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PubMed1984

Development of phonetic memory in disabled and normal readers.

The development of phonetic codes in memory of 141 pairs of normal and disabled readers from 7.8 to 16.8 years of age was tested with a task adapted from L. S. Mark, D. Shankweiler, I. Y. Liberman, and C. A. Fowler (Memory & Cognition, 1977, 5, 623-629) that measured false-positive errors in recognition memory for foil words which rhymed with words in the memory list versus foil words that did not rhyme. Our younger subjects replicated Mark et al., showing a larger difference between rhyming and nonrhyming false-positive errors for the normal readers. The older disabled readers' phonetic effect was comparable to that of the younger normal readers, suggesting a developmental lag in their use of phonetic coding in memory. Surprisingly, the normal readers' phonetic effect declined with age in the recognition task, but they maintained a significant advantage across age in the auditory WISC-R digit span recall test, and a test of phonological nonword decoding. The normals' decline with age in rhyming confusion may be due to an increase in the precision of their phonetic codes.

Adolescent↗
PubMed1999

Facial expression recognition ability among women with borderline personality disorder: implications for emotion regulation?

This study examined recognition of facial expressions of emotion among women diagnosed with borderline personality disorder (BPD; n = 21), compared to a group of women with histories of childhood sexual abuse with no current or prior diagnosis of BPD (n = 21) and a group of women with no history of sexual abuse or BPD (n = 20). Facial recognition was assessed by a slide set developed by Ekman and Matsumoto (Japanese and Caucasian Facial Expressions of Emotion and Neutral Faces, 1992), expanded and improved from previous slide sets, and utilized a coding system that allowed for free responses rather than the more typical fixed-response format. Results indicated that borderline individuals were primarily accurate perceivers of others' emotions and showed a tendency toward heightened sensitivity on recognition of fear, specifically. Results are discussed in terms of emotional appraisal ability and emotion dysregulation among individuals with BPD.

Adult↗
PubMed2001

Spectral karyotyping (SKY) of mouse meiotic chromosomes.

The spectral karyotyping procedure of in situ hybridization with chromosome-specific probes assigns a unique colour code to each of the 21 mouse mitotic chromosomes. We have adapted this procedure to meiotic prophase chromosomes, and the results show that each of the pachytene or metaphase I bivalents can be identified. This technique has the potential to recognize synaptic anomalies and chromosome-specific structural and behavioural characteristics. We confirm these potentials by the recognition of the heterologous synapsis of the X and Y chromosomes and by the variances of synaptonemal complex lengths for each of the colour-coded bivalents in eight prophase nuclei.

Animals↗
PubMed1987

Identification of the major cottontail rabbit papillomavirus late RNA cap site and mapping and quantitation of an E2 and minor E6 coding mRNA in papillomas and carcinomas.

The capsite of the 2.6- and 4.8-kb major late transcripts of cottontail rabbit papillomavirus (CRPV) has been mapped by primer extension. A leader exon of about 300 nucleotides common to both RNAs is located in the untranslated region of the genome upstream of the capsites for early transcripts. In contrast to the early capsites which are all preceded by TATA boxes, no such sequence is present 30 nucleotides upstream of the late capsite. These data indicate that the switch from early to late transcription involves recognition of a new promoter and suppression of transcription termination at the early polyadenylation site. We have also identified a minor exon with a coding potential for a putative E2 transactivating protein. Quantitation by S1 mapping of the E2 coding exon and a minor exon coding for a full-sized E6 protein unique in size to the highly oncogenic CRPV did not reveal differences in the level of transcription between papillomas and carcinomas.

Animals↗
PubMed1996

Recognition of ovine lentivirus gag gene products by serum from infected sheep.

In order to localize the immunodominant regions, 12 ovine lentivirus (OLV) gag-coding gene fragments were cloned and expressed in Escherichia coli and then tested in a Western blot (WB) assay against a panel of sera collected from US and Italian OLV-infected sheep. The most immunoreactive regions were mapped to the amino-terminal of p25 and carboxyl-terminal of p14. In addition, we found that the reactivity pattern between US and Italian sheep was very similar, suggesting the antigenic domain between US and Italian isolates in the gag gene structures could be conserved. Given the broad immunoreactivity of the amino-terminal of p25, this region could serve as an ideal diagnostic antigen for the serological identification of OLV-infected sheep.

Animals↗
PubMed1987

Anti-sense peptide recognition of sense peptides: direct quantitative characterization with the ribonuclease S-peptide system using analytical high-performance affinity chromatography.

