Science, conservation and fox-hunting.
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Accidents, Traffic↗
Biomedical subjects
R J Smith
Publications and source records attributed to R J Smith.
Elephant hunting and conservation.
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Africa↗
Mutations in the novel protocadherin PCDH15 cause Usher syndrome type 1F.
We have determined the molecular basis for Usher syndrome type 1F (USH1F) in two families segregating for this type of syndromic deafness. By fluorescence in situ hybridization, we placed the human homolog of the mouse protocadherin Pcdh15 in the linkage interval defined by the USH1F locus. We determined the genomic structure of this novel protocadherin, and found a single-base deletion in exon 10 in one USH1F family and a nonsense mutation in exon 2 in the second. Consistent with the phenotypes observed in these families, we demonstrated expression of PCDH15 in the retina and cochlea by RT-PCR and immunohistochemistry. This report shows that protocadherins are essential for maintenance of normal retinal and cochlear function.
Adult↗
Methodological issues of using observational human data in lung dosimetry models for particulates.
INTRODUCTION: The use of human data to calibrate and validate a physiologically based pharmacokinetic (PBPK) model has the clear advantage of pertaining to the species of interest, namely humans. A challenge in using these data is their often sparse, heterogeneous nature, which may require special methods. Approaches for evaluating sources of variability and uncertainty in a human lung dosimetry model are described in this study. METHODS: A multivariate optimization procedure was used to fit a dosimetry model to data of 131 U.S. coal miners. These data include workplace exposures and end-of-life particle burdens in the lungs and hilar lymph nodes. Uncertainty in model structure was investigated by fitting various model forms for particle clearance and sequestration of particles in the lung interstitium. A sensitivity analysis was performed to determine which model parameters had the most influence on model output. Distributions of clearance parameters were estimated by fitting the model to each individual's data, and this information was used to predict inter-individual differences in lung particle burdens at given exposures. The influence of smoking history, race and pulmonary fibrosis on the individual's estimated clearance parameters was also evaluated. RESULTS: The model structure that provided the best fit to these coal miner data includes a first-order interstitialization process and no dose-dependent decline in alveolar clearance. The parameter that had the largest influence on model output is fractional deposition. Race and fibrosis severity category were statistically significant predictors of individual's estimated alveolar clearance rate coefficients (P < 0.03 and P < 0.01-0.06, respectively), but smoking history (ever, never) was not (P < 0.4). Adjustments for these group differences provided some improvement in the dosimetry model fit (up to 25% reduction in the mean squared error), although unexplained inter-individual differences made up the largest source of variability. Lung burdens were inversely associated with the miners' estimated clearance parameters, e.g. individuals with slower estimated clearance had higher observed lung burdens. CONCLUSIONS: The methods described in this study were used to examine issues of uncertainty in the model structure and variability of the miners' estimated clearance parameters. Estimated individual clearance had a large influence on predicted lung burden, which would also affect disease risk. These findings are useful for risk assessment, by providing estimates of the distribution of lung burdens expected under given exposure conditions.
Body Burden↗
Cloning and characterization of SLC26A6, a novel member of the solute carrier 26 gene family.
The SLC26 gene family (solute carrier family 26) comprises five mammalian genes that encode anion transporter-related proteins. In addition to sat-1 and prestin, which were cloned from rat and gerbil, respectively, three human members have been identified and associated with specific genetic diseases (DTD, diastrophic dysplasia; CLD, congenital chloride diarrhea; PDS, Pendred syndrome). In this study we used a homology approach combined with RACE PCR to identify human SLC26A6, the sixth member of this gene family. Northern blot analysis showed the highest SLC26A6 transcript levels in kidney and pancreas. Expression in MDCK cells and in Xenopus oocytes demonstrated trafficking of the SLC26A6 protein to the cell membrane but did not reveal anion transport activity with tracer uptake or intracellular pH measurements. We determined the genomic structure of the SLC26A6 gene and excluded mutations in the 21 coding exons as the cause of DFNB6 and USH2B, which closely map to the SLC26A6 chromosomal locus (3p21).
Amino Acid Sequence↗
Genomic structures of SCN2A and SCN3A - candidate genes for deafness at the DFNA16 locus.
