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At least 253 records · Page 14Linked to original sources

PubMed1997

Periodicity coding in the primary auditory cortex of the Mongolian gerbil (Meriones unguiculatus): two different coding strategies for pitch and rhythm?

Periodic envelope or amplitude modulations (AM) with periodicities up to several thousand Hertz are characteristic for many natural sounds. Throughout the auditory pathway, signal periodicity is evident in neuronal discharges phase-locked to the envelope. In contrast to lower levels of the auditory pathway, cortical neurons do not phase-lock to periodicities above about 100 Hz. Therefore, we investigated alternative coding strategies for high envelope periodicities at the cortical level. Neuronal responses in the primary auditory cortex (AI) of gerbils to tones and AM were analysed. Two groups of stimuli were tested: (1) AM with a carrier frequency set to the unit's best frequency evoked phase-locked responses which were confined to low modulation frequencies (fms) up to about 100 Hz, and (2) AM with a spectrum completely outside the unit's frequency-response range evoked completely different responses that never showed phase-locking but a rate-tuning to high fms (50 to about 3000 Hz). In contrast to the phase-locked responses, the best fms determined from these latter responses appeared to be topographically distributed, reflecting a periodotopic organization in the AI. Implications of these results for the cortical representation of the perceptual qualities rhythm, roughness and pitch are discussed.

Acoustic Stimulation↗

PubMed1984

Segmental homologies in the coding and 3' non-coding sequences of rat liver cytochrome P-450e and P-450b cDNAs and cytochrome P-450e-like genes.

The nucleotide sequence of a cloned cDNA insert carried by pHDQ14 was determined and found to code for the 107 C-terminal amino acids of rat liver cytochrome P-450e. Comparison of the pHQ14 cDNA sequence with those of cloned cDNAs for cytochrome P-450b and of 2 P-450e-like genes revealed segmental homologies that may have resulted from gene conversion. These results suggest that gene conversion may generate sequence variants of genes for rat liver cytochrome P-450s.

Amino Acid Sequence↗

PubMed1984

Cloning of malarial genes coding for high molecular weight antigens: isolation of fragments of Plasmodium falciparum genes coding for proteins of 145 000 molecular weight.

RNA preparations from Plasmodium falciparum were shown to direct the cell free synthesis of many high molecular weight proteins, some of which could be immunoprecipitated by sera from humans immune to P. falciparum. Among these was an abundant protein with a molecular weight of 145 000. Messenger RNAs coding for high molecular weight antigens were enriched by size fractionation and used after reverse transcription to identify genomic restriction fragments in Southern blots. Genomic restriction fragments were cloned into plasmid and phage lambda vectors. Two recombinants which were recognized by the high molecular weight probe were characterized by hybrid-select-translation. In both cases the predominant in vitro translation products were proteins with a molecular weight of 145 000.

Animals↗

PubMed1993

Sequence analysis reveals that the BTG1 anti-proliferative gene is conserved throughout evolution in its coding and 3' non-coding regions.

The human BTG1 gene (expressing an anti-proliferative function) is an evolutionarily conserved gene homologous to the murine PC3/TIS21 genes. Here, we report the cloning and sequencing of the murine BTG1 coding region and chicken BTG1 cDNA. The putative human and mouse BTG1 proteins are 100% identical; the chicken BTG1 cDNA contains an open reading frame of 170 amino acids with a 91% identity to its human and murine counterparts. The 3'-untranslated region of BTG1 is also highly conserved (82% homology between human and chicken), suggesting that it plays a key role in the regulation of BTG1 expression. These data confirm that BTG1 is phylogenetically highly conserved and that BTG1 and PC3/TIS21 may constitute the first members of a new family of functionally related genes.

Amino Acid Sequence↗

PubMed1995

Simple codes versus efficient codes.

