SEARCH · PubMed Health

Results for “Coding”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources

PubMed1990

Composite descriptions associated with rare MMPI two-point code types in an adult urban psychiatric setting: codes that involve scale 0.

MMPI files of 1,016 psychiatric patients were searched for protocols with two-point codes that involved scale 0. Thirty-eight such protocols were found, which accounted for 3.7% of the sample. Salient characteristics of the cases were noted, and composite descriptions were developed for each of the code types. An additional 14 new outpatient cases from our clinic were located over the next 2 years. Base rates from the original sample, as well as descriptive statistics and composite descriptions from the extended sample, are provided for each of the eight code types.

Adult↗

PubMed1983

Coding and 3' non-coding nucleotide sequence of chalcone synthase mRNA and assignment of amino acid sequence of the enzyme.

The nucleotide sequence of an almost complete cDNA copy of chalcone synthase mRNA from cultured parsley cells (Petroselinum hortense) has been determined. The cDNA copy comprised the complete coding sequence for chalcone synthase, a short A-rich stretch of the 5' non-coding region and the complete 3' non-coding region including a poly(A) tail. The amino acid sequence deduced from the nucleotide sequence of the cDNA is consistent with a partial N-terminal sequence analysis, the total amino acid composition, the cyanogen bromide cleavage pattern, and the apparent mol. wt. of the subunit of the purified enzyme.

Journal Article↗

PubMed1985

The amino terminal half of the MS2-coded lysis protein is dispensable for function: implications for our understanding of coding region overlaps.

We have asked whether genetic overlaps only evolve to provide extra coding capacity in genomes of restricted size. As a model system we have used the lysis gene of the RNA bacteriophage MS2. This gene overlaps with the distal part of the coat protein gene and with the proximal part of the replicase gene. Using recombinant DNA procedures we have determined whether either of the two overlaps codes for amino acids that are not essential for the function of the 75 amino acid long lysis protein. We find that the first 40 amino acids of the lysis protein are dispensable for function. Thus all of the genetic information essential to the synthesis of the active C-terminal peptide lies within the overlap with the replicase gene, whereas all dispensable residues are encoded in the overlap with the coat protein gene and in the intercistronic region. This suggests that the overlap with the coat protein gene is not required for extra coding capacity but serves to regulate the expression of the lysis gene. Comparative sequence analysis is consistent with this idea.

Amino Acid Sequence↗

PubMed1986

Second gene (nifH*) coding for a nitrogenase iron protein in Azotobacter chroococcum is adjacent to a gene coding for a ferredoxin-like protein.

Azotobacter chroococcum MCD1 contains a cluster of nitrogen fixation (nif) genes coding for the structural polypeptides for nitrogenase (nifH for the Fe-protein and nifD and nifK for the MoFe protein) and a second sequence in the genome homologous to nifH. DNA fragments bearing this second nifH-like sequence were cloned and the DNA sequence around the homologous region determined. Two open reading frames were identified in this region. One codes for a protein of 289 amino acid residues and is highly homologous to other Fe-proteins but is different from the gene adjacent to the nifDK genes in A. chroococcum. This putative gene we call nifH*. The following open reading frame codes for a protein of 63 amino acids, nine of which are cysteine residues. The protein is homologous to the small low-potential ferredoxins found in anaerobic bacteria, and in particular those from Chlorobium limicola. Linkage between a structural gene for nitrogenase and a small ferredoxin has not previously been observed. Sequence analysis suggests that the two genes form an operon. Transcription of the ferredoxin gene on a 1320-bp transcript was only detectable under conditions in which A. chroococcum MCD1155, which carries a chromosomal deletion of 6.3 kb removing the entire nifHDK cluster, is capable of fixing N2, i.e. in media containing no added molybdenum or high levels of NH3. The size of the observed transcript agrees well with the predicted size for a transcript encoding nifH* and the ferredoxin genes. Expression of the nifH* promoter was not significantly activated in Escherichia coli even when nifA, the positive activator of nif genes in Klebsiella pneumoniae, was supplied in multiple copies. The results are discussed in relation to an alternative pathway for N2 fixation in A. chroococcum.

Amino Acid Sequence↗

PubMed1983

Colour coding in the cerebral cortex: the responses of wavelength-selective and colour-coded cells in monkey visual cortex to changes in wavelength composition.

