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.

Clustal W and Clustal X version 2.0.

SUMMARY: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. AVAILABILITY: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/

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.

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.

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.

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.

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.

Analysis of human crystalline lens curvature as a function of accommodative state and age.

Slit-lamp photographs from four human subjects, aged 11, 19, 29, and 45 were reanalyzed using computer-based digitization and curve-fitting methods in order to obtain more complete information on internal lens curvature changes during accommodation. All discernible curves (N = 742) could be fit to parabolas with chi 2 less than or equal to 0.001 irrespective of lens age, accommodative state, or curve location within the lens. For each lens, the coefficients of the parabolas, when displayed in graphic form, exhibit a linear relationship between location within the lens and the coefficient of the chi 2 term. The slope of this line remains unchanged over accommodation for a given lens, but is shifted in position. The slope changes as a function of age. The age 45 lens exhibits these characteristics to a limited extent only, the differences possibly related to the development of presbyopia. The further a given curve is located from the lens surface, the smaller the region of its arc that can be considered approximately circular. A roughly hourglass figure is generated by these circular bounds; the waist of the hourglass decreases with increasing accommodation, since changes in radius of curvature with accommodation are more pronounced internally. Calculations of arc lengths as a function of increasing accommodation indicate that these lengths change very little over the entire accommodative range.

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.

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.

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.

Stereotactic radiosurgery in patients with multiple brain metastases.

OBJECT: Patients with multiple brain metastases are often treated primarily with fractionated whole-brain radiation therapy (WBRT). In previous reports the authors have shown that patients with four or fewer brain metastases can benefit from stereotactic radiosurgery in addition to fractionated WBRT. In this paper the authors review their experience using linear accelerator stereotactic radiosurgery to treat patients with multiple brain metastases. METHODS: Fifty-three patients with 149 brain metastases underwent stereotactic radiosurgery. The mean age of patients was 53.1 years (range 20-78 years). There were 23 men and 30 women. The primary tumor location was lung (27 patients), melanoma (10), breast (six), ovary (six), and other (four). All patients harbored at least two metastatic tumors treated with radiosurgery; 27 patients (51%) harbored two lesions, 17 (32%) three lesions, eight (15%) four lesions, and one patient (2%) harbored five lesions. The mean radiation dose administered was 19.6 Gy (range 14-30 Gy), and the mean secondary collimator size was 15.7 mm (range 7.5-40 mm). One hundred thirty-two (89%) of the 149 treated tumors were available for review on magnetic resonance (MR) imaging at 3 months posttreatment. Fifty-two percent were smaller in size, 31% were stable, 9% had increased in size, and 8% had disappeared. New metastatic tumors appeared in 12 (23%) of the 53 patients on MR imaging within 6 months posttreatment. Radiation-induced necrosis occurred at the site of eight (5.4%) of the 149 tumors at 6 months. Seven tumors (4.7%) subsequently required surgical resection for either tumor progression (four cases) or worsening edema from radiation-induced necrosis (three cases). Median actuarial survival was 9.6 months. CONCLUSIONS: Stereotactic radiosurgery can be used to treat patients with up to four brain metastases with a 91% rate of either decrease or stabilization in tumor size and a low rate of radiation-induced necrosis. In the authors' study only a small number of patients subsequently required surgical resection of a treated lesion.

Intracranial metastases from a supraglottic carcinoma (a case report).

An extremely rare case of intracranial metastasis from a laryngeal carcinoma is reported associated with multiple pulmonary metastatic deposits.

Radical surgical treatment for extensive chronic fronto-ethmoidal sinusitis.

An unusually extensive case of fronto-ethmoidal sinusitis is presented in which normal conservative surgical measures failed to achieve clearance. A modified form of craniofacial resection was therefore performed with effective clearance of disease.

Epiglottopexy: a modification using additional hyoid suspension.

A case of non-progressive severe laryngeal incompetence is described in which, in addition to the already established operation of epiglottopexy and cricopharyngeal myotomy, a laryngeal suspension using a carbon fibre implant is performed. This provides additional protection to the laryngeal inlet, thus obviating the need for a long-term tracheostomy.

Glomus vagale: an unusual presentation.

An unusual case of glomus vagale tumour is presented where severe pain was a predominant feature. The pathological and clinical features of this rare tumour are reviewed and the investigations and treatment are discussed.