DFNA16 is a form of autosomal dominant non-syndromic hearing loss (ADNSHL) characterized by fluctuating progressive hearing impairment. Earlier, we mapped the deafness-causing gene to chromosome 2q23-24.3. In this paper, we describe fine mapping results using additional markers tightly linked to the DFNA16 candidate region. Critical recombinants at markers D2S354 and D2S124 define a 3.5-cM interval that contains the DFNA16 gene. Positional candidate genes include two members of the voltage-gated sodium channel family, the type 2 alpha subunit (SCN2A) and the type 3 alpha subunit (SCN3A). After showing that SCN2A is expressed in human fetal cochlea, we determined its genomic structure to facilitate mutation screening in our DFNA16 kindred. We also determined the genomic structure of SCN3A. These two genes are oriented head-to-head, with their 5' ends separated by approximately 40 kb; their homology is 82% at the nucleotide level, and 85% for identities and 90% for positives at the amino acid level. They share similar genomic structures and have alternative splice isoforms that are developmentally regulated and highly conserved between species. Although no DFNA16-causing mutations were found in either gene, haplotype analysis with polymorphic markers in SCN2A introns further narrowed the candidate gene interval to the region flanked by D2S354 and STS SHGC-82894.
Alternative Splicing↗
Mutations in the transcriptional activator EYA4 cause late-onset deafness at the DFNA10 locus.
We identified Eyes absent 4 (EYA4), a member of the vertebrate Eya family of transcriptional activators, as the causative gene of postlingual, progressive, autosomal dominant hearing loss at the DFNA10 locus. In two unrelated families from Belgium and the USA segregating for deafness at this locus, we found different mutations in EYA4, both of which create premature stop codons. Although EYA proteins interact with members of the SIX and DACH protein families in a conserved network that regulates early embryonic development, this finding shows that EYA4 is also important post-developmentally for continued function of the mature organ of Corti.
Age of Onset↗
A second gene for otosclerosis, OTSC2, maps to chromosome 7q34-36.
Otosclerosis due to abnormal bone homeostasis of the otic capsule is a frequent cause of hearing loss in adults. Usually, the hearing loss is conductive, resulting from fixation of the stapedial footplate, which prevents normal ossicular vibration in response to sound. An additional type of sensorineural hearing loss may be caused by otosclerotic damage to the cochlea. The etiology of the disease is unknown, and both environmental and genetic factors have been implicated. Autosomal dominant inheritance with reduced penetrance has been proposed, but large families are extremely rare. To elucidate the pathogenesis of the disease, identification of the responsible genes is essential. In this study, we completed linkage analysis in a Belgian family in which otosclerosis segregates as an autosomal dominant disease. After excluding linkage to a known locus on chromosome 15 (OTSC1), we found linkage on chromosome 7q, with a multipoint LOD score of 3.54. Analysis of key recombinant individuals maps this otosclerosis locus (OTSC2) to a 16-cM interval on chromosome 7q34-36 between markers D7S495 and D7S2426.
Alleles↗
Autosomal dominant inherited hearing impairment caused by a missense mutation in COL11A2 (DFNA13).
OBJECTIVE: To analyze the phenotype in a 5-generation DFNA13 family with a missense mutation in the COL11A2 gene that causes autosomal dominant, presumably prelingual, nonsyndromic sensorineural hearing impairment. DESIGN: Family study. SETTING: University hospital department. PATIENTS: Twenty mutation carriers from a large American kindred. METHODS: Cross-sectional analysis using pure-tone threshold measurements at 0.25, 0.5, 1, 2, 4, and 8 kHz. The audiometric configuration was evaluated according to an existing consensus protocol. The significance of features relating to audiometric configuration was tested using 1-way analysis of variance. Progression was evaluated with linear regression analyses of threshold-on-age. RESULTS: Most individuals showed midfrequency (U-shaped) characteristics. The mean threshold in generations IV and V was 44 dB at 1, 2, and 4 kHz (midfrequencies); it was 29 dB at the other frequencies (0.25, 0.5, and 8 kHz). There was no significant progression beyond presbyacusis. CONCLUSION: The trait in this family can be characterized as autosomal dominant, nonprogressive, presumably prelingual, midfrequency sensorineural hearing impairment.
Adolescent↗
Localization of the gene for familial laryngeal abductor paralysis to chromosome 6q16.
