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PubMed1977

Incidental cues and picture/word differences in recall.

80 university undergraduates attempted free recall of 20 objects presented as either (a) normally printed words, (b) words enriched with iconic sign characteristics, (c) normal line drawings, or (d) schematic line drawings constructed from a limited set of elements. Enriched words were better recalled than normal words, whereas differences in recall between the two types of line drawings just failed to reach significance. The results were discussed in reference to the dual coding- and incidental-cue hypothesis.

Cues↗
PubMed1998

Parallel coding of conjunctions in visual search.

Two experiments investigated whether the conjunctive nature of nontarget items influenced search for a conjunction target. Each experiment consisted of two conditions. In both conditions, the target item was a red bar tilted to the right, among white tilted bars and vertical red bars. As well as color and orientation, display items also differed in terms of size. Size was irrelevant to search in that the size of the target varied randomly from trial to trial. In one condition, the size of items correlated with the other attributes of display items (e.g., all red items were big and all white items were small). In the other condition, the size of items varied randomly (i.e., some red items were small and some were big, and some white items were big and some were small). Search was more efficient in the size-correlated condition, consistent with the parallel coding of conjunctions in visual search.

Adult↗
PubMed2000

Verbal coding in olfactory versus nonolfactory cognition.

Two paired-associate memory experiments were conducted to investigate verbal coding in olfactory versus nonolfactory cognition. Experiment 1 examined the effects of switching/not switching odors and visual items to words between encoding and test sessions. Experiment 2 examined switching/not switching perceptual odors and verbal-imagine versions of odors with each other. Experiment 1 showed that memory was impaired for odors but not visual cues when they were switched to their verbal form at test. Experiment 2 revealed that memory was impaired for both odors and verbal-imagine cues when they were switched in format at test and that odor sensory imagery was not accessed by the instruction to imagine a smell. Together, these findings suggest that olfaction is distinguished from other sensory systems by the degree of verbal coding involved in associated cognitive processing.

Adult↗
PubMed1992

Subjective contours 1900-1990: research trends and bibliography.

A bibliography on subjective contours and a brief summary of trends in research on this problem are presented. The bibliography covers the years 1900-1990 and contains 445 entries, each briefly annotated with a code that indicates the general content and theoretical orientation of the item.

Form Perception↗
PubMed2001

A mechanism for stop codon recognition by the ribosome: a bioinformatic approach.

Protein synthesis in ribosomes requires two kinds of tRNAs: initiation and elongation. The former initiates the process (formylmethionine tRNA in prokaryotes and special methionine tRNA in eukaryotes). The latter participates in the synthesis proper, recognizing the sense codons. Synthesis is also assisted by special proteins: initiation, elongation, and termination factors. The termination factors are necessary to recognize stop codons (UAG, UGA, and UAA) and to release the complete protein chain from the elongation tRNA preceding a stop codon. No termination tRNA capable of recognizing stop codons by their anticodons is known. The termination factors are thought to do this. In the large ribosomal RNA, we found two sites that, like tRNAs, contain the anticodon hairpin but with triplets complementary to stop codons. One site is hairpin 69 from domain IV; the other site is hairpin 89, domain V. By analogy, we call them termination tRNAs: Ter-tRNA1 and Ter-tRNA2, respectively, even though they transport no amino acids, and suggest that they directly pair to stop codons. The termination factors only aid in this recognition, making it specific and reliable. A strong argument in favor of our hypothesis comes from vertebrate mitochondria. They are known to acquire two new stop codons, AGA and AGG. In the standard code, these are two out of six arginine codons. We revealed that the corresponding anticodons, UCU and CCU, have evolved in Ter-tRNA1 of these mitochondria.

Base Sequence↗
PubMed1991

Mouse NKR-P1. A family of genes selectively coexpressed in adherent lymphokine-activated killer cells.

