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PubMed1999

Transfer RNA recognition by aminoacyl-tRNA synthetases.

The aminoacyl-tRNA synthetases are an ancient group of enzymes that catalyze the covalent attachment of an amino acid to its cognate transfer RNA. The question of specificity, that is, how each synthetase selects the correct individual or isoacceptor set of tRNAs for each amino acid, has been referred to as the second genetic code. A wealth of structural, biochemical, and genetic data on this subject has accumulated over the past 40 years. Although there are now crystal structures of sixteen of the twenty synthetases from various species, there are only a few high resolution structures of synthetases complexed with cognate tRNAs. Here we review briefly the structural information available for synthetases, and focus on the structural features of tRNA that may be used for recognition. Finally, we explore in detail the insights into specific recognition gained from classical and atomic group mutagenesis experiments performed with tRNAs, tRNA fragments, and small RNAs mimicking portions of tRNAs.

Amino Acyl-tRNA Synthetases↗
PubMed1983

Relation between pronunciation and recognition of printed words in deep and shallow orthographies.

The processes responsible for recognition and pronunciation of printed words were studied by means of lexical decision and naming experiments. Two languages were examined: English, which has a complex and deep correspondence between spelling and speech, and Serbo-Croatian, in which the correspondence is simple and direct. It was hypothesized that reliance on articulatory coding (instead of on mediation by the internal lexicon) would be greater for Serbo-Croatian because its shallow orthography would allow more efficient use of spelling-to-speech correspondences. Each target stimulus was preceded by a word that was either related or unrelated semantically. Semantic priming of target words facilitated performance in both lexical decision and naming for English, results suggesting an influence of the internal lexicon on both processes. In contrast, semantic priming facilitated only lexical decision for Serbo-Croatian, which suggests that naming, at least in that language, is not strongly influenced by the internal lexicon. Further, in Serbo-Croatian, lexical decision and naming latencies were correlated when both tasks were not semantically primed and were uncorrelated when either or both tasks received semantic priming. This suggested that articulatory coding is used in lexical decision, at least under conditions in which contextual semantic facilitation is absent. In contrast, in English, lexical decision and naming were correlated uniformly whether semantic facilitation was present or not, which, when considered with the effect of semantic facilitation on naming, suggested a stronger influence of the internal lexicon on both recognition and pronunciation.

Form Perception↗
PubMed2005

Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions.

The genetic code of nuclear genes in some ciliates was found to differ from that of other organisms in the assignment of UGA, UAG, and UAA codons, which are normally assigned as stop codons. In some ciliate species, the universal stop codons UAA and UAG instead encode glutamine. In some other ciliates, the universal stop codon UGA appears to be translated as cysteine or tryptophan. Eukaryotic release factor 1 (eRF1) is a key protein in stop codon recognition, thus, the protein is believed to play an important role in the stop codon reassignment in ciliates. We have cloned, sequenced, and analyzed the cDNA of eRF1 from four ciliate species of three different classes: Karyorelictea (Loxodes striatus), Heterotrichea (Blepharisma musculus), and Litostomatea (Didinium nasutum, Dileptus margaritifer). Phylogenetic analysis of these eRF1s supports the hypothesis that the genetic code in ciliates has deviated independently several times from the universal genetic code, and that different ciliate eRF1s may have undergone different processes to change the codon specificity. Using computational methods, we have also suggested areas on the surface of eRF1s that are important for stop codon recognition in ciliate eRF1s.

Amino Acid Sequence↗
PubMed2006

A modified SPIHT algorithm for image coding with a joint MSE and classification distortion measure.

The set partitioning in hierarchical trees (SPIHT) algorithm is an efficient wavelet-based progressive image-compression technique, designed to minimize the mean-squared error (MSE) between the original and decoded imagery. However, the MSE-based distortion measure is not in general well correlated with image-recognition quality, especially at low bit rates. Specifically, low-amplitude wavelet coefficients that may be important for classification are given low priority by conventional SPIHT. In this paper, we use the kernel matching pursuits (KMP) method to autonomously estimate the importance of each wavelet subband for distinguishing between different textures, with textural segmentation first performed via a hidden Markov tree. Based on subband importance determined via KMP, we scale the wavelet coefficients prior to SPIHT coding, with the goal of minimizing a Lagrangian distortion based jointly on the MSE and classification error. For comparison we consider Bayes tree-structured vector quantization (B-TSVQ), also designed to obtain a tradeoff between MSE and classification error. The performances of the original SPIHT, the modified SPIHT, and B-TSVQ are compared.

