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PubMedDate not supplied

Rate coding versus temporal order coding: a theoretical approach.

The belief that neurones transmit information in the form of a firing rate code is almost universal. However, we argue that at least in some situations, the efficiency of a coding strategy based on rate coding is surprisingly poor. A simple mathematical analysis reveals that, due to the stochastic nature of spike generation, even transmitting the simplest signals reliably would require either: (1) excessively long observation periods incompatible with the speed of sensory processing or (2) excessively large numbers of redundant neurones, incompatible with the anatomical constraints imposed by sensory pathways. We argue that such problems may be avoided by using alternative temporal codes which rely on the asynchrony of firing across a population of afferent neurones.

Action Potentials↗

PubMed2004

Birth-and-death evolution of protein-coding regions and concerted evolution of non-coding regions in the multi-component genomes of nanoviruses.

Genomes of the four plant viruses of the genus Nanovirus consist of multiple circular single-stranded DNA components, each of which encodes a single protein. Protein phylogenies supported the hypothesis that faba bean necrotic yellows virus (FBNYV) and milk vetch disease virus (MDV) are sister taxa; that subterranean clover stunt virus (SCSV) branched next; and that banana bunchy top virus (BBTV) is an outgroup to the three other species. The phylogeny of replication (Rep) proteins indicate that this small viral multi-gene family has evolved by a process of duplication and subsequent loss of Rep-encoding genome components, analogous to the "birth-and-death" process of evolution which has been described in eukaryotic multi-gene families. By contrast, repeated recombinational events between components were found to have homogenized the non-coding portions of several components encoding unrelated components. For example, as result of recent recombination a portion of the non-coding region is virtually identical among SCSV components 1, 3, 4, 5, and 7. Thus, there is a process of concerted evolution of non-coding regions of Nanovirus genome components, which raises the possibility that certain non-coding regions are subject to functional constraint.

Base Sequence↗

PubMed2004

3D TROSY-HNCA(coded)CB and TROSY-HNCA(coded)CO experiments: triple resonance NMR experiments with two sequential connectivity pathways and high sensitivity.

The concept of chemical shift-coding monitors chemical shifts in multi-dimensional NMR experiments without additional polarization transfer elements and evolution periods. The chemical shifts are coded in the line-shape of the cross-peak through an apparent scalar coupling dependent upon the chemical shift. This concept is applied to the three-dimensional triple-resonance experiment HNCA adding the information of (13)C(beta) or (13)C' chemical shifts. On average, the proposed TROSY-HNCA(coded)CB experiment is a factor of 2 less sensitive than the HNCA experiment. However, it contains correlations via the chemical shifts of both (13)C(alpha) and (13)C(beta), and provides up to three times higher resolution along the (13)C(alpha) chemical shift axis. Thus, it dramatically reduces ambiguities in linking the spin systems of adjacent residues in the protein sequence during the sequential assignment. The TROSY-HNCA(coded)CO experiment which is conceptually similar contains correlations via the chemical shifts of (13)C(alpha) and (13)C' without major signal losses. The proposed triple resonance experiments are applied to a approximately 70% (2)H, approximately 85% (13)C,(15)N labeled protein with a molecular weight of 25 kDa.

Nuclear Magnetic Resonance, Biomolecular↗

PubMed2025

EV DNA from pancreatic cancer patient-derived cells harbors molecular, coding, non-coding signatures and mutational hotspots.

DNA packaged into cancer cell-derived EV is not well appreciated. Here, we uncovered signatures of EV DNA secreted by pancreatic cancer cells. The cancer cells and non-cancer counterparts exhibit distinct low vs. high molecular weight (LMW vs. HMW) EV DNA fragments distribution, respectively. Genome sequencing and Single Nucleotide Variants analysis revealed that 95% of reads and 94% of SNVs map to noncoding regions of the genome. Given that ~1% of the human genome represents coding regions, the 5% mapping rate to coding regions suggests a non-random enrichment of certain coding regions and mutations. The LMW DNA fragments not only set cancer cells apart, but also harbor cancer specific enrichment of unique coding regions, the top nine being FAM135B, COL22A1, TSNARE1, KCNK9, ZFAT, JRK, MROH5, GSDMD, and MIR3667HG. Additionally, the cancer cells' LMW DNA fragments exhibit dense centromeric mapping more strikingly on chromosomes 3, 7, 9, 10, 11, 13, 17, and 20. Mutational profiling turned up close to 200 mutations specific for the cancer cells. Altogether, our analyses suggest that centromeric regions might hold clues to EV DNA content from pancreatic cancer, the molecular, mutational signatures thereof, and rationalizes the need for a new approach to DNA biomarker research.