The reaction of wavelength-selective (WL), wavelength-opponent (WLO) and colour-coded (CO) cells in monkey visual cortex to changes in the wavelength composition of the light reflected from the area in their receptive fields was studied, using multicoloured displays. Wavelength-selective and wavelength-opponent cells were found to be very sensitive to changes in the wavelength composition of the light reflected from the areas in their receptive fields, irrespective of their perceived natural and void colours. Changes in the wavelength composition of the light reflected from surrounding areas did not affect their responses. They were also sensitive to the order in which lights of various wavelengths illuminated the areas in their receptive fields. Colour-coded cells were not affected by changes in the wavelength composition nor were they sensitive to the sequence with which the area in their receptive fields was illuminated by lights of different wavelengths. However, they required that the display, with the area of their preferred colour in their receptive fields, be trichromatically illuminated. This and other evidence suggested that such cells were sensitive not only to the illumination of the area in their receptive fields, but of surrounding areas as well. This evidence reinforces further the distinction between wavelength-selective and colour-coded cells and leads to the conclusion that one function of the wavelength-selective cells must be to register the changes in wavelength composition which occur throughout the day.

Animals↗

PubMed1995

Cloning, characterization, and chromosomal localization to 4p16 of the human gene (LRPAP1) coding for the alpha 2-macroglobulin receptor-associated protein and structural comparison with the murine gene coding for the 44-kDa heparin-binding protein.

We report the molecular cloning of the human gene (symbol LRPAP1) coding for the alpha 2-macroglobulin receptor-associated protein (A2MRAP), as well as the gene coding for the 44-kDa heparin-binding protein (HBP-44), its murine counterpart. For both, genomic cosmid clones were isolated, and for the human gene a bacteriophage P1 clone containing the entire A2MRAP gene was also retrieved. The genes were characterized after subcloning: in both species, the known coding part of the cDNA is encoded by eight exons, and the position of the boundaries of the exons was conserved. The human LRPAP1 locus was assigned to chromosome 4 by PCR of human-hamster hybrid cell lines and by fluorescence in situ hybridization to band 4p16.3. This maps closely to the variable constitutional deletions of the short arm of chromosome 4, observed cytogenetically in patients with the Wolf-Hirschhorn syndrome. Metaphase spreads of two such patients were analyzed by fluorescence in situ hybridization with an LRPAP1 genomic probe. The first patient, with karyotype 46,XY,del4(p14-p16.1), had retained both copies of the LRPAP1 gene. In contrast, the other patient, with karyotype 46,XY,del4(p15.3-pter), displayed no signal for LRPAP1 on the deleted chromosome.

Abnormalities, Multiple↗

PubMed2005

Multi-criterial coding sequence prediction. Combination of GeneMark with two novel, coding-character specific quantities.

This work applies two recently formulated quantities, strongly correlated with the coding character of a sequence, as an additional "module" on GeneMark, in a three-criterial method. The difference in the statistical approaches implicated by the methods combined here, is expected to contribute to an efficient assignment of functionality to unannotated genomic sequences. The developed combined algorithm is used to fractionalize a collection of GeneMark-predicted exons into sub-collections of different expectation to be coding. A further modification of the algorithm allows for the assignment of an improved estimation of the probability to be coding, to GeneMark-predicted exons. This is on the basis of a suitable training set of GeneMark-predicted exons of known functionality.

Algorithms↗

PubMed2006

Coded excitation using biphase-coded pulse with mismatched filters for high-frequency ultrasound imaging.

A scheme of using phase-coded excitation and mismatched filter compression for high-frequency ultrasound imaging is presented in this paper. Biphase-coded pulses were constructed to excite the transducer. Received signals were compressed with mismatched filters optimized by minimizing peak-sidelobe-level (PSL). Both simulation and experiments were carried out to demonstrate the advantage of this technique. The simulation results demonstrated a possible sidelobe reduction (<-90 dB) with a slightly decrease of the signal-to-noise ratio of less than 1 dB compared with the compression using matched filters alone. The experimental results showed about 14 dB SNR improvement as well as -40 dB sidelobe level when the Barker-13 code excitation with 3-cycle sinusoidal wave carrier was used.

Acoustics↗

PubMed2006

Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota).

The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes.

Ascomycota↗

PubMed2001

Differences between coding and non-coding regions in the Trichomonas vaginalis genome: an actin gene as a locus model(1).

