Toward a molecular taxonomy

Summary The concepts of a super information source and ensemble averaging are used to estimate the amount of information stored in protein andt-RNA sequences. Specifically applied to cytochrome c and hemoglobins, information measures analogous to those found to be highly significant for DNA pair frequency data (D ₂ vs.R) by Gatlin (1968) prove to be extremely highly correlated with organism complexity. Super source stability and the possible taxonomic utility of the extraordinary clusterings obtained are discussed. A restriction on the construction of ancestral sequences and a possible handle on homology are also detailed.     

Redox thermodynamics of lactoperoxidase and eosinophil peroxidase

Eosinophil peroxidase (EPO) and lactoperoxidase (LPO) are important constituents of the innate immune system of mammals. These heme enzymes belong to the peroxidase-cyclooxygenase superfamily and catalyze the oxidation of thiocyanate, bromide and nitrite to hypothiocyanate, hypobromous acid and nitrogen dioxide that are toxic for invading pathogens. In order to gain a better understanding of the observed differences in substrate specificity and oxidation capacity in relation to heme and protein structure, a comprehensive spectro-electrochemical investigation was performed. The reduction potential (E°′) of the Fe(III)/Fe(II) couple of EPO and LPO was determined to be −126 mV and −176 mV, respectively (25 °C, pH 7.0). Variable temperature experiments show that EPO and LPO feature different reduction thermodynamics. In particular, reduction of ferric EPO is enthalpically and entropically disfavored, whereas in LPO the entropic term, which selectively stabilizes the oxidized form, prevails on the enthalpic term that favors reduction of Fe(III). The data are discussed with respect to the architecture of the heme cavity and the substrate channel. Comparison with published data for myeloperoxidase demonstrates the effect of heme to protein linkages and heme distortion on the redox chemistry of mammalian peroxidases and in consequence on the enzymatic properties of these physiologically important oxidoreductases.     

A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility

Detecting, characterizing, and interpreting gene-gene interactions or epistasis in studies of human disease susceptibility is both a mathematical and a computational challenge. To address this problem, we have previously developed a multifactor dimensionality reduction (MDR) method for collapsing high-dimensional genetic data into a single dimension (i.e. constructive induction) thus permitting interactions to be detected in relatively small sample sizes. In this paper, we describe a comprehensive and flexible framework for detecting and interpreting gene-gene interactions that utilizes advances in information theory for selecting interesting single-nucleotide polymorphisms (SNPs), MDR for constructive induction, machine learning methods for classification, and finally graphical models for interpretation. We illustrate the usefulness of this strategy using artificial datasets simulated from several different two-locus and three-locus epistasis models. We show that the accuracy, sensitivity, specificity, and precision of a na?ve Bayes classifier are significantly improved when SNPs are selected based on their information gain (i.e. class entropy removed) and reduced to a single attribute using MDR. We then apply this strategy to detecting, characterizing, and interpreting epistatic models in a genetic study (n = 500) of atrial fibrillation and show that both classification and model interpretation are significantly improved.     

Chromosome aberrations in solid tumors have a stochastic nature

An important question nowadays is whether chromosome aberrations are random events or arise from an internal deterministic mechanism, which leads to the delicate task of quantifying the degree of randomness. For this purpose, we have defined several Shannon information functions to evaluate disorder inside a tumor and between tumors of the same kind. We have considered 79 different kinds of solid tumors with 30 or more karyotypes retrieved from the Mitelman Database of Chromosome Aberrations in Cancer. The Kaplan–Meier cumulative survival was also obtained for each solid tumor type in order to correlate data with tumor malignance. The results here show that aberration spread is specific for each tumor type, with high degree of diversity for those tumor types with worst survival indices. Those tumor types with preferential variants (e.g. high proportion of a given karyotype) have shown better survival statistics, indicating that aberration recurrence is a good prognosis. Indeed, global spread of both numerical and structural abnormalities demonstrates the stochastic nature of chromosome aberrations by setting a signature of randomness associated to the production of disorder. These results also indicate that tumor malignancy correlates not only with karyotypic diversity taken from different tumor types but also taken from single tumors. Therefore, by quantifying aberration spread, we could confront diverse models and verify which of them points to the most likely outcome. Our results suggest that the generating process of chromosome aberrations is neither deterministic nor totally random, but produces variations that are distributed between these two boundaries.     

Conductometric and voltammetric studies on the bis(triphenyl phosphine) ruthenium(II) complex, cis-[RuCl2(L)(PPh3)2], where L: 2-(2′-pyridyl)quinoxaline

