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[Code of codon roots, determining the intra- and intermolecular interaction of amino acids in peptide chains].

To study the recognition processes and interaction of peptides and proteins, a model has been suggested according to which the first steps of complex formation of molecules are defined by G/C and A/U complementarity of codon roots of amino acid forming the molecules contact sites or surfaces. In contrast to amino acid--antiamino acid interaction code (L. B. Mekler, 1969), the code of codon roots involves the interaction of amino acids independently of the base structures in nucleotide triplets in positions 1 and 3. The analysis of the spectra of point mutations homologous proteins confirms the possible role of the root code.

Amino Acid Sequence↗

Ethnic categorisation of faces is not independent of face identity.

Is the extraction of a visually derived semantic code from faces (ethnicity) affected by face identity (familiarity) or not? The traditional view considers that this operation is made independently of face identity, and in parallel with the recognition of identity. However, some recent studies cast doubt on this parallel thesis regarding other visually derived semantic codes, namely: facial expression, facial speech, apparent age, and gender. Twenty-eight Caucasian participants were enrolled in an 'ethnic-decision' task on morphed faces made of an Asiatic source face and a Caucasian source face, in the proportion of 70%-30%. Half of the original faces were previously made familiar by a learning procedure (associating the face, surname, occupation, and city of residence of the person displayed), while the remaining half were unfamiliar. The results showed clearly that ethnic decision was affected by face familiarity. This adds support to the thesis according to which the identification of identity and the extraction of visually derived semantic codes are not made independently from each other and that the 'parallel-route' hypothesis becomes weakly supported.

Adult↗

Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes.

Exonic splicing enhancers (ESEs) are pre-mRNA cis-acting elements required for splice-site recognition. We previously developed a web-based program called ESEfinder that scores any sequence for the presence of ESE motifs recognized by the human SR proteins SF2/ASF, SRp40, SRp55 and SC35 (http://rulai.cshl.edu/tools/ESE/). Using ESEfinder, we have undertaken a large-scale analysis of ESE motif distribution in human protein-coding genes. Significantly higher frequencies of ESE motifs were observed in constitutive internal protein-coding exons, compared with both their flanking intronic regions and with pseudo exons. Statistical analysis of ESE motif frequency distributions revealed a complex relationship between splice-site strength and increased or decreased frequencies of particular SR protein motifs. Comparison of constitutively and alternatively spliced exons demonstrated slightly weaker splice-site scores, as well as significantly fewer ESE motifs, in the alternatively spliced group. Our results underline the importance of ESE-mediated SR protein function in the process of exon definition, in the context of both constitutive splicing and regulated alternative splicing.

Alternative Splicing↗

Influence of imaging ability on word transformation.

In the present study, we examined whether individual differences in imaging ability affect visual word recognition. Poor and vivid imagers performed a naming task that involved nonreversed (e.g., JUMP) and reversed (e.g., PMUJ) words (Experiment 1). Poor and vivid imagers were also tested on a naming task that was controlled for verbal ability; all the words were reversed and presentation time was varied (Experiment 2). In both experiments, imaging ability interacted with task difficulty, suggesting that individual differences in imaging ability affect visual word recognition. Specifically, the present data suggest that poor imagers may be less efficient than vivid imagers at processing words analytically. The data are interpreted within a limited-capacity, hybrid, word recognition model, in which words can be processed as either word-level or letter-level codes.

Adult↗

Characterization of a cDNA coding for human factor X.

A lambda gt11 cDNA library containing DNA inserts prepared from human liver mRNA has been screened with an antibody to human factor X, a plasma protein participating in the middle phase of the blood coagulation cascade. Ten positive clones were isolated from 2 X 10(6) phage and plaque purified. The cDNA in the phage containing the largest insert has been sequenced and shown to code for human factor X. This cDNA insert contained 1137 base pairs coding for a portion of the light chain of the molecule, a connecting region, the heavy chain, a stop codon, a short 3' noncoding region, and a poly(A) tail. The sequence of A-T-T-A-A-A, which functions as a potential recognition site for polyadenylylation or processing, was present in the 3' end of the coding sequence and preceded the stop codon of TGA by 1 base pair and the poly(A) tail by 14 base pairs. The amino acid sequence deduced from the cDNA indicated that factor X is synthesized as a single-chain polypeptide containing the light and heavy chains connected by an Arg-Lys-Arg tripeptide. The single-chain molecule is then converted to the light and heavy chains by cleavage of two (or more) internal peptide bonds. In plasma, these two chains are linked together by a disulfide bond. The DNA sequence coding for the active site of human factor X showed a high degree of identity with prothrombin and factor IX, two other vitamin K-dependent serine proteases that participate in blood coagulation. These data along with the protein sequence data previously published for the light chain of human factor X establish the complete amino acid sequence for the mature protein present in plasma.

Amino Acid Sequence↗

Mutations and polymorphisms in the human ornithine transcarbamylase gene.

