Small-scale association measures in epibenthic communities as a clue for allelochemical interactions

The small-scale associations in a rocky subtidal community in the northwestern Mediterranean were studied by a development of the continuous line transect method. This method allowed the overall measurement of non-randomness in interspecific contacts and the assignment of an association index to each species-pair, whose, significance was tested by Monte Carlo procedures. At the same time, the continuous recording allowed the study of the weakening of the interactions with increasing distances. Our purpose was to uncover evidence for allelochemical mechanisms of space occupation and maintenance. A strong non-randomness was found in the interspecific associations. This was mostly due to the interactions of the poecilosclerid sponge Crambe crambe (Schmidt) with its neighbours, especially its negative associations with other sponge species. The strength of the relationships fell drastically over the first few centimeters from the contact borders of the different species. The results pointed strongly to an allelochemical mechanism. The extracts of this sponge featured high bioactivity in laboratory assays, and field experiments demonstrated that the sponge can inhibit the growth of species in the community studied. Standard sampling techniques would have overlooked the spatial structure present in the data. The study emphasizes the need for both contact data and distance data in order to identify the underlying processes reliably. The line transect method provides both types of information easily and allows testing of models and identification of organisms likely to use chemical defenses in space competition. Its use as a preliminary step in studies of chemical ecology might help to detect presumptive allelochemical processes prior to experimental work on the potentially active species.     

Polypeptide folding with off-lattice Monte Carlo dynamics: the method

The MC dynamics of an off-lattice all-atom protein backbone model with rigid amide planes are studied. The only degrees of freedom are the dihedral angle pairs of the C-atoms. Conformational changes are generated by Monte Carlo (MC) moves. The MC moves considered are single rotations (simple moves, SM's) giving rise to global conformational changes or, alternatively, cooperative rotations in a window of amide planes (window moves, WM's) generating local conformational changes in the window. Outside the window the protein conformation is kept invariant by constraints. These constraints produce a bias in the distribution of dihedral angles. The WM's are corrected for this bias by suitable Jacobians. The energy function used is derived from the CHARMM force field. In a first application to polyalanine it is demonstrated that WM's sample the conformational space more efficiently than SM's.Abbreviations CPU Central Processing Unit - MC Monte Carlo - MCD Monte Carlo Dynamics - MD Molecular Dynamics - RMS Root-Mean-Square - RMSD Root-Mean-Square-Deviation - SM Simple Move - WM Window Move     

A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci. I. Methodology

A Bayesian approach to the statistical mapping of Quantitative Trait Loci (QTLs) using single markers was implemented via Markov Chain Monte Carlo (MCMC) algorithms for parameter estimation and hypothesis testing. Parameter estimators were marginal posterior means computed using a Gibbs sampler with data augmentation. Variables sampled included the augmented data (marker-QTL genotypes, polygenic effects), an indicator variable for linkage, and the parameters (allele frequency, QTL substitution effect, recombination rate, polygenic and residual variances). Several MCMC algorithms were derived for computing Bayesian tests of linkage, which consisted of the marginal posterior probability of linkage and the marginal likelihood of the QTL variance associated with the marker.     

方差组分估计方法MIVQUE和REML的模拟比较

利用ＭｏｎｔｅＣａｒｌｏ方法,对４种数据结构进行了ＭＩＶＱＵＥ和ＲＥＭＬ两种方差组分估计方法的模拟比较。方差组分估计所用的模型为奶牛育种中常用的公畜模型,它包括场年季固定效应、公牛组固定效应和公牛随机效应。４种数据结构中最大的有１２８４７个观察值,场年季效应和公牛效应水平数分别为７７８和４７,它与北京市目前可利用的奶牛头胎产奶量记录资料相当。最小的数据结构只有２００个观察值,１４８个场年季和２０头公牛。比较指标为估计值的偏差和方差（理论的或根据１０００次重复模拟所得的经验值）。结果表明,对于较大样本的数据结构,两种方法差异很小,它们间的估计值的相关接近于１,偏差小于真值的１％,方差近似相等。对于较小样本的数据结构,ＭＩＶＱＵＥ则明显优于ＲＥＭＬ。本研究还表明,对于ＲＥＭＬ来说,类似数据结构１的样本已能满足其渐近无偏性和有效性的大样本特性。     

