Vitamin D receptor knock-out mice: the expectational and the exceptional

The program General Codon Usage Analysis (GCUA) has been developed for analysing codon and amino acid usage patterns. AVAILABILITY: ftp://ftp.nhm.ac.uk/pub/gcua. Freely available for academic use, commercial users should contact the author. CONTACT: J.McInerney@nhm.ac.uk     

Analysis of effects of tRNA:message stability on frameshift frequency at the Escherichia coli RF2 programmed frameshift site

The codon that is in-frame prior to +1 frameshifting at the E.coli prfB (RF2 gene) frameshift site is randomized to create thirty-two variants. These alleles vary 1000-fold in frameshift-dependent expression in fusions to lacZ. Frameshifting is more frequent at sites where the in-frame codon ends in uridine, as if third position wobble pairs to message uridine facilitate slippage into the +1 frame. Consistent with other studies of programmed frameshift sites, efficient frameshifting depends on stable message:tRNA base pairs after rephasing. For complexes with mispairs, frameshift frequency depends on the nature, number, and position of mispairs. Central purine:purine mispairs are especially inhibitory. Relative stabilities of +1 rephased complexes are estimated from published data on the stabilities of tRNA:tRNA complexes. Stability correlates with frameshifting over its entire range, which suggests that stability is an important determinant of the probability of translation of the rephased complex.     

Carbon dioxide laser stomaplasty for tracheostomal stenosis

RESULTS: This paper describes a new program which reveals, analyses and graphically represents patterns of variability along nucleotide sequences. AVAILABILITY: The program, 'SWAN', is available from the WWW at http://evolve.zoo.ox.ac.uk/ or from the authors upon request. CONTACT: Vitali.Proutski@zoology.oxford.ac.uk     

Re-evaluation of multi-allergen skin prick test for infants with atopic dermatitis--clinical relevance and evaluation by mothers

MOTIVATION: Evolutionary models of amino acid sequences can be adapted to incorporate structure information; protein structure biologists can use phylogenetic relationships among species to improve prediction accuracy. Results : A computer program called PASSML ('Phylogeny and Secondary Structure using Maximum Likelihood') has been developed to implement an evolutionary model that combines protein secondary structure and amino acid replacement. The model is related to that of Dayhoff and co-workers, but we distinguish eight categories of structural environment: alpha helix, beta sheet, turn and coil, each further classified according to solvent accessibility, i.e. buried or exposed. The model of sequence evolution for each of the eight categories is a Markov process with discrete states in continuous time, and the organization of structure along protein sequences is described by a hidden Markov model. This paper describes the PASSML software and illustrates how it allows both the reconstruction of phylogenies and prediction of secondary structure from aligned amino acid sequences. AVAILABILITY: PASSML 'ANSI C' source code and the example data sets described here are available at http://ng-dec1.gen.cam.ac.uk/hmm/Passml.html and 'downstream' Web pages. CONTACT: P.Lio@gen.cam.ac.uk     

The majority of long non-stop reading frames on the antisense strand can be explained by biased codon usage

In recent studies it has been suggested that long reading frames on the antisense strand of open reading frames (ORFs) are more frequent than expected. The vertebrate DNA database was searched for long (greater than 900 bp) antisense non-stop reading frames (aNRFs) that overlap known coding regions. The sequences obtained were predominantly positioned in DNA with a high usage of G or C in the third codon position of the sense ORF. The major class of sequences revealed by the search was that of the heat-shock protein 70 kDa (Hsp70) family. A long Hsp70 aNRF was found in many Hsp70 sequences and occurred in species as diverse as fish, flies, fungi and bacteria. The role of codon usage bias was analysed both in the specific case of the Hsp70 genes and in a general species-wide context. The data obtained showed that even the very long aNRFs present in the Hsp70 family could be explained by codon usage bias on the sense strand. Codon usage bias is determined by GC content at the third codon position of the sense ORF and, in some species, by a high expression level of the gene in question. Such an explanation for the occurrence of long aNRFs cannot exclude that some aNRFs are transcribed and translated.     

