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PubMed2002

Recognition of tRNA backbone for aminoacylation with cysteine: evolution from Escherichia coli to human.

The underlying basis of the genetic code is specific aminoacylation of tRNAs by aminoacyl-tRNA synthetases. Although the code is conserved, bases in tRNA that establish aminoacylation are not necessarily conserved. Even when the bases are conserved, positions of backbone groups that contribute to aminoacylation may vary. We show here that, although the Escherichia coli and human cysteinyl-tRNA synthetases both recognize the same bases (U73 and the GCA anticodon) of tRNA for aminoacylation, they have different emphasis on the tRNA backbone. The E. coli enzyme recognizes two clusters of phosphate groups. One is at A36 in the anticodon and the other is in the core of the tRNA structure and includes phosphate groups at positions 9, 12, 14, and 60. Metal-ion rescue experiments show that those at positions 9, 12, and 60 are involved with binding divalent metal ions that are important for aminoacylation. The E. coli enzyme also recognizes 2'-hydroxyl groups within the same two clusters: at positions 33, 35, and 36 in the anticodon loop, and at positions 49, 55, and 61 in the core. The human enzyme, by contrast, recognizes few phosphate or 2'-hydroxy groups for aminoacylation. The evolution from the backbone-dependent recognition by the E. coli enzyme to the backbone-independent recognition by the human enzyme demonstrates a previously unrecognized shift that nonetheless has preserved the specificity for aminoacylation with cysteine.

Acylation↗

PubMed2005

Identification of mutations in the GNPTA (MGC4170) gene coding for GlcNAc-phosphotransferase alpha/beta subunits in Korean patients with mucolipidosis type II or type IIIA.

Mucolipidosis types II and III are autosomal recessive inherited diseases caused by a deficiency in the lysosomal enzyme N-acetylglucosamine-1 phosphotransferase (GlcNAc-phosphotransferase), which adds phosphate to function as a recognition marker for the uptake and transport of lysosomal enzymes. We investigated mutations in the GNPTA (MGC4170) gene, which codes for the alpha/beta subunits of phosphotransferase, and in the GNPTAG gene, which codes for its gamma subunits in five Korean patients with mucolipidosis type II or IIIA. We identified seven mutations in the GNPTA gene, but none in GNPTAG. The mutations in type II patients included p.Q104X (c.310C>T), p.R1189X (c.3565C>T), p.S1058X (c.3173C>G), p.W894X (c.2681G>A), and p.H1158fsX15 (c.3474_3475delTA), all of which are nonsense or frameshift mutations. However, a splicing site mutation, IVS13+1G>A (c.2715+1G>A) was detected along with a nonsense or a frameshift mutation (p.R1189X or p.E858fsX3 (c.2574_2575delGA)) in two mucolipidosis type IIIA patients. This report shows that mutations in the GNPTA gene coding for the alpha/beta subunits of phosphotransferase, and not mutations in the GNPTAG gene, account for most of the genetic mutations found in Korean patients with mucolipidosis type II or IIIA.

Adolescent↗

PubMed1981

Rapid saccades code a fast allocator of the generator photic stimulus.

Severe interference with generation of rapid saccades seems to result in delay of recognition of lack of novelty value of a recent stimulus. This delay was experimentally detected by the nature of bioelectric processes recorded from CA3, CA1(1) and CA1(2) hippocampal pyramidal neurons during the early phases of conditioning of the rabbit nictitating membrane reflex to an unusual visual stimulus. The results suggest that the rapid saccades contain and transmit a fast partial code of the visual stimulus that generated them. This partial code functions as a fast allocator of memory traces (of the generator photic stimulus) that are deposited in the diffuse memory system.

Animals↗

PubMedDate not supplied

Contribution of finger tracing to the recognition of Chinese characters.

Finger tracing is a simulation of the act of writing without the use of pen and paper. It is claimed to help in the processing of Chinese characters, possibly by providing additional motor coding. In this study, blindfolded subjects were equally good at identifying Chinese characters and novel visual stimuli through passive movements made with the index finger of the preferred hand and those made with the last finger of that hand. This suggests that finger tracing provides a relatively high level of coding specific to individual characters, but non-specific to motor effectors. Beginning each stroke from the same location, i.e. removing spatial information, impaired recognition of the familiar characters and the novel nonsense figures. Passively tracing the strokes in a random sequence also impaired recognition of the characters. These results therefore suggest that the beneficial effect of finger tracing on writing or recall of Chinese characters is mediated by sequence and spatial information embedded in the motor movements, and that proprioceptive channel may play a part in mediating visuo-spatial information. Finger tracing may be a useful strategy for remediation of Chinese language impairments.