Algorithms↗
PubMed1997

Further characterization of Escherichia coli endonuclease V. Mechanism of recognition for deoxyinosine, deoxyuridine, and base mismatches in DNA.

Endonuclease V from Escherichia coli has a wide substrate spectrum. In addition to deoxyinosine-containing DNA, the enzyme cleaves DNA containing urea residues, AP sites, base mismatches, insertion/deletion mismatches, flaps, and pseudo-Y structures. The gene coding for the enzyme was identified to be orf 225 or nfi (endonuclease five). Using enzyme purified from an overproducing strain, the deoxyinosine- and mismatch-specific activities of endonuclease V was found to have different divalent metal requirements. The affinity of the enzyme is greater than 20-fold higher for DNA containing deoxyinosine than deoxynebularine or base mismatches. Under optimal cleavage conditions, endonuclease V forms two stable complexes with DNA containing deoxyinosine, but not with DNA containing base mismatches or deoxynebularine, suggesting that the 6-keto group of hypoxanthine in DNA is critical for stable interactions with the protein. The enzyme recognizes deoxyuridine in DNA but exhibits a much lower affinity to DNA containing deoxyuridine compared with DNA containing deoxyinosine. Interestingly, deoxyuridine-specific endonuclease activity of endonuclease V has a divalent metal requirement similar to the mismatch activity. A model for the mechanism of substrate recognition is proposed to explain these different activities.

DNA↗
PubMed1997

Sequence of cDNAs encoding components of vascular actin single-stranded DNA-binding factor 2 establish identity to Puralpha and Purbeta.

Transcriptional repression of the mouse vascular smooth muscle alpha-actin gene in fibroblasts and myoblasts is mediated, in part, by the interaction of two single-stranded DNA binding activities with opposite strands of an essential transcription enhancer factor-1 recognition element (Sun, S., Stoflet, E. S., Cogan, J. G., Strauch, A. R., and Getz, M. J. (1995) Mol. Cell. Biol. 15, 2429-2436). One of these activities, previously designated vascular actin single-stranded DNA-binding factor 2 includes two distinct polypeptides (p44 and p46) which specifically interact with the purine-rich strand of both the enhancer and a related element in a protein coding exon of the gene (Kelm, R. J., Jr., Sun, S., Strauch, A. R., and Getz, M. J. (1996) J. Biol. Chem. 271, 24278-24285). Expression screening of a mouse lung cDNA library with a vascular actin single-stranded DNA-binding factor 2 recognition element has now resulted in the isolation of two distinct cDNA clones that encode p46 and p44. One of these proteins is identical to Puralpha, a retinoblastoma-binding protein previously implicated in both transcriptional activation and DNA replication. The other is a related family member, presumably Purbeta. Comparative band shift and Southwestern blot analyses conducted with cellular p46, p44, and cloned Pur proteins synthesized in vitro and in vivo, establish identity of p46 with Puralpha and p44 with Purbeta. This study implicates Puralpha and/or Purbeta in the control of vascular smooth muscle alpha-actin gene transcription.

Amino Acid Sequence↗
PubMed1981

[Value of the automated analysis of the electrocardiogram by the Telemed program (V version)].