JPred: a consensus secondary structure prediction server

An interactive protein secondary structure prediction Internet server is presented. The server allows a single sequence or multiple alignment to be submitted, and returns predictions from six secondary structure prediction algorithms that exploit evolutionary information from multiple sequences. A consensus prediction is also returned which improves the average Q3 accuracy of prediction by 1% to 72.9%. The server simplifies the use of current prediction algorithms and allows conservation patterns important to structure and function to be identified. AVAILABILITY: http://barton.ebi.ac.uk/servers/jpred.h tml CONTACT: geoff@ebi.ac.uk     

Expected versus observed information in SEM with incomplete normal and nonnormal data.

Maximum likelihood is the most common estimation method in structural equation modeling. Standard errors for maximum likelihood estimates are obtained from the associated information matrix, which can be estimated from the sample using either expected or observed information. It is known that, with complete data, estimates based on observed or expected information are consistent. The situation changes with incomplete data. When the data are missing at random (MAR), standard errors based on expected information are not consistent, and observed information should be used. A less known fact is that in the presence of nonnormality, the estimated information matrix also enters the robust computations (both standard errors and the test statistic). Thus, with MAR nonnormal data, the use of the expected information matrix can potentially lead to incorrect robust computations. This article summarizes the results of 2 simulation studies that investigated the effect of using observed versus expected information estimates of standard errors and test statistics with normal and nonnormal incomplete data. Observed information is preferred across all conditions. Recommendations to researchers and software developers are outlined. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Adherence to the first-AUG rule when a second AUG codon follows closely upon the first

The rule that eukaryotic ribosomes initiate translation exclusively at the 5' proximal AUG codon is abrogated under rare conditions. One circumstance that has been suggested to allow dual initiation is close apposition of a second AUG codon. A possible mechanism might be that the scanning 40S ribosomal subunit flutters back and forth instead of stopping cleanly at the first AUG. This hypothesis seems to be ruled out by evidence presented herein that in certain mRNAs, the first of two close AUG codons is recognized uniquely. To achieve this, the 5' proximal AUG has to be provided with the full consensus sequence; even small departures allow a second nearby AUG codon to be reached by leaky scanning. This context-dependent leaky scanning unexpectedly fails when the second AUG codon is moved some distance from the first. A likely explanation, based on analyzing the accessibility of a far-downstream AUG codon under conditions of initiation versus elongation, is that 80S elongating ribosomes advancing from the 5' proximal start site can mask potential downstream start sites.     

Serial order in spatial immediate memory

Serial order effects in spatial memory are investigated in three experiments. In the first an analysis of errors in recall data suggested that immediate transpositions were the most common error and that order errors over 2 or 3 adjacent items accounted for the majority of errors in recall. The first and last serial positions are less error-prone than is the middle position in sets of six and seven items. A second experiment investigated recognition of transpositions and found that immediate transpositions were hardest to recognize but that a traditional serial position effect was not found. This may be due to the difficulty of maintaining one set of spatial items when another set is presented for comparison. A probe experiment, in which subjects were asked to recognize whether a single item came from a memory set and then to assign it to its position in the set indicated that the first and last positions were remembered more accurately than were central positions. The combination of serial order data in recall and position data suggests that there are similarities between serial order and position effects in the verbal and spatial domains and that serial order in spatial sequences is position-based.     

The comparative amino acid sequences, substrate specificities and gene or cDNA nucleotide sequences of some prokaryote and eukaryote amidinotransferases: implications for evolution

The amino acid sequences of the amidinotransferases and the nucleotide sequences of their genes or cDNA from four Streptomyces species (seven genes) and from the kidneys of rat, pig, human and human pancreas were compared. The overall amino acid and nucleotide sequences of the prokaryotes and eukaryotes were very similar and further, three regions were identified that were highly identical. Evidence is presented that there is virtually zero chance that the overall and high identity regions of the amino acid sequence similarities and the overall nucleotide sequence similarities between Streptomyces and mammals represent random match. Both rat and lamprey amidinotransferases were able to use inosamine phosphate, the amidine group acceptor of Streptomyces. We have concluded that the structure and function of the amidinotransferases and their genes has been highly conserved through evolution from prokaryotes to eukaryotes. The evolution has occurred with: (1) a high degree of retention of nucleotide and amino acid sequences; (2) a high degree of retention of the primitive Streptomyces guanine + cytosine (G + C) third codon position composition in certain high identity regions of the eukaryote cDNA; (3) a decrease in the specificities for the amidine group acceptors; and (4) most of the mutations silent in the regions suggested to code for active sites in the enzymes.     

