Biomedical subjects
Publications and source records attributed to R George.
The value of medical therapy for acute exacerbations of chronic bronchitis generally increases with the severity of the episode. Antibiotics have a definite but limited benefit in severe cases. Systemic corticosteroids are valuable during hospitalization, but not after the patient has been discharged. Once recovery has occurred, pulmonary rehabilitation can improve quality of life.
Equal Symbol Fourier Transforms (FTES), characterizing nucleotide periodicity, comprise components of 5-D vectors that define base-repeat properties of a genomic sequence. This report describes a conversion of the FTES signals to a common platform of Shannon information content to facilitate comparisons of periodic data with other measures of information for genes and genomes. The autocorrelation used to compute the discrete FTES formed the basis to define repeating bases in terms of conditional probabilities. We derived a vector equation to express the Shannon information content of a sequence in a way that preserves the distinct specificity of base repeat patterns characterized by FTES vectors. We suggest application of such information vectors to study the structure of information in genes, chromosomes, and genomes by chi(2) comparisons.
BACKGROUND/AIMS: Hepatitis B mutant strains of virus emerging during treatment with the nucleoside analog lamivudine are being increasingly recognized. In the majority of lamivudine-resistant isolates the mutations have been reported to occur within the YMDD motif of the viral polymerase, either as a single mutation M552I or as M552V concomitant with L528M. We analyzed the time course and genetic succession pattern during the emergence of lamivudine resistance. METHODS: Seven patients with breakthrough viremia in the setting of chronic hepatitis (n=5) or recurrent HBV after liver transplantation (n=2) were investigated. Pre- and post-breakthrough serum samples were evaluated by single- or second-round PCR amplification and sequencing analysis. RESULTS: Genotypic succession of the virus populations was observed to occur from M552I to M552I/L528M (n=2) and from L528M to M552V/L528M (n=1). The double mutations M552I/L528M (n=4) or M552V/L528M (n=2) were found in six out of seven patients, and represented the stable virus populations throughout the follow-up period. Breakthrough viremia was not associated with the single L528M mutation. The mean duration of uninterrupted treatment with lamivudine until breakthrough was 422 days (range 182-642) and was longer in the setting of chronic hepatitis B than in recurrent hepatitis B after liver transplantation. HBV DNA levels after breakthrough were lower than pretreatment levels in the majority of patients with chronic hepatitis but higher after liver transplantation. CONCLUSION: Our observations show that the virus populations conferring resistance to lamivudine can evolve from single to double mutations at amino acid 552 and 528 of the HBV polymerase, and that M552I/ L528M or M552V/L528M seem to be the predominant mutations arising during long-term antiviral therapy with lamivudine.
UNLABELLED: The results of enhanced national surveillance of pneumococcal disease in children < 15 y of age in England and Wales are reported for the period 1996-1998. Of the 1985 cases of laboratory-confirmed invasive disease (annual incidence 6.6 per 100,000 overall and 39.7 per 100,000 in infants < 1 y of age), 485 (24%) were meningitis (annual incidence of 1.6 per 100,000 overall and 15.7 per 100,000 in infants <1 y of age). Fifty-nine deaths in children with invasive disease were identified-3% of the total reports. Thirty-one different serogroups/types were identified, with organisms in the 7-valent conjugate vaccine responsible for 69% of the infections in children < 5 y of age: this rose to 77% and 82%, respectively, for the 9-and 11-valent vaccines. Resistance to penicillin varied from 2.3% to 6.2% in different years, but erythromycin resistance remained constant at 17%. The vast majority of resistant isolates were in vaccine serotype/groups. Computerized hospital admission records for all children < 15 y of age with a discharge diagnosis code indicating probable pneumococcal disease were also analysed for 1997. The annual incidence for cases with a code specifically mentioning S. pneumoniae was 9.9 per 100,000 compared with 71.2 per 100,000 for lobar pneumonia; the mean duration of stay for both was < 1 wk. The incidence of admission for pneumococcal meningitis (1.9 overall and 19.6 for infants < 1 y of age) was similar to that derived from laboratory reports and resulted in an average duration of stay of 2 wk. CONCLUSION: This surveillance has confirmed the substantial burden of morbidity attributable to pneumococcal disease in British children and the potential public health benefits that could be achieved by the use of pneumococcal conjugate vaccines.
