Crossover Position Research Articles

Spin crossover in an elastic chain of exchange clusters beyond mean field approximation

Exact analysis of spin crossover in infinite elastic chain of two-spin exchange clusters was performed theoretically beyond mean-field approximation. Statistical mechanics of the system was exactly calculated by means of the transfer matrix technique. A possibility of spin-Peierls-like magneto-structural transition in a one-dimensional chain was shown as a result of interrelation of spin and elastic subsystems of the chain. The importance of the boundary conditions for spin crossover to occur was shown. The smoothness of spin crossover depends on the parameters of chain elasticity and the crossover position on the temperature scale is defined by the dependence of exchange integral on the cluster deformation. The proposed model qualitatively describes the main scenario of spin crossover effect in the chain polymer heterospin complex of copper(ii) hexafluoroacetylacetonate with methyl pyrazol-substituted nitronyl nitroxide containing two-spin exchange clusters.

Two types of meiotic crossovers coexist in maize.

We apply modeling approaches to investigate the distribution of late recombination nodules in maize (Zea mays). Such nodules indicate crossover positions along the synaptonemal complex. High-quality nodule data were analyzed using two different interference models: the "statistical" gamma model and the "mechanical" beam film model. For each chromosome, we exclude at a 98% significance level the hypothesis that a single pathway underlies the formation of all crossovers, pointing to the coexistence of two types of crossing-over in maize, as was previously demonstrated in other organisms. We estimate the proportion of crossovers coming from the noninterfering pathway to range from 6 to 23% depending on the chromosome, with a cell average of approximately 15%. The mean number of noninterfering crossovers per chromosome is significantly correlated with the length of the synaptonemal complex. We also quantify the intensity of interference. Finally, we develop inference tools that allow one to tackle, without much loss of power, complex crossover interference models such as the beam film. The lack of a likelihood function in such models had prevented their use for parameter estimation. This advance will allow more realistic mechanisms of crossover formation to be modeled in the future.

Visualization of Shared Genomic Regions and Meiotic Recombination in High-Density SNP Data

BackgroundA fundamental goal of single nucleotide polymorphism (SNP) genotyping is to determine the sharing of alleles between individuals across genomic loci. Such analyses have diverse applications in defining the relatedness of individuals (including unexpected relationships in nominally unrelated individuals, or consanguinity within pedigrees), analyzing meiotic crossovers, and identifying a broad range of chromosomal anomalies such as hemizygous deletions and uniparental disomy, and analyzing population structure.Principal FindingsWe present SNPduo, a command-line and web accessible tool for analyzing and visualizing the relatedness of any two individuals using identity by state. Using identity by state does not require prior knowledge of allele frequencies or pedigree information, and is more computationally tractable and is less affected by population stratification than calculating identity by descent probabilities. The web implementation visualizes shared genomic regions, and generates UCSC viewable tracks. The command-line version requires pedigree information for compatibility with existing software and determining specified relationships even though pedigrees are not required for IBS calculation, generates no visual output, is written in portable C++, and is well-suited to analyzing large datasets. We demonstrate how the SNPduo web tool identifies meiotic crossover positions in siblings, and confirm our findings by visualizing meiotic recombination in synthetic three-generation pedigrees. We applied SNPduo to 210 nominally unrelated Phase I / II HapMap samples and, consistent with previous findings, identified six undeclared pairs of related individuals. We further analyzed identity by state in 2,883 individuals from multiplex families with autism and identified a series of anomalies including related parents, an individual with mosaic loss of chromosome 18, an individual with maternal heterodisomy of chromosome 16, and unexplained replicate samples.ConclusionsSNPduo provides the ability to explore and visualize SNP data to characterize the relatedness between individuals. It is compatible with, but distinct from, other established analysis software such as PLINK, and performs favorably in benchmarking studies for the analyses of genetic relatedness.

Homologous genetic recombination in the yellow head complex of nidoviruses infecting Penaeus monodon shrimp.

