Modelling Mediterranean pasture dynamies

Pasture vegetation in an open woodland of Quercus rotundifolia subjected to periodic ploughing was sampled in spring during 8 consecutive years. The frequency of herbaceous species was recorded in a total of 69 permanent plots located on 5 adjacent sites with similar lithology, slope and orientation but differing in age since previous ploughing.Vegetation dynamics expressed as trajectories of permanent plots in a non-metric multidimensional scaling space has been modelled in terms of evironmental variables. By fitting a generalized linear model, the dynamics are shown to be related to years since last ploughing, geographical location of plots, total annual rainfall and November rainfall. Meteorological patterns of the sampling period are also described.Abbreviations GLM = Generalized Linear Model - NMDS = Non-metric Multi-Dimensional Scaling - UPGMA = Unweighted Pair-Group Method using Arithmetic Averages     

岛屿生物地理学理论：模型与应用

前言岛屿有许多显著特征,如地理隔离,生物类群简单。这些特点为重复性研究和统计学分析奠定了基础,从而有利于许多深入而细致的生物学研究。因此,岛屿为发展和检验自然选择、物种形成及演化,以及生物地理学和生态学诸领域的理论和假设,提供了重要的自然实验室。岛屿生物地理学理论(MacArthurwilson学说)即为岛屿生物学研究中所产生的著名理论之一。该理论发展之     

Simulated and measured nitrogen conditions in a manured and fertilised soil

The governing factors for soil nitrogen dynamics were identified with a simulation model. In addition, the model was used to interpret measurements from a plot fertilisation experiment in southwest Sweden.Simulated moisture and temperature conditions were the driving variables for the simulation of soil nitrogen dynamics and leaching during a 6-year period. The results of the simulation were compared with monthly observations on two plots with grain crops, one with liquid manure and commercial fertilisers applied and one with commercial fertilisers only.Simulated temporal variations of the nitrate and ammonium storages generally agreed with observations. The dominant role of the crops as a determinant of soil nitrogen conditions was demonstrated. A higher leaching loss from the plot with application of commerical fertilisers only occurred both in simulations and measurements compared to the plot with application of both commercial fertilisers and manure. The main reason was the higher N-application in the former treatment.The effect of water flows in macropores was interpreted as a delay of simulated leaching compared to observed leaching on some occasions in summer and early autumn. No direct effect of the macropores on the yearly rates of leaching could be seen.     

Anion exchange reactions in bacteria

Bacterial anion exchange now includes both carboxylate-linked reactions, in which there is an antiport of mono- and dicarboxylic acids, and Pi-linked reactions that build on phosphate (Pi) and organic phosphates. To illustrate the general features of this expanding class, this article discussed the biochemistry, physiology, and molecular biology of Pi-linked antiporters that accept glucose 6-phosphate (G6P) as their primary substrate. Kinetic and biochemical analysis suggsts that Pi-linked exchangers have a bifunctional active site that accepts a pair of negative charges. For this reason, exchange stoichiometry moves between the limits of 2:1 and 2:2 to reflect the ratio of mono- and divalent substrates at either membrane surface. This results in a particularly interesting reaction sequencein vivo, where, because cytosolic pH is relatively alkaline, one can expect the asymmetric exchange of two monovalent G6P anions against a single divalent G6P. In this way, an otherwise futile self-exchange of G6P gives a net flux driven (indirectly) by the pH gradient. Despite this biochemical and physiological complexity, Pi-linked carriers resemble all other secondary carriers at a molecular level. Indeed, sequence analysis leads one to infer a common (albeit low resolution) structural theme in which each functional unit has two sets of six trans-membrane helices separated by a central hydrophilic loop. Present examples show that this topology can derive from either a single protein, as is typical in bacteria, or from pairs of identical subunits, as found in mitochondria and chloroplasts. The finding of this common structure should make it possible to build detailed structural models that have implications for all membrane carrier proteins.     

Modeling in the museum: On the role of remnant models in the work of Joseph Grinnell

Accounts of the relation between theories and models in biology concentrate on mathematical models. In this paper I consider the dual role of models as representations of natural systems and as a material basis for theorizing. In order to explicate the dual role, I develop the concept of a remnant model, a material entity made from parts of the natural system(s) under study. I present a case study of an important but neglected naturalist, Joseph Grinnell, to illustrate the extent to which mundane practices in a museum setting constitute theorizing. I speculate that historical and sociological analyses of institutions can play a specific role in the philosophical analysis of model-building strategies.     