NK cells are a subpopulation of large granular lymphocytes. They are able to recognize and lyse a wide variety of virally infected or neoplastic target cells without previous sensitization or MHC restriction. The molecules involved in target recognition and subsequent triggering of the killing process are still undefined. Recently, a 30-kDa protein highly expressed on rat NK cells and capable of mediating transmembrane signaling was identified and the gene coding for it cloned and sequenced. To better understand the role of this protein in NK cell-mediated cytotoxicity, we cloned its mouse homologue by cross-hybridization of the rat gene to a cDNA library generated from highly purified mouse lymphokine-activated NK cells. Three messages, differing in size and sequence and encoded by different genes, are specifically cotranscribed in mouse NK cells. The protein products of this gene family express the lectin-like motif characteristic of type II transmembrane molecules. Both the rat and mouse proteins have conserved tyrosine and serine residues in their cytoplasmatic portion that are potential phosphorylation sites. They also share a sequence that could be the binding site of the P56lck tyrosine kinase. These observations are consistent with the signaling function hypothesized for these proteins.

Amino Acid Sequence↗
PubMed1994

Analysis of transforming growth factor beta 1 messenger RNA degradation by the transcript-selective, 12-O-tetradecanoylphorbol-13-acetate-regulated ribonuclease system from U937 promonocytes.

Transforming growth factor (TGF) beta 1 mRNA is selectively stabilized during 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced differentiation of U937 promonocytes. In previous studies (R. Wager and R. Assoian, Mol. Cell. Biol., 10: 5983-5990, 1990), we showed that this phenotype results from the action of a RNase system that (a) recognizes the transcript selectively and (b) is inhibited upon exposure of cells to TPA. The studies reported here were designed to localize domains of TGF-beta 1 mRNA required for recognition by this TPA-regulated, transcript-selective RNase system. By examining the degradation of several truncated TGF-beta 1 in vitro transcripts with U937 cell extracts, we show that the coding domain is sufficient to allow selective degradation of the mRNA and that this process is enhanced by either the 5' or 3' untranslated regions. The 5' and 3' untranslated regions of TGF-beta 1 mRNA are also required for TPA-mediated inhibition of the transcript-selective RNase system. In contrast, an analysis of the half-lives of the 2.1- and 1.8-kilobase TGF-beta 1 mRNAs showed that the first 270 bases, unique to the larger TGF-beta 1 mRNA, minimally affect degradation of the transcript. Finally, a survey of several transcripts showed that gamma-actin mRNA levels are also controlled by the TPA-regulated RNase system. The regulated decay of TGF-beta 1 mRNA may reflect the behavior of a class of transcripts subject to similar posttranscriptional controls on overall gene expression.

Actins↗
PubMed1996

A novel mutation in the promotor region in a family with a mild form of retinoblastoma indicates the location of a new regulatory domain for the RB1 gene.

We describe a family segregating the retinoblastoma phenotype where the affected individuals have only unifocal tumours and where linkage analysis has identified unaffected mutant gene carriers. DNA from members of this 'low penetrance' pedigree was subjected to an exon-by-exon SSCP analysis of the RB1 gene. No mutations were found in the 27 exons of the coding region but an SSCP band shift was seen for PCR products covering the RB1 promoter region. Sequencing identified a G-->C change within a GGGCGG motif which is the core of the recognition sequence of the SP1 transcription factor. Electromobility shift assays demonstrated that SP1 does not bind to oligomers from this region of the RB1 promoter but bandshifts were seen for an, as yet, unidentified protein(s) which was not seen using an oligomer containing the G-->C mutation. Thus, identification of a naturally occurring mutation in a family with only 'mild' phenotypes has identified another regulatory sequence in the RB1 promoter which binds an endogenous cellular protein(s). Identification of this protein should allow a better understanding of the control of expression of the RB1 gene.

Base Sequence↗
PubMed1990

Site-specific recombination by mutants of Tn21 resolvase with DNA recognition functions from Tn3 resolvase.

