P53基因三周期性与密码子偏好性的相关性

为了进一步研究分析P53抑癌基因的性质,对P53基因的蛋白质编码区以及对应的mRNA的三周期性进行比较分析.通过同义密码子相对使用度和拟同义密码子相对使用度方法对其分别进行计算,分析了蛋白质编码区密码子的偏好性以及mRNA密码子的偏好性.结果表明:P53蛋白质编码区具有很强的三周期性,而对应的mRNA不具有三周期性;P53蛋白质编码区的密码子偏好G或C结尾的密码子程度强于对应的mRNA.说明P53基因密码子的偏好性与三周期性紧密相关,密码子的偏好程度影响着三周期性.进一步从生物角度诠释了P53蛋白质编码区和对应mRNA三周期性的异同.结合P53基因这一特性,有助于提高其基因识别的正确率,对P53基因的深入研究具有重要的意义.     

基于拟氨基酸编码方法的同义密码子的偏好性与结合强度的相关性研究

计算了基于拟氨基酸编码方法下的同义密码子的相对使用度,分析了78个人类基因（19967个密码子）中基于拟氨基酸编码方法下的同义密码子的偏好使用情况.石秀凡等的研究结果显示了人类基因中基于基因组基因编码方法下,对同义密码子的选择在所有密码子家族中仍都呈现明显一致的偏好.即偏好使用密码子-反密码子结合作用强的密码子,恰好是以 c结尾的密码子;且避免使用结合作用中度的密码子.依据结果和数据分析, 推测人类基因对密码子的选择除了受基因组结构中 isochore和基因签名的影响外,还和密码子-反密码子结合强度密切相 关键词： 拟氨基酸编码方法 同义密码子 偏好 人类基因     

Typicality vs. Probability in Trajectory-Based Formulations of Quantum Mechanics

Bohmian mechanics represents the universe as a set of paths with a probability measure defined on it. The way in which a mathematical model of this kind can explain the observed phenomena of the universe is examined in general. It is shown that the explanation does not make use of the full probability measure, but rather of a suitable set function deriving from it, which defines relative typicality between single-time cylinder sets. Such a set function can also be derived directly from the standard quantum formalism, without the need of an underlying probability measure. The key concept for this derivation is the quantum typicality rule, which can be considered as a generalization of the Born rule. The result is a new formulation of quantum mechanics, in which particles follow definite trajectories, but which is based only on the standard formalism of quantum mechanics.     

Entropy and Fractal Dimension Study of the TDP-43 Protein Low Complexity Domain Sequence in ALS Disease Severity and SARS-CoV-2 Gene Sequences in Virulence Variability

The low complexity domain (LCD) sequence has been defined in terms of entropy using a 12 amino acid sliding window along a protein sequence in the study of disease-related genes. The amyotrophic lateral sclerosis (ALS)-related TDP-43 protein sequence with intra-LCD structural information based on cryo-EM data was published recently. An application of entropy and Higuchi fractal dimension calculations was described using the Znf521 and HAR1 sequences. A computational analysis of the intra-LCD sequence entropy and Higuchi fractal dimension values at the amino acid level and at the ATCG nucleotide level were conducted without the sliding window requirement. The computational results were consistent in predicting the intermediate entropy/fractal dimension value produced when two subsequences at two different entropy/fractal dimension values were combined. The computational method without the application of a sliding-window was extended to an analysis of the recently reported virulent genes—Orf6, Nsp6, and Orf7a—in SARS-CoV-2. The relationship between the virulence functionality and entropy values was found to have correlation coefficients between 0.84 and 0.99, using a 5% uncertainty on the cell viability data. The analysis found that the most virulent Orf6 gene sequence had the lowest nucleotide entropy and the highest protein fractal dimension, in line with extreme value theory. The Orf6 codon usage bias in relation to vaccine design was discussed.     

Statistical and linguistic features of noncoding DNA: A heterogeneous «Complex system»

Summary We present evidence supporting the idea that the DNA sequence in genes containingnoncoding regions is correlated, and that the correlation is remarkably long range-indeed, base pairsthousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene; we utilize this fact to build aCoding Sequence Finder algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. We resolve the problem of the ?non-stationarity? feature of the sequence of base pairs (that the relative concentration of purines and pyrimidines changes in different regions of the mosaic-like chain) by describing a new algorithm calledDetrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33 301 coding and 29 453 non-coding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power law correlations (and the systematic variation of the scaling exponent α with evolution) which is based upon a generalization of the classic Lévy walk. Finally, we describe briefly some recent work showing that thenoncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the ?redundancy? of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in eukaryotes may display a smaller entropy and larger redundancy than coding regions for plants and invertebrates, further supporting the possibility that noncoding regions of DNA may carry biological information. Paper presented at the I International Conference on Scaling Concepts and Complex Fluids, Copanello, Italy, July 4–8, 1994.     

