Twenty years of numerical syntaxonomy

The development of numerical syntaxonomy during its first 20 yr is reviewed. The use of methods of numerical classification and ordination is the dominating feature of the development. National and local phytosociological data banks were established, large data sets handled and many important vegetation monographs were methodically based on multivariate data analysis. Particularly the development in Italy, the Netherlands, Czechoslovakia, and Sweden contributed to new theoretical elements of numerical syntaxonomy. Ordination became a common tool of searching for reticulate synsystematic relations between community types. The most popular ordination techniques have been Principal Components Analysis and Detrended Correspondence Analysis. Hierarchical agglomerative techniques of clustering still prevail in classification, although the divisive strategy of TWINSPAN has also become an effective tool for phytosociological clustering and table sorting. Extensive program packages, also for personal computers have now become standard equipment for many vegetation scientists.     

A new dissimilarity measure and a new optimality criterion in phytosociological classification

A new dissimilarity measure, Uppsala dissimilarity, is proposed. It is a Manhattan-type measure in between the Canberra and Gower measures, based on the differences between scores in relevés compared, but it also takes both the sums of scores and the difference between maximum and minimum score into account. The measure is considered realistic for phytosociological material.A new optimality criterion has been developed after unsatisfactory results had been obtained with the DOL criterion (Popma et al. 1983) which was developed previously by our group. Problems with DOL were especially met when the criterion was applied to the distribution of only one species over the cluster array obtained. The new criterion takes both internal cluster homogeneity and between-cluster dissimilarity into account. Between-cluster dissimilarity is calculated for all other clusters and not only for the nearest neighbour, as in DOL. The new criterion has both an unweighted form: SOM, and a form with weighting for cluster size: SWOM.This new criterion was successfully applied to the evaluation of the sharpness of distribution of individual species over cluster arrays, under the name of SIM: species indication measure and SWIM, species weighted indication measure.The measures were applied to some test data. Differences between the unweighted and weighted forms were found which could not be easily interpreted.Some remarks are made on the coherence of d-SAHN and h-SAHN approaches in agglomerative clustering within the new strategy proposed.Abbreviations DOL = Detection of Optimal Level - S(W)IM = Species (Weighted) Indication Measure - S(W)OM = Standardized (Weighted) Optimality Measure - UD = Uppsala Dissimilarity measure - WPGMA = Weighted Pair-Group Method Average linking clustering - SAHN = Sequential Agglomerative Hierarchical Non-overlapping clustering     

Mechanisms of amoeboid chemotaxis: an evaluation of the cortical expansion model

In this work we evaluate the cortical expansion model for amoeboid chemotaxis with regard to new information about molecular events in the cytoskeleton following chemotactic stimulation of Dictyostelium amoebae. A rapid upshift in the concentration of chemoattractant can be used to synchronize the motile behavior of a large population of cells. This synchrony presents an opportunity to study the biochemical basis of morphological changes such as pseudopod extension that are required for amoeboid chemotaxis. Changes in the composition and activity of the cytoskeleton following stimulation can be measured with precision and correlated with important morphological changes. Such studies demonstrate that activation of actin nucleation is one of the first and most crucial events in the actin cytoskeleton following stimulation. This activation is followed by incorporation of specific actin cross-linking proteins into the cytoskeleton, which are implicated in the extension of pseudopods and filopods. These results, as well as those from studies with mutants deficient in myosin, indicate that cortical expansion, driven by focal actin polymerization, cross-linking and gel osmotic swelling, is an important force for pseudopod extension. It is concluded that whereas three forces, frontal sliding, tail contraction, and cortical expansion may cooperate to produce amoeboid movement, the cortical expansion model offers the simplest explanation of how focal stimulation with a chemoattractant causes polarized pseudopod extension.     

The barbs (Barbus spp.) of Lake Tana: a forgotten species flock?

Synopsis All living species occupy an ecological niche, and are positioned within a trophic hierarchy. Extinct organisms presumably held similar behavioral and coevolutionary characteristics in the past, and were susceptible to the same kinds of natural ecological pressures operating today. Paleoecological investigations are limited by the incompleteness of the fossil record, and particularly by a lack of behavioral data that are so fundamental to ecological studies of living communities and habitats. Opportunities to examine the coevolutionary structure of ancient communities from empirical data are extremely rare. One such opportunity is provided by the Lower Cretaceous Santana Formation of north-eastern Brazil, a series of richly fossiliferous strata approximately 110 million years old. Many fossil fishes from the Santana Formation contain identifiable prey, including decapod crustaceans and fishes. A trophic hierarchy of these organisms is reconstructed here, and their ecological relationships are discussed. Comparison is made with a similar fish fauna from the Upper Jurassic Solnhofen Limestone of Germany. Low-level, intermediate and high-level predators are identified in each fauna. Predator-prey relationships in the Santana fauna are strongly hierarchical, and are more focussed at the intermediate predator level than in Solnhofen. Comparison with a model of predator-prey relationships between fishes and benthic fauna of the Baltic Sea (which like the Araripe Basin represents a semi-enclosed environment) suggests that heavy predation on teleosts such asRhacolepis, occupying an intermediate trophic level, may have permitted benthic decapods to proliferate and exclude other benthic organisms. Less intense predation on fishes at the intermediate trophic level would allow their numbers to increase, thereby increasing the intensity of predation on the benthos at the base of the trophic hierarchy.     

