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Biomedical subjects

N P Brown

Publications and source records attributed to N P Brown.

At least 19 recordsLinked to original sources
PubMed1996

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli.

BACKGROUND: The 1.83 Megabase (Mb) sequence of the Haemophilus influenzae chromosome, the first completed genome sequence of a cellular life form, has been recently reported. Approximately 75 % of the 4.7 Mb genome sequence of Escherichia coli is also available. The life styles of the two bacteria are very different - H. influenzae is an obligate parasite that lives in human upper respiratory mucosa and can be cultivated only on rich media, whereas E. coli is a saprophyte that can grow on minimal media. A detailed comparison of the protein products encoded by these two genomes is expected to provide valuable insights into bacterial cell physiology and genome evolution. RESULTS: We describe the results of computer analysis of the amino-acid sequences of 1703 putative proteins encoded by the complete genome of H. influenzae. We detected sequence similarity to proteins in current databases for 92 % of the H. influenzae protein sequences, and at least a general functional prediction was possible for 83 %. A comparison of the H. influenzae protein sequences with those of 3010 proteins encoded by the sequenced 75 % of the E. coli genome revealed 1128 pairs of apparent orthologs, with an average of 59 % identity. In contrast to the high similarity between orthologs, the genome organization and the functional repertoire of genes in the two bacteria were remarkably different. The smaller genome size of H. influenzae is explained, to a large extent, by a reduction in the number of paralogous genes. There was no long range colinearity between the E. coli and H. influenzae gene orders, but over 70 % of the orthologous genes were found in short conserved strings, only about half of which were operons in E. coli. Superposition of the H. influenzae enzyme repertoire upon the known E. coli metabolic pathways allowed us to reconstruct similar and alternative pathways in H. influenzae and provides an explanation for the known nutritional requirements. CONCLUSIONS: By comparing proteins encoded by the two bacterial genomes, we have shown that extensive gene shuffling and variation in the extent of gene paralogy are major trends in bacterial evolution; this comparison has also allowed us to deduce crucial aspects of the largely uncharacterized metabolism of H. influenzae.

Bacterial Proteins↗
PubMed1996

The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues.

A thorough sequence analysis of the various members of the eukaryotic protein serine/threonine phosphatase 2C (PP2C) family revealed the conservation of 11 motifs. These motifs could be identified in numerous other sequences, including fungal adenylate cyclases that are predicted to contain a functionally active PP2C domain, and a family of prokaryotic serine/threonine phosphatases including SpoIIE. Phylogenetic analysis of all the proteins indicates a widespread sequence family for which a considerable number of isoenzymes can be inferred.

Amino Acid Sequence↗
PubMed1996

Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium.

The current status and future outlook of macromolecular structure databases and information handling, with particular reference to European databases, are reviewed. Issues concerning the efficiency with which data are represented, validated, archived and accessed are discussed in view of the fast growing body of information on structures of biological macromolecules.

Databases, Factual↗
PubMed1995

Identification and analysis of multigene families by comparison of exon fingerprints.

Gene families are often recognised by sequence homology using similarity searching to find relationships, however, genomic sequence data provides gene architectural information not used by conventional search methods. In particular, intron positions and phases are expected to be relatively conserved features, because mis-splicing and reading frame shifts should be selected against. A fast search technique capable of detecting possible weak sequence homologies apparent at the intron/exon level of gene organization is presented for comparing spliceosomal genes and gene fragments. FINEX compares strings of exons delimited by intron/exon boundary positions and intron phases (exon fingerprint) using a global dynamic programming algorithm with a combined intron phase identity and exon size dissimilarity score. Exon fingerprints are typically two orders of magnitude smaller than their nucleic acid sequence counterparts giving rise to fast search times: a ranked search against a library of 6755 fingerprints for a typical three exon fingerprint completes in under 30 seconds on an ordinary workstation, while a worst case largest fingerprint of 52 exons completes in just over one minute. The short "sequence" length of exon fingerprints in comparisons is compensated for by the large exon alphabet compounded of intron phase types and a wide range of exon sizes, the latter contributing the most information to alignments. FINEX performs better in some searches than conventional methods, finding matches with similar exon organization, but low sequence homology. A search using a human serum albumin finds all members of the multigene family in the FINEX database at the top of the search ranking, despite very low amino acid percentage identities between family members. The method should complement conventional sequence searching and alignment techniques, offering a means of identifying otherwise hard to detect homologies where genomic data are available.

