Protistan microbial observatory in the Cariaco Basin,Caribbean. I. Pyrosequencing vs Sanger insights into species richness

Microbial diversity and distribution are topics of intensive research. In two companion papers in this issue, we describe the results of the Cariaco Microbial Observatory (Caribbean Sea, Venezuela). The Basin contains the largest body of marine anoxic water, and presents an opportunity to study protistan communities across biogeochemical gradients. In the first paper, we survey 18S ribosomal RNA (rRNA) gene sequence diversity using both Sanger- and pyrosequencing-based approaches, employing multiple PCR primers, and state-of-the-art statistical analyses to estimate microbial richness missed by the survey. Sampling the Basin at three stations, in two seasons, and at four depths with distinct biogeochemical regimes, we obtained the largest, and arguably the least biased collection of over 6000 nearly full-length protistan rRNA gene sequences from a given oceanographic regime to date, and over 80 000 pyrosequencing tags. These represent all major and many minor protistan taxa, at frequencies globally similar between the two sequence collections. This large data set provided, via the recently developed parametric modeling, the first statistically sound prediction of the total size of protistan richness in a large and varied environment, such as the Cariaco Basin: over 36 000 species, defined as almost full-length 18S rRNA gene sequence clusters sharing over 99% sequence homology. This richness is a small fraction of the grand total of known protists (over 100 000–500 000 species), suggesting a degree of protistan endemism.     

A physiological analogy of the niche for projecting the potential distribution of plants

Aim  To develop a physiologically based model of the plant niche for use in species distribution modelling. Location  Europe. Methods  We link the Thornley transport resistance (TTR) model with functions which describe how the TTR’s model parameters are influenced by abiotic environmental factors. The TTR model considers how carbon and nutrient uptake, and the allocation of these assimilates, influence growth. We use indirect statistical methods to estimate the model parameters from a high resolution data set on tree distribution for 22 European tree species. Results  We infer, from distribution data and abiotic forcing data, the physiological niche dimensions of 22 European tree species. We found that the model fits were reasonable (AUC: 0.79–0.964). The projected distributions were characterized by a false positive rate of 0.19 and a false negative rate 0.12. The fitted models are used to generate projections of the environmental factors that limit the range boundaries of the study species. Main conclusions  We show that physiological models can be used to derive physiological niche dimensions from species distribution data. Future work should focus on including prior information on physiological rates into the parameter estimation process. Application of the TTR model to species distribution modelling suggests new avenues for establishing explicit links between distribution and physiology, and for generating hypotheses about how ecophysiological processes influence the distribution of plants.     

On computational efficiency of the hybrid Monte Carlo method applied to the multicanonical ensemble

Abstract

In the present paper, computational efficiency of the hybrid Monte Carlo (HMC) method applied to the multicanonical ensemble is studied; the HMC is an equation of motion guided Monte Carlo method. As in the standard HMC for the canonical ensemble, the multicanonical HMC calculations with high acceptance ratio show better efficiency; about 60% acceptance yields the best performance for the system examined.     

Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

We present an approach which can be used to identify native-like folds in a data base of protein conformations in the absence of any sequence homology to proteins in the data base. The method is based on a knowledge-based force field derived from a set of known protein conformations. A given sequence is mounted on all conformations in the data base and the associated energies are calculated. Using several conformations and sequences from the globin family we show that the native conformation is identified correctly. In fact the resolution of the force field is high enough to discriminate between a native fold and several closely related conformations. We then apply the procedure to several globins of known sequence but unknown three dimensional structure. The homology of these sequences to globins of known structures in the data base ranges from 49 to 17%. With one exception we find that for all globin sequences one of the known globin folds is identified as the most favorable conformation. These results are obtained using a force field derived from a data base devoid of globins of known structure. We briefly discuss useful applications in protein structural research and future development of our approach.     

Multiline varieties and disease control

Summary A general model for the evolution of pathogen populations on mixtures or multilines is developed. This model is used to extend previous analyses of the effects of the widespread cultivation of multilines on the evolution of virulence in obligate parasites to mixtures of lines carrying different numbers of resistance genes. It is concluded that the composition of an equilibrium pathogen population growing on a multiline may vary within wide limits and the prinicipal determinant of its composition is the number of components in the multiline and the resistance genes they carry. Other factors of importance are (i) the relative contribution made by each host class (with different numbers of resistance genes) to the pathogen spore pool each generation; (ii) the levels of stabilizing selection against unnecessary virulence genes; and (iii) the way in which unnecessary genes for virulence combine to reduce pathogen fitness. Conditions for the fixation of avirulent biotypes in the pathogen population and the evolution of a pathogen superrace are given for multilines of various compositions.Paper No. 9246 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, North Carolina. This investigation was supported in part by NIH Research Grant No. GM 11546 from the National Institute of General Medical Sciences     

Linkage analysis for 18 enzyme loci in Pinus rigida Mill.

Summary Estimates of recombination frequency among enzyme loci of pitch pine revealed two new linkages, Mdh3:Pgm2 (=0.01) and Pep1:Mdh4 (=0.38), and confirmed two previously established linkages. Tighter linkage (=0.30) was ruled out for nearly all gene pairs examined. In general, the Bayesian approach used in this study to test for linkage performed better than alternative methods.This work was supported by the School of Natural Resources, College of Agricultural and Life Sciences, University of Wisconsin, Madison, WI, and by McIntyre-Stennis, project no. 142-C385     

Multiline varieties and disease control

Summary Existing theoretical models have led to conflicting predictions concerning the likely effect of the widespread use of dirty crop multilines on the evolution of virulence in pathogen populations. Here we attempt to clarify these problems by extending existing models to include selection against unnecessary genes for virulence at two different stages in the life cycle of the pathogen. The results of these studies indicate that the stage of the life cycle at which selection occurs can significantly influence the evolution of virulence in pathogen populations growing on multiline varieties.     

Lipid vertical motion and related steric effects in bilayer membranes

We present a theoretical model of a lipid bilayer in its gel state which explicity couples the vertical displacements of the lipid chains to their conformational state. In this model the chains are free to move longitudinally under a potential due to the neighbouring chains. The potential is due to a restoring force with a force constant k and thus acts to keep them in the local plane as defined by their nearest neighbours. It is demonstrated that the force constant k is directly related to the internal bilayer pressure, , and that if a value =33 dynes/cm is assumed then k=17.3 dynes/cm. Steric effects are explicity included by allowing chains to twist into free volume created by the vertical displacement of neighbouring chains. The Hamiltonian is expressed in terms of the projection operators, P _ij , describing the displacement of chain i relative to a neighbour j, and G _ij describing the direction of a twist in chain i. The model is solved both analytically and via Monte Carlo simulations for a one-dimensional system. The possibility of phase-transitions in two-dimensions and the relevance to the bilayer pre-transition is discussed.This work was first presented in poster form at the Canadian Biochemical Society Conference held in Banff, Alberta, Canada, April 29–May 4, 1984Work supported in part by the Natural Sciences and Engineering Research Council of Canada, Le Fonds Formation des Chercheurs et Action a la Recherche du Quebec, and the Advisory Research Council of Queen's University