A total of 1,500 recent throat isolates of Streptococcus pyogenes collected between 1996 and 1999 from children throughout France were tested for their susceptibility to erythromycin, azithromycin, josamycin, clindamycin, and streptogramin B. The erythromycin-resistant isolates were further studied for their genetic mechanism of resistance, by means of PCR. The clonality of these strains was also investigated by means of serotyping and ribotyping. In all, 6.2% of the strains were erythromycin resistant, and 3.4 and 2.8% expressed the constitutive MLS(B) and M resistance phenotypes and harbored the ermB and mefA genes, respectively; ermTR was recovered from one isolate which also harbored the ermB gene. Ten serotypes and 8 ribotypes were identified, but we identified 17 strains by combining serotyping with ribotyping. Among the eight ribotypes, the mefA gene was recovered from six clusters, one being predominant, while the ermB gene was recovered from four clusters, of which two were predominant.
Nested PCRs for human immunodeficiency virus type 1 (HIV-1) and HIV-2 were compared with immunoblot test results. Twelve of 13 immunoblot-positive HIV-2 samples were positive by PCR. There were five INNO-LIA (Innogenetics, Zwijnaarde, Belgium) and/or HIVBLOT 2.2 (Genelabs, Singapore) samples that tested positive for dual infection. HIV-1 PCR was positive in all samples, while HIV-2 PCR was positive in two and RIBA (Chiron Corporation, San Diego, Calif.) was positive for HIV-2 in three samples. Thus the prevalence of HIV-2 is accurately estimated by the use of immunoblotting, but that of HIV-1 and -2 dual infection may be overestimated.
The oral streptococcal group (mitis phylogenetic group) currently consists of nine recognized species, although the group has been traditionally difficult to classify, with frequent changes in nomenclature over the years. The pneumococcus (Streptococcus pneumoniae), an important human pathogen, is traditionally distinguished from the most closely related oral streptococcal species Streptococcus mitis and Streptococcus oralis on the basis of three differentiating characteristics: optochin susceptibility, bile solubility, and agglutination with antipneumococcal polysaccharide capsule antibodies. However, there are many reports in the literature of pneumococci lacking one or more of these defining characteristics. Sometimes called "atypical" pneumococci, these isolates can be the source of considerable confusion in the clinical laboratory. Little is known to date about the genetic relationships of such organisms with classical S. pneumoniae isolates. Here we describe these relationships based on sequence analysis of housekeeping genes in comparison with previously characterized isolates of S. pneumoniae, S. mitis, and S. oralis. While most pneumococci were found to represent a closely related group these studies identified a subgroup of atypical pneumococcal isolates (bile insoluble and/or "acapsular") distinct from, though most closely related to, the "typical" pneumococcal isolates. However, a large proportion of isolates, found to be atypical on the basis of capsule reaction alone, did group with typical pneumococci, suggesting that they have either lost capsule production or represent as-yet-unrecognized capsular types. In contrast to typical S. pneumoniae, isolates phenotypically identified as S. mitis and S. oralis, which included isolates previously characterized in taxonomic studies, were genetically diverse. While most of the S. oralis isolates did fall into a well-separated group, S. mitis isolates did not cluster into a well-separated group. During the course of these studies we also identified a number of potentially important pathogenic isolates, which were frequently associated with respiratory disease, that phenotypically and genetically are most closely related to S. mitis but which harbor genes encoding the virulence determinants pneumolysin and autolysin classically associated with S. pneumoniae.
METHODS: The records of 106 children aged less than 5 years with invasive disease caused by Streptococcus pneumoniae were reviewed. RESULTS: The clinical manifestations were meningitis (37%), upper respiratory tract infection (24%), pneumonia (19%), and occult bacteraemia (18%). One child died and seven had persisting neurological impairment. Five serotypes caused 83% of disease and 92% of the serotypes are included in the seven valent conjugate vaccines which are undergoing trials. CONCLUSIONS: These data suggest that S pneumoniae infection is associated with a low case fatality rate but substantial morbidity in the UK.