Adult↗

PubMed2002

On the neural correlates of object recognition awareness: relationship to computational activities and activities mediating perceptual awareness.

Based on theoretical considerations of Aurell (1979) and Block (1995), we argue that object recognition awareness is distinct from purely sensory awareness and that the former is mediated by neuronal activities in areas that are separate and distinct from cortical sensory areas. We propose that two of the principal functions of neuronal activities in sensory cortex, which are to provide sensory awareness and to effect the computations that are necessary for object recognition, are dissociated. We provide examples of how this dissociation might be achieved and argue that the components of the neuronal activities which carry the computations do not directly enter the awareness of the subject. The results of these computations are sparse representations (i.e., vector or distributed codes) which are activated by the presentation of particular sensory objects and are essentially engrams for the recognition of objects. These final representations occur in the highest order areas of sensory cortex; in the visual analyzer, the areas include the anterior part of the inferior temporal cortex and the perirhinal cortex. We propose, based on lesion and connectional data, that the two areas in which activities provide recognition awareness are the temporopolar cortex and the medial orbitofrontal cortex. Activities in the temporopolar cortex provide the recognition awareness of objects learned in the remote past (consolidated object recognition), and those in the medial orbitofrontal cortex provide the recognition awareness of objects learned in the recent past. The activation of the sparse representation for a particular sensory object in turn activates neurons in one or both of these regions of cortex, and it is the activities of these neurons that provide the awareness of recognition of the object in question. The neural circuitry involved in the activation of these representations is discussed.

Awareness↗

PubMed1991

Evolutionary conservation of intron position in a subfamily of genes encoding carbohydrate-recognition domains.

The structure of the gene encoding a chicken liver receptor, the chicken hepatic lectin, which mediates endocytosis of glycoproteins has been established. The coding sequence is divided into six exons separated by five introns. The first three exons correspond to separate functional domains of the receptor polypeptide (cytoplasmic tail, transmembrane sequence, and extracellular neck region), while the final three exons encode the Ca(2+)-dependent carbohydrate-recognition domain. These results, as well as computer-assisted multiple sequence comparisons, establish this receptor as the evolutionary homolog of the mammalian asialoglycoprotein receptors. It is interesting that the chicken receptor falls into a subfamily of proteins along with the mammalian asialoglycoprotein receptors, since the saccharide-binding specificity of the chicken receptor resembles more closely that of a different set of calcium-dependent animal lectins, which includes the mannose-binding proteins. The portions of the genes encoding the carbohydrate-recognition domains of these proteins lack introns. The results suggest that divergence of intron-containing and intron-lacking carbohydrate-recognition domains preceded shuffling events in which other functional domains were associated with the carbohydrate-recognition domains. This was followed by further divergence, generating a variety of saccharide-binding specificities.

Amino Acid Sequence↗

PubMed2002

The restricted influence of sparseness of coding on the capacity of familiarity discrimination networks.

Much evidence indicates that the perirhinal cortex is involved in the familiarity discrimination aspect of recognition memory. It has been previously shown under selective conditions that neural networks performing familiarity discrimination can achieve very high storage capacity, being able to deal with many times more stimuli than associative memory networks can in associative recall. The capacity of associative memories for recall has been shown to be highly dependent on the sparseness of coding. However, previous work on the networks of Bogacz et al, Norman and O'Reilly and Sohal and Hasselmo that model familiarity discrimination in the perirhinal cortex has not investigated the effects of the sparseness of encoding on capacity. This paper explores how sparseness of coding influences the capacity of each of these published models and establishes that sparse coding influences the capacity of the different models in different ways. The capacity of the Bogacz et al model can be made independent of the sparseness of coding. Capacity increases as coding becomes sparser for a simplified version of the neocortical part of the Norman and O'Reilly model, whereas capacity decreases as coding becomes sparser for a simplified version of the Sohal and Hasselmo model. Thus in general, and in contrast to associative memory networks, sparse encoding results in little or no advantage for the capacity of familiarity discrimination networks. Hence it may be less important for coding to be sparse in the perirhinal cortex than it is in the hippocampus. Additionally, it is established that the capacities of the networks are strongly dependent on the precise form of the learning rules (synaptic plasticity) used in the network. This finding indicates that the precise characteristics of synaptic plastic changes in the real brain are likely to have major influences on storage capacity.

