On the lattice ground state of densely packed hard ellipses.

Among lattice configurations of densely packed hard ellipses, Monte Carlo simulations are used to identify the so-called parallel and diagonal lattices as the two favorable states. The free energies of these two states are computed for several system sizes employing the Einstein crystal method. An accurate calculation of the free energy difference between the two states reveals the parallel lattice as the state with the lowest free energy. The origin of the entropic difference between the two states is further elucidated by assessing the roles of the translational and rotational degrees of freedom.

Liquid-gas critical point of a two-dimensional system of hard ellipses with attractive wells.

In an effort to illuminate the general principles governing the critical behavior of model fluids, we investigate in this study how the shape and the (attractive) interaction range of the molecule affect the gas-liquid equilibrium and the critical behavior of the system. A combination of Monte Carlo simulations and analytical theory is employed to compute critical properties, i.e., temperature and density, of a system of hard-core ellipses with an attractive square-well potential in two-dimensional space. The critical temperature is found to decrease monotonically as the asphericity of the molecule is increased. This trend can be successfully explained in terms of the strength of the effective attraction acting between molecules measured, for instance, by the second virial coefficient. The critical density shows a complex dependence on both the range of attraction and the asphericity of the molecule. We find that the properties of particle clusters formed in near-critical states reproduce some of the most important features of the critical density, including multiple minima and maxima. It is shown that a model based on the extent of the overlap between attractive shells surrounding the ellipses captures the variation of the size of the clusters. Based on the obtained results, we discuss implications of varying the shape of the attraction potential for critical density.

Direct Correlation Function of a Crystalline Solid.

Direct correlation functions (DCFs), linked to the second functional derivative of the free energy with respect to the one-particle density, play a fundamental role in a statistical mechanics description of matter. This holds, in particular, for the ordered phases: DCFs contain information about the local structure including defects and encode the thermodynamic properties of crystalline solids; they open a route to the elastic constants beyond low temperature expansions. Via a demanding numerical approach, we have explicitly calculated for the first time the DCF of a solid: based on the fundamental measure concept, we provide results for the DCF of a hard sphere crystal. We demonstrate that this function differs at coexistence significantly from its liquid counterpart-both in shape as well as in its order of magnitude-because it is dominated by vacancies. We provide evidence that the traditional use of liquid DCFs in functional Taylor expansions of the free energy is conceptually wrong and show that the emergent elastic constants are in good agreement with simulation-based results.

Continuum theory for cluster morphologies of soft colloids.

We introduce a continuum description of the thermodynamics of colloids with a core-corona architecture. In the case of thick coronas, their overlap can be treated approximately by replacing the exact one-particle density distribution by a suitably shaped step profile, which provides a convenient way of modeling the spherical, columnar, lamellar, and inverted cluster morphologies predicted by numerical simulations and the more involved theories. We use the model to study monodisperse particles with the hard-core/square-shoulder pair interaction as the simplest representatives of the core-corona class. We derive approximate analytical expressions for the enthalpies of the cluster morphologies which offer a clear insight into the mechanisms at work, and we calculate the lattice spacing and the cluster size for all morphologies of the phase sequence as well as the phase-transition pressures. By comparing the results with the exact crystalline minimum-enthalpy configurations, we show that the accuracy of the theory increases with shoulder width. We discuss possible extensions of the theory that could account for the finite-temperature effects.

Assembling a puzzle of dispersed retrotransposable sequences in the genome of chickpea (Cicer arietinum L.).

Several repetitive elements are known to be present in the genome of chickpea (Cicer arietinum L.) including satellite DNA and En/Spm transposons as well as two dispersed, highly repetitive elements, CaRep1 and CaRep2. PCR was used to prove that CaRep1, CaRep2, and previously isolated CaRep3 of C. arietinum represent different segments of a highly repetitive Ty3-gypsy-like retrotransposon (Metaviridae) designated CaRep that makes up large parts of the intercalary heterochromatin. The full sequence of this element including the LTRs and untranslated internal regions was isolated by selective amplification. The restriction pattern of CaRep was different within the annual species of the genus Cicer, suggesting its rearrangement during the evolution of the genus during the last 100 000 years. In addition to CaRep, another LTR and a non-LTR retrotransposon family were isolated, and their restriction patterns and physical localization in the chickpea genome were characterized. The LINE-like element CaLin is only of comparatively low abundance and reveals a considerable heterogeneity. The Ty1-copia-like element (Pseudoviridae) CaTy is located in the distal parts of the intercalary heterochromatin and adjacent euchromatic regions, but it is absent from the centromeric regions. These results together with earlier findings allow to depict the distribution of retroelements on chickpea chromosomes, which extensively resembles the retroelement landscape of the genome of the model legume Medicago truncatula Gaertn.