Transmission of information is an important function of cortical neurons, so it is conceivable that they have evolved to transmit information efficiently, with low noise and high temporal precision. Such precision is consistent with the output generated by various working models that mimick neuronal activity, from simple integrate-and-fire models to elaborate numerical simulations of realistic-looking neurons. But our current inability to match this data with neurons' detailed spike-generating mechanisms in vivo allows us a wide latitude in interpreting the significance of the various components of their spike code. One extreme hypothesis, the 'simple' model, is that each neuron is noisy and slow, performing a simple computation and transmitting a small amount of information. A competing hypothesis, the 'efficient' model, postulates that a neuron transmits large amounts of information through precise, complex, single-spike computations. Both hypotheses are broadly consistent with the available data. The conflict may only be resolved with the development of new measurement techniques that will allow one to investigate directly the properties that make a neuron efficient--that is, to be able to measure highly transient, localized events inside the thinnest dendrites, which are currently experimentally inaccessible.

Cerebral Cortex↗

PubMed2005

The selectivity of canary HVC neurons for the Bird's Own Song: rate coding, temporal coding, or both?

The neuronal selectivity observed in the avian song system for the Bird's Own Song progressively emerged as an extraordinary fruitful model to investigate the neural code underlying the recognition of complex stimuli and the occurrence of learned behaviors. In adult zebra finch, neurons from the HVC (used as a proper name) show very selective auditory responses, firing more to presentation of the Bird's Own Song (BOS) than to reverse BOS or other conspecific songs. However, as adult zebra finches always produce the same stereotyped song, the presence of such highly selective neurons in birds with larger repertoire still remains an open question. Data presented here show that neurons selective for the BOS can be found in adult canary, a seasonal breeding bird which display a large repertoire. More precisely, we found that a large proportion of neurons (29/36) exhibits higher responses to presentation of the forward than to the reverse BOS, and that 22% of the cells were identified as selective on the basis of the d' value. For a cell that was extensively studied, we evaluated to what extent temporal stimulus-related structure predicts the acoustic stimulus using linear or non-linear artificial neural networks (ANN). These analyses indicated that the temporal structure contained in spike trains characterizes more accurately the stimulus than the firing rate. The limitations of applying ANN analyses to electrophysiological data are discussed and potential solutions to increase the confidence in these analysis are proposed.

Action Potentials↗

PubMed2005

Determination of the coding and non-coding nucleotide sequences of genuine Edmonston-Zagreb master seed and current working seed lot.

To confirm the genetic stability of the Edmonston-Zagreb vaccine strain, we determined and compared the nucleotide sequences of genuine Edmonston-Zagreb master seed (EZ D22) and current working seed lot (EZ D24 2/99). Sequence analysis and comparison of the two sequences confirmed that these two sequences are the same at the molecular level. The obtained sequences were also compared to reference strains, i.e. Edmonston wild-type (Edmonston Wt) AF266288 and Edmonston-Zagreb (EZ) AF266290 vaccine strain. The sequence of EZ D22 differed from the Edmonston Wt in 32 nucleotides. EZ D22 differed from EZ AF266290 in six nucleotides. Coding substitution at position 441 and two silent substitutions at positions 11999 and 14612 in the L gene are unique to EZ D22. The differences found between EZ from different sources can be a good reason for periodical sequence analysis of the same strain in the hands of different manufactures.

Base Sequence↗

PubMed1997

Cochlear mechanisms of frequency and intensity coding. I. The place code for pitch.