The ability of peptides coded by the anti-sense strand of DNA to interact specifically with peptides coded by the sense strand has been evaluated. The sense peptide examined, ribonuclease S-peptide, was immobilized on a coated silica affinity chromatographic matrix. Anti-sense peptides were synthesized on the basis of the anti-sense DNA sequence for the S-peptide region in native pancreatic ribonuclease A. The interaction of synthetic anti-sense peptides with sense peptide was quantitated from the degree of retardation during chromatographic elution on the sense peptide affinity matrix in buffers with and without soluble competing sense peptide. Sense/anti-sense peptide interactions were found to occur with significant affinities with each of two anti-sense 20-residue peptides of opposite amino-to-carboxyl orientations and to weaken progressively with decreasing length of anti-sense peptide. The substantial chromatographic retardation of anti-sense peptides was specific, since it decreased as expected with increasing concentration of the soluble competing S-peptide, could not be mimicked by the elution of several control peptides (including S-peptide itself) on the S-peptide matrix, and did not occur with a blank chromatographic matrix (no S-peptide attached). The stoichiometry of anti-sense peptide binding to immobilized sense peptide was found to be far greater than 1:1, and at least 4-5:1, for the two 20-mer anti-sense peptides. In sum, the analytical affinity chromatographic experiments have established quantitatively that anti-sense peptide binding to sense peptides occurs in the ribonuclease S-peptide case and have identified some structural elements that govern these interactions.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1986

Cloning and expression of cDNA for human diazepam binding inhibitor, a natural ligand of an allosteric regulatory site of the gamma-aminobutyric acid type A receptor.

Diazepam binding inhibitor (DBI) is a protein that displaces ligands bound to the beta-carboline/benzodiazepine recognition site, an allosteric modulatory site of the type A gamma-aminobutyric acid receptor complex. An incomplete rat cDNA clone coding for DBI was isolated. This rat sequence was utilized to identify a cDNA clone that encoded the entire 104 residues of human DBI. This sequence was engineered for expression in E. coli, and recombinant DBI exhibits identical biochemical and antigenic characteristics of natural human DBI. DBI is encoded by a multigene family of at least five members, but a single gene appears to account for the majority of DBI expression. DBI is expressed in a tissue-specific manner. Expression is found in central nervous system tissues and appears to extend to peripheral tissues rich in the peripheral type of high-affinity benzodiazepine recognition sites. The role of these sites and DBI in adrenal gland, testis, and kidney remains to be determined.

Amino Acid Sequence↗
PubMed2001

Prelexical phonological coding of visual words in Dutch: automatic after all.

This paper addresses a previous claim (Brysbaert & Praet, 1992) that the use of prelexical phonology in visual word recognition is optional in the Dutch language. One backward masking experiment and two masked priming experiments are reported. The experimental task was perceptual identification. Pseudohomophones, graphemic controls, and unrelated controls of the target words were used as masks or primes. The main findings were (1) unlike previous claims, the pseudohomophone effect is not strategic in Dutch, but (2) the effect is more clearly obtained with the masked priming procedure than with the backward masking procedure.

Adult↗
PubMed1997

Speech recognition at simulated soft, conversational, and raised-to-loud vocal efforts by adults with cochlear implants.

Ten postlinguistically deaf adults who used the Nucleus Cochlear Implant System and SPEAK speech coding strategy responded to vowels, consonants, words, and sentences presented sound-only at 70, 60, and 50 dB sound-pressure level. Highest group mean scores were at a raised-to-loud level of 70 dB for consonants (73%), words (44%), and sentences (87%); the highest score for vowels (70%) was at a conversational level of 60 dB. Lowest group mean scores were at a soft level of 50 dB for vowels (56%), consonants (47%), words (10%), and sentences (29%); all except subject 7 had some open-set speech recognition at this level. For the conversational level (60 dB), group mean scores for sentences and words were 72% and 29%, respectively. With this performance and sound-pressure level, it was observed that these subjects communicated successfully in a variety of listening situations. Given these subjects' speech recognition scores at 60 dB and the fact that 70 dB does not simulate the vocal effort used in everyday speaking situations, it is suggested that cochlear implant candidates and implantees be evaluated with speech tests presented at 60 dB instead of the customary 70 dB sound-pressure level to simulate benefit provided by implants in everyday life. Analysis of individuals' scores at the three levels for the four speech materials revealed different patterns of speech recognition among subjects (e.g., subjects 1 and 5). Future research on the relation between stimuli, sound processing, and subjects' responses associated with these different patterns may provide guidelines to select parameter values with which to map incoming sound onto an individual's electrical dynamic range between threshold and maximum acceptable loudness level to improve speech recognition.