Humans↗

PubMed1987

Enhanced repair of pyrimidine dimers in coding and non-coding genomic sequences in CHO cells expressing a prokaryotic DNA repair gene.

We have previously demonstrated that the active dihydrofolate reductase (DHFR) gene is efficiently repaired in Chinese hamster ovary (CHO) cells which remove only a small fraction of u.v.-induced pyrimidine dimers from the overall genome. Preferential DNA repair of essential genes may explain why the u.v. resistance of normal CHO cells is as high as that of fully repair-proficient normal human cells. In this report, we have studied the removal of pyrimidine dimers in a CHO cell line expressing the cloned denV gene from bacteriophage T4 which codes for the pyrimidine dimer specific enzyme T4 endonuclease V (T4 endo V). This cell line was derived from a u.v.-sensitive excision deficient mutant of a CHO wild type line by transformation with the denV gene, and partial restoration of u.v. resistance was achieved. We have examined an important aspect of the u.v. excision repair in these denV+ cells by studying the repair efficiencies in the active DHFR gene and in a non-coding sequence located downstream from it. In the u.v.-sensitive CHO mutant cell line from which the denV+ was derived, we detected no pyrimidine dimer removal from the gene or from the downstream sequence after irradiation of the cells with 20 J/m2 u.v. (254 nm) light. In the wild type CHO cells, approximately 50% of the pyrimidine dimers were removed from a sequence in the DHFR gene within 8 h, whereas none were removed from the downstream sequence in that period. This represents the normal pattern of preferential DNA repair of active genes, which we have described in previous communications. In the denV+ cells, approximately 70% of the pyrimidine dimers were removed from both the DHFR gene and from the downstream sequence; these cells thus repair both coding and non-coding regions of the genome and show no pattern of preferential repair. The endogenous activity that initiates excision repair in normal CHO cells is evidently much more restricted in its accessibility to DNA lesions in chromatin than is the activity in cells containing substantial amounts of the small T4 endo V enzyme.

Animals↗

PubMed1994

Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1.

We established a protocol for the prediction of the coding sequences of unidentified human genes based on the double selection and sequence analysis of cDNA clones with inserts carrying unreported 5'-terminal sequences and with insert sizes corresponding to nearly full-length transcripts. By applying the protocol, cDNA clones with inserts longer than 2 kb were isolated from a 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 20 genes contained sequences similar to known genes in the GenBank/EMBL databases. The sequences of the remaining 20 genes were entirely new, and characteristic protein motifs or domains were identified in 32 genes. Other sequence features noted were that the coding sequences of 23 genes were followed by relatively long stretches of 3'-untranslated sequences and that 5 genes contained repetitive sequences in their 3'-untranslated regions. The chromosomal location of these genes has been determined. By increasing the scale of the above analysis, the coding sequences of many unidentified genes can be predicted.

Base Sequence↗

PubMed1998

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

In our series of projects for accumulating sequence information on 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 KIAA0711 to KIAA0810. These cDNA clones were selected according to their coding potentials of large proteins (50 kDa and more) in vitro. The average sizes of the inserts and corresponding open reading frames were 4.3 kb and 2.6 kb (869 amino acid residues), respectively. Sequence analyses against the public databases indicated that the predicted coding sequences of 78 genes were similar to those of known genes, 64% of which (50 genes) were categorized as proteins functionally related to cell signaling/communication, cell structure/motility and nucleic acid management. As additional information concerning genes characterized in this study, the chromosomal locations of the clones were determined by using human-rodent hybrid panels and the expression profiles among 10 human tissues were examined by reverse transcription-coupled polymerase chain reaction which was substantially improved by enzyme-linked immunosorbent assay.