The sequence of a cloned genomic fragment of Trichomonas vaginalis containing a complete actin gene was determined. An uninterrupted open reading frame of 1128 nucleotides was found that codes for an actin gene. Two overlapped consensus promoter sequences for T. vaginalis were found 12 nucleotides upstream the actin initiation codon. In addition to actin, two incomplete open reading frames were found at the 5' and 3' ends of the clone. These two sequences are expressed and showed similarity to adenylate cyclase genes and a yeast hypothetical protein. The overall sequence showed a higher G+C content and a lower frequency of repeated sequences in the coding regions when compared with the non-coding regions. A similar unequal nucleotide distribution was found in various T. vaginalis genes retrieved from data bases.

Actins↗

PubMed1998

Cochlear mechanisms of frequency and intensity coding. II. Dynamic range and the code for loudness.

Our preceding paper described SPL-dependent changes in the shape of transfer functions recorded from inner and outer hair cells as well as supporting cells, in the 500-2500 Hz regions of the Mongolian gerbil cochlea. As SPL was increased, large shifts were observed in the peak of the transfer function. A strongly compressive nonlinearity was also observed at CF. This paper examines the data from the perspective of intensity coding in the auditory periphery. Based on the data, we offer a new explanation for the mechanisms underlying the different dynamic ranges of low and high threshold auditory neurons. We also find that, for pure tone stimuli, the growth of excitation at the characteristic place saturates rapidly, and cannot encode the wide dynamic range of loudness. The data are analyzed to explore other excitation pattern candidates for loudness coding. The growth of the peak of the IHC transfer function, as well as the growth of the response area, have been found to be linearly related to loudness growth over most of its dynamic range. Implications of the data for auditory intensity coding are discussed.

Animals↗

PubMed2004

Nucleotide composition in protein-coding and non-coding DNA in the zygomycete Phycomyces blakesleeanus.

The zygomycete Phycomyces blakesleeanus has a 30 Mb genome with a 35% content of guanine and cytosine (GC). We determined the GC content in Phycomyces genes and fragments of genes available in public databases, the frequency of nucleotides in each codon position, and the codon usage. We observed a difference of 18% between the GC content of protein-coding and non-coding DNA. This large difference allowed the visualization of protein-coding DNA by plotting the GC content along a segment of Phycomyces DNA. We have identified a high GC DNA segment linked to the pyrG genes of the zygomycete genera Phycomyces, Mucor, and Blakeslea that corresponds to the 3' end of the gene responsible for the protein kinase C.

Amino Acid Sequence↗

PubMedDate not supplied

Optimal stimulus coding by neural populations using rate codes.

We create a framework based on Fisher information for determining the most effective population coding scheme for representing a continuous-valued stimulus attribute over its entire range. Using this scheme, we derive optimal single- and multi-neuron rate codes for homogeneous populations using several statistical models frequently used to describe neural data. We show that each neuron's discharge rate should increase quadratically with the stimulus and that statistically independent neural outputs provides optimal coding. Only cooperative populations can achieve this condition in an informationally effective way.

Action Potentials↗

PubMed1997

The non-standard genetic code of Candida spp.: an evolving genetic code or a novel mechanism for adaptation?

A number of yeasts of the genus Candida translate the standard leucine-CUG codon as serine. This unique genetic code change is the only known alteration to the universal genetic code in cytoplasmic mRNAs, of either eukaryotes or prokaryotes, which involves reassignment of a sense codon. Translation of CUG as serine in these species is mediated by a novel serine-tRNA (ser-tRNACAG), which uniquely has a guanosine at position 33, 5' to the anticodon, a position that is almost invariably occupied by a pyrimidine (uridine in general) in all other tRNAs. We propose that G-33 has two important functions: lowering the decoding efficiency of the ser-tRNACAG and preventing binding of the leucyl-tRNA synthetase. This implicates this nucleotide as a key player in the evolutionary reassignment of the CUG codon. In addition, the novel ser-tRNACAG has 1-methylguanosine (m1G-37) at position 37, 3' to the anticodon, which is characteristic of leucine, but not serine tRNAs. Remarkably, m1G-37 causes leucylation of the ser-tRNACAG both in vitro and in vivo, making the CUG codon an ambiguous codon: the polysemous codon. This indicates that some Candida species tolerate ambiguous decoding and suggests either that (i) the genetic code change has not yet been fully established and is evolving at different rates in different Candida species; or (ii) CUG ambiguity is advantageous and represents the final stage of the reassignment. We propose that such dual specificity indicates that reassignment of the CUG codon evolved through a mechanism that required codon ambiguity and that ambiguous decoding evolved to generate genetic diversity and allow for rapid adaptation to environmental challenges.

