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At least 199 records · Page 11Linked to original sources
PubMed1999

Cytological, genetic and evolutionary functions of chiasmata based on chiasma graph analysis.

The nature of the chiasma as a cytological parameter for analysing cross-over was reexamined quantitatively by an improved chiasma graph method. It was reconfirmed in Mus platythrix (n =13) that interstitial chiasmata at diakinesis are distributed randomly and almost uniformly along bivalents except for the centromere and telomere regions. The size of these chiasma blank regions was consistently 0.8% of the total length of haploid autosomes in all chromosomes. There was a minimum value of chiasma interference distance between two adjacent chiasmata, which was constantly 1.8% in all chromosomes. The chiasma frequency at diakinesis was 20.1+/-2. 0 by the conventional method including terminal chiasmata. However, the primed in situ labeling technique revealed that terminal chiasmata were mostly telomere-telomere associations. From these data and also from recent molecular data we concluded that the terminal chiasma is cytologically functional for ensuring the normal disjunction of bivalents at anaphase I, but genetically non-functional for shuffling genes. The chiasma frequency excluding terminal chiasmata was 14.6+/-1.8. Reexamination of the chiasma frequency of 106 animal species revealed that the chiasma frequency increased linearly in proportion to the haploid chromosome number in spite of remarkable difference in their genome size. The increase in chiasma frequency would be evolution-adaptive, because gene shuffling is expected to be accelerated in species with high chromosome numbers.

Animals↗
PubMed1995

Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: application to the lac repressor headpiece.

A novel procedure is presented for the automatic identification of secondary structures in proteins from their corresponding NOE data. The method uses a branch of mathematics known as graph theory to identify prescribed NOE connectivity patterns characteristic of the regular secondary structures. Resonance assignment is achieved by connecting these patterns of secondary structure together, thereby matching the connected spin systems to specific segments of the protein sequence. The method known as SERENDIPITY refers to a set of routines developed in a modular fashion, where each program has one or several well-defined tasks. NOE templates for several secondary structure motifs have been developed and the method has been successfully applied to data obtained from NOESY-type spectra. The present report describes the application of the SERENDIPITY protocol to a 3D NOESY-HMQC spectrum of the 15N-labelled lac repressor headpiece protein. The application demonstrates that, under favourable conditions, fully automated identification of secondary structures and semi-automated assignment are feasible.

Amino Acid Sequence↗
PubMed1980

The graph of loudness recruitment (ABLB-test).

The ABLB-test compares the subjective loudness in patients with unilateral sensorineural hearing loss. The graph of this comparison of loudness at different suprathreshold intensities is of interest for understanding the function of the hair cells.

Auditory Threshold↗
PubMed1995

Molecular fragments associated with non-genotoxic carcinogens, as detected using a software program based on graph theory: their usefulness to predict carcinogenicity.

We assembled 390 chemicals with a structure non-alerting to DNA-reactivity (145 carcinogens and 245 non-carcinogens) for which rodent carcinogenicity data were available. These non-alerting chemicals were defined by the absence in their molecules of DNA-reactive (directly or after metabolic activation) alerting structures, as described by Ashby and coworkers (Mutat. Res., 204 (1988) 17-115; Mutat. Res., 223 (1989) 73-103; Mutat. Res., 257 (1991) 209-227; Mutat. Res., 286 (1993) 3-74). Using our software program based on graph theory we analyzed the compounds in order to estimate the program's ability to predict nonalerting carcinogens. Our software fragmented the structural formula of the chemicals into all possible fragments of contiguous atoms with size between 2 and 8 (non-hydrogen) atoms and learned about statistically significant fragments from a training set of chemicals. These fragments were used to predict carcinogenicity or lack thereof in a verification set of compounds. For 390 runs of the software program we used (n - 1) of the chemicals as a training set, to predict the excluded chemical at each run (as a test set). Using two different probability thresholds to select significant fragments (P = 0.05 and P = 0.125 1-tailed according to binomial distribution), we performed two analyses: in the better one (P = 0.05) 19% of the molecules tested lacked significant fragments, for the remaining 81% the observed level of accuracy of the prediction was 66.0% against an expected level of accuracy of 51.7%. The difference was highly significant (P < 0.0001). We also examined the more significant activating fragments (biophores) and discussed at length both their biological plausibility and the working hypothesis that additional alerting structures for carcinogenicity (not only those related to genotoxicity) can be detected using this type of SAR approach. This new class of alerting structures could identify subfamilies of congeneric analogs active through mechanisms of receptor mediated carcinogenesis.