Simulating pesticide transport from a sloped tropical soil to an adjacent stream.

Preferential flow from stream banks is an important component of pesticide transport in the mountainous areas of northern Thailand. Models can help evaluate and interpret field data and help identify the most important transport processes. We developed a simple model to simulate the loss of pesticides from a sloped litchi (Litchi chinensis Sonn.) orchard to an adjacent stream. The water regime was modeled with a two-domain reservoir model, which accounts for rapid preferential flow simultaneously with slow flow processes in the soil matrix. Preferential flow is triggered when the topsoil matrix is saturated or the infiltration capacity exceeded. In addition, close to matrix saturation, rainfall events induce water release to the fractures and lead to desorption of pesticides from fracture walls and outflow to the stream. Pesticides undergo first order degradation and equilibrium sorption to soil matrix and fracture walls. The model was able to reproduce the dynamics of the discharge reasonably well (model efficiency [EF] = 0.56). The cumulative pesticide mass (EF = 0.91) and the pesticide concentration in the stream were slightly underestimated, but the deviation from measurement data is acceptable. Shape and timing of the simulated concentration peaks occurred in the same pattern as observed data. While the effect of surface runoff and preferential interflow on pesticide mass transport could not be absolutely clarified, according to our simulations, most concentration peaks in the stream are caused by preferential interflow pointing to the important role of this flow path in the hilly areas of northern Thailand.

Genetic diversity and phylogenetic relationships in Vigna Savi germplasm revealed by DNA amplification fingerprinting.

The pantropical genus Vigna (Leguminosae) comprises 7 cultivated species that are adapted to a wide range of extreme agroclimatic conditions. Few data are available on the relationships among these cultivated species or on their importance as sources of resistance against biotic and abiotic stresses. Therefore, we optimized DNA amplification fingerprinting (DAF) to estimate the genetic diversity within, and genetic relationships among, a representative core collection of cowpea, as compared with 16 accessions representing cultivars from 6 Vigna species. A set of 26 primers was selected from 262 tested random primers and used for the characterization of 85 Vigna accessions (6 V. angularis, 4 each of V. mungo and V. radiata, 2 V. umbellata, 1 V. aconitifolia, and 68 V. unguiculata), with Phaseolus vulgaris subsp. vulgaris as outgroup. A total of 212 polymorphic bands were used for maximum parsimony analysis. Our results clearly distinguished Brazilian from African V. unguiculata genotypes. At the species level, V. angularis was the most related and V. radiata the most divergent species relative to V. unguiculata. DAF markers were also informative at the intraspecific level, detecting a large diversity between cowpea cultivars. The implications of the presented results for cowpea breeding programs are discussed.

Micro-trench experiments on interflow and lateral pesticide transport in a sloped soil in northern Thailand.

During recent decades, a change in land use in the mountainous regions of Northern Thailand has been accompanied by an increased input of agrochemicals. We identified lateral water flow and pesticide transport pathways and mechanisms in a Hapludult on a sloped litchi orchard in Northern Thailand. During two rainy seasons, two micro-trench experiments were performed at the plot scale (2 by 3 m). The first experiment was performed at the footslope of the orchard; the second was performed at a midslope position. Two salt tracers (bromide and chloride) and two pesticides {methomyl [S-methyl-N-(methylcarbamoyloxy)thioacetimidate] and chlorothalonil (2,4,5,6-Tetrachlor-1,3-benzdicarbonitril)} were applied in stripes parallel to the slope 150 and 300 cm away from the trench. At the trench, soil water was collected by wick samplers. Tensiometers and time-domain reflectometry probes were installed. At the end of the experiment, soil samples were taken and analyzed for residual concentrations of tracers and pesticides. Lateral subsurface flow of water occurred exclusively along preferential flow paths and was mainly observed at 0- to 30- and 60- to 90-cm depth. Lateral transport of pesticides was negligible, but both pesticides were found beneath the application area at 90 cm depth. Therefore, they may pose a groundwater contamination risk. The amount of wick flow and the location of interflow were mainly a function of rain amount and antecedent soil water suction. During dry periods, water flow was restricted to the topsoil. After heavy rain events and wet periods, interflow was mainly observed in the subsoil. The cumulative rain amount between samplings necessary to induce interflow was 20 mm. At the footslope, the interflow was seven times higher, and the network of water-bearing pores increased compared with the midslope position.

Quantitative trait loci governing carotenoid concentration and weight in seeds of chickpea (Cicer arietinum L.).