Adult↗
PubMed1997

Sibling recognition in the beaver: a field test for phenotype matching

The hypothesis of kin recognition by phenotype matching predicts that relatives can be identified without previous contact, and/or that cues used for recognition can be learned indirectly from a third but related individual. This hypothesis was tested in the field using 22 beaver, Castor canadensisfamilies. Individually identifiable beavers were provided with a two-way choice between two experimental scent mounds, one of which was scented with the anal gland secretion (AGS) from an unfamiliar sibling of the test subjects, the other with AGS from an unfamiliar non-relative. Beavers showed less strong territorial responses to AGS from their siblings than to that from non-relatives. The mates of the test subjects, which were not related to, or familiar with, either of the AGS donors, also responded less strongly to the AGS from their mates' siblings than to that from other unfamiliar non-relatives. This discrimination was not shown when castoreum samples were tested instead of AGS. Therefore, it was concluded that (1) information about kinship in the beaver is coded in the AGS but not in the castoreum, (2) the mechanism of phenotype matching is used in beaver sibling recognition, and (3) the cue used in phenotype matching can be learned and used for recognition of related individuals by an unrelated individual.1997The Association for the Study of Animal Behaviour

Journal Article↗
PubMed1993

Purification and cDNA cloning of HeLa cell p54nrb, a nuclear protein with two RNA recognition motifs and extensive homology to human splicing factor PSF and Drosophila NONA/BJ6.

While searching for a human homolog of the S.cerevisiae splicing factor PRP18, we found a polypeptide that reacted strongly with antibodies against PRP18. We purified this polypeptide from HeLa cells using a Western blot assay, and named it p54nrb (for nuclear RNA-binding protein, 54 kDa). cDNAs encoding p54nrb were cloned with probes derived from partial sequence of the purified protein. These cDNAs have identical coding sequences but differ as a result of alternative splicing in the 5' untranslated region. The cDNAs encode a 471 aa polypeptide that contains two RNA recognition motifs (RRMs). Human p54nrb has no homology to yeast PRP18, except for a common epitope, but is instead 71% identical to human splicing factor PSF within a 320 aa region that includes both RRMs. In addition, both p54nrb and PSF are rich in Pro and Gln residues outside the main homology region. The Drosophila puff-specific protein BJ6, one of three products encoded by the alternatively spliced no-on-transient A gene (nonA), which is required for normal vision and courtship song, is 42% identical to p54nrb in the same 320 aa region. The striking homology between p54nrb, PSF, and NONA/BJ6 defines a novel phylogenetically conserved protein segment, termed DBHS domain (for Drosophila behavior, human splicing), which may be involved in regulating diverse pathways at the level of pre-mRNA splicing.

Amino Acid Sequence↗
PubMed2005

The molecular basis of individual differences in phenylthiocarbamide and propylthiouracil bitterness perception.

Individual differences in perception are ubiquitous within the chemical senses: taste, smell, and chemical somesthesis . A hypothesis of this fact states that polymorphisms in human sensory receptor genes could alter perception by coding for functionally distinct receptor types . We have previously reported evidence that sequence variants in a presumptive bitter receptor gene (hTAS2R38) correlate with differences in bitterness recognition of phenylthiocarbamide (PTC) . Here, we map individual psychogenomic pathways for bitter taste by testing people with a variety of psychophysical tasks and linking their individual perceptions of the compounds PTC and propylthiouracil (PROP) to the in vitro responses of their TAS2R38 receptor variants. Functional expression studies demonstrate that five different haplotypes from the hTAS2R38 gene code for operatively distinct receptors. The responses of the three haplotypes we also tested in vivo correlate strongly with individuals' psychophysical bitter sensitivities to a family of compounds. These data provide a direct molecular link between heritable variability in bitter taste perception to functional variations of a single G protein coupled receptor that responds to compounds such as PTC and PROP that contain the N-C=S moiety. The molecular mechanisms of perceived bitterness variability have therapeutic implications, such as helping patients to consume beneficial bitter-tasting compounds-for example, pharmaceuticals and selected phytochemicals.

Animals↗
PubMed1993

The evolutionary change of the genetic code as restricted by the anticodon and identity of transfer RNA.

The discovery of non-universal genetic codes in several mitochondria and nuclear systems during the part ten years has necessitated a reconsideration of the concept that the genetic code is universal and frozen, as was once believed. Here, the flexibility of the relationship between codons and amino acids is discussed on the basis of the distribution of non-universal genetic codes in various organisms insofar as has been observed to date. Judging from the result of recent investigations into tRNA identity, it would appear that the non-participation of the anticodon in recognition by aminoacyl-tRNA synthetase has significantly influenced the variability of codons.