Animals↗

PubMed1990

Codon recognition mechanisms in plant chloroplasts.

In chloroplasts, all 61 sense codons are found in chloroplast (cp) DNA sequences coding for proteins. However among the sequenced cp tRNAs or tRNA genes, tRNAs with anticodons complementary to codons CUU/C (Leu), CCU/C (Pro), GCU/C (Ala) and CGC/A/G (Arg) [or CGC/A (Arg) in Marchantia] have not been found. In this paper we show that cp tRNA(Ala)(U*GC) cp tRNA(Pro)(U*GG) and cp tRNA(Arg)(ICG) are able to decode the corresponding four-codon family. In the case of leucine codons CUU/C, we show that 'U:U and U:C wobble' mechanisms can operate to allow the reading of these codons by cp tRNA(Leu)(UAm7G).

Amino Acid Sequence↗

PubMed1993

Heterologous recognition in vivo of promoter sequences from the Streptomyces coelicolor dagA gene.

The Streptomyces coelicolor dagA gene that codes for an extracellular agarase was cloned in the closely related bacterium S. lividans and transferred to the distantly related low G+C Gram-positive bacterium Bacillus subtilis and to the far more distantly related Gram-negative bacterium Escherichia coli. S1 nuclease mapping experiments identified a putative fifth promoter from which transcription of the dagA gene can take place, and accurately mapped the transcription termination site. The transcription terminator was specific for the Streptomyces strains and could terminate transcription initiated by promoters other than those of dagA. The agarase gene is efficiently transcribed in B. subtilis and E. coli, although pulse-chase experiments failed to detect the synthesis of agarase in these two bacteria.

Bacillus subtilis↗

PubMed2006

Interrater reliability and coding guide for nonpsychotic formal thought disorder.

Reliable and valid assessment of abnormal speech patterns may enable earlier recognition of nonpsychotic disorders through characteristic speech patterns. This study sought to establish interrater reliability using a standardized guide for scoring. A scoring guide defining 27 elements (e.g., inappropriate self-reference, simple loss of goal, circumstantiality) of disordered thought was developed. The seminal work of Andreasen's and Holzman's groups provided 12 elements, and 15 new elements were suggested by clinical literature. Audiotaped interviews with 12 psychiatric inpatients, adults of both sexes and various ages hospitalized for acute management of nonpsychotic psychiatric disorders, provided speech samples for observation of disordered thought by two independent raters. Using the guide's definitions and accompanying examples of elements of disordered thought, reliability in scoring was high (kappa of .85 for agreement on the presence of any abnormal speech element and kappa values from .66 to 1.00 for agreement on the presence of individual elements).

Adult↗

PubMed1983

The nucleotide sequence of the Mr = 28,500 flagellin gene of Caulobacter crescentus.

The DNA sequences which encode the Mr = 28,500 flagellin polypeptide of Caulobacter crescentus CB15 have been determined. The size of the protein, deduced from its DNA sequence (276 amino acids), is in agreement with its apparent molecular weight as measured by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The distribution of arginine residues within the protein sequence encoded by the gene correlates with their relative location as predicted by peptide alignment analysis (Gill, P.R., and Agabian, N. (1982) J. Bacteriol. 150, 925-933). DNA sequences 5' and 3' to the coding sequence were also determined. In the 5' region, DNA sequences homologous to consensus sequences associated with RNA polymerase recognition and transcription initiation sites in Escherichia coli (Pribnow box) are found. These are centered around 60, 90, and 120 base pairs upstream from the ATG codon at the beginning of the structural gene. Sequences 3' to the coding region were identified which might signal transcription termination. A typical E. coli 16 S ribosomal binding site (Shine-Dalgarno sequence) is located just 5' to the coding sequence, and for most of the amino acids there is a strong codon usage preference. Although this protein is exported from the cell (Gill, P.R., and Agabian, N. (1982) J. Bacteriol. 150, 925-933), the encoded NH2-terminal amino acid sequence is not different from the mature product.