Brain Chemistry↗

PubMed1998

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

In this paper, we report the sequences of 100 cDNA clones newly determined from a set of size-fractionated human brain cDNA libraries and predict the coding sequences of the corresponding genes, named KIAA0819 to KIAA0918. These cDNA clones were selected on the basis of their coding potentials of large proteins (50 kDa and more) by using in vitro transcription/translation assays. The sequence data showed that the average sizes of the inserts and corresponding open reading frames are 4.4 kb and 2.5 kb (831 amino acid residues), respectively. Homology and motif/domain searches against the public databases indicated that the predicted coding sequences of 83 genes were similar to those of known genes, 59% of which (49 genes) were categorized as coding for proteins functionally related to cell signaling/communication, cell structure/motility and nucleic acid management. The chromosomal locations and the expression profiles of all the genes were also examined. For 54 clones including brain-specific ones, the mRNA levels were further examined among 8 brain regions (amygdala, corpus callosum, cerebellum, caudate nucleus, hippocampus, substantia nigra, subthalamic nucleus, and thalamus), spinal cord, and fetal brain.

Amino Acid Sequence↗

PubMed1997

Trauma registry injury coding is superfluous: a comparison of outcome prediction based on trauma registry International Classification of Diseases-Ninth Revision (ICD-9) and hospital information system ICD-9 codes.

BACKGROUND: Trauma registries are an essential but expensive tool for monitoring trauma system performance. The time required to catalog patients' injuries is the source of much of this expense. Typically, 15 minutes of chart review per patient are required, which in a busy trauma center may represent 25% of a full-time employee. We hypothesized that International Classification of Disease-Ninth Revision (ICD-9) codes generated by the hospital information system (HI) would be similar to those coded by a dedicated trauma registrar (TR) and would be as accurate as TR ICD-9 codes in predicting outcome. METHODS: One thousand eight hundred twelve patients admitted to a Level I trauma center during 2 years had International Classification of Disease Injury Severity Scores (ICISS) calculated based on HI and TR ICD-9 codes. The relative predictive powers of these two ICISSs were then compared for every patient using Receiver Operator Characteristic Curve Area (ROC) and Hosmer Lemeshow Statistics. RESULTS: Eighty-nine percent of patients (1,608 of 1,812) had identical HI and TR ICISSs. Eleven patients' ICISSs differed by >0.1, and only two patients' scores differed by >0.2. ICISS proved to be a powerful predictor of outcome whether derived from HI (ROC = 0.884; 95% confidence interval (CI) = 0.850-0.917) or TR (ROC = 0.872; 95% CI = 0.837-0.908). Although these predictive powers were not significantly different (p = 0.076), the trend was for HI to perform better than TR. ISS calculated for the same data set using the MacKenzie dictionary proved significantly less predictive of outcome than either ICISS (ROC(MacKenzie) = 0.843; 95% CI = 0.792-0.884; p = 0.034). CONCLUSION: We conclude that in our hospital TR data on individual injuries can be replaced by HI data without loss of predictive power. ISS based on the MacKenzie dictionary should be abandoned because it is much less predictive of outcome than ICISS.

Adolescent↗

PubMed2000

The availability and distribution of dentists in rural ZIP codes and primary care health professional shortage areas (PC-HPSA) ZIP codes: comparison with primary care providers.

OBJECTIVE: This paper maps dentists, primary care physicians, physician assistants, nurse practitioners, and nurse midwives in rural areas and rural areas meeting criteria as underserved for primary health care. METHODS: Computer-based mapping was used to localize health care provider groups by five-digit ZIP code. For each rural and each rural primary care health professional shortage area (PC-HPSA) ZIP code, the number of providers in each group was determined. The different combinations of providers were determined. RESULTS: All providers in rural areas were present at levels substantially lower than national averages, particularly in PC-HPSA areas. Dentists were approximately equal in number to primary care physicians in rural areas and the largest group in PC-HPSAs. Approximately 75 percent of rural residents lived in ZIP code areas with dentists available. Over 5.8 million rural residents and over 50 percent of rural PC-HPSA residents had no providers available in their ZIP code areas. CONCLUSIONS: Rural areas continue to have a short supply of primary care providers and dentists. Dentists were present in many areas where primary care provider presence was absent or very low. These data, including those relating to provider co-presence, can be used to develop strategies to overcome health care access problems due to provider shortages.