Animals↗
PubMed1995

Validation of methods for the assessment of cataract progression in the Roche European-American Anticataract Trial (REACT)

The Roche European-American Anticataract Trial (REACT) will assess the effect of antioxidants on progression of cataract in humans. This report evaluates the methods used in REACT. Seventy three subjects (139 eyes) with cortical (C), posterior subcapsular (P), nuclear (N) or mixed cataract were seen twice within two weeks for eye examinations, assessments of visual function, lens photographs and CCD images. The degree of cataract and nuclear color (NC) were assessed with subjective (LOCS III) and objective (computerized, CASE 2000 CCD) methods. Repeat visit values were used to calculate intraclass correlation coefficients (r1) and 95% tolerance limits (TL). A clinically significant change (CSC) was defined as one step in LOCS III. The relative power of each method to detect cataract change and sample sizes needed to achieve statistically significant results were calculated. The r1 values for visual function tests ranged from 0.76 to 0.88; if these tests of visual function were used to detect a clinically significant change in cataract severity, sample sizes of 840 to 2707 per group would be needed. The r1 values for LOCS III were 0.88 to 0.97, and sample sizes ranged from 50 to 135 per group. The r1 values for the CCD were 0.93 to 0.98, and sample sizes ranged from 1 to 42 with poorer values relating to measurement of P. We conclude that the methods used in REACT are reproducible. The analytical algorithms in the image analysis programs did not permit differentiation between C and P opacification; therefore, P cataract is best measured with LOCS III. REACT sample sizes are adequate to detect a difference of 0.2 LOCS III units/year between the mean rates of cataract progression in two groups.

Adult↗
PubMed1994

Growing a classification tree using the apparent misclassification rate.

A method to determine the size of a classification tree is proposed. This method is based on the change of the apparent misclassification rate (AMR) of the tree at each growing stage. The method is simple and fast compared to the other classification tree methods, which are based on minimizing a cost complexity function. To test the method, it was used to classify species of fungi, and the results are in good agreement with those obtained by linear discriminant analysis. Also, 21 proteins with known structures and functions were classified using the proposed method. For this purpose the coefficient of variation for several properties of the secondary structures of these proteins has been used. Again, the results were in good agreement with the classification obtained previously using dynamic programming.

Algorithms↗
PubMed1994

Heterogeneity in ultrastructure and elemental composition of perinuclear lens retrodots.

PURPOSE: To unravel the cataractogenic process(es) leading to the birefringent lenticular bodies known as perinuclear retrodots. METHODS: Ten human lenses containing biomicroscopically verified perinuclear retrodots were systematically screened and analyzed using scanning electron microscopy and energy dispersive x-ray microanalysis to verify their ultrastructure and elemental composition. RESULTS: Three types of retrodots were distinguished, different in size, ultrastructure, and origin. Two of them contained calcium phosphate, the third probably contained calcium oxalate. All three types were separated from surrounding normal fibers and the crystalline inclusions were sequestered within membrane-lined bodies. CONCLUSIONS: Because of these observations and data found in the literature it is postulated that elevated free calcium is the initiating factor in the formation of retrodots, trapped by either oxalate or phosphate and sequestered in the retrodots. It is suggested that the oxalate is derived from ascorbate because of impaired protection against oxidative stress in the older lens. Phosphoric acid is believed to be released by calcium-induced hydrolysis of membrane phospholipids.

Calcium Oxalate↗
PubMed1993

Is cortical spoke cataract due to lens fibre breaks? The relationship between fibre folds, fibre breaks, waterclefts and spoke cataract.