BACKGROUND: Vocal fold paralysis is a common cause of neonatal stridor. Although it is usually classified as idiopathic or iatrogenic in origin, a small subset of patients have a family history of this disorder, indicating a possible genetic cause. OBJECTIVE: To identify the genetic locus of the gene that causes familial laryngeal abductor paralysis. DESIGN: A standard nonorganic protocol was used to extract DNA from whole-blood samples. The DNA samples were quantified by DNA fluorometry, and the concentration of all samples was standardized at 40 ng/microL. A pooled DNA strategy was used to facilitate rapid polymerase chain reaction screening of markers in the Weber v8.0 genome screening set. Polymerase chain reaction screening of individual DNA samples was performed using possible linked markers initially identified as having an allele that appeared with a higher incidence in the affected DNA pools. Statistical analysis of possible linkage was performed using the LINKAGE 5.1 set of linkage analysis computer programs. SUBJECTS: A family in which a form of familial laryngeal abductor paralysis segregates was ascertained. Whole blood samples were drawn from 40 participating individuals within this family after the subjects' fully informed consent was obtained. RESULTS: Initial screening of the pooled DNA specimens revealed a band pattern for D6S1021 on chromosome 6q16, indicating an allele with a higher incidence in the affected vs the nonaffected pool. Two-point analysis of individual allele patterns confirmed linkage to D6S1021 with an lod score of 3.86 (straight theta = 0.0) at a penetrance value of 0.8. Haplotype analysis with flanking markers defined a 5-centiray critical region between D6S283 and AFMA047YG1. CONCLUSION: An autosomal dominant form of familial laryngeal abductor paralysis is linked to a 5-centiray region on chromosome 6q16 surrounding D6S1021.
Alleles↗
MYO1F as a candidate gene for nonsyndromic deafness, DFNB15.
BACKGROUND: Earlier studies have mapped the autosomal recessive nonsyndromic deafness locus, DFNB15, to chromosomes 3q21.3-q25.2 and 19p13.3-13.1, identifying one of these chromosomal regions (or possibly both) as the site of a deafness-causing gene. Mutations in unconventional myosins cause deafness in mice and humans. One unconventional myosin, myosin 1F (MYO1F), is expressed in the cochlea and maps to chromosome 19p13.3-13.2. OBJECTIVE: To evaluate MYO1F as a candidate gene for deafness at the DFNB15 locus by determining its genomic structure and screening each exon for deafness-causing mutations to identify possible allele variants of MYO1F segregating in the DFNB15 family. METHODS: We used radiation hybrid mapping to localize MYO1F on chromosome arm 19p. We next determined its genomic structure using multiple long-range polymerase chain reaction experiments. Using these data, we completed mutation screening using single-stranded conformational polymorphism analysis and direct sequencing of affected and nonaffected persons in the original DFNB15 family. RESULTS: Radiation hybrid mapping placed MYO1F in the DFNB15 interval, establishing it as a positional candidate gene. Its genomic structure consists of 24 coding exons. No mutations or genomic rearrangements were found in the original DFNB15 family, making it unlikely that MYO1F is the disease-causing gene in this kindred. CONCLUSIONS: Although we did not find MYO1F allele variants in one family with autosomal recessive nonsyndromic hearing loss, the gene remains an excellent candidate for hereditary hearing impairment. Given its wide tissue expression, MYO1F might cause syndromic deafness.
Alleles↗
Pediatric otolaryngologists' knowledge and understanding of genetic testing for deafness.
OBJECTIVE: To assess the level of a cohort of pediatric otolaryngologists' knowledge and understanding of genetics and genetic testing for deafness and hard of hearing (D/HOH). METHODS: A questionnaire was designed to assess the level of knowledge and understanding of the genetic basis and genetic testing for deafness among a cohort of pediatric otolaryngologists. Three hundred questionnaires were made available to attendees of the 14th (1999) Annual Meeting of the American Society of Pediatric Otolaryngology, Palm Desert, Calif. A series of questions asked to gauge the respondent's level of knowledge of genetics and hearing impairment addressed estimating recurrence risks for deaf and normal-hearing parents and the likelihood of detecting a mutation in connexin 26 in specific clinical scenarios. RESULTS: A total of 28 questionnaires were completed and returned. All respondents reported that they regularly saw patients for D/HOH. Almost half commonly refer these patients for genetic testing and counseling. Seventeen (71%) of 24 otolaryngologists stated they offered genetic testing in all situations, while 6 offered counseling only at parental request or to address recurrence risk issues. One otolaryngologist offered genetic testing if there was a deaf sibling. Twelve (67%) of 18 offered pretest counseling, which was most frequently provided by a genetic counselor. Although 3 (19%) of 16 otolaryngologists provided the counseling themselves, 2 (13%) reported that they and a genetic counselor provided the counseling. While 24 (89%) of the 27 correctly stated that nonsyndromic D/HOH is usually autosomal recessive, recurrence risks were incorrectly estimated in several examples. CONCLUSIONS: While the surveyed pediatric otolaryngologists have a good knowledge of genetics and genetic testing for D/HOH, recurrence risks were often inaccurate. Since D/HOH testing is clinically available, it is imperative that physicians are educated about genetics and genetic testing and are able to communicate this to their patients and their patients' families.