Dentists↗

PubMed1991

The genes coding for the antigen 85 complexes of Mycobacterium tuberculosis and Mycobacterium bovis BCG are members of a gene family: cloning, sequence determination, and genomic organization of the gene coding for antigen 85-C of M. tuberculosis.

A gene encoding the 33-kDa secreted protein of Mycobacterium tuberculosis (antigen 85-C) was isolated and sequenced. The corresponding DNA sequence contains a 1,020-bp coding region. The deduced amino acid sequence corresponds to a 340-residue protein consisting of a 46-amino-acid signal peptide and a 294-amino-acid mature protein. Comparison with previously described genes for the 30-kDa antigen (the alpha antigen of M. bovis BCG, also called antigen 85-B) and the 32-kDa antigens from M. bovis BCG and M. tuberculosis (antigens 85-A) indicates that the three genes share considerable sequence homology (70.8 to 77.5%) but may also code for distinctive epitopes. Strong differences among the three sequences are clearly visible upstream and downstream from the region coding for the mature proteins. The three genes have been detected in the genome of M. bovis BCG by Southern blot hybridization with three type-specific probes. Furthermore, hybridization of large DNA fragments (100 to 1,000 kbp) from M. tuberculosis separated by pulsed-field gel electrophoresis showed that the three genes coding for the antigen 85 complex are not clustered within the bacterial genome.

Amino Acid Sequence↗

PubMed2003

Duality of rate coding and temporal coding in multilayered feedforward networks.

A functional role for precise spike timing has been proposed as an alternative hypothesis to rate coding. We show in this article that both the synchronous firing code and the population rate code can be used dually in a common framework of a single neural network model. Furthermore, these two coding mechanisms are bridged continuously by several modulatable model parameters, including shared connectivity, feedback strength, membrane leak rate, and neuron heterogeneity. The rates of change of these parameters are closely related to the response time and the timescale of learning.

Action Potentials↗

PubMed2004

Stimulus-response compatibility with wheel-rotation responses: will an incompatible response coding be used when a compatible coding is possible?

Three experiments were conducted in which subjects responded to left-right tones with clockwise-counterclockwise rotations of a steering wheel using one of two stimulus-response assignments. When the hands were at the bottom of the wheel, where hand movement is opposite to wheel movement, subjects coded responses according to the frame that yielded a compatible mapping when the instructions did not emphasize either hand or wheel movements (Experiment 1). When instructions emphasized hand movements, responses were coded relative to the hand-referenced frame (Experiment 2), and when the wheel controlled a visual cursor, responses were coded relative to a cursor-referenced frame (Experiment 3). Coding with respect to these frames occurred even when the resulting mapping was incompatible.

Cognition↗

PubMed1986

Quantification of the transition from oocyte-coded to embryo-coded glucose phosphate isomerase in mouse embryos.

A quantitative electrophoretic analysis of glucose phosphate isomerase (GPI-1) allozymes produced by heterozygous Gpi-1sa/Gpi-1sb mouse embryos has enabled us to estimate separately the contributions of GPI-1 enzyme that were oocyte coded, encoded by the embryonic, maternally derived Gpi-1sa allele and encoded by the embryonic, paternally derived Gpi-1sb allele. The oocyte-coded GPI-1 activity is stable until 2 1/2 days and then declines and is exhausted by 5 1/2 to 6 1/2 days post coitum (p.c.). The maternally and paternally derived Gpi-1s alleles are probably usually activated synchronously but several possible exceptions were observed. This activation was first detected in 2 1/2-day embryos. Total GPI-1 activity falls to a minimum around 3 1/2 to 4 1/2 days, even though embryonic gene expression has already begun. The profile of oocyte-coded GPI-1 activity is consistent with the suggestion (Harper & Monk, 1983) that there is a mechanism for the removal of oocyte-coded gene products at around 2 1/2 days p.c. The method of analysis described is applicable to other dimeric enzymes with electrophoretic variants.