In the past, several researchers have reported a substantial shift in the peak of the tone-evoked excitation pattern toward the base of the cochlea following an increase in the SPL of the stimulating tone. Evidence for such peak shifts has been found in the responses of auditory nerve fibers, cochlear microphonics, and the responses of outer hair cells and supporting cells in the cochlea, as well as in basilar membrane vibration measurements, and indirectly, in psychophysical data. However, direct evidence for such a peak shift in inner hair cell (IHC) responses has been relatively sparse. If the peak shift is preserved in the information conveyed to the auditory nerve fibers by the IHCs, the classical 'place theory' for frequency coding in the cochlea requires modification. In this study, the nature and extent of the SPL-dependent peak shift is examined with the help of recordings in the IHCs and other cells of the organ of Corti in the 0.5-2.5 kHz region of the Mongolian gerbil cochlea. It is demonstrated that the peak shift is a universal phenomenon in the diverse cell types in this region of the cochlea. Most importantly, a large SPL-dependent peak shift is demonstrated in IHC responses. On the other hand, the recordings indicate that the apical cutoff of the spatial excitation pattern is SPL-independent. We conclude, therefore, that the place theory of pitch perception must be abandoned or at least modified.

Acoustic Stimulation↗

PubMed2001

Comparison of systems performance for TT virus detection using PCR primer sets located in non-coding and coding regions of the viral genome.

BACKGROUND: the heterogeneity of the TT virus (TTV) DNA prevalence values reported from comparable human cohorts suggests that diagnostic PCR protocols still require to be optimized. OBJECTIVES: to design TTV PCR primer sets with low genotype restriction and to compare their performances with commonly used amplification systems. STUDY DESIGN: we compared full length TTV genomic sequences and identified conserved nucleotide patterns in the 5' and 3' non-coding regions of the viral genome. This permitted to design two new primer sets usable for the PCR amplification of the most divergent human isolates of TTV described to date. The performances of these amplification systems were compared with those of three other PCR systems earlier used for prevalence studies. RESULTS: the primer systems P5Bx and P3Bx exhibited higher PCR scores than the other systems tested; 14 to 34% improvement values were obtained, and divergent positive results of earlier described PCR systems were confirmed systematically by our new detection assays. CONCLUSIONS: an optimized detection of TT virus DNA is a pre-requisite for the accurate epidemiological survey of viral infection and for the realization of phylogenetic studies. Such PCR systems with low genotype restriction will be helpful in the future for a better knowledge of natural history of TT virus infection.

3' Untranslated Regions↗

PubMed2005

The influence of task instruction on action coding: constraint setting or direct coding?

In 3 experiments, the authors manipulated response instructions for 2 concurrently performed tasks. Specifically, the authors' instructions described left and right keypresses on a manual task either as left versus right or as blue versus green keypresses and required either "left" versus "right" or "blue" versus "green" concurrent verbalizations. When instructions for responses on the 2 tasks were in terms of location (Experiment 1) or color (Experiments 2a and 2b), then compatible responses on the tasks were faster than incompatible responses. However, when the verbal task required "left" versus "right" responses but instructions for manual keypresses referred to blue versus green (Experiments 3a and 3b), then no response compatibility effects were observed. These results suggest that response labels used in the instruction directly determine the codes that are used to control responding.

Adult↗

PubMed2001

Mutation frequency in coding and non-coding repeat sequences in mismatch repair deficient cells derived from normal human tissue.

Repetitive tracts within the coding regions of TGFBR2 and BAX are frequently mutated in mismatch repair deficient tumours and are implicated in tumour progression. However, there has been little study of the balance between selection pressure and inherent instability at sequences within these genes. To determine whether TGFBR2 and BAX are inherently prone to mutations in the presence of MMR defects, we studied MMR deficient cells derived from B-lymphocytes. By analysing cells derived from normal tissue we aimed to minimize the effects of selection pressures that bias the apparent frequency of mutation. We definitively show that certain sequences, usually repaired by MMR, are inherently unstable. Using a small pool PCR technique we confirmed these cells exhibit microsatellite instability. Additionally, we demonstrate that MMR deficiency results in an excess of mutations, specifically at the poly(A)(10) tract compared to other regions of the TGFBR2 gene (P<0.001). Conversely, an excess of mutations does not appear to arise at the poly(G)(8) tract of the BAX gene. These studies provide insight into the mechanism by which TGFBR2 and BAX genes become mutated during tumorigenesis. These findings invoke the notion of "unmasking" specific hypermutable sequences in particular genes adding further complexity to the concept of the mutator phenotype.