A series of 1000 12 lead ECGs recorded in 1000 consecutive ambulatory patients were analysed by the Telemed (V Version) programme and its interpretation and the precision of the French translation were compared with the interpretation of two physicians using standard criteria. The computer identified 90% of the 285 ECGs coded as "normal" by the physicians, 69% of the 57 ECGs coded as "borderline" and 96% of the 658 ECGs coded as "abnormal". The computer interpretation was correct in 74% of cases and acceptable in 87,4% of cases. The computer classified 80% of the 240 arrhythmias correctly. Atrial fibrillation was detected in 91% of cases, and ventricular and supraventricular extrasystoles in 88% of cases. The recognition of other arrhythmias was not as good but the small number of cases did not allow statistical evaluation. The 148 cases of axis deviation and 98% of ventricular conduction defects were identified. The programme detected 84% of transmural infarcts, the sensitivity being greater for anterior or lateral than inferior infarctions. The majority of undiagnosed infarcts were "possibles" according to the criteria of the Minnesota Code. Of 536 ECGs with ST-T segment abnormalities, 81% were classified correctly; ST depression of less than 0.5 mm comprised the majority of false negatives. The sensitivity of the programme to left ventricular hypertrophy was excellent (95%) with a specificity of only 92,5% as the programme uses the Romhilt-Estes criteria which are more liberal than those of the Minnesota Code. The comparison of the sensitivity and specificity for the commonest ECG changes showed excellent all round diagnostic performance of the Telemed programme. In conclusion, despite the large number of abnormal ECGs, the level of computer-physician concordance was high. The French translation of the V Version of the Telemed programme is therefore suitable for clinical use Nevertheless, the computer interpretation should still be checked by a physician.

Computers↗
PubMed2004

Performance of subjects fit with the Advanced Bionics CII and Nucleus 3G cochlear implant devices.

OBJECTIVE: To determine if subjects who used different cochlear implant devices and who were matched on consonant-vowel-consonant (CNC) identification in quiet would show differences in performance on speech-based tests of spectral and temporal resolution, speech understanding in noise, or speech understanding at low sound levels. DESIGN: The performance of 15 subjects fit with the CII Bionic Ear System (CII Bionic Ear behind-the-ear speech processor with the Hi-Resolution sound processing strategy; Advanced Bionics Corporation) was compared with the performance of 15 subjects fit with the Nucleus 24 electrode array and ESPrit 3G behind-the-ear speech processor with the advanced combination encoder speech coding strategy (cochlear corporation). SUBJECTS: Thirty adults with late-onset deafness and above-average speech perception abilities who used cochlear implants. MAIN OUTCOME MEASURES: Vowel recognition, consonant recognition, sentences in quiet (74, 64, and 54 dB SPL [sound pressure level]) and in noise (+10 and +5 dB SNR [signal-to-noise ratio]), voice discrimination, and melody recognition. RESULTS: Group differences in performance were significant in 4 conditions: vowel identification, difficult sentence material at +5 dB and +10 dB SNR, and a measure that quantified performance in noise and low input levels relative to performance in quiet. CONCLUSIONS: We have identified tasks on which there are between-group differences in performance for subjects matched on CNC word scores in quiet. We suspect that the differences in performance are due to differences in signal processing. Our next goal is to uncover the signal processing attributes of the speech processors that are responsible for the differences in performance.

Adult↗
PubMed1983

H-2D products do not affect lysis of Kk target cells by Kk-specific cytotoxic T cells.

Antigens coded by the major histocompatibility complex (MHC) stimulate a large number of cytotoxic T lymphocyte (CTL) precursors. Matzinger and Bevan have suggested that the high alloreactivity is a result of the formation of interaction antigens between MHC and non-MHC-coded antigens. Previous work by Langhorne and Fischer Lindahl did not support this hypothesis. In this report we describe are improved culture system to show that the recognition of Kk target cells by Kk-specific clones is also unaffected by H-2D products. Using such a culture system, which controls for the induction of nonspecific CTL by interleukin 2 (T cell growth factor) we were also able to confirm the original conclusion of Langhorne and Fischer Lindahl that polymorphic minor histocompatibility antigens do not significantly contribute to putative "interaction antigens" formed by MHC and other antigens.

Animals↗
PubMed1995

Characterization of murine mannose-binding protein genes Mbl1 and Mbl2 reveals features common to other collectin genes.