Child↗
Mutation screening for deafness: more than simply another diagnostic test.
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Child↗
Pendred syndrome, DFNB4, and PDS/SLC26A4 identification of eight novel mutations and possible genotype-phenotype correlations.
Mutations in PDS (SLC26A4) cause both Pendred syndrome and DFNB4, two autosomal recessive disorders that share hearing loss as a common feature. The hearing loss is associated with temporal bone abnormalities, ranging from isolated enlargement of the vestibular aqueduct (dilated vestibular aqueduct, DVA) to Mondini dysplasia, a complex malformation in which the normal cochlear spiral of 2(1/2) turns is replaced by a hypoplastic coil of 1(1/2) turns. In Pendred syndrome, thyromegaly also develops, although affected persons usually remain euthyroid. We identified PDS mutations in the proband of 14 of 47 simplex families (30%) and nine of 11 multiplex families (82%) (P=0.0023). In all cases, mutations segregated with the disease state in multiplex families. Included in the 15 different PDS allele variants we found were eight novel mutations. The two most common mutations, T416P and IVS8+1G>A, were present in 22% and 30% of families, respectively. The finding of PDS mutations in five of six multiplex families with DVA (83%) and four of five multiplex families with Mondini dysplasia (80%) implies that mutations in this gene are the major genetic cause of these temporal anomalies. Comparative analysis of phenotypic and genotypic data supports the hypothesis that the type of temporal bone anomaly may depend on the specific PDS allele variant present.
Abnormalities, Multiple↗
Novel coding-region polymorphisms in mitochondrial seryl-tRNA synthetase (SARSM) and mitoribosomal protein S12 (RPMS12) genes in DFNA4 autosomal dominant deafness families.
Two genes for components of the mitochondrial translational apparatus, mitochondrial seryl-tRNA synthetase (SARSM) and mitoribosomal protein S12 (RPMS12) lie adjacent to one another on human chromosome 19, within the critical interval for the autosomal dominant deafness locus DFNA4. Both genes are plausible candidates for DFNA4, based on the fact that deafness mutations in mtDNA have been mapped both to tRNA-ser(UCN) and to the accuracy domain of the small subunit rRNA. We have sequenced the coding regions, proximal promoters, 5' and 3' UTR and splice junctional regions of both genes in two families with DFNA4-linked deafness and in controls. Novel polymorphisms 84425C>T, 83907A>G, 79485T>G, 79406C>T, 71755A>C and 68686C>G (numbered as in GenBank AC011455) were found in one or both families, but none is a plausible disease-causing mutation. Although regulatory mutations affecting either gene could still be involved in the phenotype, structural gene mutations affecting SARSM or RPMS12 can be excluded from consideration as the cause of DFNA4-linked deafness, at least in the families identified thus far.
Chromosomes, Human, Pair 19↗
Isolation of salmon pancreas disease virus (SPDV) in cell culture and its ability to protect against infection by the 'wild-type' agent.