Thermodynamic characteristics of a biological organism: Information value of a gene and of a protein as a measure of the efficiency and as an index of selective pressure

Summary For the treatment of the information exchanged by the biological system and the external world, the concept of information amount is not sufficient because of their remoteness from equilibrium states. Further explanations are, in fact, necessary about the effects of the reception of the message,i.e. its information value that is then necessary to define for each case. We have, therefore, defined the information value of a gene and of a protein and analysed a sample of about hundred genes looking for some significative regularity in the frequency of usage of codons and amino acids allowing us to individualize the salient characteristics of a translated sequence of codons. We have found that the most used amino acids have, on the average, a low information value and, for each amino acid type, the most used codons have a lower information value. Moreover, we can say that the composition in amino acids or in codons of a sequence useful for the biological systems is such that more frequent mutations cause the smaller variation in the phenotype. All that shows that our definitions well describe the system of transmission and reception of the information value in a biological organism and that they can be considered as an index of its efficiency,i.e. of its ability to minimize the effects of the mutation of the genotype on the phenotype. To speed up publication, the authors of this paper have agreed to not receive the proofs for correction.     

The maximum entropy principle as a consequence of the principle of Laplace

The maximum entropy principle states that the probability distribution which best represents our information is the one which maximizes the entropy with the given evidence as constraints. We prove that this principle is implied from the Laplace principle of equiprobabilities applied to the setS of allN-term sequences of results which are compatible with the given evidence. We generalize to the information gain method of Kullback.     

Chaos game representation of functional protein sequences, and simulation and multifractal analysis of induced measures

Investigating the biological function of proteins is a key aspect of protein studies. Bioinformatic methods become important for studying the biological function of proteins. In this paper, we first give the chaos game representation (CGR) of randomly-linked functional protein sequences, then propose the use of the recurrent iterated function systems (RIFS) in fractal theory to simulate the measure based on their chaos game representations. This method helps to extract some features of functional protein sequences, and furthermore the biological functions of these proteins. Then multifractal analysis of the measures based on the CGRs of randomly-linked functional protein sequences are performed. We find that the CGRs have clear fractal patterns. The numerical results show that the RIFS can simulate the measure based on the CGR very well. The relative standard error and the estimated probability matrix in the RIFS do not depend on the order to link the functional protein sequences. The estimated probability matrices in the RIFS with different biological functions are evidently different. Hence the estimated probability matrices in the RIFS can be used to characterise the difference among linked functional protein sequences with different biological functions. From the values of the D_q curves, one sees that these functional protein sequences are not completely random. The D_q of all linked functional proteins studied are multifractal-like and sufficiently smooth for the C_q (analogous to specific heat) curves to be meaningful. Furthermore, the D_q curves of the measure \mu based on their CGRs for different orders to link the functional protein sequences are almost identical if q\geq 0. Finally, the C_q curves of all linked functional proteins resemble a classical phase transition at a critical point.     

Guessing probability distributions from small samples

We propose a new method for the calculation of the statistical properties, e.g., the entropy, of unknown generators of symbolic sequences. The probability distributionp(k) of the elementsk of a population can be approximated by the frequenciesf(k) of a sample provided the sample is long enough so that each elementk occurs many times. Our method yields an approximation if this precondition does not hold. For a givenf(k) we recalculate the Zipf-ordered probability distribution by optimization of the parameters of a guessed distribution. We demonstrate that our method yields reliable results.     

An inelastic threshold in electron - alkali cluster collisions

An analysis of integral cross sections for slow electron collisions with neutral sodium clusters and nanoparticles reveals that, in addition to an effective negative ion formation channel, there exists a strong inelastic threshold-type process which appears above a collision energy of 1-1.3 eV. We show that it can be plausibly associated with the onset of direct electron-induced cluster fragmentation. This result highlights the importance of understanding the dynamics of electron-vibrational energy transfer in nanoclusters, including the relative probability of direct vs. statistical energy transfer. Received 24 November 2000     

Coarse-grain reconstruction of genetic networks from expression levels

In the postgenome era many efforts have been dedicated to systematically elucidate the complex web of interacting genes and proteins. These efforts include experimental and computational methods. Microarray technology offers an opportunity for monitoring gene expression level at the genome scale. By recourse to information theory, this study proposes a mathematical approach to reconstruct gene regulatory networks at a coarse-grain level from high throughput gene expression data. The method provides the a posteriori probability that a given gene regulates positively, negatively or does not regulate each one of the network genes. This approach also allows the introduction of prior knowledge and the quantification of the information gain from experimental data used in the inference procedure. This information gain can be used to choose those genes that will be perturbed in subsequent experiments in order to refine our knowledge about the architecture of an underlying gene regulatory network. The performance of the proposed approach has been studied by in numero experiments. Our results suggest that the approach is suitable for focusing on size-limited problems, such as recovering a small subnetwork of interest by performing perturbation over selected genes.     

Tracing Life back to elements

The most ancient sequences, of proteins and nucleic acids, active in their early times, can be still recognized amongst modern sequences. That allows reconstruction of all steps of evolution of the triplet code, and of the earliest stages of evolution of genes and proteins. According to the reconstruction, the very first protein activities of living matter have been ATP binding and ATPase, responsible for energy supply. Respective modern proteins and genes are projected back to their earliest primordial forms. In particular, it is demonstrated that these two earliest activities have been encoded originally in the complementary strands of the same duplex gene.     

