The fractal dimension as a measure for characterizing genetic variation of the human genome

Motivated by the characteristics of highly clustered single nucleotide polymorphism (SNP) across the human genome, we propose a set of chromosome-wise fractal dimensions as a measure for identifying an individual for human polymorphism. The fractal dimension quantifies the degree of clustered distribution of SNPs and represents parsimoniously the genetic variation in a chromosome. In this sense, the proposed scheme projects the SNP genotype data into a new space which is simpler and lower in dimension. As an illustrative example, we estimate the chromosome-wise fractal dimensions of SNPs that are extracted from the HapMap of Phase III data set. To determine the validity of the proposed measure, we apply principal component analysis (PCA) to the set of estimated fractal dimensions and demonstrate that the set more or less described the population structure of 11 global populations. We also use multidimensional scaling to relate the genetic distances based on PCA to the geographical distances between global populations. This shows that, similar to the SNP genotype data, the fractal dimensions also has a role in genetic distance in the population structure. In addition, we apply the proposed measure to a signature for the classification of global populations by developing a support vector machine model. The selected feature model predicts the global population with a balanced accuracy of about 77%. These results support that the fractal dimension is an efficient way to describe the genetic variation of global populations.     

A framework for the development of STR genotyping in domestic animal species: Characterization and population study of 12 canine X‐chromosome loci

This study reports the methodology used to search, select and characterize STR loci on the canine X chromosome using publicly available genome resources and following the current guidelines for human and non‐human forensic testing. After several rounds of selection, 12 X‐STR markers were optimized for simultaneous co‐amplification in a single PCR, and genetic profiles were determined in a sample of 103 unrelated dogs. Mendelian inheritance was verified and mutation rates were assessed using family groups. Alleles that varied in size were sequenced to create a standardized nomenclature proposal based on the number of repeats. All loci conformed to Hardy–Weinberg expectations. The resulting panel showed high forensic efficiency, presenting high values of power of discrimination (in males and females) and mean exclusion chance, both in trios involving female offspring and in duos composed of dam and male offspring. Its use may complement the information obtained by autosomal STR analysis and contribute to the resolution of complex cases of kinship in dogs. The presented methodology for the de novo construction of an STR multiplex may also provide a helpful framework for analogous work in other animal species. As an increasing number of reference genomes become available, convenient tools for individual identification and parentage testing based on STR loci selected from autosomes or sex chromosomes' sequences may be created following this strategy.     

Detection of heteroplasmy in individual mitochondrial particles

Mitochondrial DNA (mtDNA) mutations have been associated with disease and aging. Since each cell has thousands of mtDNA copies, clustered into nucleoids of five to ten mtDNA molecules each, determining the effects of a given mtDNA mutation and their connection with disease phenotype is not straightforward. It has been postulated that heteroplasmy (coexistence of mutated and wild-type DNA) follows simple probability rules dictated by the random distribution of mtDNA molecules at the nucleoid level. This model has been used to explain how mutation levels correlate with the onset of disease phenotype and loss of cellular function. Nonetheless, experimental evidence of heteroplasmy at the nucleoid level is scarce. Here, we report a new method to determine heteroplasmy of individual mitochondrial particles containing one or more nucleoids. The method uses capillary cytometry with laser-induced fluorescence detection to detect individual mitochondrial particles stained with PicoGreen, which makes it possible to quantify the mtDNA copy number of each particle. After detection, one or more particles are collected into polymerase chain reaction (PCR) wells and then subjected to real-time multiplexed PCR amplification. This PCR strategy is suitable to obtain the relative abundance of mutated and wild-type mtDNA. The results obtained here indicate that individual mitochondrial particles and nucleoids contained within these particles are not heteroplasmic. The results presented here suggest that current models of mtDNA segregation and distribution (i.e., heteroplasmic nucleoids) need further consideration.     

An analytical model of gene evolution with six mutation parameters: an application to archaeal circular codes

We develop here an analytical evolutionary model based on a trinucleotide mutation matrix 64 x 64 with six substitution parameters associated with the transitions and transversions in the three trinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4 x 4 and the trinucleotide mutation matrix 64 x 64 with three parameters. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to six substitution parameters. An application of this model allows an evolutionary study of the common circular code COM and the 15 archaeal circular codes X which have been recently identified in several archaeal genomes. The main property of a circular code is the retrieval of the reading frames in genes, both locally, i.e. anywhere in genes and in particular without a start codon, and automatically with a window of a few nucleotides. In genes, the circular code is superimposed on the traditional genetic one. Very unexpectedly, the evolutionary model demonstrates that the archaeal circular codes can derive from the common circular code subjected to random substitutions with particular values for six substitutions parameters. It has a strong correlation with the statistical observations of three archaeal codes in actual genes. Furthermore, the properties of these substitution rates allow proposal of an evolutionary classification of the 15 archaeal codes into three main classes according to this model. In almost all the cases, they agree with the actual degeneracy of the genetic code with substitutions more frequent in the third trinucleotide site and with transitions more frequent that transversions in any trinucleotide site.     

