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/

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.

The development and maintenance of emmetropia.

The human eye is programmed to achieve emmetropia in youth and to maintain emmetropia with advancing years. This is despite the changes in all eye dimensions during the period of growth and the continuing growth of the lens throughout life. The process of emmetropisation in the child's eye is indicated by a shift from the Gaussian distribution of refractive errors around a hypermetropic mean value at birth to the non-Gaussian leptokurtosis around an emmetropic mean value in the adult. Emmetropisation is the result of both passive and active processes. The passive process is that of proportional enlargement of the eye in the child. The proportional enlargement of the eye reduces the power of the dioptric system in proportion to the increasing axial length. The power of the cornea is reduced by lengthening of the radius of curvature. The power of the lens is reduced by lengthening radii of curvature and the effectivity of the lens is reduced by deepening of the anterior chamber. Ametropia results when these changes are not proportional. The active mechanism involves the feedback of image focus information from the retina and consequent adjustment of the axial length. Defective image formation interferes with this feedback and ametropia then results. Heredity determines the tendency to certain globe proportions and environment plays a part in influencing the action of active emmetropisation. The maintenance of emmetropia in the adult in spite of continuing lens growth with increasing lens thickness and increasing lens curvature, which is known as the lens paradox, is due to the refractive index changes balancing the effect of the increased curvature. These changes may be due to the differences between nucleus and cortex or to gradient changes within the cortex.

Iterated sequence databank search methods.

Iterated sequence databank search methods were assessed from the viewpoint of someone with the sequence of a novel gene product wishing to find distant relatives to their protein and, with the specific searches against the PDB, also hoping to find a relative of known structure. We examined three methods in detail, spanning a range from simple pattern-matching to sophisticated weighted profiles. Rather than apply these methods 'blindly' (with default parameters) to a large number of test queries, we have concentrated on the globins, so allowing a more detailed investigation of each method on different data subsets with different parameter settings. Despite their widespread use, regular-expression matching proved to be very limited-seldom extending beyond the sub-family from which the pattern was derived. To attain any generality, the patterns had to be 'stripped-down' to include only the most highly conserved parts. The QUEST program avoided these problems by introducing a more flexible (weighted) matching. On the PDB sequences this was highly effective, missing only a few globins with probes based on each sub-family or even a single representative from each sub-family. In addition, very few false-positives were encountered, and those that did match, often only did so for a few cycles before being lost again. On the larger sequence collection, however, QUEST encountered problems with maintaining (or achieving) the alignment of the full globin family. psi-BLAST also recognised almost all the globins when matching against the PDB sequences, typically, missing three or four of the most distantly related sequences while picking-up a few false-positives. In contrast to QUEST, psi-BLAST performed very well on the larger databank, getting almost a full collection of globins although still retaining the same proportion of false-positives. SAM applied to the PDB sequences performed reasonably well with the myoglobin and hemoglobin families as probes, missing, typically several of the more difficult proteins but performed poorly with the leghemoglobin probe. Only with the full family range as a probe did it produce results comparable to psi-BLAST and QUEST. With the larger databank, SAM produced a good result but, again, this was only achieved using the full range of sequence variation with the default regulariser and use of Dirichlet mixtures completely failed in this situation.

Automated genome sequence analysis and annotation.

MOTIVATION: Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. RESULTS: We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. AVAILABILITY: The GeneQuiz system is publicly available for analysis of protein sequences through a Web server at http://www.sander.ebi.ac. uk/gqsrv/submit

Frame: detection of genomic sequencing errors.

MOTIVATION: The underlying error rate for genomic sequencing sometimes results in the introduction of artificial frameshifts and in-frame stop codons into putative protein encoding genes. Severe errors are then introduced into the inferred transcripts through mis-translation or premature termination. RESULTS: We describe a system for screening segments of DNA for frameshift and in-frame stop errors in coding regions. The method is based on homology matching using blastx to compare all six reading frames of the query nucleotide sequence against selected protein sequence databases. Fragments of protein matching neighbouring regions of the query DNA are united and extended laterally to define candidate open reading frames, within which, frameshifts and stops are identified. Suitable targets include prokaryotic or other intron-free genomic sequence and complementary DNAs. As an example of its use, we report here two frameshifted ORFs that deviate from the original TIGR sequence annotations for the recently released Helicobacter pylori genome. AVAILABILITY: The tool is accessible via the URL http://www.sander.ebi.ac.uk/frame/. CONTACT: brown@ebi.ac.uk.

MView: a web-compatible database search or multiple alignment viewer.

UNLABELLED: MView is a tool for converting the results of a sequence database search into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment can be processed. In either case, the output is simply HTML, so the result is platform independent and does not require a separate application or applet to be loaded. AVAILABILITY: Free from http://www.sander.ebi.ac.uk/mview/ subject to copyright restrictions. CONTACT: brown@ebi.ac.uk

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.

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.

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.

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.

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.

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.

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.

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.

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.

Anterior segment photography using the Oxford retro-illumination camera.

The use of the Oxford retro-illumination camera in documenting cataract is now well established. Repeatability has been shown to be good. This article describes its use in photographing the anterior segment of the eye.