Chickpea is a staple protein source in many Asian and Middle Eastern countries. The seeds contain carotenoids such as beta-carotene, cryptoxanthin, lutein and zeaxanthin in amounts above the engineered beta-carotene-containing "golden rice" level. Thus, breeding for high carotenoid concentration in seeds is of nutritional, socio-economic, and economic importance. To study the genetics governing seed carotenoids in chickpea, we studied the relationship between seed weight and concentrations of beta-carotene and lutein by means of high-performance liquid chromatography in segregating progeny from a cross between an Israeli cultivar and wild Cicer reticulatum Ladiz. Seeds of the cross progeny varied with respect to their carotenoid concentration (heritability estimates ranged from 0.5 to 0.9), and a negative genetic correlation was found between mean seed weight and carotenoid concentration in the F(3). To determine the loci responsible for the genetic variation observed, the population was genotyped using 91 sequence tagged microsatellite site markers and two CytP450 markers to generate a genetic map consisting of nine linkage groups and a total length of 344.6 cM. Using quantitative data collected for beta-carotene and lutein concentration and seed weight of the seeds of the F(2) population, we were able to identify quantitative trait loci (QTLs) by interval mapping. At a LOD score of 2, four QTLs for beta-carotene concentration, a single QTL for lutein concentration and three QTLs for seed weight were detected. The results of this investigation may assist in improving the nutritional quality of chickpea.

Ionic microgels as model systems for colloids with an ultrasoft electrosteric repulsion: structure and thermodynamics.

We present a theoretical analysis of the structural properties and phase behavior of spherical, loosely cross-linked ionic microgels that possess a low monomer concentration. The analysis is based on the recently derived effective interaction potential between such particles [A. R. Denton, Phys. Rev. E 67, 011804 (2003)]. By employing standard tools from the theory of the liquid state, we quantitatively analyze the pair correlations in the fluid and find anomalous behavior above the overlap concentration, similar to the cases of star-branched neutral and charged polymers. We also employ an evolutionary algorithm in order to predict the crystalline phases of the system without any a priori assumptions regarding their symmetry class. A very rich phase diagram is obtained, featuring two reentrant melting transitions and a number of unusual crystal structures. At high densities, both the Hansen-Verlet freezing criterion [J.-P. Hansen and L. Verlet, Phys. Rev. 184, 151 (1969)] and the Lindemann melting criterion [F. A. Lindemann, Phys. Z. 11, 609 (1910)] lose their validity. The topology of the phase diagram is altered when the steric interactions between the polymer segments become strong enough, in which case the lower-density reentrant melting disappears and the region of stability of the fluid is split into two disconnected domains, separated by intervening fcc and bcc regions.

Phase behavior of ionic microgels.

We employ effective interaction potentials between spherical polyelectrolyte microgels in order to investigate theoretically the structure, thermodynamics, and phase behavior of ionic microgel solutions. Combining a genetic algorithm with accurate free energy calculations we are able to perform an unrestricted search of candidate crystal structures. Hexagonal, body-centered orthogonal, and trigonal crystals are found to be stable at high concentrations and charges of the microgels, accompanied by reentrant melting behavior and fluid-fcc-bcc transitions below the overlap concentration.

Molecular mapping of Fusarium oxysporum f. sp. ciceris race 3 resistance gene in chickpea.

Sequence-tagged microsatellite site (STMS) and sequence-tagged site (STS) markers linked closely to Fusarium oxysporum f. sp. ciceris race 3 resistance gene in chickpea were identified, and linkage between three wilt resistance genes was elucidated. The resistance to race 3 in chickpea germplasm accession WR-315 was inherited as a single gene, designated foc-3, in 100 F(7) recombinant inbred lines derived from the cross of WR-315 (resistant) x C-104 (susceptible). The foc-3 gene was mapped 0.6 cM from STMS markers TA96 and TA27 and STS marker CS27A. Another STMS marker, TA194, at 14.3 cM, flanked the gene on the other side. Linkage between foc-3 and two other chickpea wilt resistance genes, foc-1 (syn. h(1)) and foc-4, was established. foc-3 was mapped 9.8 cM from foc-1 and 8.7 cM from foc-4, whereas foc-1 and foc-4 are closely linked at 1.1 cM. The identification of closely linked markers to resistance genes will facilitate marker-assisted selection for introgression of the race 3 resistance gene to susceptible chickpea lines.

Theoretical description of phase coexistence in model C60.

