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PubMed1984

[Visual and phonological access to the mental lexicon].

In a lexical decision experiment we investigated whether the mental lexicon is accessed directly by a visual code or by phonological mediation. Subjects were asked to make lexical decisions where phonological coding was either beneficial or detrimental. It was found that subjects used phonological coding when it was helpful and abandoned this strategy when it was a hindrance. These results support the hypothesis that lexical decisions can be based on variable coding operations. The fact that subjects were faster in classifying words when they did not rely on phonological codes is consistent with the assumption of faster visual access to the mental lexicon. Taken as a whole, these results are consistent with models which assume phonological coding to take place after lexical access as well as with models postulating parallel access to the mental lexicon. They are not compatible with models postulating mandatory prelexical phonological coding.

Decision Making↗

PubMed1998

Xa21D encodes a receptor-like molecule with a leucine-rich repeat domain that determines race-specific recognition and is subject to adaptive evolution.

The rice Xa21 gene confers resistance to Xanthomonas oryzae pv oryzae in a race-specific manner. Analysis of the inheritance patterns and resistance spectra of transgenic plants carrying six Xa21 gene family members indicated that one member, designated Xa21D, displayed a resistance spectrum identical to that observed for Xa21 but conferred only partial resistance. Xa21D encodes a receptor-like protein carrying leucine-rich repeat (LRR) motifs in the presumed extracellular domain. The Xa21D transcript terminates shortly after the stop codon introduced by the retrotransposon Retrofit. Comparison of nucleotide substitutions in the LRR coding regions of Xa21 and Xa21D provided evidence of adaptive selection. Both functional and evolutionary evidence indicates that the Xa21D LRR domain controls race-specific pathogen recognition.

Adaptation, Physiological↗

PubMed1998

Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations.

Specific amino acid binding by aminoacyl-tRNA synthetases is necessary for correct translation of the genetic code. To obtain insight into the origin of the specificity, the binding to aspartyl-tRNA synthetase (AspRS) of the negatively charged substrate aspartic acid and the neutral analogue asparagine are compared by use of molecular dynamics and free energy simulations. Simulations of the Asn-AspRS complex show that although Asn cannot bind in the same position as Asp, several possible positions exist 1.5 to 2 A away from the Asp site. The binding free energy of Asn in three of these positions was compared to that of Asp through alchemical free energy simulations, in which Asp is gradually mutated ito Asn in the complex with the enzyme. To correctly account for the electrostatic interactions in the system (including bulk solvent), a recently developed hybrid approach was used, in which the region of the mutation site is treated microscopically, whereas distant protein and solvent are treated by continuum electrostatics. Seven free energy simulations were performed in the protein and two in solution. The various Asn positions and orientations sampled at the Asn endpoints of the protein simulations yielded very similar free energy differences. The calculated Asp-->Asn free energy change is 79.8(+/-1.5) kcal/mol in solution and 95.1(+/-2.8) kcal/mol in the complex with the protein. Thus, the substrate Asp is predicted to bind much more strongly than Asn, with a binding free energy difference of 15.3 kcal/mol. This implies that erroneous binding of Asn by AspRS is highly improbable, and cannot account for any errors in the translation of the genetic code. Almost all of the protein contributions to the Asp versus Asn binding free energy difference arise from an arginine and a lysine residue that hydrogen bond to the substrate carboxylate group and an Asp and a Glu that hydrogen bond to these; all four amino acid residues are completely conserved in AspRSs. The protein effectively "solvates" the Asp side-chain more strongly than water does. The simulations are analyzed to determine the interactions that Asn is able to make in the binding pocket, and which sequence differences between AspRS and the highly homologous AsnRS are important for modifying the amino acid specificity. A double or triple mutation of AspRS that could make it specific for Asn is proposed, and supported by preliminary simulations of a mutant complex.

Amino Acid Sequence↗

PubMed2000

Hidden variables: unstable Abeta chain genes encoding antigen recognition structures in tumor survivors.