Fibre folds, previously called lamellar separation of the lens, have been found by electron microscopy to be associated with fibre breaks, which are seen in vivo as the circular shades of Obazawa. This led to the present study to determine the relationship between fibre folds, fibre breaks, waterclefts and spoke cataract. All lenses with fibre folds were found to have circular shades. A few instances of circular shades without fibre folds were found, suggesting that the fibre break may be the primary pathology. It was found that circular shades occurred in association with spoke cataract only when fibre folds were also present. Thus there is no essential causal relationship between fibre breaks and spoke cataract. The occurrence of waterclefts was unrelated to the presence of the other features. The lower nasal quadrant of the lens was the most common site for the four features. The depth of spoke cataracts was found to be unrelated to the age of the patient, which makes it unlikely that accommodational stress at the time of onset of presbyopia is causative.

Age of Onset↗
PubMed1993

Morphologic characteristics and chemical composition of Christmas tree cataract.

PURPOSE: Christmas tree cataract consists of highly refractile multicolored "needles" crisscrossing the lens fibers of the deep cortex. The fact that the colors vary according to the angle of the incident light, and that in retroillumination only a dim outline of the cataract is seen, would suggest that Christmas tree cataract is a diffractive phenomenon. This study was performed to unravel the ultrastructure and chemical composition of the Christmas tree needles. METHODS: Eight lenses from donor eyes and four extracapsularly extracted lenses with Christmas tree cataract were investigated by scanning and transmission electron microscopy. The chemical composition was studied with energy-dispersive x-ray microanalysis and Raman microspectroscopy. RESULTS: Scanning electron microscope examination showed that the needles are smooth, rectangular, plate-like elements bordered by membranes and amorphous material and running crisscross through the lens. In the specimens for transmission electron microscopic examination, the needles proved to be largely dissolved, but the remains showed regular spacings of approximately 5 nm. Material identical in spacing and electron density was found in neighboring cells bound to a reticular membranous network originating from the fiber-limiting membranes. Energy-dispersive x-ray and Raman microanalysis showed that the needles have a high sulfur content and pronounced S-S, CS-SC, and C-S vibrations. The cytoplasm adjacent to the needles and reticular meshwork had an elevated Ca++ content. CONCLUSIONS: It is concluded that cystine is the most likely candidate for the Christmas tree needles and that the needles probably are formed as the result of an age-related aberrant breakdown of crystallins induced by elevated Ca++ levels.

Aged↗
PubMed1992

Fast structure alignment for protein databank searching.

A fast method is described for searching and analyzing the protein structure databank. It uses secondary structure followed by residue matching to compare protein structures and is developed from a previous structural alignment method based on dynamic programming. Linear representations of secondary structures are derived and their features compared to identify equivalent elements in two proteins. The secondary structure alignment then constrains the residue alignment, which compares only residues within aligned secondary structures and with similar buried areas and torsional angles. The initial secondary structure alignment improves accuracy and provides a means of filtering out unrelated proteins before the slower residue alignment stage. It is possible to search or sort the protein structure databank very quickly using just secondary structure comparisons. A search through 720 structures with a probe protein of 10 secondary structures required 1.7 CPU hours on a Sun 4/280. Alternatively, combined secondary structure and residue alignments, with a cutoff on the secondary structure score to remove pairs of unrelated proteins from further analysis, took 10.1 CPU hours. The method was applied in searches on different classes of proteins and to cluster a subset of the databank into structurally related groups. Relationships were consistent with known families of protein structure.

Amino Acid Sequence↗
PubMed1992

The relationship between central nuclear scatter and perinuclear retrodots in the human crystalline lens.

Retrodots are common perinuclear features of age-related cataract. Clinical observation suggested that retrodots were associated with increased nuclear scatter. To test this hypothesis, retrospective data were analysed from 78 non-diabetic subjects (118 eyes), of at least 50 years of age, who had neither subscapsular nor axial spoke opacities. Retrodots were graded using the Oxford Clinical Cataract Classification and Grading system and central nuclear scatter was assessed by image analysis of Scheimpflug photographic negatives. Regression analysis in groups was performed according to the "intra-class correlation model" either considering retrodots as a graded feature (grades 0-5) or as a dichotomous variable (present or absent). After adjusting for age (treated as a co-variate), a highly significant association (P < 10(-6) was found between retrodots and increased nuclear scatter in each analysis. It is suggested that the co-existence of these two cataract types may reflect a common cataractogenic mechanism, possibly oxidative stress.

