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PubMed1996

Prediction of the coding sequences of unidentified human genes. V. The coding sequences of 40 new genes (KIAA0161-KIAA0200) deduced by analysis of cDNA clones from human cell line KG-1.

As part of our continuing efforts to accumulate information on the coding region of unidentified human genes, we newly determined the sequences of 40 cDNA clones of human cell line KG-1 which correspond to relatively long and nearly full-length transcripts, and predicted the coding sequences of the corresponding genes, named KIAA0161 to 0200. The average size of the cDNA clones analyzed was approximately 5.0 kb. A computer search of the sequences in public databases indicated that the sequences of 20 genes were unrelated to any reported genes, while the remaining 20 genes carried sequences which show some similarities to known genes. Among the genes in the latter category, KIAA0167 contained a Zn-finger motif with significant structural similarity to that of the yeast transcription factor GCS1, and KIAA0189 was classified into the RhoGAP gene family. Stretches of typical CAG (Gln) repeats, which were often correlated with genetic disorders, were found in KIAA0181 and KIAA0192. Another novel repeat composed of alternating Arg and Glu was identified in KIAA0182. Northern hybridization analysis demonstrated that 10 genes are expressed in a cell- or tissue-specific manner.

Amino Acid Sequence↗

PubMed1997

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

In this series of projects of sequencing human cDNA clones which correspond to relatively long transcripts, we newly determined the entire sequences of 100 cDNA clones which were screened on the basis of the potentiality of coding for large proteins in vitro. The cDNA libraries used were the fractions with average insert sizes from 5.3 to 7.0 kb of the size-fractionated cDNA libraries from human brain. The randomly sampled clones were single-pass sequenced from both the ends to select clones that are not registered in the public database. Then their protein-coding potentialities were examined by an in vitro transcription/translation system, and the clones that generated proteins larger than 60 kDa were entirely sequenced. Each clone gave a distinct open reading frame (ORF), and the length of the ORF was roughly coincident with the approximate molecular mass of the in vitro product estimated from its mobility on SDS-polyacrylamide gel electrophoresis. The average size of the cDNA clones sequenced was 6.1 kb, and that of the ORFs corresponded to 1200 amino acid residues. By computer-assisted analysis of the sequences with DNA and protein-motif databases (GenBank and PROSITE databases), the functions of at least 73% of the gene products could be anticipated, and 88% of them (the products of 64 clones) were assigned to the functional categories of proteins relating to cell signaling/communication, nucleic acid managing, and cell structure/motility. The expression profiles in a variety of tissues and chromosomal locations of the sequenced clones have been determined. According to the expression spectra, approximately 11 genes appeared to be predominantly expressed in brain. Most of the remaining genes were categorized into one of the following classes: either the expression occurs in a limited number of tissues (31 genes) or the expression occurs ubiquitously in all but a few tissues (47 genes).

Blotting, Northern↗

PubMed1998

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

As an extension of a series of projects for sequencing human cDNA clones derived from relatively long transcripts, we herein report the entire sequences of 100 newly determined cDNA clones with the potential of coding for large proteins in vitro. The cDNA clones were isolated from size-fractionated human brain cDNA libraries with insert sizes between 4.5 and 8.3 kb. The sequencing of these clones revealed that the average size of the cDNA inserts and of their open reading frames was 5.3 kb and 2.8 kb (930 amino acid residues), respectively. Homology search against public databases indicated that the predicted coding sequences of 86 clones exhibited significant similarities to known genes; 51 of them (59%) were related to those for cell signaling/communication, nucleic acid management, and cell structure/motility. All the clones characterized in this study are accompanied by their expression profiles in 14 human tissues examined by reverse transcription-coupled polymerase chain reaction and the chromosomal mapping data.