Yellow head virus (YHV) is a highly virulent pathogen of Penaeus monodon shrimp. It is one of six known genotypes in the yellow head complex of nidoviruses which also includes mildly pathogenic gill-associated virus (GAV, genotype 2) and four other genotypes (genotypes 3–6) that have been detected only in healthy shrimp. In this study, comparative phylogenetic analyses conducted on replicase- (ORF1b) and glycoprotein- (ORF3) gene amplicons identified 10 putative natural recombinants amongst 28 viruses representing all six genotypes from across the Indo-Pacific region. The ∼ 4.6 kb genomic region spanning the two amplicons was sequenced for three putative recombinant viruses from Vietnam (genotype 3/5), the Philippines (genotype 5/2) and Indonesia (genotype 3/2). SimPlot analysis using these and representative parental virus sequences confirmed that each was a recombinant genotype and identified a recombination hotspot in a region just upstream of the ORF1b C-terminus. Maximum-likelihood breakpoint analysis predicted identical crossover positions in the Vietnamese and Indonesian recombinants, and a crossover position 12 nt upstream in the Philippine recombinant. Homologous genetic recombination in the same genome region was also demonstrated in recombinants generated experimentally in shrimp co-infected with YHV and GAV. The high frequency with which natural recombinants were identified indicates that genetic exchange amongst genotypes is occurring commonly in Asia and playing a significant role in expanding the genetic diversity in the yellow head complex. This is the first evidence of genetic recombination in viruses infecting crustaceans and has significant implications for the pathogenesis of infection and diagnosis of these newly emerging invertebrate pathogens.

Distribution of MLH1 foci and inter-focal distances in spermatocytes of infertile men

In a previous study on severely infertile men, we observed alterations in the number of meiotic crossovers; however, it is unknown if these men also show alterations in the position of crossovers. Spermatocytes from 15 men (5 control men and 10 infertile men) were immunostained to observe the synaptonemal complex and MLH1 foci, which localize to sites of crossovers. Fluorescent in situ hybridization was performed to identify chromosomes 13, 18 and 21. Chromosome bivalents were separated into those with single and double crossover configurations, and the distribution of MLH1 foci along each chromosome arm was calculated. The inter-focal distances on chromosome 13 and 18 bivalents with double crossovers were also calculated. Four of the infertile men displayed an altered MLH1 distribution on at least one of the chromosome arms studied. Of these four men, two displayed reduced rates of meiotic recombination. Only one man displayed an abnormality in crossover interference, with inter-focal distances reduced on chromosome 13 bivalents. Recombination defects in infertile men may include alterations in the number of crossovers, the position of crossovers or both. Alterations in both the number and position of crossovers may increase the risk of aneuploid sperm in infertile men.

Mars and Mercury rotation variations from altimetry crossover data: Feasibility study

Knowledge of the interior structure of terrestrial planets can be achieved by studying the changes of their rotation and orientation in time. We simulate the use of time deviations of altimetry crossover positions to infer information on the nutations of Mars and on the librations of Mercury. The analysis is based on the least squares estimator and uses simulated crossover points. The simulations demonstrate that the use of crossover data improves the estimates of the observed libration amplitude and obliquity of Mercury and allows detecting the nutations of Mars.

Lens theory of non-paraxial rays for electron gun characterization

It has been attempted to characterize the cathode rays inside electron guns by utilizing the optical concepts familiar in the paraxial lens theory. We have proposed the Canonical Mapping Transformation (CMT) theory to obtain the gun optical parameters. The method is based on the Lagrange differential invariant theorem known in analytical mechanics. It has been found that major electron source properties, such as the crossover position, crossover size, and the angular current intensity, are all deducible from the four CMT optical parameters ( zco , f , Csg , and Ccg ), which in turn can be estimated by calculating the normal electron rays, whose emanation vectors on the cathode surface are in the surface normal direction. Since the normal electron rays can in many cases be regarded as paraxial, a scheme has been proposed to calculate the relevant optical parameters by a modification of the conventional paraxial trajectory calculation. It is shown that the normal electron ray of the CMT theory corresponds to (1, 0) principal trajectory in the paraxial method, g(z) . The conventional perturbation characteristic function integral method can be employed for the evaluation of the CMT aberration coefficients. Two realistic electron gun models (a single-crystal LaB6 cathode gun and a Schottky emitter source) were analyzed by use of the CMT optical parameters. Both the ray tracing of the normal electrons and the modified paraxial calculation method were employed for the analyses. It has been found that the guns with quite different nature in the source properties can well be described by the CMT optical parameters proposed. The paraxial calculations have been shown to produce accurate enough results and the authors hope their use would help electron optical column designers both in reducing the work load and in having clear physical images of their gun characteristics. © 2008 Elsevier B.V. All rights

The mismatch repair protein MLH1 marks a subset of strongly interfering crossovers in tomato.