We have investigated the phase diagram of a pair interaction model of C60 fullerene [L. A. Girifalco, J. Phys. Chem. 96, 858 (1992)], in the framework provided by two integral equation theories of the liquid state, namely, the modified hypernetted chain (MHNC) implemented under a global thermodynamic consistency constraint, and the self-consistent Ornstein-Zernike approximation (SCOZA), and by a perturbation theory (PT) with various degrees of refinement, for the free energy of the solid phase. We present an extended assessment of such theories as set against a recent Monte Carlo study of the same model [D. Costa, G. Pellicane, C. Caccamo, and M. C. Abramo, J. Chem. Phys. 118, 304 (2003)]. We have compared the theoretical predictions with the corresponding simulation results for several thermodynamic properties such as the free energy, the pressure, and the internal energy. Then we have determined the phase diagram of the model, by using either the SCOZA, the MHNC, or the PT predictions for one of the coexisting phases, and the simulation data for the other phase, in order to separately ascertain the accuracy of each theory. It turns out that the overall appearance of the phase portrait is reproduced fairly well by all theories, with remarkable accuracy as for the melting line and the solid-vapor equilibrium. All theories show a more or less pronounced discrepancy with the simulated fluid-solid coexistence pressure, above the triple point. The MHNC and SCOZA results for the liquid-vapor coexistence, as well as for the corresponding critical points, are quite accurate; the SCOZA tends to underestimate the density corresponding to the freezing line. All results are discussed in terms of the basic assumptions underlying each theory. We have then selected the MHNC for the fluid and the first-order PT for the solid phase, as the most accurate tools to investigate the phase behavior of the model in terms of purely theoretical approaches. It emerges that the use of different procedures to characterize the fluid and the solid phases provides a semiquantitative reproduction of the thermodynamic properties of the C60 model at issue. The overall results appear as a robust benchmark for further theoretical investigations on higher order C(n>60) fullerenes, as well as on other fullerene-related materials, whose description can be based on a modelization similar to that adopted in this work.

Mapping of gene-specific markers on the genetic map of chickpea (Cicer arietinum L.).

With the exception of the fact that it is made up of eight different chromosomes, the physical organization of the 738-Mb genome of the important legume crop chickpea (Cicer arietinum L.) is unknown. In an attempt to increase our knowledge of the basic structure of this genome, we determined the map positions of a series of genes involved in plant defence responses (DR) by genetic linkage analysis. Exploiting the sequence data available in GenBank, we selected genes known to be induced in chickpea and other plants by pathogen attack. Gene-specific primers were designed based on conserved regions, and used to detect the corresponding gene sequences in a segregating population derived from an interspecific cross between Cicer arietinum and C. reticulatum. Forty-seven gene-specific markers were integrated into an existing map based on STMS, AFLP, DAF and other anonymous markers. The potential of this approach is discussed.

Molecular markers closely linked to fusarium resistance genes in chickpea show significant alignments to pathogenesis-related genes located on Arabidopsis chromosomes 1 and 5.

A population of 131 recombinant inbred lines from a wide cross between chickpea ( Cicer arietinum L., resistant parent) and Cicer reticulatum (susceptible parent) segregating for the closely linked resistances against Fusarium oxysporum f.sp. ciceri races 4 and 5 was used to develop DNA amplification fingerprinting markers linked to both resistance loci. Bulked segregant analysis revealed 19 new markers on linkage group 2 of the genetic map on which the resistance genes are located. Closest linkage (2.0 cM) was observed between marker R-2609-1 and the race 4 resistance locus. Seven other markers flanked this locus in a range from 4.1 to 9.0 cM. These are the most closely linked markers available for this locus up to date. The sequences of the linked markers were highly similar to genes encoding proteins involved in plant pathogen response, such as a PR-5 thaumatin-like protein and an important regulator of the phytoalexin pathway, anthranilate N-hydroxycinnamoyl-benzoyltransferase. Others showed significant alignments to genes encoding housekeeping enzymes such as the MutS2 DNA-mismatch repair protein. In the Arabidopsis genome, similar genes are located on short segments of chromosome 1 and 5, respectively, suggesting synteny between the fusarium resistance gene cluster of chickpea and the corresponding regions in the Arabidopsis genome. Three marker sequences were similar to retrotransposon-derived and/or satellite DNA sequences. The markers developed here provide a starting point for physical mapping and map-based cloning of the fusarium resistance genes and exploration of synteny in this highly interesting region of the chickpea genome.

Resistance gene analogues of chickpea ( Cicer arietinum L.): isolation, genetic mapping and association with a Fusarium resistance gene cluster.

