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At least 1,009 records · Page 56Linked to original sources
PubMed2003

MANIFOLD: protein fold recognition based on secondary structure, sequence similarity and enzyme classification.

We present a protein fold recognition method, MANIFOLD, which uses the similarity between target and template proteins in predicted secondary structure, sequence and enzyme code to predict the fold of the target protein. We developed a non-linear ranking scheme in order to combine the scores of the three different similarity measures used. For a difficult test set of proteins with very little sequence similarity, the program predicts the fold class correctly in 34% of cases. This is an over twofold increase in accuracy compared with sequence-based methods such as PSI-BLAST or GenTHREADER, which score 13-14% correct first hits for the same test set. The functional similarity term increases the prediction accuracy by up to 3% compared with using the combination of secondary structure similarity and PSI-BLAST alone. We argue that using functional and secondary structure information can increase the fold recognition beyond sequence similarity.

Algorithms↗
PubMed1996

Pattern discrimination with increment and decrement Craik-Cornsweet-O'Brien stimuli.

Previous studies have reported that the magnitude of induced brightness in Craik-Cornsweet-O'Brien (CCOB) figures is greater for decrement compared with increment figures. Moulden and Kingdom (Spatial Vision, 1990, 5, 101-121) suggested this was due to larger Off-centre compared with On-centre receptive fields. Such an explanation would also predict an increment-decrement difference in the contrast threshold for discriminating a CCOB stimulus from its step-edge equivalent. To test this prediction contrast thresholds were measured for discriminating 'cusp' from 'square-bar' stimuli, for both increment and decrement forms. Contrary to prediction however, no difference was found between increment and decrement discrimination thresholds. These findings suggest that On- versus Off-centre receptive field size differences are unlikely to underlie the polarity-based asymmetry in induced brightness in CCOB figures. More generally they demonstrate that the magnitude of induced brightness in CCOB figures does not have a direct parallel in the ability of observers to discriminate those stimuli from their step-edge equivalents. The significance of these findings for models of brightness coding is discussed.

Contrast Sensitivity↗
PubMed2006

Processing of chemical sensor arrays with a biologically inspired model of olfactory coding.

This paper presents a computational model for chemical sensor arrays inspired by the first two stages in the olfactory pathway: distributed coding with olfactory receptor neurons and chemotopic convergence onto glomerular units. We propose a monotonic concentration-response model that maps conventional sensor-array inputs into a distributed activation pattern across a large population of neuroreceptors. Projection onto glomerular units in the olfactory bulb is then simulated with a self-organizing model of chemotopic convergence. The pattern recognition performance of the model is characterized using a database of odor patterns from an array of temperature modulated chemical sensors. The chemotopic code achieved by the proposed model is shown to improve the signal-to-noise ratio available at the sensor inputs while being consistent with results from neurobiology.

Models, Biological↗
PubMed1990

Genomic organization of mouse Fc gamma receptor genes.

We have isolated and characterized the gene coding for the mouse Fc receptor that is termed Fc gamma RIIa. The gene contains five exons and spans approximately 9 kilobases. Unlike most members of the immunoglobulin gene superfamily, this gene utilizes multiple exons to encode its leader peptide. The first exon encodes the hydrophobic region of the signal sequence; the second exon, which contains only 21 base pairs, encodes a segment of the signal peptidase recognition site; and the beginning of the third exon encodes the predicted site of peptidase cleavage. The third and fourth exons each code for immunoglobulin-like extracellular domains. The fifth exon encodes the hydrophobic transmembrane domain and the cytoplasmic tail. Partial characterization of the Fc gamma RIIb gene indicates that it also contains multiple leader exons, including a 21-base-pair exon and two exons coding for homologous immunoglobulin-like extracellular domains. However, the Fc gamma RIIb gene uses four exons to encode its intracytoplasmic region. Analysis using contour-clamped homogeneous electric field (CHEF) gels indicates that the Fc gamma RIIa and Fc gamma RIIb genes are linked within 160 kilobases on mouse chromosome 1.

Amino Acid Sequence↗
PubMed1980

[Aid to the diagnosis of epilepsy. Codification of EEG tracings for the characterization of detectable non-stationary phenomena].

The aim of automatic EEG analysis is to detect and class the significant events of the signal. For the detection phase an autoregressive model is developed giving rise to non-stationary points. The model used to analyse information in each event goes further than the problem of existence or non-existence. It is possible to understand qualitative aspects regarding the recognition of typical patterns of epilepsy such as 'spike and waves' providing a preliminary classification of the pattern. Such a classification based on sentence coding established from quantities provided from the model leads to a qualitative understanding of the phenomenon. The first results are presented.

Computers↗
PubMed2002

Odor discrimination by G protein-coupled olfactory receptors.