Amino Acid Sequence↗

PubMed1995

Analytic importance of the coding features for the discrimination of vowels in the cochlear implant signal.

The present study considers the analytic importance of the excitation pulse features delivered by a Nucleus cochlear implant using the F0F1F2 strategy. Four cochlear implant patients and 10 speakers uttering two 48-item lists constructed from four basic French vowels participated in this study. Patterns were presented to the patients and played at the input of an acquisition system in order to record the pulse features. Confusion matrices obtained with the patients and with automatic recognition procedures were then compared in order to find out the best-matching models simulating the patients' performances, out of 255 possibilities. The automatic recognition was carried out according to fuzzy logic based on the elementary features of the pulses coding the vowels. Results show that the essential features strongly depended on the subject.

Adult↗

PubMed2003

Facial recognition reactivates the primary visual cortex: an functional magnetic resonance imaging study in humans.

In order to investigate how the brain represents sensory-specific information during memory retrieval, we examined functional magnetic resonance imaging's during a face-recognition task. When compared with activation associated with viewing of novel faces, recognition of faces presented 5 min before scanning activated the primary visual cortex, consistent with the hypothesis that retrieved facial information is coded by the reactivation of the brain regions engaged during sensory perception. This reactivation was not observed 14 weeks following initial presentation of the faces despite no significant difference in recognition rate between the two intervals. This suggests that accessing of visual information during memory retrieval is associated with the primary visual cortex, and that its activation is time-dependent--probably related to the memory transformation or consolidation.

Adult↗

PubMed1985

Interaction of alpha 1 with alpha 2 region in class I MHC proteins contributes determinants recognized by antibodies and cytotoxic T cells.

The structure-function relationship of individual coding regions of class I mouse major histocompatibility complex proteins was studied by a combination of recombinant DNA, gene transfer techniques, and serologic and functional characterization. To examine the role of alpha 1 and alpha 2 regions in antibody and CTL recognition, the third exon of H-2Dd, Kd, and Ld transplantation antigen genes was replaced by the homologous coding region of the Qa-2-coded class I gene, Q6. We have chosen to carry out the exon shuffling experiments between these two different types of class I genes, because they are structurally similar and did not evolve to carry out identical functions. Therefore, it is less likely that the hybrid proteins will fortuitously recreate alpha 1-alpha 2 controlled functionally important determinants. The replacement of H-2 alpha 2 coding region with its Q6 counterpart had different effects on the expression of the three genes. The mutant H-2Dd gene transfected into L cells was expressed at high levels and retained several of the serologic determinants found on parental H-2Dd and Q6 domains. The serologic epitopes on the mutant H-2Kd-transfected cells were detectable at very low levels, whereas the product of the mutant H-2Ld gene could not be identified at all. Analysis of cells transfected with mutant H-2Dd gene with alloreactive and minor antigen(s)-restricted cytotoxic T cells indicated that the hybrid proteins lost the ability to be recognized by T cells. Our data suggest that cytotoxic T cells recognize conformational determinants composed of amino acids from alpha 1 and alpha 2 regions. Alternatively, it could be proposed that T cell recognition sites located in a single alpha 1 or alpha 2 protein region are susceptible to distortion upon alpha 1-alpha 2 interactions. Such susceptibility to conformational changes of the amino-terminal domain of transplantation antigens could be of functional importance for H-2-restricted antigen presentation.

Animals↗

PubMed1982

Synthesis of a human insulin gene. V. Enzymatic assembly, cloning and characterization of the human proinsulin DNA.

To form a 258-bp sequence coding for human proinsulin, 41 synthetic deoxyribo-oligonucleotide fragments of 11 to 15 nucleotides in length were assembled by enzymatic methods. The coding sequence is preceded by ATG and following by TGA for translation start and stop signals, and terminated in an EcoRI and a BamHI recognition sequence. The complete synthetic sequence was ligated to a plasmid and cloned in Escherichia coli. The cloned DNA was shown to have the correct human proinsulin coding sequence.

