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PubMed1992

Protein tertiary structure recognition using optimized Hamiltonians with local interactions.

Protein folding codes embodying local interactions including surface and secondary structure propensities and residue-residue contacts are optimized for a set of training proteins by using spin-glass theory. A screening method based on these codes correctly matches the structure of a set of test proteins with proteins of similar topology with 100% accuracy, even with limited sequence similarity between the test proteins and the structural homologs and the absence of any structurally similar proteins in the training set.

Amino Acids↗

PubMed1981

Modality effects in short term recognition memory.

Retention was assessed using a four-alternative recognition test in a modified Brown-Peterson paradigm. Performance decreased with the length of the distraction interval at a faster rate when the test modality (auditory or visual) did not match the presentation modality than when test and presentation modalities did match. These results, which were replicated in a second experiment, were interpreted in terms of a dual-access model of the recognition process and a feature conception of memory codes. Also, in Experiment 1, modality-specific encoding was not circumvented by dual-modality presentation (auditory plus visual): dual-modality presentation resulted in performance comparable to that observed following visual presentation. When subjects were instructed to attend to both modalities equally in Experiment 2, the pattern of results reflected a corresponding shift in attentional bias but modality-dependent encoding was circumvented only partially. This result was interpreted as being inconsistent with either the notion of modality-specific processing capacities or dual-code theory.

Adult↗

PubMed1990

Mechanism of escape of endogenous murine leukemia virus emv-14 from recognition by anti-AKR/Gross virus cytolytic T lymphocytes.

It was previously shown that spleen cells from endogenous ecotropic murine leukemia virus emv-14+ AKXL-5 mice fail to stimulate an anti-AKR/Gross virus cytolytic T-lymphocyte (CTL) response in a mixed lymphocyte culture with primed C57BL/6 responder spleen cells, whereas spleen cells from AKXL strains carrying the very similar emv-11 provirus do stimulate a response (Green and Graziano, Immunogenetics 23:106-110, 1986). We wished to determine whether the lack of response with AKXL-5 spleen cells was at the level of recognition between effector cell and target cell and whether the relevant mutation was within the emv-14 provirus. It is shown here that EMV-negative SC-1 fibroblast cells transfected with the major histocompatibility complex class I Kb gene and infected with virus isolated from the AKXL-5 strain (SC.Kb/5 cells) were not lysed by H-2b-restricted anti-AKR/Gross virus CTL. SC.Kb cells infected with virus isolated from emv-11+ strains, however, were efficiently lysed by anti-AKR/Gross virus CTL, indicating that there is nothing intrinsic to EMV-infected SC.Kb cells that would prevent them from being recognized and lysed efficiently by anti-AKR/Gross virus CTL. Analysis of virus expression for the infected SC.Kb cells by XC plaque assay and by flow cytometry indicated that emv-14 virus expression for SC.Kb/5 cells was not significantly different from that for emv-11-containing SC.Kb/9 or SC.Kb/21 cells. These data show that the mutation responsible for the lack of CTL recognition and lysis is at the level of recognition between target cell and effector cell. Furthermore, these data strongly suggest that the mutation is within the emv-14 genome. Flow cytometry experiments with monoclonal antibodies against a number of viral determinants indicated that there was no gross mutation detectable in the viral determinants analyzed. The data suggest that the relevant mutation may be a point mutation or a small insertion or deletion within a coding sequence that is critical for CTL recognition.

AKR murine leukemia virus↗

PubMed1994

LIM domain recognition of a tyrosine-containing tight turn.

Endocytosis of cell surface receptors requires sequence "codes" consisting of tight turn structures with an essential Tyr or Phe residue. To determine mechanisms through which cells recognize this information, we utilized exon 16 of the human insulin receptor in the two-hybrid system to isolate a novel 455-amino acid cytoplasmic protein that contains two LIM domains within its carboxyl terminus. Mutational analyses indicate that one of the Cys-rich Zn2+ binding LIM domains specifically recognizes active but not inactive endocytic codes contained in exon 16. These findings suggest that LIM domain structures in proteins provide molecular recognition of Tyr-containing tight turn structures.