In most eukaryotes, the prospective chromosomal positions of meiotic crossovers are marked during meiotic prophase by protein complexes called late recombination nodules (LNs). In tomato (Solanum lycopersicum), a cytological recombination map has been constructed based on LN positions. We demonstrate that the mismatch repair protein MLH1 occurs in LNs. We determined the positions of MLH1 foci along the 12 tomato chromosome pairs (bivalents) during meiotic prophase and compared the map of MLH1 focus positions with that of LN positions. On all 12 bivalents, the number of MLH1 foci was approximately 70% of the number of LNs. Bivalents with zero MLH1 foci were rare, which argues against random failure of detecting MLH1 in the LNs. We inferred that there are two types of LNs, MLH1-positive and MLH1-negative LNs, and that each bivalent gets an obligate MLH1-positive LN. The two LN types are differently distributed along the bivalents. Furthermore, cytological interference among MLH1 foci was much stronger than interference among LNs, implying that MLH1 marks the positions of a subset of strongly interfering crossovers. Based on the distances between MLH1 foci or LNs, we propose that MLH1-positive and MLH1-negative LNs stem from the same population of weakly interfering precursors.

Determination of geoid over South China Sea and Philippine Sea from multi-satellite altimetry data

A new computational procedure for derivation of marine geoid on a 2.5′ × 2.5′ grid in a non-tidal system over the South China Sea and the Philippine Sea from multi-satellite altimeter sea surface heights is discussed. Single-and dual-satellite crossovers were performed, and components of deflections of the vertical were determined at the crossover positions using Sandwell’s computational theory, and gridded onto a 2.5′ × 2.5′ resolution grid by employing the Shepard’s interpolation procedure. 2.5′ × 2.5′ grid of EGM96-derived components of deflections of the vertical and geoid heights were then used as reference global geopotential model quantities in a remove-restore procedure to implement the Molodensky-like formula via 1D-FFT technique to predict the geoid heights over the South China Sea and the Philippine Sea from the gridded altimeter-derived components of deflections of the vertical. Statistical comparisons between the altimeter-and the EGM96-derived geoid heights showed that there was a root-mean-square agreement of ±0.35 m between them in a region of less tectonically active geological structures. However, over areas of tectonically active structures such as the Philippine trench, differences of about −19.9 m were obtained.

Structure-guided SCHEMA recombination of distantly related β-lactamases

We constructed a library of beta-lactamases by recombining three naturally occurring homologs (TEM-1, PSE-4, SED-1) that share 34-42% sequence identity. Most chimeras created by recombining such distantly related proteins are unfolded due to unfavorable side-chain interactions that destabilize the folded structure. To enhance the fraction of properly folded chimeras, we designed the library using SCHEMA, a structure-guided approach to choosing the least disruptive crossover locations. Recombination at seven selected crossover positions generated 6561 chimeric sequences that differ from their closest parent at an average of 66 positions. Of 553 unique characterized chimeras, 111 (20%) retained beta-lactamase activity; the library contains hundreds more novel beta-lactamases. The functional chimeras share as little as 70% sequence identity with any known sequence and are characterized by low SCHEMA disruption (E) compared to the average nonfunctional chimera. Furthermore, many nonfunctional chimeras with low E are readily rescued by low error-rate random mutagenesis or by the introduction of a known stabilizing mutation (TEM-1 M182T). These results show that structure-guided recombination effectively generates a family of diverse, folded proteins even when the parents exhibit only 34% sequence identity. Furthermore, the fraction of sequences that encode folded and functional proteins can be enhanced by utilizing previously stabilized parental sequences.

Human Imprinted Chromosomal Regions Are Historical Hot-Spots of Recombination

Human recombination rates vary along the chromosomes as well as between the two sexes. There is growing evidence that epigenetic factors may have an important influence on recombination rates, as well as on crossover position. Using both public database analysis and wet-bench approaches, we revisited the relationship between increased rates of meiotic recombination and genome imprinting. We constructed metric linkage disequilibrium (LD) maps for all human chromosomal regions known to contain one or more imprinted genes. We show that imprinted regions contain significantly more LD units (LDU) and have significantly more haplotype blocks of smaller sizes than flanking nonimprinted regions. There is also an excess of hot-spots of recombination at imprinted regions, and this is likely to do with the presence of imprinted genes, per se. These findings indicate that imprinted chromosomal regions are historical “hot-spots” of recombination. We also demonstrate, by direct segregation analysis at the 11p15.5 imprinted region, that there is remarkable agreement between sites of meiotic recombination and steps in LD maps. Although the increase in LDU/Megabase at imprinted regions is not associated with any significant enrichment for any particular sequence class, major sequence determinants of recombination rates seem to differ between imprinted and control regions. Interestingly, fine-mapping of recombination events within the most male meiosis–specific recombination hot-spot of Chromosome 11p15.5 indicates that many events may occur within or directly adjacent to regions that are differentially methylated in somatic cells. Taken together, these findings support the involvement of a combination of specific DNA sequences and epigenetic factors as major determinants of hot-spots of recombination at imprinted chromosomal regions.