Abnormal adhesion of T cells to extracellular matrix proteins in hemodialysis patients

MOTIVATION: The BioCatalog is a database of information on software of interest in molecular biology and genetics. The programs are grouped by domain of interest. AVAILABILITY: The BioCatalog is freely distributed as ASCII files. It can be searched through its Web interface at http://www.ebi.ac.uk/biocat. CONTACT: biocat@ebi. ac.uk     

Pointing errors reflect biases in the perception of the initial hand position

By comparing the visuomotor performance of 10 adult, normal subjects in three tasks, we investigated whether errors in pointing movements reflect biased estimations of the hand starting position. In a manual pointing task with no visual feedback, subjects aimed at 48 targets spaced regularly around two starting positions. Nine subjects exhibited a similar pattern of systematic errors across targets, i.e., a parallel shift of the end points that accounted, on average, for 49% of the total variability. The direction of the shift depended on the starting location. Systematic errors decreased dramatically in the second condition where subjects were allowed to see their hand before movement onset. The third task was to use a joystick held by the left hand to estimate the location of their (unseen) right hand. The systematic perceptual errors in this condition were found to be highly correlated with the motor errors in the first condition. The results support the following conclusions. 1) Kinesthetic estimation of hand position may be consistently biased. Some of the mechanisms responsible for these biases are always active, irrespective of whether position is estimated overtly (e.g., with a matching paradigm), or covertly as part of the motor planning for aimed movements. 2) Pointing errors reflect to a significant extent the erroneous estimation of initial hand position. This suggests that aimed hand movements are planned vectorially, i.e., in terms of distance and direction, rather than in terms of absolute position in space.     

Effect of ignoring random sire and dam effects on estimates and standard errors of breed comparisons

Data were weights of F1 calves and weaning weights of top-cross progeny from sires and maternal grandsires of 13 breeds. Three analyses were performed on each trait to obtain estimates and standard errors of breed effects needed to calculate across-breed EPD and accuracies. Model (R) for records of F1 progeny contained fixed effects for birth year and date of birth, sex, age and breed of dam, and breed of sire, and a random residual effect. The second analysis included random effects for sires (RS), and the third analysis included random effects for sires and dams (RSD). In maternal analysis of top-cross progeny, model (Rm) contained fixed effects for cycle of experiment, age of dam, year of birth, sex, breeds of maternal grandam and grandsire, and breed of sire, and a random residual effect. In addition, the second and third analyses fit random effects for maternal grandsires (RSm) and for maternal grandsires and daughters of maternal grandsires (RSDm). Estimates of breed of sire effects changed only slightly for different models. Total variance increased in RSD and RS relative to R. Standard errors of breed of sire comparisons were underestimated with Model R, compared to Models RS and RSD. Standard errors of other contrasts were generally not affected. Variance components, breed effects, and standard errors followed patterns for Rm, RSm, and RSDm similar to those for R, RS, and RSD. Ignoring random variation due to sires and dams underestimated standard errors of breed of sire comparisons.     

Statistical properties of a DNA sample under the finite-sites model

Statistical properties of a DNA sample from a random-mating population of constant size are studied under the finite-sites model. It is assumed that there is no migration and no recombination occurs within the locus. A Markov process model is used for nucleotide substitution, allowing for multiple substitutions at a single site. The evolutionary rates among sites are treated as either constant or variable. The general likelihood calculation using numerical integration involves intensive computation and is feasible for three or four sequences only, it may be used for validating approximate algorithms. Methods are developed to approximate the probability distribution of the number of segregating sites in a random sample of n sequences, with either constant or variable substitution rates across sites. Calculations using parameter estimates obtained for human D-loop mitochondrial DNAs show that among-site rate variation has a major effect on the distribution of the number of segregating sites; the distribution under the finite-sites model with variable rates among sites is quite different from that under the infinite-sites model.     