The resolvases from the transposons Tn3 and Tn21 are homologous proteins but they possess distinct specificities for the DNA sequence at their respective res sites. The DNA binding domain of resolvase contains an amino acid sequence that can be aligned with the helix-turn-helix motif of other DNA binding proteins. Mutations in the gene for Tn21 resolvase were made by replacing the section of DNA that codes for the helix-turn-helix with synthetic oligonucleotides. Each mutation substituted one amino acid in Tn21 resolvase with either the corresponding residue from Tn3 resolvase or a residue that lacks hydrogen bonding functions. The ability of these proteins to mediate recombination between res sites from either Tn21 or Tn3 was measured in vivo and in vitro. With one exception, where a glutamate residue had been replaced by leucine, the activity of these mutants was similar to that of wild-type Tn21 resolvase. A further mutation was made in which the complete recognition helix of Tn21 resolvase was replaced with that from Tn3 resolvase. This protein retained activity in recombining Tn21 res sites, though at a reduced level relative to wild-type; the reduction can be assigned entirely to weakened binding to this DNA. Neither this mutant nor any other derivative of Tn21 resolvase had any detectable activity for recombination between res sites from Tn3. The exchange of this section of amino acid sequence between the two resolvases is therefore insufficient to alter the DNA sequence specificity for recombination.

Amino Acid Sequence↗
PubMed1979

Word context effects on letter recognition.

24 subjects were asked to determine whether a target letter was present in a tachistoscopically exposed word. The presence of the target was detected faster if the target was clarly sounded in the word, that is, the target G in the word TIGER was detected faster than the target G in the word RIGHT. This effect was strongest among subjects whose over-all response time was below the median value. This result was interpreted as evidence that (1) a word is recognized as a whole before its component parts are analyzed, (2) the transformation of the word from visual to acoustic code occurs before the analysis of the individual letters, and (3) individual differences in efficiency of target detection depend on a subject's over-all response time.

Adolescent↗
PubMed1998

The neural development and organization of letter recognition: evidence from functional neuroimaging, computational modeling, and behavioral studies.

Although much of the brain's functional organization is genetically predetermined, it appears that some noninnate functions can come to depend on dedicated and segregated neural tissue. In this paper, we describe a series of experiments that have investigated the neural development and organization of one such noninnate function: letter recognition. Functional neuroimaging demonstrates that letter and digit recognition depend on different neural substrates in some literate adults. How could the processing of two stimulus categories that are distinguished solely by cultural conventions become segregated in the brain? One possibility is that correlation-based learning in the brain leads to a spatial organization in cortex that reflects the temporal and spatial clustering of letters with letters in the environment. Simulations confirm that environmental co-occurrence does indeed lead to spatial localization in a neural network that uses correlation-based learning. Furthermore, behavioral studies confirm one critical prediction of this co-occurrence hypothesis, namely, that subjects exposed to a visual environment in which letters and digits occur together rather than separately (postal workers who process letters and digits together in Canadian postal codes) do indeed show less behavioral evidence for segregated letter and digit processing.

Adult↗
PubMed2006

Time-domain signal divergence and discrimination without receptor modification in sympatric morphs of electric fishes.

Polymorphism in an animal communication channel provides a framework for studying proximate rules of signal design as well as ultimate mechanisms of signal diversification. Reproductively isolated mormyrid fishes from Gabon's Brienomyrus species flock emit distinctive electric organ discharges (EODs) thought to function in species and sex recognition. Species boundaries and EODs appear congruent in these fishes, with the notable exception of three morphs designated types I, II and III. Within the species flock, these morphs compose a monophyletic group that has recently been called the magnostipes complex. Co-occurring morphs of this complex express distinctive EODs, yet they appear genetically indistinguishable at several nuclear loci. In this study, we investigated EOD discrimination by these morphs using both behavioral and physiological experiments. During the breeding season, wild-caught type I and type II males showed evidence that they can discriminate their own morph's EOD waveform from that of a sympatric and genetically distinct reference species. However, we found that type I and type II males exhibited an asymmetry in unconditioned responses to paired playback of EODs recorded from type I versus type II females. Males of the type II morph responded preferentially to EODs of type II females, whereas type I males did not appear to discriminate homotypic and heterotypic EODs in our experimental paradigm. Part of this behavioral asymmetry may have resulted from a previously undetected difference in adult size, which may have enhanced apparent discrimination by the smaller morph (type II) due to a relatively higher risk of injury from the larger morph (type I). Knollenorgan receptors, which mediate electrical communication in mormyrids, showed similar spectral tuning in type I and type II. These electroreceptors coded temporal features of any single magnostipes-complex EOD with similar patterns of time-locked spikes in both morphs. By contrast, Knollenorgans exhibited distinctive responses to different EOD waveforms. These results suggest that discrete EOD variation in this rapidly diversifying complex is functional in terms of morph-specific advertisement and recognition. Time-domain signal divergence has outpaced frequency-domain divergence between sympatric morphs, requiring little to no change in receptor response properties. We discuss our findings in light of a model for EOD time-coding by the Knollenorgan pathway, as well as evolutionary hypotheses concerning sympatric signal diversification in the magnostipes complex.