Deletions of variable size involving one or more exons, 29 different missense, nonsense, or frameshift mutations, and three polymorphisms have been found in patients with ornithine transcarbamylase (OTC) deficiency. Most of the deletions and mutations were found in patients with severe disease manifested clinically as acute neonatal hyperammonemia. A small number of mutations or somatic mosaicism for deletions were found in males with "late onset" disease and heterozygous females who were symptomatic. Approximately 10-15% of all molecular alterations associated with OTC deficiency are large deletions involving all or part of the OTC gene with or without contiguous genes on the short arm of the X chromosome. Approximately 10% of all point mutations involve the CpG dinucleotide of codon 141 with a CGA-->CAA transition producing a deleterious Arg-->Gln substitution in position 109 of the mature enzyme and causing the elimination of a TaqI recognition site. The majority of the remaining mutations in the OTC gene are unique to the affected family and are usually not found in unrelated patients. To date, two mutations have been described in the sequence of the "leader" peptide, 23 mutations have been found in the coding sequence of the "mature" enzyme, and four mutations have been discovered in splicing recognition sites. Approximately 20 single base polymorphisms have been postulated to exist by comparing two reported OTC gene sequences; six of these substitutions cause amino acid changes of which three have been confirmed in patients. Of the known point mutations, 27 are single base substitutions: 17 missense, 6 nonsense, 4 splice site, and the remaining 2 are single base deletions.

Amino Acid Sequence↗

Properties of a temporal population code.

The temporal patterning of neuronal activity may play a substantial role in the representation of sensory stimuli. One particular hypothesis suggests that visual stimuli are represented by the temporal evolution of the instantaneous firing rate averaged over a whole population of neurons. Using an implementation in a cortical type network with lateral interactions, we could previously show that this scheme can be successfully applied to a pattern recognition task. Here, we use a large set of artificially generated stimuli to investigate the coding properties of the network in detail. The temporal population code generated by the network is intrinsically invariant to stimulus translations. We show that the encoding is invariant to small deformations of the stimuli and robust with respect to static and dynamic variations in synaptic strength of the lateral connections in the network. Furthermore, we present several measures which indicate that the encoding maps the stimuli into a high-dimensional space. These results show that a temporal population code is a promising approach for the encoding of relevant stimulus properties while simultaneously discarding the irrelevant information.

Animals↗

A programme for computer-aided recognition of electrocardiographic patterns.

A programme for pattern recognition and automatic diagnosis on digitally converted electrocardiograms is described. Pattern recognition is carried out on the 12 classical leads and diagnosis is given in the Minnesota Code, 1968 variant. The programme was written in FORTRAN and tested in a FELIX C 256 computer.

Computers↗

Prognostic value of round-window psychophysical testing with cochlear-implant candidates.

The preimplant, psychophysical-test results obtained with a single-ball, round-window electrode for 32 peri- or postlingually deafened, adult, Nucleus 22-channel cochlear-implant users were analyzed and correlated with their postimplant, open-set, speech recognition performance. The results revealed that some preimplant measures do have value as predictors of speech recognition abilities in this group of subjects. All subjects used the MPEAK speech-coding strategy and had been using their device for at least 6 months. The psychophysical measures that were found to correlate most highly with postimplant performance included the detection threshold at 400 Hz and the threshold slope function from 50 to 400 Hz, with lower values associated with higher speech recognition. To a lesser extent, detection thresholds at 100 and 200 Hz, the dynamic range at 200 and 400 Hz, and the gap detection threshold at 100 Hz correlated with speech performance. As well, duration-of-deafness variables were found to correlate significantly with postimplant performance.

Adult↗

Cloning, nucleotide sequence, and regulation of MET14, the gene encoding the APS kinase of Saccharomyces cerevisiae.

The MET14 gene of Saccharomyces cerevisiae, encoding APS kinase (ATP:adenylylsulfate-3'-phosphotransferase, EC 2.7.1.25), has been cloned. The nucleotide sequence predicts a protein of 202 amino acids with a molecular mass of 23,060 dalton. Translational fusions of MET14 with the beta-galactosidase gene (lacZ) of Escherichia coli confirmed the results of primer extension and Northern blot analyses indicating that the ca. 0.7 kb mRNA is transcriptionally repressed by the presence of methionine in the growth medium. By primer extension the MET14 transcripts were found to start between positions -25 and -45 upstream of the initiator codon. Located upstream of the MET14 gene is a perfect match (positions -222 to -229) with the previously proposed methionine-specific upstream activating sequence (UASMet). This is the same as the consensus sequence of the Centromere DNA Element I (CDEI) that binds the Centromere Promoter Factor I (CPFI) and of two regulatory elements of the PHO5 gene to which the yeast protein PHO4 binds. The human oncogenic protein c-Myc also has the same recognition sequence. Furthermore, in the 270 bp upstream of the MET14 coding region there are several matches with a methionine-specific upstream negative (URSMet) control element. The significance of these sequences was investigated using different upstream deletion mutations of the MET14 gene which were fused to the lacZ gene of E. coli and chromosomally integrated. We find that the methionine-specific UASMet and one of the URSMet lie in regions necessary for strong activation and weak repression of MET14 transcription, respectively. We propose that both types of control are exerted on MET14.