Amino Acid Sequence↗

PubMed1995

Evolution of tRNA recognition systems and tRNA gene sequences.

The aminoacylation of tRNAs by the aminoacyl-tRNA synthetases recapitulates the genetic code by dictating the association between amino acids and tRNA anticodons. The sequences of tRNAs were analyzed to investigate the nature of primordial recognition systems and to make inferences about the evolution of tRNA gene sequences and the evolution of the genetic code. Evidence is presented that primordial synthetases recognized acceptor stem nucleotides prior to the establishment of the three major phylogenetic lineages. However, acceptor stem sequences probably did not achieve a level of sequence diversity sufficient to faithfully specify the anticodon assignments of all 20 amino acids. This putative bottleneck in the evolution of the genetic code may have been alleviated by the advent of anticodon recognition. A phylogenetic analysis of tRNA gene sequences from the deep Archaea revealed groups that are united by sequence motifs which are located within a region of the tRNA that is involved in determining its tertiary structure. An association between the third anticodon nucleotide (N36) and these sequence motifs suggests that a tRNA-like structure existed close to the time that amino acid-anticodon assignments were being established. The sequence analysis also revealed that tRNA genes may evolve by anticodon mutations that recruit tRNAs from one isoaccepting group to another. Thus tRNA gene evolution may not always be monophyletic with respect to each isoaccepting group.

Amino Acyl-tRNA Synthetases↗

PubMed1991

Allospecific recognition of hemic cells in vitro by natural killer cells from athymic rats: evidence that allodeterminants coded for by single major histocompatibility complex haplotypes are recognized.

We have previously shown that large granular lymphocyte (LGL)-enriched cell populations have the capacity to spontaneously recognize and kill allogeneic small lymphocytes and bone marrow cells (BMC) in vitro in certain strain combinations of rats. Here, we have studied the alloreactivity of natural killer (NK) cells from PVG nude (RT1c) rats against a panel of major histocompatibility complex (MHC) incompatible hemic cells. Both lymphocytes and BMC from the AO (RT1u), DA (RT1a), BN (RT1n) as well as the MHC-congenic PVG-RT1u (RT1u) rat strains were efficiently killed in vitro, whereas cells from syngeneic PVG rats were spared. The structures recognized on lymphocytes and BMC were probably similar since the two cell populations inhibited each other in cross-competition experiments. A number of features aligned the alloreactive effector cells with NK cells and not T cells. (a) Only about 5% of the effector cells from nude spleens expressed the T cell antigens CD3, CD5 or T cell receptor (TcR) alpha/beta whereas greater than 50% of the cells expressed markers present on NK cells (CD2, CD8, OX52 and the rat NK cell-specific marker NKR-P1 recognized by the monoclonal antibody 3.2.3). (b) The alloreactive cells were granular since pretreatment of nude spleen cells with the lysosomotropic agent L-leucine methyl ester which eliminated LGL, simultaneously abolished the cytolysis of both allogeneic lymphocytes and YAC-1 tumor cells. (c) Nude spleen cells stimulated with human recombinant interleukin 2 for 1 week in vitro generated large granular proliferating cells which were CD3-, CD5-, TcR alpha/beta-, but greater than 95% 3.2.3+. These cells efficiently killed allogeneic hemic cells from the same rat strains as did freshly isolated effector cells. (d) The cytolysis of allogeneic hemic cells could effectively be inhibited with unlabelled NK-sensitive (YAC-1 and K-562), but not NK-resistant (Roser leukemia) tumor cells. Cross-competition studies showed that PVG nude NK cells discriminated between AO, BN and DA BMC, suggesting that different alloantigens were positively recognized by subsets of NK cells. The mode of inheritance of the allodeterminant specifically recognized on AO BMC was investigated in crosses and backcrosses between AO and BN or DA rats. A gene dosage effect was observed in that this determinant was expressed at a slightly reduced level in F1 hybrids.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2001

Decoding "drug imprints" at the millennium: a proposal to increase accuracy and reduce costs.