Monte Carlo study of the effect of β2-microglobulin on the binding cleft of the HLA-A2 complex

Peptide recognition by class I products of the major histocompatibility complex requires association of the class I heavy chain with β₂-microglobulin. We present results of Monte Carlo simulations of the β-pleated sheet floor of the human class I MHC molecule, HLA-A2, with and without β₂-microglobulin. We find a significant effect of β₂-microglobulin on the side chains of residues near a region that would accommodate the C-terminus of a bound peptide. By modeling simultaneously each loop and its neighboring strand at either end of the class I cleft, we find that β₂-microglobulin restricts the conformational space of residues that are central to binding peptides. The effect is most pronounced for R97 and H114 and somewhat less important for Y99 and Y116, the latter forming strong hydrogen bonds with neighboring residues in the heavy chain itself.     

Optimization of the electrostatic interactions in proteins of different functional and folding type

The 3-dimensional optimization of the electrostatic interactions between the charged amino acid residues was studied by Monte Carlo simulations on an extended representative set of 141 protein structures with known atomic coordinates. The proteins were classified by different functional and structural criteria, and the optimization of the electrostatic interactions was analyzed. The optimization parameters were obtained by comparison of the contribution of charge-charge interactions to the free energy of the native protein structures and for a large number of randomly distributed charge constellations obtained by the Monte Carlo technique. On the basis of the results obtained, one can conclude that the charge-charge interactions are better optimized in the enzymes than in the proteins without enzymatic functions. Proteins that belong to the mixed αβ folding type are electrostatically better optimized than pure α-helical or β-strand structures. Proteins that are stabilized by disulfide bonds show a lower degree of electrostatic optimization. The electrostatic interactions in a native protein are effectively optimized by rejection of the conformers that lead to repulsive charge-charge interactions. Particularly, the rejection of the repulsive contacts seems to be a major goal in the protein folding process. The dependence of the optimization parameters on the choice of the potential function was tested. The majority of the potential functions gave practically identical results.     

Development and maturation of surghum seeds on detached panicles grown in vitro

Summary A procedure for culturing detached panicles of sorghum, Sorghum bicolor (L.) Moench, was developed to achieve flowering, fertilization, and subsequent seed development and maturation in vitro. Sixteen sorghum genotypes (five high and eleven low in tannin) were tested for their ability to develop normally in culture. Panicles collected one to two days before the initiation of anthesis were cultured in flasks containing liquid medium. Contamination and medium darkening were the major obstacles encountered. Up to 55% of the panicles cultured reached physiological maturity in vitro. The frequency of seed set ranged from 30 to 97% depending upon genotype and medium. Seed and glume color were normal. Seed produced in vitro resembled those grown in vivo and germinated well, but were smaller than normal (100 kernel weight reached 50 to 70% of the control). Grain polyphenols were synthesized in the cultured panicles. Seed of high tannin genotypes produced in vitro were lower in total phenols and tannins and higher in flavan-4-ols and the 3-deoxyanthocyanidin pigments than control seed. This technique can be used for harvesting late-maturing stocks and for various sorghum studies.     

Crop responses to CO2 enrichment

Carbon dioxide is rising in the global atmosphere, and this increase can be expected to continue into the foreseeable future. This compound is an essential input to plant life. Crop function is affected across all scales from biochemical to agro-ecosystem. An array of methods (leaf cuvettes, field chambers, free-air release systems) are available for experimental studies of CO₂ effects. Carbon dioxide enrichment of the air in which crops grow usually stimulates their growth and yield. Plant structure and physiology are markedly altered. Interactions between CO₂ and environmental factors that influence plants are known to occur. Implications for crop growth and yield are enormous. Strategies designed to assure future global food security must include a consideration of crop responses to elevated atmospheric CO₂. Future research should include these targets: search for new insights, development of new techniques, construction of better simulation models, investigation of belowground processes, study of interactions, and the elimination of major discrepancies in the scientific knowledge base.