Adaptation, Physiological↗

PubMed2001

Plasminogen activator inhibitor type 2 contains mRNA instability elements within exon 4 of the coding region. Sequence homology to coding region instability determinants in other mRNAs.

Plasminogen activator inhibitor type 2 (PAI-2) is a serine protease inhibitor that inhibits urokinase. Constitutive and regulated PAI-2 gene expression involves post-transcriptional events, and an AU-rich mRNA instability motif within the 3'-untranslated region of PAI-2 mRNA is required for this process (Maurer, F., Tierney, M., and Medcalf, R. L. (1999) Nucleic Acids Res. 27, 1664-1673). Here we show that instability determinants are present within various exons of the PAI-2 coding region, most notably within exon 4. Deletion of exon 4 from the full-length PAI-2 cDNA results in a doubling in the half-life of PAI-2 mRNA, whereas a 28-nucleotide region within exon 4 contains binding sites for cytoplasmic proteins. Inducible stabilization of PAI-2 mRNA in HT-1080 cells treated with phorbol ester and tumor necrosis factor does not alter the binding of proteins to the exon 4 instability determinant, but resulted in a transient increase in the binding of factors to the AU-rich RNA instability element. Hence, PAI-2 mRNA stability is influenced by elements located within both the coding region and the 3'-untranslated region and that cytoplasmic mRNA binding factors may influence steady state and inducible PAI-2 mRNA expression. Finally a 10-nucleotide region flanking the exon 4 protein-binding site is homologous to instability elements within five other transcripts, suggesting that a common coding region determinant may exist.

3' Untranslated Regions↗

PubMed1997

Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro.

As a part of our project for accumulating sequence information of the coding regions of unidentified human genes, we herein report the sequence features of 78 new cDNA clones isolated from human brain cDNA libraries as those which may code for large proteins. The sequence data showed that the average size of the cDNA inserts and their open reading frames was 6.0 kb and 2.8 kb (925 amino acid residues), respectively, and these clones produced the corresponding sizes of protein products in an in vitro transcription/translation system. Homology search against the public databases indicated that the predicted coding sequences of 68 genes contained sequences similar to known genes, 69% of which (47 genes) were related to cell signaling/communication, nucleic acid management, and cell structure/motility. The expression profiles of these genes in 14 different tissues have been analyzed by the reverse transcription-coupled polymerase chain reaction method, and 8 genes were found to be predominantly expressed in the brain.

Brain Chemistry↗

PubMed1998

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

As an extension of our cDNA analysis for deducing the coding sequences of unidentified human genes, we have newly determined the sequences of 100 cDNA clones from a set of size-fractionated human brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA0611 to KIAA0710. In vitro transcription-coupled translation assay was applied as the first screening to select cDNA clones which produce proteins with apparent molecular mass of 50 kDa and over. One hundred unidentified cDNA clones thus selected were then subjected to sequencing of entire inserts. The average size of the inserts and corresponding open reading frames was 4.9 kb and 2.8 kb (922 amino acid residues), respectively. Computer search of the sequences against the public databases indicated that predicted coding sequences of 87 genes were similar to those of known genes, 62% of which (54 genes) were categorized as proteins related to cell signaling/communication, cell structure/motility and nucleic acid management. The expression profiles in 10 human tissues of all the clones characterized in this study were examined by reverse transcription-coupled polymerase chain reaction and the chromosomal locations of the clones were determined by using human-rodent hybrid panels.

Brain Chemistry↗

PubMed1999

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

As a part of our cDNA project for deducing the coding sequence of unidentified human genes, we newly determined the sequences of 100 cDNA clones from a set of size-fractionated human brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA0919 to KIAA1018. The sequencing of these clones revealed that the average sizes of the inserts and corresponding open reading frames were 4.9 kb and 2.6 kb (882 amino acid residues), respectively. A computer search of the sequences against the public databases indicated that predicted coding sequences of 87 genes contained sequences similar to known genes, 53% of which (46 genes) were categorized as proteins relating to cell signaling/communication, cell structure/motility and nucleic acid management. 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.

Animals↗