Novel single exon genes Abeta4-7 comprising the Abeta6 gene family have been cloned from mouse mutants surviving transplantable metastatic tumors. Their protein coding sequences are similar to H2-Ab cDNA which encodes antigen-binding molecules of antigen presenting cells (APC); their promoters and/or signal sequences are unrelated to Ab sequences but found in other eukaryotic genes. Abeta4(b) protein was demonstrated on macrophages and B cells that are APC. The Abeta6(w302) appears to be an ancient gene ancestral to major histocompatibility complex (MHC) class II beta genes. However, unlike the MHC class II, the Abeta4-7 genes are not involved in skin graft rejection. Despite inbreeding, the Abeta6(w302) locus remains unfixed in several strains of mice. The number of Abeta genes and their alleles varied between individual mice; they do not map into the H2 region but appear to be scattered over the genome. The Abeta6 gene family is molecularly unstable in Abeta6(w302)-positive (but not in Abeta6(w302)-negative) mice which are somatic mosaics for these genes. Biological features of Abeta4-7 genes make them remarkably different from the classical MHC gene system. All available evidence strongly suggests that these genes control susceptibility/resistance to the spread of metastatic tumors.

Animals↗

PubMed1991

The rat H+/K(+)-ATPase beta subunit gene and recognition of its control region by gastric DNA binding protein.

The rat gastric H+/K(+)-ATPase beta subunit gene was cloned, and its nucleotide sequence was determined. The coding region is separated by 6 introns, whereas the related human Na+/K(+)-ATPase beta subunit gene was shown to have 5 introns (Lane, L.K., Shull, M.M., Whitmer, K.R., and Lingrel, J.B. (1989) Genomics 5, 445-453). The positions of introns 1, 2, and 5 of the two genes were the same. The similarities in intron/exon organizations and primary structures (30-40% identical residues) suggest that the beta subunit genes for H+/K(+)-ATPases were derived from a common ancestor. The upstream region of the rat H+/K(+)-ATPase beta subunit gene contains direct repeat sequences and palindromes, potential binding sites for RNA polymerase II and E4TF1, and CACCC box sequences. Gel retardation assay demonstrated that the stomach, but not other tissues (liver, brain, kidney, spleen, and lung), has a nuclear protein(s) capable of binding to the regions upstream of the potential RNA polymerase II binding sites (TATA box). The nuclear protein(s) are suggested to recognize three tandem GATAGC sequences and may be important for controlled transcription of the H+/K(+)-ATPase beta subunit gene in gastric parietal cells.

Adenosine Triphosphatases↗

PubMed1996

Single sequence of a helix-loop peptide confers functional anticodon recognition on two tRNA synthetases.

The specific aminoacylation of RNA oligonucleotides whose sequences are based on the acceptor stems of tRNAs can be viewed as an operational RNA code for amino acids that may be related to the development of the genetic code. Many synthetases also have direct interactions with tRNA anticodon triplets and, in some cases, these interactions are thought to be essential for aminoacylation specificity. In these instances, an unresolved question is whether interactions with parts of the tRNA outside of the anticodon are sufficient for decoding genetic information. Escherichia coli isoleucyl- and methionyl-tRNA synthetases are closely related enzymes that interact with their respective anticodons. We used binary combinatorial mutagenesis of a 10 amino acid anticodon binding peptide in these two enzymes to identify composite sequences that would confer function to both enzymes despite their recognizing different anticodons. A single peptide was found that confers function to both enzymes in vivo and in vitro. Thus, even in enzymes where anticodon interactions are normally important for distinguishing one tRNA from another, these interactions can be 'neutralized' without losing specificity of amino-acylation. We suggest that acceptor helix interactions may play a role in providing the needed specificity.

Amino Acid Sequence↗

PubMed2006

Structural basis of RNA-dependent recruitment of glutamine to the genetic code.

