Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains

Matrix generator techniques have been adapted to account for precise structural features of the nucleotide repeating unit and to translate the primary sequence of DNA base pairs into three-dimensional structures. Chains have been constructed to reflect the local sequence-dependent differences of bending and twisting of adjacent residues and various overall chain properties, including the average unperturbed moments of the end-to-end vector r and the mean angular orientation (〈γ〉 between base pair normals, 〈?₁〉 between long axes, and 〈?₂〉 between short axes) of terminal chain residues, have been computed. The chain backbone is treated implicitly in terms of the spatial fluctuations of successive base pairs. Motions are limited to low-energy perturbations of the standard B-DNA helix. Approximate potential energy schemes are used to represent the rules governing the patterns of local base–base morphology and flexibility. Theoretical predictions are compared with experimental observations at both the local and the macro-molecular level. Initial applications are limited to the rodlike poly(dA) · poly(dT) and poly(dG) · poly(dC) helices. The former duplex is found to be more compressed and the latter more extended than random-sequence DNA of the same chain length. The flexibility of the duplexes as a whole is described in terms of the average higher moments of the displacement vector ρ = r - 〈r〉 and the likelihood of chain cyclization is estimated from the three-dimensional Hermite series expansions of the displacement tensors. Emphasis is placed on theoretical methodology and the practical relevance of the calculated chain moments to observed physical properties.     

Configurational statistics of polysaccharide chains. Part III. Linear β-(1 → 4′) xylan and mannan

The characteristic ratio C_N = 〈r²〉₀/Nl_v² of the β-D (1 → 4′)-linked polysaccharides xylan and mannan has been computed as a function of the angle τ at the bridge oxygen atom and the degree of polymerization N. The calculated values of the characteristic ratio C_N are very high relative to their free rotational dimensions. The characteristic ratio of these polysaecharides converges to the asymptotic value at low degree of polymerization at higher τ values. The low values of the calculated characteristic ratio of xylan compared to cellulose and mannan for the same τ value indicate that the former is more flexible and assumes a compact configuration. A pronounced difference in the values of the characteristic ratio C_N of cellulose and mannan has also been observed lower τ angles (<120°). On the other hand, nearly the same values of C_N have been obtained at higher τ angles (120°–125°), which suggests that, cellulose and mannan may have similar configuralons in certain solvents.     

Configurational statistics of 1,6-linked glycans

We have calculated the unperturbed dimensions of some 1,6-linked glycans by regarding the homopolymer as a ‘copolymer’ in which the different ‘comonomers’ are conformers characterized by the dihedral angle about the C5C6 bond.We find that the characteristic ratio is small (e.g. for the α-glucan it is about 3·3 to 3·4). From the results of some model calculations in which the dihedral angle about the C5C6 bond is fixed, we argue that these low values arise from bonding geometry effects, which are at least as important as the additional conformational freedom from rotation about the C5C6 bond.     

Kinetics of polysaccharide degradation during ethanol–alkali delignification of giant reed—Part 1. Cellulose and xylan

The degradation kinetics of the principal polysaccharides (cellulose and xylan) of the agro-fibre crop Arundo donax L. (giant reed) during ethanol–alkali delignification is reported. Based on the properties of a multi-component reaction system, the degradation kinetics of both polysaccharides was accurately described in terms of two simultaneous irreversible first-order reactions corresponding to removal of two kinetically homogeneous fractions. The moderate cellulose losses during pulping (about 4.5%) result mainly from the removal of the more reactive cellulose fraction, that accounted for 4% of initial cellulose. The bulk of the cellulose (96%) degrades slowly with three orders lower rate with pulping progress. The apparent activation energy of cellulose fractions degradation was estimated as 105.2 and 106.5 kJ mol⁻¹, respectively. Substantial loss of xylan during pulping (about 55%, as a homoxylan) is caused by fast removal of the first very reactive fraction, covering about 48% of total xylan. The degradation rate of the second xylan fraction is only one order higher of the bulk cellulose degradation. The activation energy of xylan fractions degradation was found as 74.4 and 140.9 kJ mol⁻¹, respectively.     

LD-SPatt: large deviations statistics for patterns on Markov chains.