The State of Washington mandated the use of imprints on all prescription drugs in 1980 and for "OTC's" in 1991. The FDA implemented federal requirements in 1995. Unfortunately, the FDA permitted the continued use of symbols, logotypes, and trademarks as code components, limiting the use of automated recognition systems. Analyses of several week-long samples of phone inquiries documented imprinting calls, the staff's ability to respond with an identification, the information sources used, and apparent reasons for any failure. In the first week we received 666 decoding requests, which when projected for the year amounted to > 25,000 calls. A review of 1999 data exceeded that number. Staff was able to reach drug identification in 93.8% of inquiries. Uninterpretable symbols and absence of code listings contributed to the 36 failures. Projecting over the US suggested as many as 1.25 million calls costing poison centers $25 million/y. A touch-tone telephone or website response system could permit automated responses. Neither solution is feasible without the elimination of symbols or logotypes when using an exclusively alpha-numeric code.

Drug Labeling↗

PubMed2003

Does jugde activate COURT? Transposed-letter similarity effects in masked associative priming.

Transposed-letter (TL) nonwords (e.g., jugde) can be easily misperceived as words, a fact that is somewhat inconsistent with the letter-position-coding schemes employed by most current models of visual word recognition. To examine this issue further, we conducted four masked semantic/associative priming experiments, using a lexical decision task. In Experiment 1, the related primes could be words, TL-internal nonwords, or replacement-letter (RL) nonwords (e.g., judge, jugde, or judpe, respectively; the target would be COURT). Relative to an unrelated condition, masked TL-internal primes produced a significant semantic/associative priming effect, an effect that was only slightly smaller than the priming effect for word primes. No effect, however, was observed for RL-nonword primes. In Experiment 2, the TL-nonword primes were created by switching the two final letters of the primes (e.g., judeg). The results again showed a semantic/associative priming effect for word primes, but not for TL-final nonword primes or for RL-nonword primes. Experiment 3 replicated the associative/semantic priming effect for TL-internal nonword primes, with, again, no effect for TL-final nonword primes. Finally, Experiment 4 again failed to yield a priming effect for TL-final nonword primes. The implications of these results for the choice of a letter-position-coding scheme in visual word recognition models are discussed.

Association↗

PubMed2004

Selective recognition of acetylated histones by bromodomain proteins visualized in living cells.

Acetylation and other modifications on histones comprise histone codes that govern transcriptional regulatory processes in chromatin. Yet little is known how different histone codes are translated and put into action. Using fluorescence resonance energy transfer, we show that bromodomain-containing proteins recognize different patterns of acetylated histones in intact nuclei of living cells. The bromodomain protein Brd2 selectively interacted with acetylated lysine 12 on histone H4, whereas TAF(II)250 and PCAF recognized H3 and other acetylated histones, indicating fine specificity of histone recognition by different bromodomains. This hierarchy of interactions was also seen in direct peptide binding assays. Interaction with acetylated histone was essential for Brd2 to amplify transcription. Moreover association of Brd2, but not other bromodomain proteins, with acetylated chromatin persisted on chromosomes during mitosis. Thus the recognition of histone acetylation code by bromodomains is selective, is involved in transcription, and potentially conveys transcriptional memory across cell divisions.

Acetylation↗

PubMed2005

Hospital admissions for 'drug-induced' disorders in England: a study using the Hospital Episodes Statistics (HES) database.