The vertebrate olfactory system possesses a remarkable capacity to recognize and discriminate a variety of odorants by sending the coding information from peripheral olfactory sensory neurons in the olfactory epithelium to the olfactory bulb of the brain. The recognition of odorants appear to be mediated by a G protein-coupled receptor superfamily that consists of approximately 1% of total genes in vertebrates. Since the first discovery of the olfactory receptor gene superfamily in the rat, similar chemosensory receptors have been found in various species across different phyla. The functions of these receptors, however, had been uncharacterized until the recently successful functional expression and ligand screening of some olfactory receptors in various cell expression systems. The functional cloning of odorant receptors from single olfactory neurons allowed for the identification of multiple receptors that recognized a particular odorant of interest. Reconstitution of the odorant responses demonstrated that odorant receptors recognized various structurally-related odorant molecules with a specific molecular receptive range, and that odor discrimination is established based on a combinatorial receptor code model in which the identities of different odorants are encoded by a combination of odorant receptors. The receptor code for an odorant changes at different odorant concentrations, consistent with our experience that perceived quality of an odorant changes at different concentrations. The molecular bases of odor discrimination at the level of olfactory receptors appear to correlate well with the receptive field in the olfactory bulb where the input signal is further processed to create the specific odor maps.

Animals↗
PubMed1996

Transmembrane segment 10 is important for substrate recognition in Ga12 and Hxt2 sugar transporters in the yeast Saccharomyces cerevisiae.

A systematic series of chimeras between Ga12 galactose transporter and Hxt2 glucose transporter in yeast was produced to delineate the essential domain for substrate recognition. A domain of 101 amino acids close to the COOH-terminus that has been previously identified as the critical substrate recognition region was further divided into four subdomains, by introducing five restriction enzyme sites at exactly corresponding locations of both genes without changing coding amino acids. When each of all possible 16 modified genes was expressed, all the galactose transport-active chimeras were found to possess Ga12-derived transmembrane segment (TM) 10. Of the 35 amino acids in the TM1O region, only 12 differ between Ga12 and Hxt2, indicating that these 12 amino acids include the critical residue(s) responsible for the differential recognition of galactose and glucose in these transporters.

Amino Acid Sequence↗
PubMed1994

Requirement for a zinc motif for template recognition by the bacteriophage T7 primase.

Gene 4 of bacteriophage T7 encodes two proteins, a 63 kDa and a colinear 56 kDa protein. The coding sequence of the 56 kDa protein begins at the residues encoding an internal methionine located 64 amino acids from the N-terminus of the 63 kDa protein. The 56 kDa gene 4 protein is a helicase and the 63 kDa gene 4 protein is a helicase and a primase. The unique 7 kDa N-terminus of the 63 kDa gene 4 protein is essential for primer synthesis and contains sequences with homology to a Cys4 metal binding motif, Cys-X2-Cys-X17-Cys-X2-Cys. The zinc content of the 63 kDa gene 4 protein is 1.1 g-atom/mol protein, while the zinc content of the 56 kDa gene 4 protein is < 0.01, as determined by atomic absorption spectrometry. A bacteriophage deleted for gene 4, T7 delta 4-1, is incapable of growing on Escherichia coli strains that contain plasmids expressing gene 4 proteins with single amino acid substitutions of Ser at each of the four conserved Cys residues (efficiency of plating, 10(-7)). Primase containing a substitution of the third Cys for Ser has been overexpressed in E. coli and purified to homogeneity. This mutant primase cannot catalyze template-directed synthesis of oligoribonucleotides although it is able to catalyze the synthesis of random diribonucleotides in a template-independent fashion. The mutant primase has reduced helicase activity although it catalyzes single-stranded DNA-dependent hydrolysis of dTTP at rates comparable with wild type primase. The zinc content of the mutant primase is 0.5 g-atom/mol protein.

Amino Acid Sequence↗
PubMed2001

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.

Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to incorporate artificial amino acid residues into proteins in vivo. In a previous paper, the binding to aspartyl-tRNA synthetase of the substrate Asp and the analogue Asn were compared by molecular dynamics free energy simulations. Molecular dynamics combined with Poisson-Boltzmann free energy calculations represent a less expensive approach, suitable for examining multiple active site mutations in an engineering effort. Here, Poisson-Boltzmann free energy calculations for aspartyl-tRNA synthetase are first validated by their ability to reproduce selected molecular dynamics binding free energy differences, then used to examine the possibility of Asn binding to native and mutant aspartyl-tRNA synthetase. A component analysis of the Poisson-Boltzmann free energies is employed to identify specific interactions that determine the binding affinities. The combined use of molecular dynamics free energy simulations to study one binding process thoroughly, followed by molecular dynamics and Poisson-Boltzmann free energy calculations to study a series of related ligands or mutations is proposed as a paradigm for protein or ligand design. The binding of Asn in an alternate, "head-to-tail" orientation observed in the homologous asparagine synthetase is analyzed, and found to be more stable than the "Asp-like" orientation studied earlier. The new orientation is probably unsuitable for catalysis. A conserved active site lysine (Lys198 in Escherichia coli) that recognizes the Asp side-chain is changed to a leucine residue, found at the corresponding position in asparaginyl-tRNA synthetase. It is interesting that the binding of Asp is calculated to increase slightly (rather than to decrease), while that of Asn is calculated, as expected, to increase strongly, to the same level as Asp binding. Insight into the origin of these changes is provided by the component analyses. The double mutation (K198L,D233E) has a similar effect, while the triple mutation (K198L,Q199E,D233E) reduces Asp binding strongly. No binding measurements are available, but the three mutants are known to have no ability to adenylate Asn, despite the "Asp-like" binding affinities calculated here. In molecular dynamics simulations of all three mutants, the Asn ligand backbone shifts by 1-2 A compared to the experimental Asp:AspRS complex, and significant side-chain rearrangements occur around the pocket. These could reduce the ATP binding constant and/or the adenylation reaction rate, explaining the lack of catalytic activity in these complexes. Finally, Asn binding to AspRS with neutral K198 or charged H449 is considered, and shown to be less favorable than with the charged K198 and neutral H449 used in the analysis.