Alleles↗

PubMed1982

Coding sequence for the pT181 repC product: a plasmid-coded protein uniquely required for replication.

pT181 is a 4.4-kilobase plasmid from Staphylococcus aureus specifying tetracycline resistance and present in about 20 copies per cell. The existence of a diffusible pT181 product required for plasmid replication has been proposed on the basis of trans-complementable thermosensitive mutants defective in plasmid maintenance (phenotype Tsr). In this report, the Tsr mutants are shown to have primary replication defects, and the genetic complementation data are confirmed biochemically. All of five mutations are in a single cistron, the repC cistron; interruption of the plasmid DNA molecule at any of three neighboring restriction sites inactivates repC function. Analysis of the DNA sequence in this region reveals an open reading frame of 939 base pairs which encodes the repC product, a 313-amino acid protein. pT181 replication has been demonstrated in cell-free extracts to require specifically a pT181-coded protein of approximately the same size, and it is proposed that this protein is, indeed, the repC product. Preliminary evidence is discussed suggesting that the pT181 replication rate is controlled at the level of synthesis of the repC protein.

Bacterial Proteins↗

PubMed2004

Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana.

MOTIVATION: Simple sequence repeats or microsatellites have been found abundantly in many genomes. However, the significance of distribution preference has not been completely understood. Completion of the Arabidopsis genome sequencing allows us to better understand and characterize microsatellites. RESULTS: Microsatellite distribution was more abundant in 5'-flanking regions of genes compared with that expected in the whole genome, with an over-representation of AG and AAG repeats; there were clear differences from distributions in 3'-flanks and coding fractions, where triplet frequencies evidently corresponded to codon usage. We identified 1140 full-length genes that contained at least one locus of AG or AAG repeats in their upstream sequences, and whose functional characteristics were significantly associated with the repeats. This observation indicates that selective pressure markedly differed in the three transcribed regions, with positive selection of AG and AAG repeats in 5'-flanks close to those genes whose products are preferentially involved in transcription.

Algorithms↗

PubMed1994

Prediction of the coding sequences of unidentified human genes. II. The coding sequences of 40 new genes (KIAA0041-KIAA0080) deduced by analysis of cDNA clones from human cell line KG-1.

By applying the protocol previously established, we isolated and sequenced full-length cDNA clones longer than 2 kb from cDNA library of human immature myeloid cell line KG-1, and the coding sequences of 40 new genes were predicted. A computer search of the sequences indicated that 29 genes contained sequences with similarities to reported genes in the GenBank/EMBL databases. Significant transmembrane domains were identified in 9 genes, 5 of which harbored multiple hydrophobic regions. Protein motifs that matched those in the PROSITE motif database were identified in 13 genes. In terms of sequence similarities and protein motifs, 5 genes were related to transcriptional factors. Repetitive sequences were found in the 3'-untranslated region of 8 genes. Northern hybridization demonstrated that the expression of 9 genes was tissue-specific, while the remaining 31 genes were expressed ubiquitously. It was also noted that 17 genes yielded different sizes of bands possibly due to either alternative splicing or alternative initiation. The chromosomal location of these genes has been determined.

Amino Acid Sequence↗

PubMed1995

Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1.

We isolated full-length cDNA clones from size-fractionated cDNA libraries of human immature myeloid cell line KG-1, and the coding sequences of 40 genes were newly predicted. A computer search of the GenBank/EMBL databases indicated that the sequences of 14 genes were unrelated to any reported genes, while the remaining 26 genes carried some sequences with similarities to known genes. Significant transmembrane domains were identified in 17 genes, and protein motifs that matched those in the PROSITE motif database were identified in 11 genes. Northern hybridization analysis with 18 different cells and tissues demonstrated that 10 genes were apparently expressed in a cell-specific or tissue-specific manner. Among the genes predicted, half were isolated from the medium-sized cDNA library and the other half from the small-sized cDNA library, and their average sizes were 4 kb and 1.4 kb, respectively. As judged by Northern hybridization profiles, small-sized cDNAs appeared to be expressed more ubiquitously and abundantly in various tissues, compared with that of medium-sized cDNAs.