AIMS: To review Hospital Episode Statistics (HES) data for England coded as being 'drug induced' during 1996-2000 and to consider their potential utility for assessing the public health burden of adverse drug reactions (ADRs) and studying drug safety. METHODS: ICD-10 codes including the words 'drug-induced' or 'due to' a medicine or which are recognized to be invariably caused by a drug were extracted along with external cause codes indicating that a drug was implicated (i.e. Y40-59 in ICD-10). We also calculated the proportions of patients with each 'drug-induced' code for whom an external cause code had been applied. RESULTS: During the 5-year study period there were almost 53.8 million hospital admissions in England, of which 44 411 (0.083%) were coded as 'drug-induced' and 168 958 (0.314%) were associated with a relevant external cause code. The numbers of patients with 'drug-induced' codes used were generally stable during the study period (range 7454-8860 per year) but the application of external cause codes increased in each year and by 40% overall (from 24 786 in 1996 to 34 843 in 2000). The overall proportion of 'drug-induced' codes associated with a relevant external cause code was quite low (12-15%) but there was considerable variation between codes. CONCLUSIONS: Comparisons with published studies indicate that HES data grossly underestimate the burden of drug-induced disorders as a cause of hospital admission. There are likely to be multiple underlying reasons including under-recognition, under-recording and limitations of the coding system. The potential of these data for identifying previously unrecognized serious ADRs is limited by constraints on the availability of detailed data regarding individual cases.

Drug-Related Side Effects and Adverse Reactions↗

PubMed2003

Analysis of bacterial RM-systems through genome-scale analysis and related taxonomy issues.

Recognition sites for type II restriction and modification enzymes in genomes of several bacteria are recognized as semi-palindromic motifs and are avoided at a significant degree. The key idea of contrast word analysis with respect to RMS recognition sites, is that under-represented words are likely to be selected against. Starting from over- or underrepresented words corresponding to RMS recognition sites in specific clades, the specificity of unknown R-M systems can be highlighted. Among the known restriction enzymes, that are described in the REBASE database of restriction and modification systems, many of their recognition sites are still uncharacterized. Eventually, this motivates studies aimed at assessing horizontal transferring events of RMS in micro-organisms through the analysis of word usage biases in well-determined genomic regions. A probabilistic model is built on a first-order Markovian chain. Statistics on the k-neighborhood of a word is carried out to assess the biological significance of a genomic motif. Efficient word counting procedures have been implemented and statistics are used for the assessment of the significance of individual words in large sequences. On the basis of the set of most avoided words, and in accordance to the IUPAC coding standards, suggestions are made regarding potential recognition sequences. In certain cases, a comparison of avoided palindromic words in taxonomically related bacteria shows a pattern of relatedness of their R-M systems. For strengthening this analysis, the primary protein structure of all type II R-M systems known in REBASE have been blasted against the nr-GENBANK database. The combination of these analyses has revealed some interesting examples of possible horizontal transfer events of R-M systems.

Amino Acid Sequence↗

PubMed1987

Advanced cardiac life support refresher course using standardized objective-based Mega Code testing.

The American Heart Association (AHA) recommends that those whose daily work requires knowledge and skills in advanced cardiac life support (ACLS) not only be trained in ACLS, but also be given a refresher training at least every 2 yr. However, AMA offers no recommended course for retraining; no systematic studies of retraining have been conducted on which to base these recommendations. In this paper we review and present our recommendation for a standardized approach to refresher training. Using the goals and objectives of the ACLS training program as evaluation criteria, we tested with the Mega Code a sample population who had previously been trained in ACLS. The results revealed deficiencies in ACLS knowledge and skills in the areas of assessment, defibrillation, drug therapy, and determining the cause of an abnormal blood gas value. We combined this information with our knowledge of other deficiencies identified during actual resuscitation attempts and other basic life-support and ACLS teaching experiences. We then designed a refresher course which was consistent with the overall goals and objectives of the ACLS training program, but which placed emphasis on the deficiencies identified in the pretesting. We taught our newly designed refresher course in three sessions, which included basic life support, endotracheal intubation, arrhythmia recognition and therapeutic modalities, defibrillation, and Mega Code practice. In a fourth session, using Mega Code testing, we evaluated knowledge and skill learning immediately after training. We similarly tested retention 2 to 4 months later. Performance immediately after refresher training showed improvement in all areas where performance had been weak.(ABSTRACT TRUNCATED AT 250 WORDS)

Critical Care↗

PubMed2004

Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA.