Predicting the melting point of human C-type lysozyme mutants

A complete understanding of the relationships between protein structure and stability remains an open problem. Much of our insight comes from laborious experimental analyses that perturb structure via directed mutation. The glycolytic enzyme lysozyme is among the most well characterized proteins under this paradigm, due to its abundance and ease of manipulation. To speed up such analyses, efficient computational models that can accurately predict mutation effects are needed. We employ a minimal Distance Constraint Model (mDCM) to predict the stability of a series of lysozyme mutants (specifically, human wild-type C-type lysozyme and 14 point mutations). With three phenomenological parameters that characterize microscopic interactions, the mDCM parameters are determined by obtaining the least squares error between predicted and experimental heat capacity curves. The mutants are chemically and structurally diverse, but have been experimentally characterized under nearly identical thermodynamic conditions (pH, ionic strength, etc.). The parameters found from best fits to heat capacity curves for one or more lysozyme structures are subsequently used to predict the heat capacity on the remaining. We simulate a typical experimental situation, where prediction of relative stabilities in an untested mutated structure is based on known results as they accumulate. From the statistical significance of these simulations, we establish that the mDCM is a viable predictor for relative stability of protein mutants. Remarkably, using parameters from any single fitting yields an average percent error of 4.3%. Across the dataset, the mDCM reproduces experimental trends sufficiently well (R = 0.64) to be of practical value to experimentalists when making decisions about which mutations to invest time and funds for characterization.     

人类Y染色体回文序列中的重复序列与碱基关联

利用信息论和统计学的方法并结合生物学的特征研究人类Y染色体回文序列的互信息、“n字”熵、条件熵,定量分析了回文序列的长程关联和短程关联,发现其中既存在长程关联也存在短程关联,并且它们主要是由序列中的重复序列引起的．研究表明重复序列含量越高碱基之间的关联越强．     

On the calculation of a limit for infinite systems from data on finite systems

We propose a mathematical model for the calculation of physical or chemical properties of infinite polymers, based on data for structurally closely related finite molecules. The modelling is phenomenological but permits a physical interpretation of the parameters involved in the equations. Received: 11 June 1996 / Accepted: 5 June 1997     

Thermal decomposition study on nickel(ii) complexes of 1,2-(diimino-4’-antipyrinyl)ethane with varying counter ions

The phenomenological, kinetic and mechanistic aspects of the nitrate, chloride, bromide and iodide complexes of nickel(II) with1,2-(diimino-4’-antipyrinyl)ethane (GA) have been studied by TG and DTG techniques. The kinetic parameters like activation energy, pre-exponential factor and entropy of activation were computed. The rate controlling process in all stages of decomposition is random nucleation with one nucleus on each particle (Mampel model).     

Phototactic orientation mechanism in the ciliate Fabrea salina, as inferred from numerical simulations

The marine ciliate Fabrea salina shows a clear positive phototaxis, but the mechanism by which a single cell is able to detect the direction of light and orient its swimming accordingly is still unknown. A simple model of phototaxis is that of a biased random walk, where the bias due to light can affect one or more of the parameters that characterize a random walk, i.e., the mean speed, the frequency distribution of the angles of directional changes and the frequency of directional changes. Since experimental evidence has shown no effect of light on the mean speed of Fabrea salina, we have excluded models depending on this parameter. We have, therefore, investigated the phototactic orientation of Fabrea salina by computer simulation of two simple models, the first where light affects the frequency distribution of the angles of directional changes (model M1) and the second where the light bias modifies the frequency of directional changes (model M2). Simulated M1 cells directly orient their swimming towards the direction of light, regardless of their current swimming orientation; simulated M2 cells, on the contrary, are unable to actively orient their motion, but remain locked along the light direction once they find it by chance. The simulations show that these two orientation models lead to different macroscopic behaviours of the simulated cell populations. By comparing the results of the simulations with the experimental ones, we have found that the phototactic behaviour of real cells is more similar to that of the M2 model.     