Cell Line↗

PubMed1995

Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1.

In this series of projects regarding the accumulation of sequence information of unidentified human genes, we newly deduced the sequences of 40 full-length cDNA clones of human cell line KG-1, and predicted the coding sequences of the corresponding genes, named KIAA0121 to 0160. The results of a computer search of public databases indicated that the sequences of 13 genes were unrelated to any reported genes, while the remaining 27 genes carried sequences which showed some similarities to known genes. Obvious unique sequences noted were as follows. A stretch of triplet repeats was contained in each of three genes: These were GAG(Glu) in KIAA0122 and KIAA0147, and TCC(Ser) in KIAA0150. A stretch of 10 amino acid-residues was repeated 21 times in KIAA0139, and a homologous sequence of 76-78 nucleotides was found repeated 6 times in the untranslated region of KIAA0125. Northern hybridization analysis demonstrated that 13 genes were expressed in a cell- or tissue-specific manner. Although a vast number of expressed sequence tags (ESTs) have been registered for comprehensive analysis of cDNA clones, our sequence data indicated that their distribution is very unbalanced: e.g. while no EST hit 7 genes, 85 ESTs fell in a single gene.

Amino Acid Sequence↗

PubMed1996

Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain.

In this series of projects of sequencing human cDNA clones which correspond to relatively long and nearly full-length transcripts, we newly determined the sequences of 80 clones, and predicted the coding sequences of the corresponding genes, named KIAA0201 to KIAA0280. Among the sequenced clones, 68 were obtained from human immature myeloid cell line KG-1 and 12 from human brain. The average size of the clones was 5.3 kb, and that of distinct ORFs in clones was 2.8 kb, corresponding to a protein of approximately 100 kDa. Computer search against the public databases indicated that the sequences of 22 genes were unrelated to any reported genes, while the remaining 58 genes carried sequences which show some similarities to known genes. Protein motifs that matched those in the PROSITE motif database were found in 25 genes and significant transmembrane domains were identified in 30 genes. Among the known genes to which significant similarity was shown, the genes that play key roles in regulation of developmental stages, apoptosis and cell-to-cell interaction were included. Taking into account of both the search data on sequence similarity and protein motifs, at least seven genes were considered to be related to transcriptional regulation and six genes to signal transduction. When the expression profiles of the cDNA clones were examined with different human tissues, about half of the clones from brain (5 of 11) showed significant tissue-specificity, while approximately 80% of the genes from KG-1 were expressed ubiquitously.

Amino Acid Sequence↗

PubMed1999

Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.

To extend our cDNA project for accumulating basic information on unidentified human genes, we newly determined the sequences of 100 cDNA clones from a set of size-fractionated human adult and fetal brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA1019 to KIAA1118. The sequencing of these clones revealed that the average size of the inserts and corresponding open reading frames were 5.0 kb and 2.6 kb (880 amino acid residues), respectively. Database search of the predicted amino acid sequences classified 58 predicted gene products into the five functional categories, such as cell signaling/communication, cell structure/motility, nucleic acid management, protein management and cell division. It was also found that, for 34 gene products, homologues were detected in the databases, which were similar in sequence through almost the entire regions. The chromosomal locations of the genes were determined by using human-rodent hybrid panels unless their mapping data were already available in the public databases. The expression profiles of all the genes among 10 human tissues, 8 brain regions (amygdala, corpus callosum, cerebellum, caudate nucleus, hippocampus, substania nigra, subthalamic nucleus, and thalamus), spinal cord, fetal brain and fetal liver were also examined by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.

Adult↗