Electronic properties of interstitial iron and iron-boron pairs determined by means of advanced lifetime spectroscopy

As dissolved iron is one of the most common lifetime-killing contaminants in silicon, its coexisting defect configurations, interstitial iron (Fei) and iron-boron pairs (FeB), are investigated on an intentionally iron-contaminated silicon sample by means of temperature-dependent lifetime spectroscopy (TDLS) and injection-dependent lifetime spectroscopy (IDLS). In good agreement with the literature, the study identifies the known Fei donor level at Et−EV=(0.394±0.005)eV and determines its symmetry factor as k=σn∕σp=51±5, which is an order of magnitude lower than expected from the literature. Using the well-confirmed k factor, the poorly confirmed electron-capture cross section is redetermined as σn=(3.6±0.4)×10−15cm2 at 300K. In addition, the observed exponential σ(T) dependence identifies the multiphonon emission mechanism as the dominant capture mechanism for electrons with an activation energy E∞=0.024eV. Concerning the defect related to the iron-boron pair, the study unambiguously identifies the deep FeB acceptor level as the dominant FeB recombination center. While the known average value EC−Et=(0.26±0.03)eV for the energy level is well confirmed, the symmetry factor is determined as k=0.45, which represents an intermediate value among the scattered results from the literature. Additional spectroscopic information from the defect transformation allows both capture cross sections of the FeB defect to be determined (σn=2.5×10−15cm2 and σp=5.5×10−15cm2). Being suggested as a fingerprint of iron in the literature, the crossover position of the Fei- and FeB-dominated IDLS curves (at 300K) is experimentally proved to be doping dependent which is accurately predicted on the basis of the extracted set of Fei and FeB defect parameters. An additional fingerprint of iron is found by the qualitative change of the TDLS curve upon illumination and its S-like shape under dark conditions, which represents a robust criterion for unambiguous identification of iron in silicon. As the most sensitive technique to detect and determine an iron contamination in silicon heavily relies on the Fei and FeB defect parameters, the spectroscopic results are of special practical importance.

Estimating the Charged Particle Beam Parameters in View of the Space Charge Forces

A method for estimating the main parameters of a paraxial axially symmetric charged particle beam taking into account the contribution of space charge forces is described. This method is based on the general equation for a beam envelope. The data characterizing its convergence and stability for experimental errors are presented. The errors in determining the crossover position and the beam radius in the crossover do not exceed 15%, and the error in estimating the emittance depends on the relationship between the emittance and space charge forces. This method has been used to estimate the parameters of an actual electron gun with an energy of 50 keV and a current of 0.64 A. The results obtained are in good agreement with the design values. The technique described may be generalized to the case in which axial symmetry is absent.

Design of combinatorial protein libraries of optimal size

In this article we introduce a computational procedure, OPTCOMB (Optimal Pattern of Tiling for COMBinatorial library design), for designing protein hybrid libraries that optimally balance library size with quality. The proposed procedure is directly applicable to oligonucleotide ligation-based protocols such as GeneReassembly, DHR, SISDC, and many more. Given a set of parental sequences and the size ranges of the parental sequence fragments, OPTCOMB determines the optimal junction points (i.e., crossover positions) and the fragment contributing parental sequences at each one of the junction points. By rationally selecting the junction points and the contributing parental sequences, the number of clashes (i.e., unfavorable interactions) in the library is systematically minimized with the aim of improving the overall library quality. Using OPTCOMB, hybrid libraries containing fragments from three different dihydrofolate reductase sequences (Escherichia coli, Bacillus subtilis, and Lactobacillus casei) are computationally designed. Notably, we find that there exists an optimal library size when both the number of clashes between the fragments composing the library and the average number of clashes per hybrid in the library are minimized. Results reveal that the best library designs typically involve complex tiling patterns of parental segments of unequal size hard to infer without relying on computational means.