On the Distribution of Surface Extrema in Several One- and Two-dimensional Random Landscapes

We study here a standard next-nearest-neighbor (NNN) model of ballistic growth on one-and two-dimensional substrates focusing our analysis on the probability distribution function P(M,L) of the number M of maximal points (i.e., local “peaks”) of growing surfaces. Our analysis is based on two central results: (i) the proof (presented here) of the fact that uniform one-dimensional ballistic growth process in the steady state can be mapped onto “rise-and-descent” sequences in the ensemble of random permutation matrices; and (ii) the fact, established in Ref. [G. Oshanin and R. Voituriez, J. Phys. A: Math. Gen. 37:6221 (2004)], that different characteristics of “rise-and-descent” patterns in random permutations can be interpreted in terms of a certain continuous-space Hammersley-type process. For one-dimensional system we compute P(M,L) exactly and also present explicit results for the correlation function characterizing the enveloping surface. For surfaces grown on 2d substrates, we pursue similar approach considering the ensemble of permutation matrices with long-ranged correlations. Determining exactly the first three cumulants of the corresponding distribution function, we define it in the scaling limit using an expansion in the Edgeworth series, and show that it converges to a Gaussian function as L → ∞.     

Molecular evolution of toxin genes in Elapidae snakes

The venom of the sea krait, Laticauda semifasciata, consists primarily of two toxic proteins, phospholipase A₂ (PLA₂) and a three-finger-structure toxin. We have cloned both toxic protein genes, including the upstream region. PLA₂ genes contain three types of inserted sequences: an AG-rich region, a chicken repeat 1-like long interspersed nucleotide element sequence and an intron II 3′ side repeat sequence. The molecular divergence of L. semifasciata PLA₂ genes was defined on the basis of the inserted sequences and their sequence homology. The length of intron I in the three-finger-structure toxin genes differs from species to species. The alignment analysis of intron I of the three-finger-structure toxin genes revealed that the intron I sequence of the ancestral gene comprised ten genetic regions. A hypothetical evolutionary process for the three-finger-structure toxin genes has also been developed.     

Change in the order parameter symmetry in the vicinity of the surface of a superconductor with <Emphasis Type="Italic">s</Emphasis><Subscript>±</Subscript> pairing

The behavior of the order parameter and the local density of states near the impenetrable surface have been theoretically studied in a two-band superconductor in which the gapless state with s _± symmetry of the superconducting order parameter is realized. It has been shown that, over a wide range of the parameters, the spatial behavior of the order parameter on the surface is not reduced to a standard suppression. If the probability of the interband reflection on the surface is of the order of or higher than the probability of the intraband reflection, it can be energetically more favorable to change the symmetry of the superconducting state near the surface from s _± symmetry to common s symmetry. The region of existence of the surface s-superconductivity is very sensitive to relative values of the interband and intraband pairing potentials. It has also been shown that the self-consistent calculation (i.e., with allowance made for the dissimilarity of the near-surface order parameter from the bulk value) can lead to a qualitatively different behavior of the near-surface local density of states as compared to the results of the non-self-consistent calculation.     

X-ray fluorescence intensity distribution in circular specimens

Summary The relative X-ray fluorescence (XRF) intensities for annular source and various annular specimen are measured with a Ge-Li detection system and calculated by the Monte Carlo numerical techniques (MCNT).Kα X-ray intensities of annular specimens with different radii prepared from a pure-molybdenum foil are measured and it is seen that the measured values are in good agreement with the values calculated by MCNT. The variation of the fluorescence intensity due to the collimator radius is also studied. The differences between the MCNT and experimental results are discussed in terms of the possible sources of errors.     

Block persistence

We define a block persistence probability p _l (t) as the probability that the order parameter integrated on a block of linear size l has never changed sign since the initial time in a phase-ordering process at finite temperature T<T _c . We argue that in the scaling limit of large blocks, where z is the growth exponent (), is the global (magnetization) persistence exponent and f(x) decays with the local (single spin) exponent for large x. This scaling is demonstrated at zero temperature for the diffusion equation and the large-n model, and generically it can be used to determine easily from simulations of coarsening models. We also argue that and the scaling function do not depend on temperature, leading to a definition of at finite temperature, whereas the local persistence probability decays exponentially due to thermal fluctuations. These ideas are applied to the study of persistence for conserved models. We illustrate our discussions by extensive numerical results. We also comment on the relation between this method and an alternative definition of at finite temperature recently introduced by Derrida [Phys. Rev. E 55, 3705 (1997)]. Received: 25 February 1998 / Revised: 24 July 1998 / Accepted: 27 July 1998     

LETTER: Quantum Creation of BTZ Black Hole

The constrained instanton method is used to study quantum creation of a BTZ black hole. It is found that the relative creation probability is the exponential of the negative sum of the entropy associated with the outer and inner black hole horizons. The quantum creations of the 4- or higher dimensional versions of the BTZ black hole are also studied.