Mannose-binding protein (MBP) is a member of a family of collagenous lectins (collectins), which are believed to play an important role in first-line host defense. In this study, the two genes encoding MBP in mice--Mbl1 and Mbl2--have been isolated and their exon-intron structure studied to understand their evolutionary relationship to the single human (MBL) and the two rat MBP genes. Mouse Mbl1 and Mbl2 have five and six exons, respectively. The structure of the mouse Mbl genes is similar to that of the rat and human MBP genes and shows homology to the other collectin genes, with the entire carbohydrate recognition domain being encoded in a single exon and all introns being in phase 1. The MBP encoded by mouse Mbl1 with three cysteines in the first coding exon, like the rat Mbl1 and human MBL, is capable of a higher degree of multimerization and has apparent ability to fix complement in the absence of antibody or C1q. However, the structural features of other exons, that is, the larger size of collagen domain region in the first coding exon (64 bp in Mbl2 vs 46 bp in Mbl1) and the smaller size of the exon encoding the trimerization domain (69 bp in Mbl2 vs 75 bp in Mbl1) reveal that the single human MBL gene is closely related to rodent Mbl2 rather than rodent Mbl1. The findings in this study suggest that in contrast to the evolution of another collectin gene--bovine surfactant protein-D--which duplicated in bovidae after divergence from humans, MBP gene most likely duplicated prior to human-rodent divergence, and that the human homolog to Mbl1 was perhaps lost during evolution.

Amino Acid Sequence↗
PubMed1991

An upstream regulatory element of the NCAM promoter contains a binding site for homeodomains.

In the present study, we have analyzed an upstream regulatory element of the neural cell adhesion molecule (NCAM) promoter which is required for full promoter activity. It contains an ATTATTA motif that resembles the core recognition sequence of homeodomain (HD) proteins of the Antennapedia (Antp) and related types. Electrophoretic mobility shift (EMSA) and DNase I footprinting analyses revealed that the Drosophila HDs coded by the Antp and the zerknüllt (zen) genes bind this site in vitro. In contrast, the engrailed (en) protein did not produce a detectable footprint. The functional relevance of the ATTATTA motif was demonstrated by showing that a two-nucleotide exchange curtailed stimulation of an heterologous promoter. An oligonucleotide known to be recognized with high affinity by Antp-like HDs efficiently competed for endogenous factor binding. These results suggest that the NCAM gene may be a target for HD proteins.

Animals↗
PubMed1984

Semantic and visual memory codes in learning disabled readers.

Two experiments investigated whether learning disabled readers' impaired recall is due to multiple coding deficiencies. In Experiment 1, learning disabled and skilled readers viewed nonsense pictures without names or with either relevant or irrelevant names with respect to the distinctive characteristics of the picture. Both types of names improved recall of nondisabled readers, while learning disabled readers exhibited better recall for unnamed pictures. No significant difference in recall was found between name training (relevant, irrelevant) conditions within reading groups. In Experiment 2, both reading groups participated in recall training for complex visual forms labeled with unrelated words, hierarchically related words, or without labels. A subsequent reproduction transfer task showed a facilitation in performance in skilled readers due to labeling, with learning disabled readers exhibiting better reproduction for unnamed pictures. Measures of output organization (clustering) indicated that recall is related to the development of superordinate categories. The results suggest that learning disabled children's reading difficulties are due to an inability to activate a semantic representation that interconnects visual and verbal codes.

Adolescent↗
PubMed1985

Nucleotide sequence of the immunity region of Bacillus subtilis bacteriophage phi 105: identification of the repressor gene and its mRNA and protein products.

A gene involved in the regulation of lysogeny in the temperate Bacillus subtilis phage phi 105 has been identified and isolated. A plasmid, pDC4, was constructed that contains a 740-bp HindIII-PvuII fragment that is derived from the phi 105 immunity region and is capable of rendering B. subtilis immune to infection by phi 105. Three different hybrid plasmids that contain the 740-bp fragment, pAG101 [Cully and Garro, J. Virol. 34 (1980) 789-791], pDC1 and pDC2, were found to synthesize a common 18-kDal polypeptide in B. subtilis minicells and Escherichia coli maxicells. The nucleotide (nt) sequence of this region revealed three open reading frames (ORFs) that predict proteins with Mrs of 16521, 7332, and 5516. In vivo synthesized phi 105 prophage RNA was mapped by primer extension and shown to be transcribed from the DNA strand coding for the Mr 16521 protein. The 5' end of the phi 105 lysogen RNA was mapped to a region that contains conserved sequences for RNA polymerase recognition.