Crossover interference

Crossover interference

Inter-sex variation in synaptonemal complex lengths largely determine the different recombination rates in male and female germ cells

Meiotic chromosomes in human oocytes are packaged differently than in spermatocytes at the pachytene stage of meiosis I, when crossing-over takes place. Thus the meiosis-specific pairing structure, the synaptonemal complex (SC), is considerably longer in oocytes in comparison to spermatocytes. The aim of the present study was to examine the influence of this length factor on meiotic recombination in male and female human germ cells. The positions of crossovers were identified by the DNA mismatch repair protein MLH1. Spermatocytes have approximately 50 crossovers per cell in comparison to more than 70 in oocytes. Analyses of inter-crossover distances (and presumptively crossover interference) along SCs suggested that while there might be inter-individual variation, there was no consistent difference between sexes. Thus the higher rate of recombination in human oocytes is not a consequence of more closely spaced crossovers along the SCs. The rate of recombination per unit length of SC is higher in spermatocytes than oocytes. However, when the so-called obligate chiasma is excluded from the analysis, then the rates of recombination per unit length of SC are essentially identical in the two sexes. Our analyses indicate that the inter-sex difference in recombination is largely a consequence of the difference in meiotic chromosome architecture in the two sexes. We propose that SC length per se, and therefore the size of the physical platform for crossing-over (and not the DNA content) is the principal factor determining the difference in rate of recombination in male and female germ cells. A preliminary investigation of SC loop size by fluorescence in situ hybridization (FISH) indicated loops may be shorter in oocytes than in spermatocytes.

FamClash: a method for ranking the activity of engineered enzymes.

This article introduces the computational procedure FamClash for analyzing incompatibilities in engineered protein hybrids by using protein family sequence data. All pairs of residue positions in the sequence alignment that conserve the property triplet of charge, volume, and hydrophobicity are first identified, and significant deviations are denoted as residue-residue clashes. This approach moves beyond earlier efforts aimed at solely classifying hybrids as functional or nonfunctional by correlating the rank ordering of these hybrids based on their activity levels. Experimental testing of this approach was performed in parallel to assess the predictive ability of FamClash. As a model system, single-crossover ITCHY (incremental truncation for the creation of hybrid enzymes) libraries were prepared from the Escherichia coli and Bacillus subtilis dihydrofolate reductases, and the activities of functional hybrids were determined. Comparisons of the predicted clash map as a function of crossover position revealed good agreement with activity data, reproducing the observed V shape and matching the location of a local peak in activity.

Diagnosis and dynamics in a simple low energy medium current electron beam channel

We present a simple experimental setup and an associated method enabling both the non-destructive diagnosis and the calculation of the beam evolution in a low energy medium current electron beam channel, where the space-charge and emittance effects are comparable. The diagnosis makes use of an axially symmetric magnetic lens while a second lens is added to increase the flexibility in the beam processing. The paper emphasizes the three steps involved in the method: the evaluation of the lenses' magnetic field by numerical simulation, the beam diagnosis, and the computation of the beam envelope. The calculation of the magnetic field is based on the finite element method. Subsequently, the beam parameters at the electron source exit – emittance and cross-over radius and position – are found with the modified three gradient method. Finally, the beam dynamics are modeled with the K–V equation adapted for the particular case of axial symmetry. The results obtained in this paper can be used to optimize technological processes, such as welding, hardening, cladding, and surface alloying.

Using Incremental Truncation to Create Libraries of Hybrid Enzymes

This chapter describes the use of incremental truncation to create libraries of hybrid enzymes. The creation of genetic diversity through mutagenesis and selection is essential for organisms to adapt to the changing environments. In the laboratory, these processes can be enhanced and accelerated to evolve proteins for specific functions. The most commonly used method of protein engineering is DNA shuffling and the numerous variations of this technique. Incremental truncation is successfully used to convert monomeric enzymes into heterodimers and to create libraries of hybrid enzymes. These methods are generally referred to as incremental truncation for the creation of hybrid enzymes (ITCHY). To start the ITCHY method, the plasmid is linearized with restriction enzyme R1and truncated incrementally using Exo III. It is found that for each ITCHY library, checking crossover distribution is also important. Usually, 20 isolates are sequenced from each library and the crossover positions are plotted to check for adequate distribution. It is suggested that libraries can become biased from insufficient or excessive Exo III digestion and need to be reconstructed.

Measuring anti-correlations in the nordic electricity spot market by wavelets

We consider the Nordic electricity spot market from mid-1992 to the end of year 2000. This market is found to be well approximated by an anti-persistent self-affine (mean-reverting) walk. It is characterized by a Hurst exponent of H≃0.41 over three orders of magnitude in time ranging from days to years. We argue that in order to see such a good scaling behavior, and to locate cross-overs, it is crucial that an analyzing technique is used that decouples scales. This is in our case achieved by utilizing a (multi-scale) wavelet approach. The shortcomings of methods that do not decouple scales are illustrated by applying, to the same data set, the classic R/ S- and Fourier techniques, for which scaling regimes and/or positions of cross-overs are hard to define.