Influence of the packing heterogeneity on the performance of liquid chromatography supports

We report on a series of plate height and flow resistance data obtained via computational fluid dynamics simulations in a simplified two-dimensional (2D) mimic of real packed bed and monolithic columns. By varying the external porosity (0.4 < epsilon < 0.8) and the degree of packing randomness, a good qualitative insight in the relationship between the packing porosity and heterogeneity and the general chromatographic performance parameters is obtained, unbiased by any differences in phase retention factor k', mobile phase diffusivity or viscosity or intra-skeleton porosity. The results provide a quantitative support for the use of domain size reduced plate heights as a means to compare the performance of chromatographic beds with a different porosity, as it was found that packings with a similar degree of packing heterogeneity yield very similar domain size reduced h(min)-values, nearly completely independent of the porosity. The study also clearly shows that the presence of preferential flow paths (inevitably accompanied by the presence of more clustered regions) leads to a decrease of the flow resistance, but also leads to a strong increase of the band broadening if supports with the same porosity epsilon and the same radial width are compared. For the presently considered 2D system, the flow resistance reduction is too small to overcome the corresponding strong increase in band broadening, such that the presence of preferential flow paths always leads to an overall increase of the separation impedance.     

Chromosome segregation in Escherichia coli division: a free energy-driven string model

Although the mechanisms of eukaryotic chromosome segregation and cell division have been elucidated to a certain extent, those for bacteria remain largely unknown. Here we present a computational string model for simulating the dynamics of Escherichia coli chromosome segregation. A novel thermal-average force field accounting for stretching, bending, volume exclusion, friction and random fluctuation is introduced. A Langevin equation is used to simulate the chromosome structural changes. The mechanism of chromosome segregation is thereby postulated as a result of free energy-driven structural optimization with replication introduced chromosomal mass increase. Predictions of the model agree well with observations of fluorescence labeled chromosome loci movement in living cells. The results demonstrate the possibility of a mechanism of chromosome segregation that does not involve cytoskeletal guidance or advanced apparatus in an E. coli cell. The model also shows that DNA condensation of locally compacted domains is a requirement for successful chromosome segregation. Simulations also imply that the shape-determining protein MreB may play a role in the segregation via modification of the membrane pressure.     

Nucleic acid affinity of clustered-charge anion exchange adsorbents: effects of ionic strength and ligand density

In previous work we demonstrated the improved protein-binding capacity and selectivity of ion-exchange adsorbents displaying a "clustered" rather than random, distribution of surface charges. For example, anion-exchange adsorbents displaying 5 mM of positive charge in the form of 1 mM penta-argininamide show much higher affinity and capacity for alpha-lactalbumin than do adsorbents displaying the same 5 mM total charge in the form of single dispersed argininamide charges. We also found that clustered adsorbents selectively favor proteins with inherent charge clustering. In the present work, "clustered" penta-argininamide adsorbents showed DNA binding capacity comparable to that of conventional dispersed adsorbents with 10-100-fold higher ligand density. We also observed that at moderate ionic strength the DNA affinity of all adsorbents tested increased with salt while RNA affinity decreased, so that selectivity for DNA over RNA was enhanced as salt concentration increased.     

Torsional interaction in 2-haloethanols: infrared data,ab initio results and treatment of a two-dimensional model

The splittings of the hydroxyl torsional absorption bands observed in the gas phase IR spectra of 2-haloethanols, XCH₂-CH₂-OH are reported for X = Cl, Br, I. The satellite absorptions, assigned to excited states of the skeletal torsion, appear on the low-frequency side of the fundamental, possibly because of weakening of the internal hydrogen bond. The torsional potential surface is investigated by calculations using a two-dimensional model based on the known experimental data for the compound with X = Cl, and by ab initio calculations for the haloethanols with X = F and X = Cl. Models based on the assumption of pure torsion and simple dipole-dipole or central force interaction terms failed to reproduce the observed data for 2-chloroethanol, but good agreement was obtained after local modification of the potential surface interpolated from the ab initio calculations. The results may help devise the phenomenological theory of potential energy needed for quantitative study of the internal hydrogen bond.     