Animals↗

PubMed1986

New statistical approach to discriminate between protein coding and non-coding regions in DNA sequences and its evaluation.

We propose a new approach to study protein coding and non-coding regions in DNA sequences, by making use of two complementary statistical methods. The principal component analysis (PCA) is a graphical method to represent DNA sequences which are characterized by some quantitative parameters: it is a help to the intuition. The discriminating analysis (DA) is a quantitative method which permits to classify the DNA sequences. It leads to an evaluation of the first method and to a decision. The value of this approach has been confirmed since we also have found some results which had been described recently in the literature. Furthermore, this general methodology has permitted us to show the existence of parameters which identify the nucleic acid sequence functional domains, without having to make use of the properties of the genetic code.

Animals↗

PubMed1998

The role of the genetic code in generating new coding sequences inside existing genes.

The genetic code has a very interesting property--it generates an open reading frame (ORF) inside a coding sequence, in a specific phase of the antisense strand with much higher probability than in the random DNA sequences. Furthermore, these antisense ORFs (A-ORFs) possess the same features as real genes--the asymmetry in the nucleotide composition at the first and second positions in codons. About two thirds of the 2997 overlapping ORFs in the yeast genome possess this feature. Thus, the question arises: has this feature of the genetic code been exploited in the evolution of genes? We have searched the FASTA data bases for homologies with the antisense translation products of a specific class of genes and we have found some sequences with relatively high homology. Many of them have scores which could be randomly found in the searched data bases with a probability lower than 10(-6). We conclude that some genes could arise by positioning a copy of the original gene under a promoter in the opposite direction in such a way that both, the original gene and its copy initially use the same nucleotides in the third, degenerated positions in codons.

DNA, Antisense↗

PubMed2003

The early phases of genetic code origin: conjectures on the evolution of coded catalysis.

A review of the most significant contributions on the early phases of genetic code origin is presented. After stressing the importance of the key intermediary role played in protein synthesis, by peptidyl-tRNA, which is attributed with a primary function in ancestral catalysis, the general lines leading to the codification of the first amino acids in the genetic code are discussed. This is achieved by means of a model of protoribosome evolution which sees protoribosome as the central organiser of ancestral biosynthesis and the mediator of the encounter between compounds (metabolite-pre-tRNAs) and catalysts (peptidyl-pre-tRNAs). The encounter between peptidyl-pre-tRNA catalysts in protoribosome is favoured by metabolic pre-mRNAs and later resulted (given the high temperature at which this evolution is supposed to have taken place) in the evolution of mRNAs with codons of the type GNS. These mRNAs codified only for those amino acids that the coevolution theory of genetic code origin sees as the precursors of all other amino acids. Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule (tmRNA) which is here considered a molecular fossil of ancestral protein synthesis.

Amino Acids↗

PubMed1999

Elucidating sequence codes: three codes for evolution.

The sequences are related to evolution in several ways. First, they carry traces of a distant past. Two sequence features point to the earliest sequence organization. The universal hidden GCU-periodical pattern in mRNA suggests the earliest codons: GCU and its nine-point-change derivatives. They code for seven amino acids that by several criteria are also the oldest. Together it makes the earliest form of the triplet code, still recognizable in the extant sequences. Another feature present in the sequences, apparently, since separation of prokaryotes and eukaryotes, is hidden genome segmentation. Both protein-coding and noncoding sequences appear to have been formed by fusion of standard size units, about 360 bp (120 aa) in eukaryotes and 450 bp (150 aa) in prokaryotes. Presumably, the units have been functioning at some stage of evolution as autonomous single-gene size elements. There are sequence designs that promote evolution. One such design suitable for fast adaptation is the tandem repetition of identical sequences, so that their copy numbers in the repeat arrays would modulate (tune) the expression of nearby genes. The tandem repeat expansion diseases illustrate this mechanism in a dramatic way: overtuning of the respective gene expression leads to the disease.

Adaptation, Biological↗