In June 1997 a postal questionnaire was sent to all palliative medicine trainees in the United Kingdom to ascertain the resources available to facilitate education and research, and the experiences of trainees who had undertaken research. Questions posed related to protected study time, library facilities, information technology (IT) support, postgraduate educational activities, details of research projects undertaken, level of senior supervision and overall impressions. The response rate was 85%. Thirty-six per cent of respondents were undertaking postgraduate educational courses and 30% of those remaining planned to do so. Protected time for study was allocated to almost all trainees, but access to educational resources was more variable. The availability of several journals and of information technology support was lower than their perceived importance. Satisfaction scores for the availability of books covering areas related to clinical practice were high, but were lower for availability of the internet and of books covering specific training issues. Ninety-one per cent of respondents had been involved in research/audit projects, two-thirds had published at least one article and half had presented an oral or written paper. Details of 162 projects were received, together with problems encountered. The results indicate that many of the foundations for specialist education in palliative medicine are in place and that trainees are highly motivated towards conducting research. The aspects in need of improvement on the educational side include IT facilities and the availability of specific speciality related journals. There is a need for more accessible supervision from senior colleagues and training in research methodology.
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A surgical approach designed to reliably attain the modern goal of small incision cataract surgery 99.8% of the time is described. Phacoemulsification as well as a manual small incision technique is utilised to achieve the desired outcome as often as possible and for all types of cataracts. The logic, and required surgical steps are described and illustrated. This surgical technique allows the advantages of small incision surgery to be reliably achieved. The method is flexible and allows decisions and steps to be modified depending on the skill and comfort zone of the individual surgeon.
Tail-anchored proteins are inserted into intracellular membranes via a C-terminal transmembrane domain. The topology of the protein is such that insertion must occur post-translationally, since the insertion sequence is not available for membrane insertion until after translation of the tail-anchored polypeptide is completed. Here, we show that the targeting information in one such tail-anchored protein, translocase in the outer mitochondrial membrane 22, is contained in a short region flanking the transmembrane domain. An equivalent region is sufficient to specify the localisation of Bcl2 and SNARE proteins to the secretory membranes. We discuss the targeting process for directing members of this protein family to the secretory and mitochondrial membranes in vivo.
A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized "Adh region." A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species. Before beginning a Hunt, it is wise to ask someone what you are looking for before you begin looking for it. Milne 1926
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We have used fluorescent amplified-fragment length polymorphism (FAFLP) analysis to subtype clinical isolates of Streptococcus pyogenes serotype M1. Established typing methods define most M1 isolates as members of a clone that has a worldwide distribution and that is strongly associated with invasive diseases. FAFLP analysis simultaneously sampled 90 to 120 loci throughout the M1 genome. Its discriminatory power, precision, and reproducibility were compared with those of other molecular typing methods. Irrespective of disease symptomatology or geographic origin, the majority of the clinical M1 isolates shared a single ribotype, pulsed-field gel electrophoresis macrorestriction profile, and emm1 gene sequence. Nonetheless, among these isolates, FAFLP analysis could differentiate 17 distinct profiles, including seven multi-isolate groups. The FAFLP profiles of M1 isolates reproducibly exhibited between 1 and more than 20 amplified fragment differences. The high discriminatory power of genotyping by FAFLP analysis revealed genetic microheterogeneity and differentiated otherwise "identical" M1 isolates as members of a clone complex.