Carcinogens↗
PubMed1978

Bond graphs and the exploitation of power conserving transformations.

Use is made of the guaranteed energy conservation property of any bond graph model (presuming that consistent energy variables are used). Thus power transformations are power conserving, and this property is exploited with respect to multiport transformers where many effort and flow variables may be involved. In these cases the relationship among the effort (flow) variables across the transformer may be easier to derive than the relationship among the flows (efforts). The power conserving nature of the transformer permits immediate derivation of the alternate variable relationship. This formulation procedure is applied to the reflex reaction of the arm.

Energy Metabolism↗
PubMed1992

Three-dimensional structural resemblance between leucine aminopeptidase and carboxypeptidase A revealed by graph-theoretical techniques.

Using 3-D searching techniques based on algorithms derived from graph theory we have established a striking structural similarity between the structure of bovine carboxypeptidase A and that of the C-terminal domain of bovine leucine aminopeptidase. There is no significant sequence homology between the aminopeptidases and the carboxypeptidases but the strong structural relationship detected in this complex fold suggests that there may be a very remote divergent evolutionary relationship between these two enzyme classes.

Animals↗
PubMed1993

Three-dimensional structural resemblance between the ribonuclease H and connection domains of HIV reverse transcriptase and the ATPase fold revealed using graph theoretical techniques.

Using 3D searching techniques based on algorithms derived from graph theory, we have established two previously unreported structural similarities involving the ribonuclease H (RNase H) domain of HIV-1 reverse transcriptase (RT). First, we report that there is a strong similarity between the 3D folds of the RNase H domain of RT and the 'ATPase folds' of hexokinase, the 70 kDa heat-shock cognate protein and actin. Like RNase H, these enzymes are involved in nucleotide binding and metal ion-catalysed cleavage of a phosphodiester bond. Similarities of the folding motif and the position of the metal-binding site in these enzymes suggest possible functional analogies and evolutionary relationships with RNase H. Second, we find there is a strong resemblance between the folds of the RNase H domain and of the p66 and p51 'connection' domains of RT. It is possible that this striking similarity within the RT structure indicates a possible ancestral gene doubling event. The similarity may also indicate that the connection domains possess functional roles in addition to those previously suggested, and they may therefore represent a further target for the design of therapeutic agents.

Adenosine Triphosphatases↗
PubMed1985

Amino acid transport across the human blood-CSF barrier. An evaluation graph for amino acid concentrations in cerebrospinal fluid.

The correlation of cerebrospinal fluid (CSF)/serum concentration quotients was used as a method for identification of amino acids which are transported by a common carrier system across the blood-CSF barrier. Isoleucine, leucine, valine, phenylalanine, tyrosine and lysine were found to compete for the same carrier system. This group of amino acids in man was found to be different from the system described as a neutral amino acid carrier at the blood-brain barrier in rats. In man, methionine and tryptophan do not compete with the other neutral amino acids for the same carrier system. In contrast, lysine as a basic amino acid is found to be correlated with the same transport system as the five neutral amino acids. A graph for the evaluation of pathological amino acid concentrations in CSF is presented. Patients with a blood-CSF barrier dysfunction for proteins showed partly normal, partly increased, CSF/serum concentration quotients for the amino acids. Hydroxyproline could be identified as a constituent of the amino acid pool in CSF. For proline and hydroxyproline a special control system has to be suggested because of their smaller biological variance in CSF than in blood. Contrary to the other amino acids proline and hydroxyproline have a smaller biological variation in CSF than in serum.

Adolescent↗
PubMed1976

The corticosteroid dose graph. Use in determination of corticosteroid requirements, characterization of patients, and prevention of seasonal exacerbation in corticosteroid-dependent patients.