Animal Communication↗
PubMed1998

Differential modulation of CYP2E1 activity by cAMP-dependent protein kinase upon Ser129 replacement.

Many toxic compounds are activated by cytochrome P450 (CYP) 2E1 to reactive metabolites, which represents a potential hazard for cellular homeostasis. Therefore knowledge about CYP2E1 regulation could be of great biological importance. It has been shown that CYP2E1 is controlled transcriptionally and post-translationally by phosphorylation. In the present study we investigated the role of serine-129 (Ser129) in the protein kinase A (PKA) recognition sequence motif Arg-Arg-Phe-Ser129. To gain further insights into the possible relevance of Ser129 for CYP2E1 function, Ser129 was replaced by alanine (Ala) or glycine (Gly) by site-directed mutations of the cDNA coding for CYP2E1. The mutant cDNAs were transfected into Chinese hamster lung fibroblast V79 cells. Despite the mutation in the PKA phosphorylation motif, all strains produced catalytically active CYP2E1. However, there was a marked change in the substrate preference: The Gly129-containing strains hydroxylated p-nitrophenol (PNP) to a markedly higher extent than the wild-type cDNA-containing cells, while they demethylated N-nitrosodimethylamine (NDMA) to a markedly lower extent than the wild-type cells. All the strains activated NDMA to mutagenic products. Treatment with the membrane-permeating cAMP derivative db-cAMP reduced markedly both the PNP hydroxylase and the NDMA demethylase activities as well as the mutation frequency induced by NDMA in the Ser129-containing strain. This decrease in activity was not accompanied by a decrease in CYP2E1 content. In addition, the catalytic activities of CYP2E1 were decreased in microsomes from rat hepatocytes treated with db-cAMP. Also in this case, the decrease in activities was not accompanied by a decrease in enzyme protein. These findings argue that involvement of Ser129 and its phosphorylation is not in determining CYP2E1 protein level, but rather in controlling its catalytic activity. In contrast, in the strains containing Ala129 or Gly129, treatment with db-cAMP caused a marked increase in both PNP hydroxylase and NDMA demethylase. In these strains a similar db-cAMP-mediated increase was also observed in the mutation frequency, resulting from the treatment with the promutagen NDMA, which is activated by CYP2E1. Our results show that CYP2E1 in V79 cells responds in two separate ways to db-cAMP exposure depending on the amino acid residue present in the PKA recognition sequence. The enzyme is committed to a negative regulation by db-cAMP if Ser129 is the target amino acid for PKA, leading to a decrease in the metabolic activation to mutagenic and carcinogenic species. On the other hand, Ala129 or Gly129 substitution directed CYP2E1 toward a positive regulation by increasing its catalytic activities and metabolic activation to mutagenic intermediates in the presence of db-cAMP. We also obtained evidence that cAMP-mediated downregulation of wild-type (Ser129) CYP2E1 was not accompanied by its destruction but instead by its stabilization, which shows that Ser129 is not involved in CYP2E1 degradation but dictates requirements for its specific activities.

Amino Acid Substitution↗
PubMed1990

Improved transformation frequency and heterologous promoter recognition in Aspergillus niger.