Hydration of 3-cyanopyridine to nicotinamide by crude extract nitrile hydratase

Summary The kinetic and stability characteristics of crude extract nitrile hydratase fromBrevibacterium R-312 were studied for the hydration of 3-cyanopyridine to nicotinamide. The enzyme was substrate and product inhibited and had the following kinetic constants:K _m =28 mM;K _p =36 mM;K _s =155 mM;V _m =5.8 mol/min/mg protein (25°C). Itsmaximum temperature and pH (phosphate buffer) were 35°C and 8.0, respectively and it had half-lives of 50 days, 10 days and 1 day at 4°C, 10°C and 25°C, respectively. The crude extract also exhibited amidase activity on nicotinamide, but it became significant only at nicotinamide concentrations greater than 300 mM. Mathematical models for batch and fed-batch hydrations were developed to account for substrate and product inhibitions and for enzyme decay. They predicted to within 10% experimental results for initial substrate and final product concentrations up to 300 mM; the accuracies decreased at higher concentrations primarily because of the relatively rapid hydrolysis of nicotinamide.     

PROBLEMS WITH TESTING INBREEDING AVOIDANCE: THE CASE OF THE COLLARED FLYCATCHER

Four year's data on collared flycatchers, Ficedula albicollis, breeding in a nestbox plot on the island of Gotland, Sweden, was used to investigate whether individuals avoid mating with close kin (i.e., parents or sibs). Only one case of close inbreeding (0.5% of all pairs) was observed during the years of study. The observed frequency of close inbreeding was compared to expected frequencies based on two different null models. Assuming no inbreeding avoidance behaviors (e.g., dispersal or kin recognition), but taking into account the fact that mortality, and different arrival and pairing times of individuals reduce the probability of mating with close kin, the expected frequency of close inbreeding is 10% and 15% for female and male recruits (i.e., born in the study plot), respectively. However, assuming mating to be random within the study plot reduced the expected frequency of close inbreeding to 1% or less for both males and females. Consequently, conclusions drawn concerning inbreeding avoidance depend on the null model used. Contrasting estimated costs of tolerating close inbreeding with those of avoiding it (by dispersal to other plots), however, suggests that the costs of avoiding close inbreeding are substantially greater than those of tolerating it. Therefore, although inbreeding avoidance cannot be rejected as a cause of dispersal of this species, it is not the primary cause, and particularly not for sex-biased dispersal. The general problems of investigating inbreeding avoidance are discussed. It is argued that all previous null models based on random mating in finite populations produce expected frequencies of close inbreeding that in fact include inbreeding avoidance, since they implicitly assume random dispersal within a finite population. Thus, comparisons between observed and expected frequencies of close inbreeding based on random mating are inadequate. The most promising method of investigating inbreeding avoidance is to experimentally study individual movements and mating preferences in the presence and absence of close kin.     

Modeling competition between Laurencia obtusa (Ceramiales,Rhodophyta) and Hypnea spinella (Gigartinales,Rhodophyta) at Cabo Frio Island,Rio de Janeiro,Brazil

The Lotka-Volterra competition model was used to represent the interaction between Laurencia obtusa and Hypnea spinella. A new model that considers effects of competition on algal carrying capacity is suggested. To test the models, data from field experiments conducted in an intertidal region at Cabo Frio Island, Rio de Janeiro, Brazil, were used. Both models showed that Hypnea was a stronger competitor than Laurencia. The model of interaction through the carrying capacity showed a stable coexistence between the algal populations and better represented the experimental data.     

Construction of hermes shuttle vectors: a versatile system useful for genetic complementation of transformable and non-transformableNeisseria mutants

A versatile shuttle system has been developed for genetic complementation with cloned genes of transformable and non-transformableNeisseria mutants. By random insertion of a selectable marker into the conjugativeNeisseria plasmidptetM25.2, a site within this plasmid was identified that is compatible with plasmid replication and with conjugative transfer of plasmid. Regions flanking the permissive insertion site of ptetM25.2 were cloned inEscherichia coli and served as a basis for the construction of the Hermes vectors. Hermes vectors are composed of anE. coli replicon that does not support autonomous replication inNeisseria, e.g. ColE1, p15A, orori _fd, fused with a shuttle consisting of a selectable marker and a multiple cloning site flanked by the integration region of ptetM25.2. Complementation of a non-transformableNeisseria strain involves a three-step process: (i) insertion of the desired gene into a Hermes vector; (ii) transformation of Hermes into aNeisseria strain containing ptetM25.2 to create a hybrid ptetM25.2 via gene replacement by the Hermes shuttle cassette; and (iii) conjugative transfer of the hybrid ptetM25.2 into the finalNeisseria recipient. Several applications for the genetic manipulation of pathogenicNeisseriae are described.