In silico explanation for the causalities of deleterious RNF213 SNPs in Moyamoya disease and insulin resistance

Moyamoya disease (MMD), a cerebrovascular disorder caused by the RNF213 gene, is a cerebrovascular, neurological disorder leading to ischemic strokes. Our previous work suggested that RNF213 might be involved in the pro-inflammatory TNFα-mediated insulin-resistance pathway in adipocytes. Insulin resistance can lead to cerebrovascular diseases and ischemic strokes. Though p. R4810 K has been reported as the founder mutation for Asian population with this disease, there are several mutations continuously reported in clinical diagnosis. We are interested to know whether these mutations can modulate insulin resistance. Also, we are intended to understand the causalities of RNF213 and its associated mutations in MMD. For this, we have adopted a computational approach to characterize RNF213 and its naturally occurring SNPs. Clinically reported SNPs and the predicted SNPs were analyzed for their pathogenicity and effect on the biological function of the protein. To increase accuracy, this was performed through three different analysis software (PROVEAN, SIFT, and SNAP2). The mutations that were found to be deleterious in all the three platforms were further analyzed for their effect on the thermal stability of the protein through I-mutant and iStable. It was found that R4810 K and other mutations decreased the thermodynamic stability of the protein. Loss of function of RNF213 was suggested in some reports. Contrary to this, some studies reported a gain of function state due to the R4810K mutation. To understand this we have measured the ligand-binding ability of this mutated protein through COFACTOR and COACH. An increase in ligand binding is always related to the functional stability of a protein. We have observed that the R4810K mutation might increase the iron-binding efficiency of the amino acid residues. This increase in binding was further validated by analyzing the binding efficiencies by docking. Since RNF213 was previously reported as a target for Protein Tyrosine Phosphatase 1B (PTP1B), we have also analyzed whether PTP1B-binding positions are susceptible to mutations. We have re-analyzed our earlier report on the differential expression pattern of RNF213 in cancer and obese samples. We have provided a detailed analysis of the most deleterious SNPs related to RNF213. Also, we provide a prediction for the loss of function and gain of function attributes of RNF213 and its predicted causalities in MMD and insulin resistance.     

Landau theory-based estimates for viscosity coefficients of uniaxial and biaxial nematic liquid crystals

Using Landau theory, it is shown that eight phenomenological parameters are needed to describe and distinguish the twelve viscosity coefficients of a biaxial nematic phase, or the five viscosity coefficients of a uniaxial nematic phase. The dependence of the coefficients on the macroscopic uniaxial and biaxial order parameters is established. Since these order parameters are determined by the anisotropies of the dielectric constant, we show that it should be possible to determine values for all eight of the phenomenological parameters of the theory from measurements of the temperature dependence of the five viscosities of a uniaxial phase.     

超离子导体CaF2中的Ca2+亚晶格和F-亚晶格

CaF_2在熔化以前为超离子导体相。一些实验和理论的研究表明,在超离子导体相中,Ca~(2+)仍维持原有的面心立方骨架,而F~-则在Ca~(2+)骨架中运动。早期的分子动力学模拟结果表明Ca~(2+)的均方根位移仅约0.3A,而F~-的扩散系数可达2.6×10~(-5)cm·s~(-1),已是熔盐扩散系数量级。近年来的中子散射实验表明在扩散离子和近邻离子间存在着某种动力学相关。为解释这些事实,新近Gillan的分子动力学模拟表明扩散离子伴随着F~-亚晶格变形,而Kaneko和Ueda的分子动力学模拟则表明扩散离子伴随着近邻离子在同一运动方向的相关运动。进一步的研究尚待进行。八十年代初,Nelson等人提出了描述晶体、非晶和液态中键取向的键球谐函数方法。     

Ion induced lamellar-lamellar phase transition in charged surfactant systems

We propose a model for the liquid-liquid (L(alpha)-->L(alpha(') )) phase transition observed in osmotic pressure measurements of certain charged lamellae-forming amphiphiles. The model free energy combines mean-field electrostatic and phenomenological nonelectrostatic interactions, while the number of dissociated counterions is treated as a variable degree of freedom that is determined self-consistently. The model, therefore, joins two well-known theories: the Poisson-Boltzmann theory for ionic solutions between charged lamellae and the Langmuir-Frumkin-Davies adsorption isotherm modified to account for charged adsorbing species. Minimizing the appropriate free energy for each interlamellar spacing, we find the ionic density profiles and the resulting osmotic pressure. While in the simple Poisson-Boltzmann theory the osmotic pressure isotherms are always smooth, we observe a discontinuous liquid-liquid phase transition when the Poisson-Boltzmann theory is self-consistently augmented by the Langmuir-Frumkin-Davies adsorption. This phase transition depends on the area per amphiphilic head group, as well as on nonelectrostatic interactions of the counterions with the lamellae and interactions between counterion-bound and counterion-dissociated surfactants. Coupling the lateral phase transition in the bilayer plane with electrostatic interactions in the bulk, our results offer a qualitative explanation for the existence of the L(alpha)-->L(alpha(') ) phase transition of didodecyldimethylammonium bromide (DDABr), but the transition's apparent absence for the chloride and the iodide homologs. More quantitative comparisons with experiment require better understanding of the microscopic basis of the phenomenological model parameters.     