Conductometric investigation on the bis(triphenyl phosphine) ruthenium(II) complex, cis-[RuCl₂(L)(PPh₃)₂] (A) (where PPh₃: triphenyl phosphine and L: 2-(2′-pyridyl)quinoxaline, C₁₃N₃H₉), in dimethylsulfoxide (DMSO) was performed at temperatures ranging from 25 to 50 °C. In addition, cyclic voltammograms of A were recorded on platinum working electrode in dichloromethane (DCM) and dimethylsulfoxide (DMSO) using n-tetrabutylammonium hexafluorophosphate (NBu₄PF₆) as supporting electrolyte at 25 °C. The molar conductivities (Λ) demonstrate that A behaves as uni-univalent electrolyte in DMSO over the whole temperature range. This behavior can be explained in terms of the replacement upon dissolution of chlorine and PPh₃ ligands by DMSO molecules, and consequently, the formation of the ion-pair [RuCl(L)(PPh₃)(DMSO)₂]Cl [B⁺Cl⁻] which is dissociated in some extent. The Λ values were analyzed by means of the Lee-Wheaton conductivity equation in order to estimate the limiting molar conductivities (Λ^o) and the ion-pair association constants (K_A) of [B⁺Cl⁻]. The limiting ion conductivities for the B⁺ ion were evaluated using n-tetrabutylammonium chloride (NBu₄Cl) as “reference electrolyte”. The thermodynamic functions related with the ion association, such as Gibbs free energy , enthalpy , and entropy , were evaluated as well. The mobility of B⁺ was found to increase linearly with rising temperature and the consequent decrease of the viscosity (η) of DMSO. The K_A and values indicate that the association of [B⁺Cl⁻] increases to some extent with the rise of the temperature followed by the decrease of the dielectric constant (ε) of DMSO. The voltammetric experiments indicated that the couple Ru^3+/2+ is reversible and diffusion controlled in DCM and completely irreversible in DMSO.     

Modelling the potential distribution of the Bridled Skink,Trachylepis vittata (Olivier, 1804), in the Middle East

The Bridled Skink, Trachylepis vittata, is widespread in the Middle East and eastern coastal Mediterranean areas and inhabits foothills throughout the arid regions of the Middle East. With the help of more than 146 distribution records from Iran, Turkey, Syria, Israel, Jordan, Cyprus, Egypt, Lebanon and Libya, we analysed the influence of climate on the distribution pattern. According to the Maximum Entropy model, the most influential factors that determined T. vittata distribution are: precipitation of coldest quarter, Normalised Difference Vegetation Index (NDVI) and precipitation in the warmest quarter. The model suggests that the western slopes of the Zagros Mountains in Iran and slopes in the southern regions of Anatolia around the Mediterranean Sea are suitable for this species. The species is associated with areas with intermediate NDVI (150-180) (a measure of primary productivity), high winter precipitation (>300?mm) and dry summer (<50mm). The association with rainy winter limits the presence of the species in lowlands. The Zagros Mountains may act as a biogeographic barrier that limits the species dispersal eastward, because of their scarce precipitation.     

基于广义线性模型和最大熵模型的黑龙江省林火空间分布模拟

林火分布模型是在较大区域上描述林火空间分布的强有力工具,并可以确定影响林火分布的控制因子.本研究基于黑龙江省1996-2006年的历史火烧记录数据,分别采用广义线性模型和最大熵模型分析了地形、人类活动和土地覆被类型等环境控制因子对黑龙江省林火空间分布的影响,并比较了模型预测精度、评价环境变量重要性及预测火点概率分布图等.结果表明:两个模型的预测精度达中等水平,而最大熵模型的预测精度要略高于广义线性模型.总体而言,与人类活动相关的变量是林火分布模型最佳的环境变量,地形变量次之.尽管两个模型在预测精度和环境变量重要性方面都有很大的相似性,但最大熵模型产生的火点概率图空间格局与广义线性模型产生的明显不同.本研究说明,为了更加精确地确定森林火灾发生的热点地区,应该采用不同模型进行比较,或者有选择性地进行组合以产生综合的预测结果,从而为森林防火工作提供更加合理高效的建议.     

Stereotyped and non-stereotyped features of the temporal patterning of singing sessions in the ovenbird Seiurus auricapillus

Temporal patterning of recorded singing sessions of 26 different male ovenbirds Seiurus auricapillus (Fringillidae: Parulini) was analyzed computationally, in order to test whether differences among songs are potentially informative or merely reflect performance errors. Repeated songs within a singing session by a given male showed relatively little inter-individual variation in the duration of the song or in the number of units composing it, although these features varied substantially among individuals. On the other hand, within a session of singing by an individual male, the most variable and potentially informative aspect of temporal patterning was the relative placement of the peak amplitude within the song. These results support the hypothesis that diversity in the vocalization sessions of oscine passerines can be produced by other means than the use of a varied song repertoire, even in a species like the ovenbird that uses just one song type. Because variation among song was focused on a single feature, performance errors are an unlikely explanation, suggesting that the temporal patterning of singing sessions may play an informative role, such as the minimization of habituation on the part of receivers.     

The significance of sex

Sexual and asexual modes of proliferation are associated with advantages and disadvantages, yet a profound percept that would account for both ways of reproduction is missing. On the basis of the 2nd law of thermodynamics we find that both sexual and asexual reproduction can be regarded as a means to consume free energy in least time. Parthenogenesis is a fast way to consume a rich repository of free energy, e.g., an ample stock of food with a large number of individuals, whereas sexual reproduction is a fast way to consume diverse and dispersed resources with a large variety of individuals. Most organisms have adapted to their surroundings accordingly and some organisms switch from one mode of reproduction to the other depending on the amount and dispersion of free-energy sources. We conclude that the least-time free energy consumption in respective surroundings, as the general criterion of natural selection, determines also sexual and asexual modes of reproduction.