Glutaminyl-transfer RNA (Gln-tRNA(Gln)) in archaea is synthesized in a pretranslational amidation of misacylated Glu-tRNA(Gln) by the heterodimeric Glu-tRNA(Gln) amidotransferase GatDE. Here we report the crystal structure of the Methanothermobacter thermautotrophicus GatDE complexed to tRNA(Gln) at 3.15 angstroms resolution. Biochemical analysis of GatDE and of tRNA(Gln) mutants characterized the catalytic centers for the enzyme's three reactions (glutaminase, kinase, and amidotransferase activity). A 40 angstrom-long channel for ammonia transport connects the active sites in GatD and GatE. tRNA(Gln) recognition by indirect readout based on shape complementarity of the D loop suggests an early anticodon-independent RNA-based mechanism for adding glutamine to the genetic code.

Acylation↗

PubMed2002

Accurate translation of the genetic code depends on tRNA modified nucleosides.

Transfer RNA molecules translate the genetic code by recognizing cognate mRNA codons during protein synthesis. The anticodon wobble at position 34 and the nucleotide immediately 3' to the anticodon triplet at position 37 display a large diversity of modified nucleosides in the tRNAs of all organisms. We show that tRNA species translating 2-fold degenerate codons require a modified U(34) to enable recognition of their cognate codons ending in A or G but restrict reading of noncognate or near-cognate codons ending in U and C that specify a different amino acid. In particular, the nucleoside modifications 2-thiouridine at position 34 (s(2)U(34)), 5-methylaminomethyluridine at position 34 (mnm(5)U(34)), and 6-threonylcarbamoyladenosine at position 37 (t(6)A(37)) were essential for Watson-Crick (AAA) and wobble (AAG) cognate codon recognition by tRNA(UUU)(Lys) at the ribosomal aminoacyl and peptidyl sites but did not enable the recognition of the asparagine codons (AAU and AAC). We conclude that modified nucleosides evolved to modulate an anticodon domain structure necessary for many tRNA species to accurately translate the genetic code.

Adenosine↗

PubMed2001

Many-to-one and one-to-many associative learning in a naturalistic task.

Associative learning of a coding scheme for alternative and augmentative communication devices requires the formation of multiple associations to 1 stimulus or 1 response. Alternative study presentations differ on several important factors, including recognition versus recall responses and many-to-one versus one-to-many associative learning. Also, the directionality of the association emphasized at study does not necessarily parallel the use of the association, raising questions concerning retention. Two experiments tested expectations regarding the efficacy of 2 study presentations. The study presentations produced dissociative effects for acquisition versus retention of the coding scheme for normal and intellectually disabled participants. Consideration of the results and the manner in which the coding scheme is used recommends many-to-one training in which vocabulary items are given as stimuli and icons are learned as responses.

Adolescent↗

PubMed1999

[Rate discrimination and tone recognition in mandarin-speaking cochlear-implant listeners].

OBJECTIVE: To explore the relationship between the rate discrimination and the tone recognition with psychophysical method, and provide a basis for evaluating the results from mandarin-speaking cochlear implantees who used multi-channel cochlear implant and designing new speech coding strategies of the speech processor. METHODS: Four postlingually-deafened adults with cochlear implant participated in this study. We used the method of constant stimuli to measure the rate discrimination as a function of the standard rate at 50, 100, 200, 400 Hz on electrode pairs (E1, E3), (E7, E9), (E14, E16), and (E20, E22), respectively. We also measured tone recognition in 25 consonant-vowel syllables, each of which has four tonal variations, resulting in a total of 100 words. These words were recorded by a male talker and were presented five times each to the implant users via their speech processors. The tone recognition results were scored in overall percent correct and analyzed by error patterns in the confusion matrix and fundamental frequency. RESULTS: The rate discrimination thresholds, defined at the 75% correct level, varied greatly among individuals and ranged from several Hz to hundreds of Hz. A three-way ANOVA indicated significant effect (P < 0.05) on rate discrimination for the standard rate, electrode position, and patient variable. The tone recognition ranged from 40% to 80% and tones 1 and 3 were more easily identified than tones 2 and 4. Preliminary analysis using linear regression revealed highly significant correlation between rate discrimination and tone recognition. CONCLUSION: These results suggest that identification of tones relies on good rate discrimination in cochlear implant listeners. Clinical rehabilitation strategies in improving rate discrimination were discussed.