Amino Acid Sequence↗

A real-time gesture recognizer based on dynamic programming.

Coded gestures are physical movements to which precise meanings have been attached. Their use with an electronic pointing device potentially increases the power of the pointer by allowing several distinct control functions to be incorporated. The formation of a coded gesture is invariably subject to distortions which make its automatic recognition difficult. After particular consideration of three techniques, a dynamic programming algorithm was developed and was used in the design of a real-time gesture recognizer that allows mouse-driven software to be operated purely by means of an electronic pointer. The decision was taken to implement the gesture recognizer using a widely available, obsolescent microcomputer in order to keep down costs. Despite the inevitable technical compromises in this approach, results of preliminary trials using 10 normal subjects show an average gesture recognition rate of 98.3% and a gesture confusion rate of only 0.4%.

Algorithms↗

Polymorphic site study at codon 347 of apolipoprotein A-IV in a Japanese population.

In a population of Japanese subjects, we surveyed codon 347 of the apolipoprotein (apo) A-IV gene and found that the frequency of a rare allele at this point was extremely low compared to that in western populations. Only one of 850 unrelated samples showed mutation at the enzyme recognition site by agarose gel electrophoresis. However, direct sequencing of the coding region revealed that it did not result from the ACT (Thr) to TCT (Ser) mutation which has been reported in western countries, but from an ACT to ACG (Thr) mutation, which does not affect the primary structure of apo A-IV. Two additional family members showed the same point mutation at codon 347.

Adult↗

Evidence and diagnostic reporting in the IHE context.

Capturing clinical observations and findings during the diagnostic imaging process is increasingly becoming a critical step in diagnostic reporting. Standards developers-notably HL7 and DICOM-are making significant progress toward standards that enable exchanging clinical observations and findings among the various information systems of the healthcare enterprise. DICOM-like the HL7 Clinical Document Architecture (CDA) -uses templates and constrained, coded vocabulary (SNOMED, LOINC, etc.). Such a representation facilitates automated software recognition of findings and observations, intrapatient comparison, correlation to norms, and outcomes research. The scope of DICOM Structured Reporting (SR) includes many findings that products routinely create in digital form (measurements, computed estimates, etc.). In the Integrating the Healthcare Enterprise (IHE) framework, two Integration Profiles are defined for clinical data capture and diagnostic reporting: Evidence Document, and Simple Image and Numeric Report. This report describes these two DICOM SR-based integration profiles in the diagnostic reporting process.

Computer Systems↗

Discrimination and association processes for faces and non-faces: the effect of rotation.

Most current theories of face perception claim that inversion leaves the coding of non-face stimuli largely unaffected, while causing a qualitative change in the coding of faces. Empirical support for this hypothesis mainly stems from recognition studies which typically show a larger inversion decrement for faces than for other stimuli. Several recent studies using experimental paradigms that do not contain a substantial memory component have however yielded contradicting results. This observation suggests that the disproportionate effect of inversion for faces might be related to the presence, or absence, of a memory component in the experimental task. In order to explore this hypothesis we investigated the effect of inversion within a discrimination learning paradigm, which contains a memory component comparable to that included in a recognition paradigm. We compared the effect of rotation on discrimination and association processes for faces and cars, Subjects learned to discriminate pairs of similar faces and similar cars and to associated them with neutral responses. The stimulus pairs were presented upright, inverted, and additionally in two intermediate orientations. We found that discrimination performance was generally better for faces than for cars and that associations were learned faster for faces than for cars. However, we did not find any evidence that rotation affected discrimination and association processes for faces differently than for cars. In this sense, our results provide no evidence for the hypothesis that memory processes are responsible for disproportionate effect of inversion which is found in recognition experiments.

Adult↗

Alpha-thalassaemia caused by a polyadenylation signal mutation.

Most eukaryotic messenger RNAs have the sequence AAUAAA 11-30 nucleotides from the 3'-terminal poly(A) tract. Since this is the only significant sequence homology in the 3' non-coding region it has been suggested that it may be a recognition site for enzymes involved in polyadenylation and/or termination of polymerase II transcription. This idea is strengthened by observations on the effect of deletion mutations in or around the AATAAA sequence on polyadenylation of late simian virus 40 (SV40) mRNA; removal of this sequence prevents poly(A) addition. Naturally occurring variants of this hexanucleotide are rare and hitherto their functional significance has not been assessed. We have now identified a human alpha 2-globin gene which contains a single point mutation in this hexanucleotide (AATAAA leads to AATAAG). The paired alpha 1 gene on the same chromosome is completely inactivated by a frame-shift mutation. This unique combination has enabled the expression of the mutant alpha 2 gene to be studied in vivo where it has been found that the accumulated level of alpha 2-specific mRNA in erythroid cells is reduced. Furthermore, readthrough transcripts extending beyond the normal poly(A) addition site are detected in mRNA obtained from HeLa cells transfected with cloned DNA from the mutant alpha 2 gene, suggesting that the single nucleotide change in the AATAAA sequence is the cause of its abnormal expression.

Base Sequence↗

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.

We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).

Escherichia coli↗