Amino Acid Sequence↗
PubMed2004

Identification and characterization of two novel brain-derived immunoglobulin superfamily members with a unique structural organization.

We recently used a differential display PCR screen to identify secreted and transmembrane proteins that are highly expressed in the developing rat basilar pons, a prominent ventral hindbrain nucleus used as a model for studies of neuronal migration, axon outgrowth, and axon-target recognition. Here we describe cloning and characterization of one of these molecules, now called MDGA1, and a closely related homologue, MDGA2. Analyses of the full-length coding region of MDGA1 and MDGA2 indicate that they encode proteins that comprise a novel subgroup of the Ig superfamily and have a unique structural organization consisting of six immunoglobulin (Ig)-like domains followed by a single MAM domain. Biochemical characterization demonstrates that MDGA1 and MDGA2 proteins are highly glycosylated, and that MDGA1 is tethered to the cell membrane by a GPI anchor. The MDGAs are differentially expressed by subpopulations of neurons in both the central and peripheral nervous systems, including neurons of the basilar pons, inferior olive, cerebellum, cerebral cortex, olfactory bulb, spinal cord, and dorsal root and trigeminal ganglia. Little or no MDGA expression is detected outside of the nervous system of developing rats. The similarity of MDGAs to other Ig-containing molecules and their temporal-spatial patterns of expression within restricted neuronal populations, for example migrating pontine neurons and D1 spinal interneurons, suggest a role for these novel proteins in regulating neuronal migration, as well as other aspects of neural development, including axon guidance.

Amino Acid Sequence↗
PubMed2006

Detection of multidimensional targets in visual search.

Search performance for targets defined along multiple dimensions was investigated with an accuracy visual search task. Initially, threshold was measured for targets that differed from homogeneous distractors along a single dimension (e.g., a reddish target among achromatic distractors, or a right-tilted target among vertically oriented distractors). Threshold was then measured for a multidimensional target (a redundant target) that differed from homogeneous distractors along two dimensions (e.g., a reddish AND right-tilted target among achromatic, vertically oriented distractors). Search performance for multidimensional target combinations of chromaticity and luminance, chromaticity and orientation, and chromaticity and spatial frequency was tested. Measurements were evaluated within several summation models, allowing for a test of the mechanisms mediating the detection of multidimensional targets in search. Measurements were generally consistent with probability summation suggesting the particular combinations of stimulus dimensions tested were coded along independent, noisy, neural mechanisms.

Adult↗
PubMed2003

FNR-mediated regulation of hyp expression in Escherichia coli.

The hypA-E operon is involved in the maturation of all three NiFe hydrogenases in Escherichia coli. Two hyp promoters have been described; a sigma54-dependent promoter upstream of hypA, and a sigma70-dependent promoter (PhypA) within the hypA coding region. Here it is shown that the oxygen-responsive transcription factor FNR regulates PhypA under anaerobic conditions only. PhypA does not possess a canonical FNR recognition sequence, but two FNR half-sites are present. Studies using PHYPA::lacZ fusions carrying lesions in one or both FNR half-sites indicated that although some residual anaerobic activity was retained by the promoter containing only the downstream FNR half-site, both half-sites are required for maximal PhypA activity in vivo. In vitro gel retardation analysis suggested that the primary interaction occurs at the downstream FNR half-site. Possible explanations for these observations and the implications for other FNR-regulated promoters are discussed.

Anaerobiosis↗
PubMed1998

Identification of protein-coding regions in Arabidopsis thaliana genome based on quadratic discriminant analysis.

A new method (MZEF) for predicting internal coding exons in genomic DNA sequences has been developed. This method is based on a prediction algorithm that uses the quadratic discriminant function for multivariate statistical pattern recognition. With improved feature measures, an Arabidopsis thaliana-specific implementation of MZEF is completed and made available to the plant genome community.

Algorithms↗