Amino Acid Sequence↗

PubMed1999

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

In order to obtain information on the coding sequences of unidentified human genes, we newly determined the sequences of 100 cDNA clones of unknown human genes, which we named KIAA1193 to KIAA1292, from two sets of size-fractionated human adult and fetal brain cDNA libraries. The results of our particular strategy to select cDNA clones which have the potentiality of coding for large proteins in vitro revealed that the average sizes of the inserts and the corresponding open reading frames reached 5.2 kb and 2.8 kb (933 amino acid residues), respectively. By the computational analysis of the predicted amino acid sequences against the OWL and Pfam databases, 58 predicted gene products were classified into the following five functional categories: cell signaling/communication, cell structure/motility, nucleic acid management, protein management and metabolism. It was also found that 30 gene products had homologues in the public databases which were similar in sequence throughout almost their entire regions to the newly identified genes. The chromosomal loci of the genes were assigned by using human-rodent hybrid panels unless their mapping data were already available in the public databases. The expression profiles of the genes were studied in 10 human tissues, 8 brain regions, spinal cord, fetal brain and fetal liver by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.

Adult↗

PubMed2001

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

To accumulate information on the coding sequences of unidentified genes, we have carried out a sequencing project of human cDNA clones which encode large proteins. We herein present the entire sequences of 100 cDNA clones of unidentified human genes, named KIAA1776 and KIAA1780-KIAA1878, from size-fractionated cDNA libraries derived from human fetal brain, adult whole brain, hippocampus and amygdala. Most of the cDNA clones to be entirely sequenced were selected as cDNAs which were shown to have coding potentiality by in vitro transcription/translation experiments, and some clones were chosen by using computer-assisted analysis of terminal sequences of cDNAs. Three of these clones (fibrillin2/KIAA1776, MEGF10/KIAA1780 and MEGF11/KIAA1781) were isolated as genes encoding proteins with multiple EGF-like domains by motif-trap screening. The average sizes of the inserts and corresponding open reading frames of eDNA clones analyzed here reached 4.7 kb and 2.4 kb (785 amino acid residues), respectively. From the results of homology and motif searches against the public databases, the functional categories of the predicted gene products of 54 genes were determined; 93% of these predicted gene products (50 gene products) were classified as proteins related to cell signaling/communication, nucleic acid management, or cell structure/motility. To collect additional information on these genes, their expression profiles were also studied in 10 human tissues, 8 brain regions, spinal cord, fetal brain and fetal liver by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.

Adult↗

PubMed2001

Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins.

As an extension of a sequencing project of human cDNA clones which encode large proteins of unidentified genes, we herein present the entire sequences of 60 cDNA clones for the genes named KIAA1879-KIAA1938. The cDNA clones were isolated from size-fractionated cDNA libraries derived from human fetal brain, adult whole brain and amygdala, and their protein-coding sequences were predicted. Thirty-seven cDNA clones entirely sequenced in this study were selected as cDNAs which have coding potentiality by in vitro transcription/translation experiments, and the remaining 23 cDNA clones were chosen by computer-assisted analysis of terminal sequences of cDNAs. The average sizes of the inserts and corresponding open reading frames of cDNA clones analyzed here were 4.5 kb and 2.2 kb (733 amino acid residues), respectively. Sequence analyses against the public databases enabled us to annotate the functions of the predicted products of the 25 genes; 84% of these predicted gene products (21 gene products) were classified into proteins related to cell signaling/communication, nucleic acid management, and cell structure/motility. In addition to the sequence information about these 60 genes, their expression profiles were also studied in some human tissues including brain regions by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.

Adult↗

PubMed2001

Prediction of the coding sequences of unidentified human genes. XXII. The complete sequences of 50 new cDNA clones which code for large proteins.

As an extension of human cDNA projects for accumulating sequence information on the coding sequences of unidentified genes, we herein present the entire sequences of 50 cDNA clones, named KIAA1939-KIAA1988. cDNA clones to be entirely sequenced were selected by two approaches based on their protein-coding potentialities prior to sequencing: 10 cDNA clones were chosen because their encoding proteins had a molecular mass larger than 50 kDa in an in vitro transcription/translation system; the remaining 40 cDNA clones were selected because their putative proteins-as determined by analysis of the genomic sequences flanked by both the terminal sequences of cDNAs using the GENSCAN gene prediction program-were larger than 400 amino acid residues. According to the sequence data, the average sizes of the inserts and corresponding open reading frames of cDNA clones analyzed here were 4.6 kb and 1.9 kb (643 amino acid residues), respectively. From the results of homology and motif searches against the public databases, the functional categories of the 31 predicted gene products could be assigned; 25 of these predicted gene products (81%) were classified into proteins relating to cell signaling/communication, nucleic acid management, and cell structure/motility. The expression profiles of the genes were also studied in 10 human tissues, 8 brain regions, spinal cord, fetal brain and fetal liver by reverse transcription-coupled polymerase chain reaction, the products of which were quantified by enzyme-linked immunosorbent assay.