Small-scale plant species turnover in a limestone grassland: the carousel model and some comments on the niche concept

Abstract. This study reports on small-scale changes in the distribution of plant species in a 2.5 m² plot of grazed, species-rich Veronica spicata - Avenula pratensis grassland on shallow, dry, nutrient-poor soil in the Great Alvar area (Stora Alvaret) of southern Öland, southeastern Sweden. Multivari-ate analysis of 0.001 m² and 0.25 m² quadrats within the plot showed that there is little floristic variation without any trend in the plot. Average species richness varied little throughout the study period from 1986 to 1991 with 1986 averages of 7.0 on 0.001m², 16.3 on 0.01 m², and 26.1 on 0.25 m². On 0.001 m²the highest species number found was 12, on 0.01 m², 27. However, cumulative species richness, i.e. species number in the first year plus new species appearing in later years (averaged over 40 quadrats) increased over the same period, on 0.001 m² from 7.0 in 1986 to 14.9 in 1991, and on 0.01 m² from 16.3 to 24.1. Cumulative frequency, i.e. number of quadrats out of 40 where a species occurred in the first year or/and in later years, increased as well; the number of cumulatively highly frequent (> 80%) species increased from 5 in 1986 to 18 in 1991. Species mobility on the scale of the small quadrats used implies both appearance and disappearance from these quadrats. Using six examples, species mobility is shown to vary individualistically, both in rate and degree. We postulate that in homogeneous, grazed, nutrient- and water-deficient environments many species can reach virtually all microsites within the plot, which we express through the idea of the ‘carousel model’. We also question the usefulness of the niche concept and re-interpret it by stating that all species of this plant community have the same habitat niche, while most of them are short-lived and have the same regeneration niche. The essential variation amongst the species is their individual ability to establish or re-establish by making use of favourable conditions appearing in microsites in an unknown, complex spatio-temporal pattern.     

Dynamic genome-scale modeling of Saccharomyces cerevisiae unravels mechanisms for ester formation during alcoholic fermentation

Fermentation employing Saccharomyces cerevisiae has produced alcoholic beverages and bread for millennia. More recently, S. cerevisiae has been used to manufacture specific metabolites for the food, pharmaceutical, and cosmetic industries. Among the most important of these metabolites are compounds associated with desirable aromas and flavors, including higher alcohols and esters. Although the physiology of yeast has been well-studied, its metabolic modulation leading to aroma production in relevant industrial scenarios such as winemaking is still unclear. Here we ask what are the underlying metabolic mechanisms that explain the conserved and varying behavior of different yeasts regarding aroma formation under enological conditions? We employed dynamic flux balance analysis (dFBA) to answer this key question using the latest genome-scale metabolic model (GEM) of S. cerevisiae. The model revealed several conserved mechanisms among wine yeasts, for example, acetate ester formation is dependent on intracellular metabolic acetyl-CoA/CoA levels, and the formation of ethyl esters facilitates the removal of toxic fatty acids from cells using CoA. Species-specific mechanisms were also found, such as a preference for the shikimate pathway leading to more 2-phenylethanol production in the Opale strain as well as strain behavior varying notably during the carbohydrate accumulation phase and carbohydrate accumulation inducing redox restrictions during a later cell growth phase for strain Uvaferm. In conclusion, our new metabolic model of yeast under enological conditions revealed key metabolic mechanisms in wine yeasts, which will aid future research strategies to optimize their behavior in industrial settings.     

Stage-specific expression of three cell surface carbohydrate antigens during murine spermatogenesis detected with monoclonal antibodies

We have identified three germ cell surface carbohydrate antigens that exhibit a common, stage-specific pattern of expression during spermatogenesis in the mouse. IgM-class monoclonal antibodies designated "J1," "C6," and "A5" were absorbed by adult testis, but not by any adult somatic tissue tested. In indirect immunofluorescence assays using collagenase-dissociated prepuberal and adult testicular cells, these antibodies labeled the surfaces of early and late pachytene spermatocytes and round spermatids. Gonocytes from fetal and neonatal testes were not labeled. In paraffin sections of prepuberal and adult testes, sialidase treatment exposed antigens recognized by antibodies C6 and A5 on preleptotene, leptotene, and zygotene spermatocytes located near the perimeter of seminiferous tubules. The determinants recognized by antibodies J1, C6, and A5 were characterized partially using a sugar hapten inhibition assay. The binding of J1 to adult testicular cells was inhibited specifically by N-acetylglucosamine and the binding of both C6 and A5 was inhibited by N-acetyllactosamine. The glycoconjugates recognized by J1, C6, and A5 eluted from gel filtration columns with an apparent molecular weight greater than 1 X 10(6) and were sensitive to endo-beta-galactosidase (keratanase) treatment. The apparent high molecular weight of these glycoconjugates was confirmed by immunolabeling Western blots of testis extracts separated by SDS-polyacrylamide gel electrophoresis. The results suggest that polylactosamine (keratan) glycoconjugates of high molecular weight are associated with the plasma membranes of meiotic and haploid male germ cells. The effects of sialidase on antibody labeling patterns suggest that changes in cell surface sialylation accompany the transition of early meiotic germ cells to pachytene spermatocytes during spermatogenesis.