Sixty-three corticosteroid(CS)-dependent asthmatics were evaluated by a method which records asthmatic exacerbations as a function of change in CS dosage. This method, the Corticosteroid Dose Graph (CSDG), is a graphic representation of the patients' narrative charts. It is useful in assessing and directing the care of these patients and in evaluating the efficacy of altered therapeutic regimens in asthmatics. The CSDG categorizes cooperative patients (CP) and distinguishes these patients from those who are less cooperative (LCP). Evaluation of the progress of CP by the graphic analysis system showed that CP have fewer severe exacerbations of asthma than LCPs. Evaluation of the 63 patients by this graphic method shows a significantly increased incidence of asthmatic exacerbations in the Chicago area in October as compared to other months. The CSDG also demonstrates that some individuals experienced significantly increased numbers of asthma exacerbations at certain times of the year unique to themselves. Because the CSDG predicts exacerbations, it was shown to be applicable to prevent such exacerbations by prophylactic increase in CS dose during a high-risk season for selected CS-dependent asthmatics.

Adolescent↗
PubMed1992

MEPS parameters and graph analysis for the use of recombination to construct ordered sets of overlapping clones.

Homologous recombination can provide a basis for the construction of an ordered set of overlapping clones. The principle is to make two libraries, each in a vector that has a different selectable marker flanking the insert site. Recombination between the flanking markers, leading to a selectable phenotype, can only occur as the consequence of crossing over between inserts. The two libraries are crossed in a matrix, allowing the construction of an ordered set. The logic, akin to S. Benzer's (1961, Genetics 47:403-415) for the arrangement of deletion and point mutations, has a graph theoretic formulation, which helps to cope with the complex and noisy data inherent in the physical mapping of genomes rich in repeated sequences. The minimum length of identity required for homologous recombination is called the MEPS (minimum efficient processing segment) and is a property of each recombination pathway. The amount and the type of sequence similarity required for two sequences to recombine is different from that implied by either the conservation of restriction sites or by most procedures of hybridization.

Chromosome Deletion↗
PubMed2026

Robust error-minimization in the genetic code across physicochemical metrics and variant codes: A graph-theoretic analysis in GF(2)6.

The standard genetic code reduces the impact of point mutations, but the robustness of this property across physicochemical metrics, naturally occurring variant codes, and codon-reassignment mechanisms remains incompletely quantified. Embedding the 64 codons in GF(2)6 represents the hypercube Q6 as a coordinate-dependent subgraph of the encoding-independent single-nucleotide mutation graph H(3,4), and enables continuous &#x3c1;-interpolation between the two. Under a quartet-pattern shuffle null (n=10,000), the standard code is significantly low-cost across four established, code-independent physicochemical distance metrics with partially overlapping content (Grant ham p=0.0062; Miyata p<0.001; Woese polar requirement p=0.003; Kyte-Doolittle hydropathy p=0.001), and the signal strengthens monotonically as &#x3c1; moves Q6&#x2192;H(3,4). A structure-aware sensitivity analysis under the alignment-derived ProtSub matrix (Jia & Jernigan 2021) yields the most extreme percentile of any measure tested (p=0.0004; all five p-values pass Bonferroni at &#x3b1;=0.05). Across the 27 NCBI translation tables, near-optimality is preserved: 11 of 12 informative-distance variants retain top-5% placement after BH-FDR correction. Natural codon reassignments avoid disrupting codon-family connectivity: under the encoding-independent H(3,4) adjacency, observed events are topology-breaking at relative risk 0.32 versus the candidate landscape (permutation p&#x2264;10-4). The H(3,4) result is stable by construction; the Q6 decomposition is representation-specific and fails to show depletion under 8 of 24 base-to-bit encodings, so we report H(3,4) as the primary test and Q6 as a sensitivity. Event-level conditional-logit modelling shows that topology avoidance and local physicochemical cost provide complementary, only weakly correlated signal (rs=0.15), and that topology adds explanatory value beyond physicochemistry under both Q6 and encoding-independent H(3,4) adjacency. Retrospective reanalysis of nine genome-recoding datasets is consistent with codon-family topology operating as an evolutionary-trajectory constraint distinct from acute engineering fitness. The contribution is the second axis: code evolution is jointly constrained by physicochemical smoothness and codon-family topological integrity, and these two constraints are partly independent.