Adult↗

PubMed1990

Use of coded mortality data to assess area cancer rates: impact of residence reporting and coding errors.

In spite of their limitations, mortality data are used in many epidemiologic and public health settings. In this investigation, the authors examined the extent to which community cancer mortality rates were affected by incorrect reporting or coding of residence on death certificates. Observed and expected cancer mortality for two adjacent communities in northern rural Minnesota for the periods 1970-1974 and 1980-1984 were obtained from computerized state mortality data. Using statewide rates to obtain expected values, standardized mortality ratios for total cancers for both periods combined were 138 for men (101 observed deaths) and 148 for women (86 observed deaths). These excesses were statistically significant (p less than 0.05). However, after review of data from the actual death certificates, city maps, and information from city officials, 44 of the 187 total cancer deaths (24%) were found to have had an incorrectly reported or coded residence status. After removal of these cases, the standardized mortality ratio for total cancers for males went from 138 to 107, and for females the standardized mortality ratio went from 148 to 111. No standardized mortality ratios remained statistically significant. These findings may have implications for those who use mortality data for assessing cancer rates in communities in rural areas.

Death Certificates↗

PubMed2005

Comparison of synchrotron radiation calculations between analytical codes (STAC8, photon) and Monte Carlo codes (FLUKA, EGS4).

STAC8 is a significant improvement upon its predecessor PHOTON and is a valuable analytical code for quick and conservative beamline shielding designs for synchrotron radiation (SR) facilities. In order to check the applicability, accuracy and limitations of STAC8, studies were conducted to compare the results of STAC8 with those of PHOTON with calculations using the FLUKA and EGS4 Monte Carlo codes. Doses and spectra for scattered SR in a few beam-target-shield geometries were calculated, with and without photon linear polarisation effects. Areas for expanding the STAC8 capabilities, for example, features of the mirror-reflected lights and double-Compton light calculations and the use of monochromatic light have been identified. Some of these features have been implemented and benchmarked against Monte Carlo calculations. Reasonable agreements were found between the STAC8 and Monte Carlo calculations.

Algorithms↗

PubMed1999

Anatomy of a code. How do you feel at the start of a code blue?

Prepare for a code by recognizing breathing and circulation signs before trouble occurs. Know when to call a code, and how to move past your adrenaline rush to act effectively.

Algorithms↗

PubMed2001

Evolutionarily conserved RNA secondary structures in coding and non-coding sequences at the 3' end of the hepatitis G virus/GB-virus C genome.

Hepatitis G virus (HGV)/GB virus C (GBV-C) causes persistent, non-pathogenic infection in a large proportion of the human population. Epidemiological and genetic evidence indicates a long-term association between HGV/GBV-C and related viruses and a range of primate species, and the co-speciation of these viruses with their hosts during primate evolution. Using a combination of covariance scanning and analysis of variability at synonymous sites, we previously demonstrated that the coding regions of HGV/GBV-C may contain extensive secondary structure of undefined function (Simmonds & Smith, Journal of Virology 73, 5787-5794, 1999 ). In this study we have carried out a detailed comparison of the structure of the 3'untranslated region (3'UTR) of HGV/GBV-C with that of the upstream NS5B coding sequence. By investigation of free energies on folding, secondary structure predictive algorithms and analysis of covariance between HGV/GBV-C genotypes 1-4 and the more distantly related HGV/GBV-C chimpanzee variant, we obtained evidence for extensive RNA secondary structure formation in both regions. In particular, the NS5B region contained long stem-loop structures of up to 38 internally paired nucleotides which were evolutionarily conserved between human and chimpanzee HGV/GBV-C variants. The prediction of similar structures in the same region of hepatitis C virus may allow the functions of these structures to be determined with a more tractable experimental model.