OBJECTIVE: As a direct or indirect result of antiphospholipid antibody production, subjective laboratory interpretation, and false positive results, the common serologic tests for syphilis have been inherently inaccurate diagnostic tests in patients with systemic lupus erythematosus (SLE) and other autoimmune diseases. We assessed the diagnostic accuracy of syphilis testing in patients with SLE and other autoimmune diseases using the treponemal Western blot (TWB) as the gold standard. METHODS: A prospective cohort study carried out at a tertiary care medical center. We studied 107 patients with autoimmune disease, 50 with at least one positive serologic test for syphilis and 57 disease matched controls. Prior to enrollment all eligible patients underwent a clinical assessment performed by at least 2 rheumatologists to confirm a diagnosis of rheumatic disease. All subjects underwent serologic testing, in blinded fashion, for syphilis using the rapid plasma reagin test (RPR), Venereal Disease Research Laboratory test (VDRL), fluorescent treponemal antibody absorption test (FTA-ABS), and the TWB. RESULTS: Eighty-seven percent of the patients studied were female, the mean age was 46.5 years, and the most common diagnosis at the time of enrollment was SLE. Using the TWB as the gold standard diagnostic test for syphilis, the sensitivity, specificity, and positive predictive values for each syphilis test were calculated. The sensitivity and specificity for the RPR in patients with rheumatic disease was 62.5% (95% confidence interval 24.5 to 91.5%) and 91.9% (95% CI 84.2 to 96.2%), respectively. The sensitivity and specificity for the VDRL were 37.5% (95% CI 8.5 to 75.5%) and 89.9% (95% CI 81.8 to 94.8%), respectively. Confirmatory syphilis testing using the FTA-ABS showed a sensitivity of 100% (95% CI 68.6 to 100%) and a specificity of 67.7% (95% CI 57.4 to 76.5%). Eight patients tested positive for syphilis by Western blotting. For the FTA-ABS test, there was a significantly higher number of false positive results (n = 32) compared to false negative results (n = 0), p < 0.0005. CONCLUSION: The FTA-ABS is not an accurate confirmatory test for syphilis in patients with SLE and other autoimmune diseases. While a negative FTA-ABS may exclude syphilis infection in the majority of cases, a positive FTA-ABS test result cannot assuredly confirm syphilis infection in this population. Western blotting is an accurate confirmatory test for syphilis and may be necessary to unequivocally discern the immunological response of syphilis from that of an underlying autoimmune disease.
Homologous recombination was used to construct a series of hybrid chaperonin genes, containing various lengths of Escherichia coli groEL replaced by the equivalent region from the homologous cpn60-1 gene of Rhizobium leguminosarum. Analysis of proteins produced by these hybrids showed that many of them formed structures with properties consistent with their being single heptameric rings under some conditions, as opposed to the double ring form in which both the GroEL and the Cpn60-1 proteins are found. By determining precise cross-over points, two regions in Cpn60-1 were defined which appeared to be critical for ring-ring interactions. Within one of these regions is a highly conserved arginine residue (Arg101), which we hypothesised to interact with a residue or residues toward the C terminus of the protein, this contact being required for double rings to form. To test this hypothesis, we mutagenised this residue from arginine to threonine in chaperonin genes from two different species of Rhizobium. In both cases, proteins which ran on non-denaturing gels as single rings were produced. Conversion of Arg101 to serine also had the same effect, whereas conversion of Arg101 to lysine did not. Two different single rings created by homologous recombination could be converted back to double rings by changing the threonine, which naturally occurs at this position in E. coli GroEL, back to arginine. The in vivo properties of the proteins were investigated by complementation following deletion of the chromosomal copy of the groEL gene, and by monitoring the ability of cells expressing the hybrid proteins to plate bacteriophage. Most of the hybrid and mutant proteins were functional in these assays, despite their altered properties compared to wild-type GroEL.
The yeast nascent polypeptide-associated complex (NAC) is encoded by two genes, EGD1 and EGD2, and is associated with cytoplasmic ribosomes. Yeast mutants lacking NAC (Deltaegd2) are viable but suffer slight defects in the targeting of nascent polypeptides to several locations including the endoplasmic reticulum and mitochondria. If both NAC and Mft52p are missing from yeast cells, inefficient targeting of mitochondrial precursor proteins leads to defects in both mitochondrial function and morphology. We suggest that NAC provides a ribosomal environment for nascent mitochondrial targeting sequences to achieve secondary structure, thereby enhancing the efficiency of protein targeting.