Base Sequence↗

PubMed2005

Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition.

At least half of all human pre-mRNAs are subject to alternative 3' processing that may modulate both the coding capacity of the message and the array of post-transcriptional regulatory elements embedded within the 3' UTR. Vertebrate poly(A) site selection appears to rely primarily on the binding of CPSF to an A(A/U)UAAA hexamer upstream of the cleavage site and CstF to a downstream GU-rich element. At least one-quarter of all human poly(A) sites, however, lack the A(A/U)UAAA motif. We report that sequence-specific RNA binding of the human 3' processing factor CFI(m) can function as a primary determinant of poly(A) site recognition in the absence of the A(A/U)UAAA motif. CFI(m) is sufficient to direct sequence-specific, A(A/U)UAAA-independent poly(A) addition in vitro through the recruitment of the CPSF subunit hFip1 and poly(A) polymerase to the RNA substrate. ChIP analysis indicates that CFI(m) is recruited to the transcription unit, along with CPSF and CstF, during the initial stages of transcription, supporting a direct role for CFI(m) in poly(A) site recognition. The recognition of three distinct sequence elements by CFI(m), CPSF, and CstF suggests that vertebrate poly(A) site definition is mechanistically more similar to that of yeast and plants than anticipated.

3' Untranslated Regions↗

PubMed1994

Organization and sequence of the SalI restriction-modification system.

The organization and nucleotide (nt) sequences were determined for the genes encoding the SalI restriction and modification (R-M) system (recognition sequence 5'-GTCGAC-3') from Streptomyces albus G. The system comprises two genes, salIR, coding for the restriction endonuclease (ENase, R.SalI; probably 315 amino acids (aa), a predicted M(r) of 35,305; product, G'TCGAC) and salIM, coding for the methyltransferase (MTase, M.SalI; probably 587 aa, a predicted M(r) of 64,943; product, GTCGm6AC). The genes are adjacent, they have the same orientation, and they occur in the order salIR then salIM. R.SalI contains a putative magnesium-binding motif similar to those at the active sites of R.EcoRI and R.EcoRV, but otherwise it bears little aa sequence similarity to other ENases. M.SalI is a member of the m6A gamma class of MTases. In aa sequence it resembles M.AccI, another m6A gamma-MTase whose recognition sequence includes the SalI recognition sequence as a subset.

Amino Acid Sequence↗

PubMed1990

Cloning and characterization of two tandemly arranged DNA methyltransferase genes of Neisseria lactamica: an adenine-specific M.NlaIII and a cytosine-type methylase.

The gene encoding the Neisseria lactamica III DNA methyltransferase (M.NlaIII) which recognizes the sequence CATG has been cloned and expressed in Escherichia coli. DNA sequencing of a 3.125 kb EcoRI-PstI fragment localizes the M. NlaIII gene to a 334 codon open reading frame (ORF) and identifies, 468 bp downstream, a second ORF of 313 amino acids, which is referred to as M.NlaX. Both proteins are detectable in the E. coli coupled in vitro transcription-translation system; they are apparently expressed from separate N. lactamica promoters. The N-terminal half of the previously characterized M.FokI, which methylates adenine in one of the DNA strands with its asymmetric recognition sequence (GGATG), is found to have 41% sequence identity and a further 11.7% sequence similarity with M.NlaIII. Among the conserved amino acids is the wellknown DPPY sequence motif. With one exception, analysis of the nucleotides coding for the DP dipeptide in all known DPPY sequences shows the presence of an inherent DNA adenine methylation (dam) recognition site of GATC. A low level of expression of M.NlaX in E. coli prevents the elucidation of its sequence recognition specificity. Sequence analysis of M.NlaX shows that it is closely related to the group of monospecific 5-methylcytosine DNA methyltransferases (M.EcoRII, Dcm, M.HpaII and M.HhaI) which all have a modified cytosine at the second position of the recognition sequences. Both M.EcoRII and Dcm amino acid sequences are about 50% identical with M.NlaX; a considerable degree of sequence identity is found in the so-called variable region which is believed to be responsible for sequence recognition specificity. M.NlaX is probably the counterpart to the E. coli Dcm in N. lactamica.

Amino Acid Sequence↗