3' Untranslated Regions↗

PubMed2002

Bridging rate coding and temporal spike coding by effect of noise.

It is controversial whether temporal spike coding or rate coding is dominant in the information processing of the brain. We show by a two-layered neural network model with noise that, when noise is small, cortical neurons fire synchronously and intervals of synchronous firing robustly encode the signal information, but that the neurons desynchronize with moderately strong noise to encode waveforms of the signal more accurately. Further increase of noise just deteriorates the encoding. A positive role of noise in the brain is suggested in a meaning different from stochastic resonance, coherence resonance, and deterministic chaos.

Action Potentials↗

PubMed1996

ISBT Code 128 and code changes as part of the implementation of a national IT system for the English National Blood Service.

The implementation of PULSE within the NBS will bring considerable advantages to the Service and to hospitals. A system of dual labelling has been developed to overcome intrinsic constraints identified with the ABC Codabar system. This should not, however, impact directly on hospitals which will be able to continue to utilize the ABC Codabar system. The dual labelling system incorporates the use of the ISBT Code 128 barcode system for transfusion centre use. This must be clearly differentiated from the implementation of ISBT code 128 within the UK. This latter development would bring considerable benefit to transfusion practice, increasing the overall safety of blood transfusion. It is, however, recognized that extensive discussion with appropriate stakeholders will be necessary before any implementation date can be determined for this initiative, particularly so given the significant logistical and financial implications inherent in such a change.

Blood Banks↗

PubMedDate not supplied

Assessing the effectiveness of coding and non-coding regions in antisense ribosome inhibition of gene expression in Tetrahymena.

In Tetrahymena thermophila, an "antisense ribosome" technology has been developed for inhibiting gene expression and generating novel mutants. Short segments of genes are inserted in antisense orientation into an rDNA vector in a region corresponding to an external loop of the folded rRNA. DNA segments derived from the 5'-ends of genes have proven most effective in reducing cognate gene expression. To investigate the efficacy of other genic regions, we generated Tetrahymena cell lines with antisense ribosome constructs containing 100-bp DNA segments derived from the 5'-ends, 3'-ends, and internal coding regions of two non-essential genes, granule lattice protein 1 and macronuclear histone H1. The 5'- and 3'-end constructs inhibited gene expression, but antisense ribosomes derived exclusively from coding regions had little effect.

Animals↗

PubMed1994

A perceptual study of source coding of Fourier phase and amplitude of the linear predictive coding residual of vowel sounds.

A practical question in a Fourier transform coding of speech signals is to what accuracy their amplitude and phase spectra have to be represented without perceptible distortions. In this paper a concern is with the audibility of quantization noise signals which are produced by quantizing the amplitude and phase spectra of vowel sounds. Experiments show that the detection of the noise targets with maskers of a low fundamental frequency is determined mainly by the sharpest temporal resolution of the auditory system in the high-frequency region. For maskers of a high fundamental frequency the detection is determined mainly by the sharpest spectral resolution in the low-frequency region. Noise targets with global random phase and amplitude are relatively more difficult to detect than those produced by a local randomization. Local random phase noise targets are generally more detectable than those produced by local amplitude randomization. The relative importance of phase and magnitude spectra in the Fourier transform coding is strongly dependent on the fundamental frequency of the vowel sounds and the window size used in the short-time Fourier analysis.

Auditory Perception↗

PubMed1998

Ribosomal S27a coding sequences upstream of ubiquitin coding sequences in the genome of a pestivirus.