Codon reassignment↗
PubMed1997

The selection of ELISA cut-off points for testing antibody to Newcastle disease by two-graph receiver operating characteristic (TG-ROC) analysis.

Two hundred and sixty field serum samples were tested for Newcastle disease (ND) antibodies using a commercial enzyme-linked immunosorbent assay (ELISA) and the haemagglutination inhibition test (HI). The HI test was regarded as the reference method. Reciprocal titres of 16 and above were considered positive. In this study the two-graph receiver operating characteristic (TG-ROC) analysis was used as a tool for selecting cut-off points. Sensitivity, specificity, efficiency and Youden's index were used as indices of test accuracy. The positive and negative predictive values of the ELISA results were analysed for various prevalence rates.

Animals↗
PubMed1992

Propagation of information in MetaNet graph models.

Information flow in metabolic networks has been studied with a graph model which represents the biochemical transformations occurring in the system under investigation. The "signal strength", an algebraic expression which estimates the probability that an intermediate metabolite is bound to a given enzyme, has been used to derive the "signal transmittance", the fraction of the informational signal at one intermediate that reaches another intermediate. The transmittance has been used to derive the "response ratio", the sensitivity of the rate of change of information at one metabolite consequent to a perturbation at another metabolite. Because the graphical representation corresponds to the biochemical events presumed to occur in the network, these quantities can be used to design experiments to confirm or falsify the hypotheses underlying the model and aid in understanding the regulatory properties of the system. The technique is illustrated by an example model, and its predictions are shown to be sensitive to modest structural changes in the network.

Animals↗
PubMed1999

Graph-theoretic description of the interplay between non-linearity and connectivity in biological systems.

The purpose of this article is to stress the implications that the consideration of nonlinearity has upon the extension and strength of connectivity, if this is understood as a characterization of the degree of interrelation between parts of the system. This objective is reached within the QP formalism for non-linear ODEs. The formalism is developed in a graph-theoretic setting, with the help of which the connectionist aspect of non-linearity becomes apparent. Topology-preserving transformations involve an exchange between the degree of non-linearity and the strengths of interactions, thus assembling systems of apparently different nature into classes of equivalence. We argue that, if we have in mind a classification of systems according to behavior, these classes of equivalence should be given their proper singularity. We characterize globally the connectivity of a class with an index, although we point out during the discussion that the mathematical conception of the complex idea of connectivity is still incomplete.

Linear Models↗
PubMedDate not supplied

Correlation of graph-theoretical parameters with biological activity.

Ośmialowski and Kaliszan calculated graph-theoretical indices for substituted isonicotinic hydrazides and used simple and multiple regression to search (unsuccessfully) for correlations with biological activity. The present paper describes successful searches for correlation in the same data set using principal component analysis (PCA) with multivariate outlier testing and also using stepwise multiple regression. Following PCA, correlation with biological activity always appeared in the second principal component, not the first, that is, after projection of the data points into the (n - 1)-space orthogonal to the first principal component axis. In that space, the principal component score was a more accurate predictor of biological activity than were equations provided by multiple regression or stepwise multiple regression using the underlying variables. A multivariate outlier test identified one observation as discordant, and removing that observation improved prediction further.

Data Interpretation, Statistical↗
PubMedDate not supplied

Graph theory and group contributions in the estimation of boiling points.

Estimation of normal boiling points of organic compounds using a group contribution method is known to be unsatisfactory and an attempt has been made to improve the accuracy of the estimations by including chemical graph information in the regressions. This leads to a measurable improvement in the results obtained for both a set of 63 alcohols and also a set of 541 structurally diverse organic compounds. This new approach was found to have better predictive ability than the group contribution approach both in the cross-validation tests and in predicting the normal boiling points for 32 new compounds.

Alcohols↗