Adult↗

PubMed2002

Object recognition using three-dimensional optical quasi-correlation.

A novel method of three-dimensional (3-D) object recognition is proposed. Several projections of a 3-D target are recorded under white-light illumination and fused into a single complex two-dimensional function. After proper filtering, the resulting function is coded into a computer-generated hologram. When this hologram is coherently illuminated, a correlation space is reconstructed such that light peaks indicate the existence and locations of true targets in the observed 3-D scene. Experimental results and comparisons with results of another 3-D object recognition technique are presented.

Journal Article↗

PubMed2003

Programming peptidomimetic syntheses by translating genetic codes designed de novo.

Although the universal genetic code exhibits only minor variations in nature, Francis Crick proposed in 1955 that "the adaptor hypothesis allows one to construct, in theory, codes of bewildering variety." The existing code has been expanded to enable incorporation of a variety of unnatural amino acids at one or two nonadjacent sites within a protein by using nonsense or frameshift suppressor aminoacyl-tRNAs (aa-tRNAs) as adaptors. However, the suppressor strategy is inherently limited by compatibility with only a small subset of codons, by the ways such codons can be combined, and by variation in the efficiency of incorporation. Here, by preventing competing reactions with aa-tRNA synthetases, aa-tRNAs, and release factors during translation and by using nonsuppressor aa-tRNA substrates, we realize a potentially generalizable approach for template-encoded polymer synthesis that unmasks the substantially broader versatility of the core translation apparatus as a catalyst. We show that several adjacent, arbitrarily chosen sense codons can be completely reassigned to various unnatural amino acids according to de novo genetic codes by translating mRNAs into specific peptide analog polymers (peptidomimetics). Unnatural aa-tRNA substrates do not uniformly function as well as natural substrates, revealing important recognition elements for the translation apparatus. Genetic programming of peptidomimetic synthesis should facilitate mechanistic studies of translation and may ultimately enable the directed evolution of small molecules with desirable catalytic or pharmacological properties.

Base Sequence↗

PubMed1995

Prediction of function in DNA sequence analysis.

Recognition of function of newly sequenced DNA fragments is an important area of computational molecular biology. Here we present an extensive review of methods for prediction of functional sites, tRNA, and protein-coding genes and discuss possible further directions of research in this area.

Algorithms↗

PubMedDate not supplied

Patient pain in primary care: factors that influence physician diagnosis.

BACKGROUND: The accurate recognition of patient pain is a crucial, but sometimes difficult, task in medical care. This study explored factors related to the physician's diagnosis of pain in primary care patients. METHODS: New adult patients were prospectively randomized to care by primary care providers at a university medical center clinic. Study participants were interviewed prior to the initial visit, and their level of self-reported pain was measured with the Visual Analog Pain Scale and the Medical Outcomes Study Short Form-36. The medical encounter was videotaped in its entirety and later analyzed using the Davis Observation Code to characterize physician practice style. Patient satisfaction was measured immediately after the visit. A review of the medical record was used to assess physician recognition of patient pain. RESULTS: For all patients (N = 509), as the amount of pain increased, the percentage of patients having pain diagnosed by the physician also increased. Female patients reported a greater amount of pain than male patients. When women were in severe pain, they were more likely than men to have their pain accurately recognized by their physician. The correct diagnosis of pain was not significantly related to patient satisfaction. Physician practice styles emphasizing technically oriented activities and health behavior discussions were strongly predictive of the physician diagnosing patient pain. CONCLUSIONS: The diagnosis of pain is influenced by the severity of patient pain, patient gender, and physician practice style. If the routine use of pain assessment tools is found to be effective in improving physician recognition and treatment of patients' pain, then application of these tools in patient care settings should be encouraged.