Prediction of splice sites in non-coding regions of genes is one of the most challenging aspects of gene structure recognition. We perform a rigorous analysis of such splice sites embedded in human 5' untranslated regions (UTRs), and investigate correlations between this class of splice sites and other features found in the adjacent exons and introns. By restricting the training of neural network algorithms to 'pure' UTRs (not extending partially into protein coding regions), we for the first time investigate the predictive power of the splicing signal proper, in contrast to conventional splice site prediction, which typically relies on the change in sequence at the transition from protein coding to non-coding. By doing so, the algorithms were able to pick up subtler splicing signals that were otherwise masked by 'coding' noise, thus enhancing significantly the prediction of 5' UTR splice sites. For example, the non-coding splice site predicting networks pick up compositional and positional bias in the 3' ends of non-coding exons and 5' non-coding intron ends, where cytosine and guanine are over-represented. This compositional bias at the true UTR donor sites is also visible in the synaptic weights of the neural networks trained to identify UTR donor sites. Conventional splice site prediction methods perform poorly in UTRs because the reading frame pattern is absent. The NetUTR method presented here performs 2-3-fold better compared with NetGene2 and GenScan in 5' UTRs. We also tested the 5' UTR trained method on protein coding regions, and discovered, surprisingly, that it works quite well (although it cannot compete with NetGene2). This indicates that the local splicing pattern in UTRs and coding regions is largely the same. The NetUTR method is made publicly available at www.cbs.dtu.dk/services/NetUTR.

5' Untranslated Regions↗

PubMed1994

Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage.

We have used two selection techniques to study sequence-specific DNA recognition by the zinc finger, a small, modular DNA-binding minidomain. We have chosen zinc fingers because they bind as independent modules and so can be linked together in a peptide designed to bind a predetermined DNA site. In this paper, we describe how a library of zinc fingers displayed on the surface of bacteriophage enables selection of fingers capable of binding to given DNA triplets. The amino acid sequences of selected fingers which bind the same triplet are compared to examine how sequence-specific DNA recognition occurs. Our results can be rationalized in terms of coded interactions between zinc fingers and DNA, involving base contacts from a few alpha-helical positions. In the paper following this one, we describe a complementary technique which confirms the identity of amino acids capable of DNA sequence discrimination from these positions.

Amino Acid Sequence↗

PubMed1993

A cytoplasmic actin gene from the silkworm Bombyx mori is expressed in tissues of endodermal origin and previtellogenic germ cells of transgenic Drosophila.

A cytoplasmic actin gene from Bombyx mori introduced into Drosophila melanogaster by P-element mediated transformation, is efficiently transcribed in larvae, pupae and adults of the host. The exogenous mRNA has the same size as the one observed in the Bombyx cells and the intron located within the coding region is properly excised, indicating a correct recognition of the exogenous sequences by the Drosophila transcriptional and splicing machineries. The expression of the Bombyx gene in Drosophila tissues was determined by transforming flies with a hybrid gene in which a large part of the Bombyx actin coding sequences was replaced by those of the bacterial lac Z gene. This chimaeric gene is specifically and highly expressed, from the embryo to the adult of the transgenic lines, in tissues of endodermal origin, the midgut and its derivatives, i.e. gastric caeca, the outer layer of the proventriculus, and in the Malpighian tubules. This gene is also expressed, at a lower level, in germ cells but restricted to the sixteen cell cysts during previtellogenesis. The expression of the Bombyx gene during development of transgenic flies was compared to that of the two Drosophila endogenous cytoplasmic actin genes and the results are discussed.

Actins↗

PubMed2006

Investigation of the mechanism of meiotic DNA cleavage by VMA1-derived endonuclease uncovers a meiotic alteration in chromatin structure around the target site.

