0.591 for theta = 0.2). An 'interesting' lod score was obtained with Bf and a haplotype generated by the markers DQA and DXA (1.575 for theta = 0.1 and 0.979 for theta = 0.2, respectively). Further testing of markers on chromosome 6p are indicated. Although ty-pos OCA in Southern Africa is likely to be a homogeneous disorder, genetic heterogeneity cannot be excluded as differences due to the presence/absence of ephelides within families have been observed. To date 57% of the genome has been excluded from linkage with ty-pos OCA.

Albinism, Oculocutaneous↗
PubMed1989

The usefulness of various polymorphisms in paternity testing. Experience with three southern African populations.

Genetic studies have been carried out on 1,059 cases (involving 3,177 blood samples) of disputed paternity. Seventeen polymorphic systems, representing 21 loci, have been used on all the cases and an additional 11 system (12 loci) were used when an exclusion on only one of the system was obtained. The overall rate of exclusion was 34.0% and the data were analysed according to the population from which the case came (white, 'coloured' or black). HLA is the most informative system in all three populations, followed by PGM1, with the rhesus blood group the next most useful in the whites and 'coloured's, whereas ABO is the next most useful in the blacks. The probability of excluding a man falsely accused of paternity was 99.1% in the black, 99.4% in the white and 99.7% in the 'coloured' populations. The data were also used to calculate the probability of paternity in the cases in which an exclusion could not be demonstrated; values of over 98% were found in 98.5% of whites, 98.8% of 'coloureds' and 90% of blacks; a further 9.1% of blacks gave values of 95.1 - 98.0%. The range of genetic markers, representing red cell antigen, red cell enzyme, serum protein and HLA polymorphisms used in this study, meets the requirements of an efficient paternity testing service.

Black People↗
PubMed1987

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.

Black People↗
PubMed1986

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.

Africa, Southern↗
PubMed1985

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.

Alleles↗
PubMed1985

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.

Amphotericin B↗