Amino Acid Substitution↗
PubMed2003

Legislative recognition in France of psychological harassment at work.

The recent French Law on Social Modernisation of 17 January 2002 introduced into the French Labour Code and into the French Criminal Code, the concept of "moral" harassment. The definition of psychological harassment under this law adopts quite a broad conception of the notion of psychological harassment. The legislator has established a means for "friendly" settlement of disputes: mediation. When it has not been possible to settle the dispute internally, the Courts have a number of sanctions available to them. The French Labour Code provides that any termination of the contract of employment resulting from a situation of psychological harassment is automatically null and void. Such nullification should therefore be applicable whatever the nature of the termination: dismissal, resignation or negotiated departure and it punishes psychological harassment at work by imprisonment for one year and a fine of 3,750 Euros. The French Criminal Code prescribes penalties of one year and 15,000 Euros.

Civil Rights↗
PubMed1992

Effects of channel number and place of stimulation on performance with the Cochlear Corporation multichannel implant.

The effects of active channel number and place of stimulation on auditory-only performance with the Cochlear Corporation multichannel cochlear implant were investigated in seven subjects. A balanced crossover design was employed; subjects were initially programmed with either 10 basal or the full complement of 20 to 21 active electrodes. Following a 6-month period with the initial coding strategy, subjects were programmed with the alternate configuration, which they used for an additional 6 months. Auditory-only performance on suprasegmental, phoneme (vowel and consonant) open- and closed-set speech recognition was compared between the two electrode configurations. Additionally, performance with the first configuration and performance with the second configuration 3 days following programming were also compared. While a trend for increased scores was noted with 20 electrodes, especially with open-set speech recognition tasks, none of the differences between the two configurations reached statistical significance, as indicated by a Wilcoxon test. A comparison of performance at the end of the first 6-month period and 3 days following programming with the second configuration revealed a trend for reduced scores, especially on vowel tests. Overall, our results indicate that the feature extraction coding strategy associated with the Cochlear Corporation device allows patients to function well with only 10 basal electrodes and that speech recognition is only mildly affected initially when patients are programmed with a different encoding strategy.

Acoustic Stimulation↗
PubMed2006

Self recognition versus recognition of others by biological motion: viewpoint-dependent effects.

We investigated the influence of viewing angle on performance in recognising the identity of one's own person and familiar individuals such as friends or colleagues from walking patterns. Viewpoint-dependent recognition performance was tested in two groups of twelve persons who knew each other very well. Participants' motion data were acquired by recording their walking patterns in three-dimensional space with the use of a motion capture system. Size-normalised point-light displays of biological motion of these walking patterns, including one's own, were presented to the same group members on a computer screen in frontal view, half-profile view, and profile view. Observers were requested to assign the person's name to the individual gait pattern. No feedback was given. Whereas recognition performance of one's own walking patterns was viewpoint independent, recognition rate for other familiar individuals was better for frontal and half-profile view than for profile view. These findings are discussed in the context of the theory of common coding of motor and visual body representations.

Adult↗
PubMedDate not supplied

Calibration and quantification of fast intracellular motion (FIM) in living cells using correlation analysis.

Video rate confocal laser scanning microscopy at the highest spatial and temporal resolution of backscattered light (BSL) imaging allowed for regular observation of fast intracellular motion (FIM) first revealed in living neoplastic cells. However, the absence of an objective evaluation has hampered further study of the mechanisms and biological significance of FIM. Particularly, a quantification of apparent differences in velocities that would complement and improve the current demonstration of FIM by color coding using the combination of red-green-blue (RGB) images had been missing. Standard methods of tracking or pattern recognition could not be applied because of the fuzzy nature of images of FIM. A search for a suitable method led to correlation analysis. It was calibrated on Brownian motion and a known type of motion, such as cell marginal ruffling, compared with FIM. Results approved its explanatory potential. Therefore, several crucial incidences of FIM could be analyzed. Apart from an argument against viewing FIM as a manifestation of simple Brownian motion, the correlation analysis of FIM in the adjacent peripheries of a rat fibroblast and a K4 rat sarcoma cell confirmed the notion of higher and uneven distribution of velocity of FIM in a tumor cell so far shown in color-coded images only. This result and other yet unpublished observations indicate that the velocity and topology of FIM can also contribute to a biological distinction between neoplastic and normal cells. Regular application of the correlation analysis should further expand the study of FIM for its mechanisms and predictive value. Such an approach should be thoroughly examined for a contribution to the knowledge of cancer cells.

Animals↗