Resistance gene analogues (RGAs) of Cicer were isolated by different PCR approaches and mapped in an inter-specific cross segregating for fusarium wilt by RFLP and CAPS analysis. Initially, two pairs of degenerate primers targeting sequences encoded at nucleotide-binding sites (NBS), which are conserved in plant disease resistance genes such as RPS2, L6 and N, were selected for amplification. Cloning and sequence analysis of amplified products from C. arietinum DNA revealed eight different RGAs. Additionally, five RGAs were identified after characterisation of the presumptive RGA alleles from C. reticulatum. Therefore, a total of 13 different RGAs were isolated from Cicer and classified through pair-wise comparison into nine distinct classes with sequence similarities below a 68% amino acid identity threshold. Sequence comparison of seven RGA alleles of C. arietinum and C. reticulatum revealed polymorphisms in four RGAs with identical numbers of synonymous and non-synonymous substitutions. An NlaIII site, unique in the RGA-A allele of C. arietinum, was exploited for CAPS analysis. Genomic organisation and map position of the NBS-LRR candidate resistance genes was probed by RFLP analysis. Both single-copy as well as multi-copy sequence families were present for the selected RGAs, which represented eight different classes. Five RGAs were mapped in an inter-specific population segregating for three race-specific Fusarium resistances. All RGAs mapped to four of the previously established eight linkage groups for chickpea. Two NBS-LRR clusters were identified that could not be resolved in our mapping population. One of these clusters, which is characterised by RFLP probe CaRGA-D, mapped to the linkage group harbouring two of three Fusarium resistance genes characterised in the inter-specific population. Our study provides a starting point for the characterisation and genetic mapping of candidate resistance genes in Cicer that is useful for marker-assisted selection and as a pool for resistance genes of Cicer.

Development of flow cytogenetics and physical genome mapping in chickpea (Cicer arietinum L.).

Procedures for flow cytometric analysis and sorting of mitotic chromosomes (flow cytogenetics) have been developed for chickpea (Cicer arietinum). Suspensions of intact chromosomes were prepared from root tips treated to achieve a high degree of metaphase synchrony. The optimal protocol consisted of a treatment of roots with 2 mmol/L hydroxyurea for 18 h, a 4.5-h recovery in hydroxyurea-free medium, 2 h incubation with 10 micromol/L oryzalin, and ice-water treatment overnight. This procedure resulted in an average metaphase index of 47%. Synchronized root tips were fixed in 2% formaldehyde for 20 min, and chromosome suspensions prepared by mechanical homogenization of fixed root tips. More than 4 x 10(5) morphologically intact chromosomes could be isolated from 15 root tips. Flow cytometric analysis of DAPI-stained chromosomes resulted in histograms of relative fluorescence intensity (flow karyotypes) containing eight peaks, representing individual chromosomes and/or groups of chromosomes with a similar relative DNA content. Five peaks could be assigned to individual chromosomes (A, B, C, G, H). The parity of sorted chromosome fractions was high, and chromosomes B and H could be sorted with 100% purity. PCR on flow-sorted chromosome fractions with primers for sequence-tagged microsatellite site (STMS) markers permitted assignment of the genetic linkage group LG8 to the smallest chickpea chromosome H. This study extends the number of legume species for which flow cytogenetics is available, and demonstrates the potential of flow cytogenetics for genome mapping in chickpea.

A PCR-based assay to detect En/Spm-like transposon sequences in plants.

Degenerate primers deduced from the TPase region of plant En/Spm-like transposons allowed the amplification of similar sequences from various plant species including sugar beet, wheat and pea. These primers are efficient tools for the detection of this family of transposons in many plant genomes irrespective of sequence knowledge or phenotypic pecularities. An efficient PCR assay was therefore developed for these class II transposons, similar to assays already available for Ty1-copia-, Ty3-gypsy- or LINEs. This approach allowed us not only to show the widespread almost-ubiquitous presence of En/Spm-elements in plant genomes, but also to characterize their genomic organization and chromosomal distribution in the genome of chickpea (Cicer arietinum L.) and its abundance in related Cicer species. This approach can be used for the detection and characterization of endogenous DNA transposable elements in plant species, their complete isolation and evaluation of their use for genome analysis.

Thermodynamic properties of a polydisperse system.

We use the virial theorem to derive a closed analytic form of the Helmholtz free energy for a polydisperse system of sticky hard spheres (SHS) within the mean spherical model (MSM). To this end we calculate the free energy of the MSM for an N-component mixture of SHS via the virial route and apply to it-after imposing a Lorentz-Berthelot type rule on the interactions-the stochastic (i.e., polydisperse) limit. The resulting excess free energy of this polydisperse system is of the truncatable moment free energy format. We also discuss the compressibility and the energy routes.