Adult↗

PubMed1986

Viral recognition by influenza A virus cross-reactive cytotoxic T (Tc) cells: the proportion of Tc cells that recognize nucleoprotein varies between individual mice.

L cells (H-2k) transfected with DNA coding for the A/NT/60/68 influenza nucleoprotein (NP) gene have been found previously to provide a target cell for cytotoxic T (Tc) cells. In this report we have studied the repertoire of cytotoxic memory cells in mice of different strains primed by infection with several influenza A subtypes. L cells transfected with NP and Db genes enabled us to estimate the proportion of A virus cross-reactive Tc cells specific for NP. The most striking feature of our results was variation in the frequency of NP-specific Tc cells between individuals of an inbred mouse strain. Occasional individuals, although showing a strong A virus cross-reactive Tc response, had no A virus cross-reactive Tc cells that recognized NP. The NP-directed Tc repertoire represented between 0-40% of lysis of target cells infected with a heterologous type A virus. Thus, a significant proportion of A virus cross-reactive Tc cells must have different specificities for type A influenza virus. In C3H-H-2o2 mice, Dk is a low responder allele for NP recognition by Tc cells.

Alleles↗

PubMed1998

Cloning, characterization, and the complete 56.8-kilobase DNA sequence of the human NOTCH4 gene.

The first complete mammalian genomic sequence reported thus far in the Notch gene family, including a putative promoter region and 30 exons of the human NOTCH4 gene spanning 56.8 kb of DNA, were sequenced. The NOTCH4 locus contains a TATA-less promoter with two putative transcription initiation sites (Inr), three RBP-Jkappa sites, and two GATA recognition sites. Two cDNA isoforms, NOTCH4(L) and NOTCH4(S),were identified. Whereas the NOTCH4(S) isoform contains the entire coding sequence, the NOTCH4(L) isoform has two unspliced intronic sequences between exons 11 and 12 and exons 20 and 21 and a misspliced exon 6. Consistent with these results, two alternatively spliced isoforms of transcripts of approximately 9.3 and 6.7 kb were detected by Northern blot analysis. The predicted amino acid sequence of the NOTCH4 protein based on the NOTCH4(S) cDNA sequence contains 2003 amino acids and includes the predominant motifs of the Notch family: 29 epidermal growth factor (EGF)-like repeats, 3 Notch/lin-12 repeats, a transmembrane region, 6 cdc10/Ankyrin repeats, and a PEST domain.

Adult↗

PubMed1990

Identification of atypical strains of Streptococcus pneumoniae by a specific DNA probe.

A specific DNA probe containing a 0.65 Kb fragment coding for the aminoterminal region of the major pneumococcal autolysin (amidase) was constructed, deleting the region involved in the specific recognition of cell wall choline residues. The high specificity of this probe was demonstrated in tests with Streptococcus pneumoniae related species including Streptococcus oralis, which contains choline in its cell wall. The probe was used to characterize pneumococcal isolates showing atypical responses in conventional identification tests. The hybridization obtained with 27 atypical pneumococci and 11 of 17 isolates presumptively identified as viridans streptococci confirmed that the probe is suitable for diagnostic use.

DNA Probes↗

PubMed1990

Orthographic processing in visual word identification.

A series of experiments is reported examining orthographic priming effects between briefly presented pairs of letter strings. The experiments investigate the effects of the number and position of letters shared by primes and targets, and the effects of prime-target length. Priming effects increase nonlinearly as a function of both the number and the position of shared letters, and they are dependent on the positions of letters relative to both the end positions in the string and to the identities of their nearest neighbours. There is little effect of absolute string length on priming. These priming effects can be distinguished from intrusion errors where letters from primes are reported in response to targets. An account of orthographic processing is outlined which attributes priming to cooperative interactions between coarse relative-position coded letter cluster representations activated by primes and targets. The implications of the findings for understanding other effects in word recognition and reading are discussed.

Adult↗