Animals↗
PubMed2006

YASSPP: better kernels and coding schemes lead to improvements in protein secondary structure prediction.

The accurate prediction of a protein's secondary structure plays an increasingly critical role in predicting its function and tertiary structure, as it is utilized by many of the current state-of-the-art methods for remote homology, fold recognition, and ab initio structure prediction. We developed a new secondary structure prediction algorithm called YASSPP, which uses a pair of cascaded models constructed from two sets of binary SVM-based models. YASSPP uses an input coding scheme that combines both position-specific and nonposition-specific information, utilizes a kernel function designed to capture the sequence conservation signals around the local window of each residue, and constructs a second-level model by incorporating both the three-state predictions produced by the first-level model and information about the original sequence. Experiments on three standard datasets (RS126, CB513, and EVA common subset 4) show that YASSPP is capable of producing the highest Q3 and SOV scores than that achieved by existing widely used schemes such as PSIPRED, SSPro 4.0, SAM-T99sec, as well as previously developed SVM-based schemes. On the EVA dataset it achieves a Q3 and SOV score of 79.34 and 78.65%, which are considerably higher than the best reported scores of 77.64 and 76.05%, respectively.

Algorithms↗
PubMed1987

Sequence of the mglB gene from Escherichia coli K12: comparison of wild-type and mutant galactose chemoreceptors.

The mglB gene of Escherichia coli codes for a galactose-binding protein (GBP) that serves both as the galactose chemoreceptor and as the recognition component of the beta-methylgalactoside transport system. The mglB551 mutation eliminates the chemotactic function of GBP without altering its transport or substrate-binding properties. To investigate the interaction between GBP and Trg, the chemotactic signal transducer for galactose, we sequenced the mglB genes from wild-type and mglB551 mutant strains. The mutation causes the replacement of Gly74 of GBP by Asp. This residue is located in alpha-Helix III at the tip of the P domain in the GBP tertiary structure farthest removed from the substrate-binding cleft between the P and Q domains. We conclude that Helix III must be part of, or at least adjacent to, the recognition site for Trg. Our sequence also included part of the mglA gene, which is immediately distal to mglB. The amino acid sequence deduced for the beginning of the MglA protein showed homology with a family of polypeptides that contain an ATP-binding site and are components of binding-protein-dependent transport systems.

Amino Acid Sequence↗
PubMed1996

Genetic diagnosis of familial hypercholesterolemia in affected relatives using pedigree tracing.

OBJECTIVES: To describe a process of diagnosing familial hypercholesterolemia (FH) at the DNA level in selected family members of affected individuals. DESIGN AND METHODS: A 63-year-old male patient presented with cholesterol elevations consistent with heterozygous familial hypercholesterolemia. Through participation with the international "MEDPED FH" project to detect affected relatives and to identify their LDL-receptor mutation, the patient was discovered to carry the Lebanese mutation, whereby the codon for cysteine at residue 660 instead codes for a premature termination (C660X), thus truncating the protein product. This mutation also created a new restriction recognition site for the endonuclease Hinfl, which permitted rapid detection of the mutation in selected family members using restriction fragment-length polymorphisms. RESULTS: The patient's son, who had cholesterol levels consistent with heterozygous FH, was also found to be a heterozygote for the C660X variant of the LDL-receptor. CONCLUSIONS: Diagnosis of familial hypercholesterolemia at the DNA level is possible as a relatively rapid screening technique in families with a known LDL-receptor mutation, established through participation with the MED-PED FH project.

Female↗
PubMed2006

The Simon effect in vocal responses.

The Simon effect refers to the finding that faster responses are made to non-spatial stimulus features (e.g., color) when the positions of stimulus and response correspond than when they do not correspond. The usual explanation is that a spatial stimulus code automatically activates a corresponding spatial response code. Recently, however, the Simon effect has also been observed in vocal responses. The present study investigated the properties of Simon effects in the vocal modality. Experiment 1 compared horizontal and vertical Simon effects in vocal responses and found similar patterns of sequential modulations, but different time-courses. Yet the observed results are similar to those described in the literature for manual Simon effects. Experiments 2 and 3 used a dual-task procedure to investigate the impact of manual response codes on the encoding of irrelevant location and the initiation of vocal responses, respectively. Results suggest close links between manual response codes and conceptually corresponding vocal response codes.

Adult↗