A Scottish salmon pancreas disease virus (SPDV) has been isolated and its optimum growth conditions determined. Although several fish cell lines have been tested, successful culture was achieved only with CHSE-214 cells. Cytopathic effects were observed after 5 days. The highest virus titres, calculated by microtitration assay, were reached at 15 degrees C. After 7-9 days post-inoculation, CHSE-214 cell supernatants contained between 10(7)-10(5) TCID50 ml(-1) The cultured isolate is chloroform- and pH 3.0-sensitive, and virions are 50-60 nm in diameter. These characteristics are similar to the Irish SPDV isolates. The culture isolate induced typical pancreas disease (PD) lesions in experimentally infected Atlantic salmon and convalescent fish were resistant to experimental infection with PD-infective kidney homogenates obtained by serial in vivo passages from a PD-infected farmed salmon (termed wild-type SPDV). Furthermore, fish immunised with the inactivated cultured virus were protected against a cohabitation challenge with the wild-type virus. Immunised fish sera showed virus-neutralising activity before challenge (7 weeks post-immunisation) and from 3-6 weeks post-challenge, when sera from non-immunised fish did not neutralise the virus. At 6 weeks post-cohabitation challenge, previously immunised fish had neutralising titres of up to 1:65. Following intraperitoneal (i.p.) challenge, immunised fish showed neutralising titres as high as 1:226 at 8 weeks post-challenge. Non-immunised fish injected i.p. with the wild-type virus developed serum-neutralising activity against the cultured isolate when sampled 8 weeks after infection, confirming an antigenic relationship between the wild-type and cultured virus. The results demonstrate that the tissue culture-adapted isolate of SPDV could be successfully used to protect against challenge by the wild-type virus and could therefore have potential use as an inactivated vaccine against PD.
Alphavirus↗
A biomathematical model of particle clearance and retention in the lungs of coal miners.
To understand better the factors influencing the relationships among airborne particle exposure, lung burden, and fibrotic lung disease, we developed a biologically based kinetic model to predict the long-term retention of particles in the lungs of coal miners. This model includes alveolar, interstitial, and hilar lymph node compartments. The 131 miners in this study had worked in the Beckley, West Virginia, area and died during the 1960s. The data used to develop this model include exposure to respirable coal mine dust by intensity and duration within each job, lung and lymph node dust burdens at autopsy, pathological classification of fibrotic lung disease, and smoking history. Initial parameter estimates for this model were based on both human and animal data of particle deposition and clearance and on the biological and physical factors influencing these processes. Parameter estimation and model fit to the data were determined using least squares. Results show that the end-of-life lung dust burdens in these coal miners were substantially higher than expected from first-order clearance kinetics, yet lower than expected from the overloading of alveolar clearance predicted from rodent studies. The best-fitting and most parsimonious model includes processes for first-order alveolar-macrophage-mediated clearance and transfer of particles to the lung interstitium. These results are consistent with the particle retention patterns observed previously in the lungs of primates. The findings indicate that rodent models extrapolated to humans, without adjustment for the kinetic differences in particle clearance and retention, would be inadequate for predicting lung dust burdens in humans. Also, this human lung kinetic model predicts greater retained lung dust burdens from occupational exposure than predicted from current human models based on lower exposure data. This model is useful for risk assessment of particle-induced lung diseases, by estimating equivalent internal doses in rodents and humans and predicting lung burdens in humans with occupational dust exposures.
Air Pollutants, Occupational↗
A biomathematical model of particle clearance and retention in the lungs of coal miners. II. Evaluation of variability and uncertainty.
The objective of this study is to investigate the sources of variability and uncertainty in a previously developed human lung dosimetry model. That three-compartment model describes the retention and clearance kinetics of respirable particles in the gas-exchange region of the lungs. It was calibrated using exposure histories and lung dust burden data in U.S. coal miners. A multivariate parameter estimation and optimization method was developed for fitting the dosimetry model to these human data. Models with various assumptions about overloading of alveolar clearance and interstitialization (sequestration) of particles were evaluated. Variability in the estimated clearance rate coefficients was assessed empirically by fitting the model to groups' and to each miner's data. Distributions of lung and lymph node particle burdens were computed at working lifetime exposures, using the variability in the estimated individual clearance rate coefficients. These findings confirm those of the earlier analysis; i.e., the best-fitting exposure-dose model to these data has substantial interstitialization/sequestration of particles and no dose-dependent decline in alveolar clearance. Among miners with different characteristics for smoking, disease, and race, the group median estimated alveolar clearance rate coefficients varied by a factor of approximately 4. Adjustment for these group differences provided some improvement in the dosimetry model fit to all miners (up to 25% reduction in MSE), although unexplained interindividual differences made up the largest source of variability. The predicted mean lung and lymph node particle burdens at age 75 after exposure to respirable coal mine dust at 2 mg/m(2) for a 45-year working lifetime were 12 g (5th and 95th percentiles, 3.0-26 g) and 1.9 g (0.26-5.3), respectively. This study provides quantitative information on variability in particle retention and clearance kinetics in humans. It is useful for risk assessment by providing estimated lung dust burdens associated with occupational exposure to respirable particles.
Adult↗