Molecular characterization of cytopathogenic (cp) bovine viral diarrhea virus (BVDV) strain CP Rit, a temperature-sensitive strain widely used for vaccination, revealed that the viral genomic RNA is about 15.2 kb long, which is about 2.9 kb longer than the one of noncytopathogenic (noncp) BVDV strains. Molecular cloning and nucleotide sequencing of parts of the genome resulted in the identification of a duplication of the genomic region encoding nonstructural proteins NS3, NS4A, and part of NS4B. In addition, a nonviral sequence was found directly upstream of the second copy of the NS3 gene. The 3' part of this inserted sequence encodes an N-terminally truncated ubiquitin monomer. This is remarkable since all described cp BVDV strains with ubiquitin coding sequences contain at least one complete ubiquitin monomer. The 5' region of the nonviral sequence did not show any homology to cellular sequences identified thus far in cp BVDV strains. Databank searches revealed that this second cellular insertion encodes part of ribosomal protein S27a. Further analyses included molecular cloning and nucleotide sequencing of the cellular recombination partner. Sequence comparisons strongly suggest that the S27a and the ubiquitin coding sequences found in the genome of CP Rit were both derived from a bovine mRNA encoding a hybrid protein with the structure NH2-ubiquitin-S27a-COOH. Polyprotein processing in the genomic region encoding the N-terminal part of NS4B, the two cellular insertions, and NS3 was studied by a transient-expression assay. The respective analyses showed that the S27a-derived polypeptide, together with the truncated ubiquitin, served as processing signal to yield NS3, whereas the truncated ubiquitin alone was not capable of mediating the cleavage. Since the expression of NS3 is strictly correlated with the cp phenotype of BVDV, the altered genome organization leading to expression of NS3 most probably represents the genetic basis of cytopathogenicity of CP Rit.

Amino Acid Sequence↗

PubMed2003

Response properties of single neurons in the zebra finch auditory midbrain: response patterns, frequency coding, intensity coding, and spike latencies.

The avian mesencephalicus lateralis, dorsalis (MLd) is the auditory midbrain nucleus in which multiple parallel inputs from lower brain stem converge and through which most auditory information passes to reach the forebrain. Auditory processing in the MLd has not been investigated in songbirds. We studied the tuning properties of single MLd neurons in adult male zebra finches. Pure tones were used to examine tonotopy, temporal response patterns, frequency coding, intensity coding, spike latencies, and duration tuning. Most neurons had no spontaneous activity. The tonotopy of MLd is like that of other birds and mammals; characteristic frequencies (CFs) increase in a dorsal to ventral direction. Four major response patterns were found: 1) onset (49% of cells); 2) primary-like (20%); 3) sustained (19%); and 4) primary-like with notch (12%). CFs ranged between 0.9 and 6.1 kHz, matching the zebra finch hearing range and the power spectrum of song. Tuning curves were generally V-shaped, but complex curves, with multiple peaks or noncontiguous excitatory regions, were observed in 22% of cells. Rate-level functions indicated that 51% of nononset cells showed monotonic relationships between spike rate and sound level. Other cells showed low saturation or nonmonotonic responses. Spike latencies ranged from 4 to 40 ms, measured at CF. Spike latencies generally decreased with increasing sound pressure level (SPL), although paradoxical latency shifts were observed in 16% of units. For onset cells, changes in SPL produced smaller latency changes than for cells showing other response types. Results suggest that auditory midbrain neurons may be particularly suited for processing temporally complex signals with a high degree of precision.

Acoustic Stimulation↗

PubMed2003

Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions.

BACKGROUND: The variant surface antigen family Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors. The sequence diversity and organization of the 3D7 PfEMP1 repertoire was investigated on the basis of the complete genome sequence. METHODS: Using two tree-building methods we analysed the coding and non-coding sequences of 3D7 var and rif genes as well as var genes of other parasite strains. RESULTS: var genes can be sub-grouped into three major groups (group A, B and C) and two intermediate groups B/A and B/C representing transitions between the three major groups. The best defined var group, group A, comprises telomeric genes transcribed towards the telomere encoding PfEMP1s with complex domain structures different from the 4-domain type dominant of groups B and C. Two sequences belonging to the var1 and var2 subfamilies formed independent groups. A rif subgroup transcribed towards the centromere was found neighbouring var genes of group A such that the rif and var 5' regions merged. This organization appeared to be unique for the group A var genes CONCLUSION: The grouping of var genes implies that var gene recombination preferentially occurs within var gene groups and it is speculated that the groups reflect a functional diversification evolved to cope with the varying conditions of transmission and host immune response met by the parasite.

Animals↗