VMA1-derived endonuclease (VDE), a homing endonuclease in Saccharomyces cerevisiae, is encoded by the mobile intein-coding sequence within the nuclear VMA1 gene. VDE recognizes and cleaves DNA at the 31-bp VDE recognition sequence (VRS) in the VMA1 gene lacking the intein-coding sequence during meiosis to insert a copy of the intein-coding sequence at the cleaved site. The mechanism underlying the meiosis specificity of VMA1 intein-coding sequence homing remains unclear. We studied various factors that might influence the cleavage activity in vivo and found that VDE binding to the VRS can be detected only when DNA cleavage by VDE takes place, implying that meiosis-specific DNA cleavage is regulated by the accessibility of VDE to its target site. As a possible candidate for the determinant of this accessibility, we analyzed chromatin structure around the VRS and revealed that local chromatin structure near the VRS is altered during meiosis. Although the meiotic chromatin alteration exhibits correlations with DNA binding and cleavage by VDE at the VMA1 locus, such a chromatin alteration is not necessarily observed when the VRS is embedded in ectopic gene loci. This suggests that nucleosome positioning or occupancy around the VRS by itself is not the sole mechanism for the regulation of meiosis-specific DNA cleavage by VDE and that other mechanisms are involved in the regulation.

Active Transport, Cell Nucleus↗

PubMed1998

Why morphometrics is not special: coding quantitative data for phylogenetic analysis.

Thorpe (1984) and Chappill (1989) argued that selection of a coding method should be [figure: see text] based on the purpose of coding. In our view, the purpose of coding is dictated by the principles of phylogenetic systematics. The foundation of phylogenetic systematics is the observation that monophyletic groups can be recognized if homologous character states, shared evolutionary novelties, can be identified (Hennig, 1966). Unfortunately, characters do not have labels indicating their homology. Instead, a systematist must propose a hypothesis of homology and evaluate its congruence with independent hypotheses based on other traits. In this context, the purpose of coding is to represent those hypotheses. The major obstacle to coding is that the a priori groups under analysis (i.e., taxa) often have ranges of variation that overlap to some degree. This is true whether traits are described qualitatively or quantitatively. One advantage of quantitative description is that it permits a more detailed analysis of how much the ranges of variation overlap. It may seem appropriate to use statistical methods to summarize the amount of overlap and even to decide objectively (on a priori grounds) whether taxa are similar or different. Above, we demonstrated some of the problems resulting from these uses of statistical analysis. In our view, the most important problem is the implication that similarity of the feature across taxa is the basis for inferring homology. The similarity that is relevant to phylogenetic analysis is not proximity in morphospace, but shared novelty. Statistical methods can describe proximity, but they cannot recognize novelty. The method of coding we recommend uses graphical displays of individual values. Coding decisions are based on all of the individuals in each taxon, not on summaries derived from models of expected distributions. Then, the evidence for inferring divergence is independently evaluated for each pair of overlapping taxa. Coding decisions are not based on a priori rules that have no bearing on recognition of evolutionary novelty. This is the same approach that is used to code qualitatively described traits.

Animals↗

PubMed2006

Pulses, patterns and paths: neurobiology of acoustic behaviour in crickets.

Crickets use acoustic communication for pair formation. Males sing with rhythmical movements of their wings and the mute females approach the singing males by phonotaxis. Females walking on a trackball rapidly steer towards single sound pulses when exposed to split-song paradigms. Their walking path emerges from consecutive reactive steering responses, which show no temporal selectivity. Temporal pattern recognition is tuned to the species-specific syllable rate and gradually changes the gain of auditory steering. If pattern recognition is based on instantaneous discharge rate coding, then the tuning to the species-specific song pattern may already be present at the level of thoracic interneurons. During the processing of song patterns, changes in cytosolic Ca(2+ )concentrations occur in phase with the chirp rhythm in the local auditory interneurone. Male singing behaviour is controlled by command neurons descending from the brain. The neuropil controlling singing behaviour is located in the anterior protocerebrum next to the mushroom bodies. Singing behaviour is released by injection of cholinergic agonists and inhibited by gamma-butyric acid (GABA). During singing, the sensitivity of the peripheral auditory system remains unchanged but a corollary discharge inhibits auditory processing in afferents and interneurons within the prothoracic auditory neuropil and prevents the auditory neurons from desensitisation.

Animals↗