Wild-type strains of Aspergillus niger were transformed with integrative vectors. The number of stable transformants varied from approximately 20-30/micrograms up to 17,000/micrograms using acetamide and hygromycin B selection, respectively. The introduction of deletions of 5' and 3' non-coding regions of the acetamidase gene (amdS+) revealed that these sequences influenced the number of transformants. The molecular characterization of A. niger transformants revealed that several copies of the vectors were tandemly integrated into the nuclear DNA. These oligomers were stably inherited, even after 100 days of growth on non-selective medium. The expression of the vector-encoded genes was confirmed by evidence from the mRNAs and corresponding proteins encoded by the selectable marker genes.

Acetamides↗
PubMed2000

Abasic site recognition by two apurinic/apyrimidinic endonuclease families in DNA base excision repair: the 3' ends justify the means.

DNA damage occurs unceasingly in all cells. Spontaneous DNA base loss, as well as the removal of damaged DNA bases by specific enzymes targeted to distinct base lesions, creates non-coding and lethal apurinic/apyrimidinic (AP) sites. AP sites are the central intermediate in DNA base excision repair (BER) and must be processed by 5' AP endonucleases. These pivotal enzymes detect, recognize, and cleave the DNA phosphodiester backbone 5' of, AP sites to create a free 3'-OH end for DNA polymerase repair synthesis. In humans, AP sites are processed by APE1, whereas in yeast the primary AP endonuclease is termed APN1, and these enzymes are the major constitutively expressed AP endonucleases in these organisms and are homologous to the Escherichia coli enzymes Exonuclease III (Exo III) and Endonuclease IV (Endo IV), respectively. These enzymes represent both of the conserved 5' AP endonuclease enzyme families that exist in biology. Crystal structures of APE1 and Endo IV, both bound to AP site-containing DNA reveal how abasic sites are recognized and the DNA phosphodiester backbone cleaved by these two structurally unrelated enzymes with distinct chemical mechanisms. Both enzymes orient the AP-DNA via positively charged complementary surfaces and insert loops into the DNA base stack, bending and kinking the DNA to promote flipping of the AP site into a sequestered enzyme pocket that excludes undamaged nucleotides. Each enzyme-DNA complex exhibits distinctly different DNA conformations, which may impact upon the biological functions of each enzyme within BER signal-transduction pathways.

Apurinic Acid↗
PubMed2004

Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1.

The 2694 ORFs originally annotated as potential genes in the genome of Aeropyrum pernix can be categorized into three clusters (A, B, C), according to their nucleotide composition at three codon positions. Coding potential was found to be responsible for the phenomenon of three clusters in a 9-dimensional space derived from the nucleotide composition of ORFs: ORFs assigned to cluster A are coding ones, while those assigned to clusters B and C are non-coding ORFs. A "codingness" index called the AZ score is defined based on a clustering method used to recognize protein-coding genes in the A. pernix genome. The criterion for a coding or non-coding ORF is based on the AZ score. ORFs with AZ > 0 or AZ < 0 are coding or non-coding, respectively. Consequently, 620 out of 632 ORFs with putative functions based on the original annotation are contained in cluster A, which have positive AZ scores. In addition, all 29 ORFs encoding putative or conserved proteins newly added in RefSeq annotation also have positive AZ scores. Accordingly, the number of re-recognized protein-coding genes in the A. pernix genome is 1610, which is significantly less than 2694 in the original annotation and also much less than 1841 in the RefSeq annotation curated by NCBI staff. Annotation information of re-recognized genes and their AZ scores are available at: http://tubic.tju.edu.cn/Aper/.

Aeropyrum↗
PubMed1992

[Chemical-enzymatic synthesis and cloning in Escherichia coli of a gene coding for human granulocyte-colony stimulating factor].

Two artificial genes, encoding two forms of human granulocyte colony stimulating factor as products of a normal and an alternative splicing, have been by a chemical-enzymatic way synthesized and cloned in Escherichia coli. The genes are supplied with recognition sites of restriction endonucleases to facilitate the further cassette mutagenesis.

Amino Acid Sequence↗