Measurement of plasma total homocysteine by HPLC with coulometric detection

Vertebrate MitBASE is a specialized database where all the vertebrate mitochondrial DNA entries from primary databases are collected, revised and integrated with new information emerging from the literature. Variant sequences are also analyzed, aligned and linked to reference sequences. Data related to the same species and fragment can be viewed over the WWW. The database has a flexible interface and a retrieval system to help non-expert users and contains information not currently available in the primary databases. Vertebrate MitBASE is now available through the MitBASE home page at URL: http://www.ebi.ac.uk/htbin/Mitbase/mitb ase.pl. This work is part of a larger project, MitBASE which is a network of databases covering the full panorama of knowledge on mitochondrial DNA from protists to human sequences.     

Phylogenetic analyses of the rbcL sequences from haptophytes and heterokont algae suggest their chloroplasts are unrelated

Using the large subunit of RuBisCo (rbcL) sequences from cyanobacteria, proteobacteria, and diverse groups of algae and green plants, we evaluated the plastid relationship between haptophytes and heterokont algae. The rbcL sequences were determined from three taxa of heterokont algae (Bumilleriopsis filiformis, Pelagomonas calceolata, and Pseudopedinella elastica) and added to 25 published sequences to obtain a data set comprising 1,434 unambiguously aligned sites (approximately 98% of the total rbcL gene). Higher levels of mutational saturation in third codon positions were observed by plotting the pairwise substitutions with and without corrections for multiple substitutions at the same site for first and second codon positions only and for third positions only. In accordance with this finding phylogeny reconstructions were completed by omitting third codon positions, thus using 956 bp in weighted-parsimony and maximum-likelihood analyses. The midpoint-rooted phylogenies showed two major clusters, one containing cyanobacteria, glaucocystophytes, a phototrophic euglenoid, chlorophytes, and embryophytes (the green lineage), the other containing proteobacteria, haptophytes, red algae, a cryptophyte, and heterokont algae (the non-green lineage). In the nongreen lineage, the haptophytes formed a sister group to the clade containing heterokont algae, red algae, and the cryptophyte Guillardia theta. This branching pattern was well supported in terms of bootstrap values in weighted-parsimony and maximum-likelihood analyses (100% and 92%, respectively). However, the phylogenetic relationship among red algae, heterokonts, and a cryptophyte taxon was not especially well resolved. A four-cluster analysis was performed to further explore the statistical significance of the relationship between proteobacteria, red algae (including and excluding Guillardia theta), haptophytes, and heterokont algae. This test strongly favored the hypothesis that the heterokonts and red algae are more closely related to each other than either is to proteobacteria or haptophytes. Hence, this molecular study based on a plastid-encoded gene provides additional evidence for a distant relationship between haptophytes and the heterokont algae. It suggests an evolutionary scenario in which the ancestor of the haptophyte lineage engulfed a phototrophic eukaryote and, more recently, the heterokont lineage became phototrophic by engulfing a red alga.     

COFFEE: an objective function for multiple sequence alignments

MOTIVATION: In order to increase the accuracy of multiple sequence alignments, we designed a new strategy for optimizing multiple sequence alignments by genetic algorithm. We named it COFFEE (Consistency based Objective Function For alignmEnt Evaluation). The COFFEE score reflects the level of consistency between a multiple sequence alignment and a library containing pairwise alignments of the same sequences. RESULTS: We show that multiple sequence alignments can be optimized for their COFFEE score with the genetic algorithm package SAGA. The COFFEE function is tested on 11 test cases made of structural alignments extracted from 3D_ali. These alignments are compared to those produced using five alternative methods. Results indicate that COFFEE outperforms the other methods when the level of identity between the sequences is low. Accuracy is evaluated by comparison with the structural alignments used as references. We also show that the COFFEE score can be used as a reliability index on multiple sequence alignments. Finally, we show that given a library of structure-based pairwise sequence alignments extracted from FSSP, SAGA can produce high-quality multiple sequence alignments. The main advantage of COFFEE is its flexibility. With COFFEE, any method suitable for making pairwise alignments can be extended to making multiple alignments. AVAILABILITY: The package is available along with the test cases through the WWW: http://www. ebi.ac.uk/cedric CONTACT: cedric.notredame@ebi.ac.uk