Statistics on Markov chains are widely used for the study of patterns in biological sequences. Statistics on these models can be done through several approaches. Central limit theorem (CLT) producing Gaussian approximations are one of the most popular ones. Unfortunately, in order to find a pattern of interest, these methods have to deal with tail distribution events where CLT is especially bad. In this paper, we propose a new approach based on the large deviations theory to assess pattern statistics. We first recall theoretical results for empiric mean (level 1) as well as empiric distribution (level 2) large deviations on Markov chains. Then, we present the applications of these results focusing on numerical issues. LD-SPatt is the name of GPL software implementing these algorithms. We compare this approach to several existing ones in terms of complexity and reliability and show that the large deviations are more reliable than the Gaussian approximations in absolute values as well as in terms of ranking and are at least as reliable as compound Poisson approximations. We then finally discuss some further possible improvements and applications of this new method.     

Estimating statistics of neuronal dynamics via Markov chains

We present an efficient computational method for estimating the mean and variance of interspike intervals defined by the timing of spikes in typical orbits of one-dimensional neuronal maps. This is equivalent to finding the mean and variance of return times of orbits to particular regions of phase space. Rather than computing estimates directly from time series, the system is modelled as a finite state Markov chain to extract stationary behaviour in the form of invariant measures and average absorption times. Ergodic-theoretic formulae are then applied to produce the estimates without the need to generate orbits directly. The approach may be applied to both deterministic and randomly forced systems. Received: 26 January 2000 / Accepted in revised form: 9 June 2000     

Cellulose as extracellular polysaccharide of hot spring sulfur-turf bacterial mat

The carbohydrate fraction of a hot spring sulfur-turf bacterial mat was shown to contain cellulose by the examination of neutral sugar composition, methylation analysis, and the identification of free oligosacchrides obtained from an acetolyzate of the desulfurized sulfur-turf mat. This suggested that the sulfur-oxidizing bacteria composing the sulfur-turf were producers of cellulose.     

Configurational entropy of native proteins.

Simulations of the residual configurational entropy of a protein in the native state suggest that it is nearly an order of magnitude larger than the entropy of denaturation. The implications of this result are discussed.     

Staining of O-specific polysaccharide chains of lipopolysaccharides with ruthenium red

S-form lipopolysaccharides (LPS) from Klebsiella strain LEN-1 (O3: K1-) and from Salmonella minnesota strain 1114 were positively stained with ruthenium red, whereas R-form LPS from Klebsiella strain LEN-111 (O3-: K1-) and Ra, Rb1, RcP+, Rd1P-, and Re LPS from the respective mutant strains of S. minnesota were not or only faintly stained by such treatment. From these results it was concluded that ruthenium red stains the O-specific polysaccharide chains of LPS. The appearance of stained preparations of S-form LPS suggested that the material responsible for this positive staining corresponded to the surface projections which were seen by the negative staining technique as attached to the ribbon-like structures and spherules of the LPS.     

Configurational variants of oncornavirus RNAs.

Heating oncornavirus RNAs at temperatures insufficient for complete denaturation results in forms migrating between the native form (vRNA) and the completely denatured form (vRNA) after gel electrophoresis. Intermediate forms from Rous sarcoma virus or murine leukemia virus were isolated after heating of vRNA's at 58 degrees C and sedimenting in sucrose gradients, and at least four intermediates could be identified in each case. Melting of feline virus (RD-114) RNA produced one major intermediate which required a comparatively high temperature to denature, and a second intermediate occurring in conditions of low ionic strength. Although the subunit model for oncornavirus RNA is not excluded by these data, we propose that vRNA, vRNA', and intermediates may be configurational variants of the same molecule, and a monomer model for oncornavirus RNA is presented.     

S-SPatt: simple statistics for patterns on Markov chains

SUMMARY: S-SPatt allows the counting of patterns occurrences in text files and, assuming these texts are generated from a random Markovian source, the computation of the P-value of a given observation using a simple binomial approximation.     

Pattern statistics on Markov chains and sensitivity to parameter estimation

Background:  

In order to compute pattern statistics in computational biology a Markov model is commonly used to take into account the sequence composition. Usually its parameter must be estimated. The aim of this paper is to determine how sensitive these statistics are to parameter estimation, and what are the consequences of this variability on pattern studies (finding the most over-represented words in a genome, the most significant common words to a set of sequences,...).