Aged↗
PubMed1991

Growth spurt in a lens with a posterior subcapsular cataract.

Over a period of 5 years, the lenses of a patient with a unilateral posterior subcapsular cataract were documented using Scheimpflug slit-image photography. For the first time ever, a growth spurt was observed of the cataractous lens. It is postulated that this could be a reflection of either a mitotic spurt of the lens epithelium or a failure of compaction of the deeper lens fibres.

Adult↗
PubMed1990

The lens after renal transplantation.

A single masked observer examined 55 non-diabetic patients chosen randomly from a population of patients who had undergone renal transplant. The mean age was 41 years and mean time from transplant was 4.4 years (1-10 years). Fourteen patients were found to have a posterior subcapsular cataract (PSC). The axial thickness of the right lens of the renal transplant population, even in the presence of a PSC, was significantly larger than in a control population of 99 patients with clear lenses. The PSC of renal transplantation is readily distinguished from age related PSC because the opacity lies in the superficial cortex at a depth proportional to time from transplant and the lens maintains a normal anterior clear zone. It is proposed that this type of cataract be called 'recovering' PSC. It is concluded that the cataractogenic insult occurs mainly during the peritransplant period. Maintenance doses of immunosuppressives or steroids are therefore probably not cataractogenic.

Adult↗
PubMed1989

Dynamic nature of posterior subcapsular cataract.

Posterior subcapsular cataracts were studied in 10 patients (19 eyes) and were photographed at four to 12 weeks intervals by the Oxford Retroillumination Camera. Changes in the fine structure of PSC may occur in as short a time as four weeks. Posterior subcapsular cataracts are shown to be in a state of flux and are not, as might be assumed, slowly but relentlessly progressive. This could imply the existence of a repair mechanism in the lens.

Adult↗
PubMed1988

Human lens nuclear colour matching and brunescence grading in vivo.

The nuclear colour of in vivo human lenses has been investigated by means of a colour matching technique, using 'Munsell' colour samples. Observations covered an extended age range, and included all degrees of nuclear pigmentation. A positive correlation was noted between increasing nuclear pigmentation and age. The colour matching data generated was used as a basis for establishing a system of nuclear brunescence grading. The system of grading consists of a Grade 0 for absence of brunescence, and Grade 1 to Grade 5 for increasing brunescence. The 'Munsell' notation for samples representing these grades are: Grade 0 (5GY 6/1), Grade 1 (5Y 7/4), Grade 2 (2.5Y 7/8), Grade 3 (7.5YR 6/8), Grade 4 (5YR 4/6), and Grade 5 (2.5YR 2.5/2). Assessments of both inter- and intra-observer variability in the use of the derived scale have shown the new colour grading system to be reliable. The measure is simple to use during biomicroscopic slit-lamp examination of the lens, and has the potential for routine clinical application as well as for use in clinical trials where detailed documentation of lens morphology is required. The new colour scale may be used either as an isolated measure, or as part of a battery of lens measures in the Oxford Clinical Cataract Classification and Grading system.

Aging↗
PubMed1988

Inter-observer and intra-observer variability of the Oxford clinical cataract classification and grading system.

Intra-observer (within observers) and inter-observer (between observers) variability of the Oxford Clinical Cataract Classification and Grading System were studied. Twenty cataracts were examined and scored independently by four observers. On a separate occasion two of the observers repeated the assessments of the same cataracts in the absence of information from the initial observations. The chance corrected and weighted kappa statistics for observer agreement, both for inter-observer and intra-observer variability demonstrated satisfactory repeatability of the cataract grading system. The overall intra-observer mean weighted kappa was kappa w = +0.68 (range SE kappa = 0.012-0.052) and the overall inter-observer mean weighted kappa was kappa w = +0.55 (range SE kappa = 0.011-0.043).

Cataract↗