Periodic sequence distribution of product ion abundances in electron capture dissociation of amphipathic peptides and proteins

The rules for product ion formation in electron capture dissociation (ECD) mass spectrometry of peptides and proteins remain unclear. Random backbone cleavage probability and the nonspecific nature of ECD toward amino acid sequence have been reported, contrary to preferential channels of fragmentation in slow heating-based tandem mass spectrometry. Here we demonstrate that for amphipathic peptides and proteins, modulation of ECD product ion abundance (PIA) along the sequence is pronounced. Moreover, because of the specific primary (and presumably secondary) structure of amphipathic peptides, PIA in ECD demonstrates a clear and reproducible periodic sequence distribution. On the one hand, the period of ECD PIA corresponds to periodic distribution of spatially separated hydrophobic and hydrophilic domains within the peptide primary sequence. On the other hand, the same period correlates with secondary structure units, such as α-helical turns, known for solution-phase structure. Based on a number of examples, we formulate a set of characteristic features for ECD of amphipathic peptides and proteins: (1) periodic distribution of PIA is observed and is reproducible in a wide range of ECD parameters and on different experimental platforms; (2) local maxima of PIA are not necessarily located near the charged site; (3) ion activation before ECD not only extends product ion sequence coverage but also preserves ion yield modulation; (4) the most efficient cleavage (e.g. global maximum of ECD PIA distribution) can be remote from the charged site; (5) the number and location of PIA maxima correlate with amino acid hydrophobicity maxima generally to within a single amino acid displacement; and (6) preferential cleavage sites follow a selected hydrogen spine in an α-helical peptide segment. Presently proposed novel insights into ECD behavior are important for advancing understanding of the ECD mechanism, particularly the role of peptide sequence on PIA. An improved ECD model could facilitate protein sequencing and improve identification of unknown proteins in proteomics technologies. In structural biology, the periodic/preferential product ion yield in ECD of α-helical structures potentially opens the way toward de novo site-specific secondary structure determination of peptides and proteins in the gas phase and its correlation with solution-phase structure.     

Stuffer‐free multiplex ligation‐dependent probe amplification based on conformation‐sensitive capillary electrophoresis: A novel technology for robust multiplex determination of copy number variation

Developing diagnostic tools based on the application of known disease/phenotype‐associated copy number variations (CNVs) requires the capacity to measure CNVs in a multiplex format with sufficient reliability and methodological simplicity. In this study, we developed a reliable and user‐friendly multiplex CNV detection method, termed stuffer‐free MLPA‐CE‐SSCP, that combines a variation of multiplex ligation‐dependent probe amplification (MLPA) with CE‐SSCP. In this variation, MLPA probes were designed without the conventionally required stuffer sequences. To separate the similar‐sized stuffer‐free MLPA products, we adopted CE‐SSCP rather than length‐dependent conventional CE analysis. An examination of the genomic DNA from five cell lines known to vary in X‐chromosome copy number (1–5) revealed that copy number determinations using stuffer‐free MLPA‐CE‐SSCP were more accurate than those of conventional MLPA, and the CV of the measured copy numbers was significantly lower. Applying our system to measure the CNVs on autosomes between two HapMap individuals, we found that all peaks for CNV targets showed the expected copy number changes. Taken together, our results indicate that this new strategy can overcome the limitations of conventional MLPA, which are mainly related to long probe length and difficulties of probe preparation.     

Linear regression model of DNA sequences and its application

We constructed six new models to analyze the DNA sequences. First, we regarded a DNA primary sequence as a random process in t and gave three ways to define nucleotides' random distribution functions. We extracted some parameters from the linear model and analyzed the changes of the nucleotides' distributions. In order to facilitate the comparison of DNA sequences, we proposed two ways to measure their similarities. Finally, we compared the six models by analyzing the similarities of the DNA primary sequences presented in Table 1 and selected the optimal one.