The Onset and Extinction of Neural Spiking: A Numerical Bifurcation Approach

We study the onset of neural spiking when the equilibrium rest state loses stability by the change of a critical parameter, the applied current. In the case of the well-known Morris-Lecar model, we start from a complete numerical study of the bifurcation diagram in the most relevant two-parameter range. This diagram includes all equilibrium and limit cycle bifurcations, thus correcting and completing earlier studies.We discuss and classify the behavior of the spiking orbits, when increasing or decreasing the applied current. A complete classification can be extracted from the complete bifurcation diagram. It is based on three components: bifurcation type of the equilibrium at the loss of stability, subcritical behavior in the limit of decreasing the applied current and supercritical behavior in the limit of increasing the applied current.     

EDD, a novel phosphotransferase domain common to mannose transporter EIIA, dihydroxyacetone kinase, and DegV

Using a recently developed program (SCOPmap) designed to automatically assign new protein structures to existing evolutionary-based classification schemes, we identify a evolutionarily conserved domain (EDD) common to three different folds: mannose transporter EIIA domain (EIIA-man), dihydroxyacetone kinase (Dak), and DegV. Several lines of evidence support unification of these three folds into a single superfamily: statistically significant sequence similarity detected by PSI-BLAST; "closed structural grouping" using DALI Z-scores (each protein inside a group finds all other group members with scores higher than those to proteins outside the group) that includes only these proteins sharing a unique alpha-helical hairpin at the C-terminus and excludes all other proteins with similar topology; similar domain fusions connect Dak and DegV, and genomic neighborhood organizations connect Dak and EIIA-man. Finally, both Dak and EIIA-man perform similar phosphotransfer reactions, suggesting a phosphotransferase activity for the DegV-like family of proteins, whose function other than lipid binding revealed in the crystal structure remains unknown.     

Restoration ecology meets carabidology: effects of floodplain restitution on ground beetles (Coleoptera,Carabidae)

The effects of different restoration activities on floodplain-inhabiting ground beetles were studied at a lowland river in northwestern Germany. In the 6-km² project area the bank reinforcement was stopped, the dikes that bordered the river on both sides were removed and two oxbows (disconnected parts of the main stream course) were reconnected to the river. We investigated the banks at two sites at the main river, at the two reconnected oxbows and at two unconnected oxbows as reference sites. To analyse the effects of the removal of the dikes we chose three floodplain sites in front and two reference sites behind the new dike. As a consequence of the lack of bank reinforcement and the reconnection of the oxbows, the area of open river banks, a rare bank structure at rivers in northwestern Germany, increased by a factor of 4.6 during the 4 years of investigation. Numerous stenotopic ground beetle species colonized the newly developed habitats at the main river and at the reconnected oxbows quickly, during several weeks or months, and established new populations as indicated by newly hatched individuals. The removal of the dikes should lead to a rewetting of the floodplain area that is incorporated in the flood dynamics, an important aspect of the development of typical floodplain habitats such as wet meadows, reeds and alluvial forests, while reference sites on the other side of the removed dike remained uninfluenced. Four years after the removal of the dikes no species turnover at the sites with a potentially changed water regime was recorded that indicated a shift of the carabid assemblages towards hygrophilous species. One reason could be the low frequency of inundations and their short duration during the investigation period. The flood dynamics could be sustained by the elevation and enlargement of the river bed, and periodic floods are the key factor for a development of floodplain habitats.     

Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences

A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA (1855 bp), rbcL (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early‐branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schi‐sandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well‐supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well‐supported eudicot clade, the early‐diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise six well‐supported subclades: (1) Berberidopsidaceae/Aextoxicaceae; (2) Myrothamnaceae/ Gunneraceae; (3) Saxifragales, which are the sister to Vitaceae (including Leea) plus a strongly supported eurosid clade; (4) Santalales; (5) Caryophyllales, to which Dilleniaceae are sister; and (6) an asterid clade. The relationships among these six subclades of core eudicots do not receive strong support. This large data set has also helped place a number of enigmatic angiosperm families, including Podostemaceae, Aphloiaceae, and Ixerbaceae. This analysis further illustrates the tractability of large data sets and supports a recent, phylogenetically based, ordinal‐level reclassification of the angiosperms based largely, but not exclusively, on molecular (DNA sequence) data.     

Software dependent phenetic relationships of non-nodulating African species ofAcacia

The phenetic analysis of non-nodulatingAcacia species by Harrier et al. (1997) was repeated to illustrate how different computer programs may generate alternative UPGMA trees for the very same data, even in the absence of data input order effects (ties). For example, all Harrier et al.'s UPGMA dendrograms produced by software from the Scottish Agricultural Statistics Service differed from those obtained by the packages NTSYS and MVSP87. Particularly, the positions ofA. albida, A. rovumae, andA. pentagona, as well as the relationships betweenDiacanthae andTriacanthae were affected by this phenomenon. Hence, whenever clustering techniques are used, care should be taken to consider possible software-dependent caveats and artefacts. Nevertheless, all programs provided clusterings that largely coincided with the subgeneric and sectional groupings proposed by Vassal (1972) although the positions of some species varied depending on whether morphological or molecular data were considered (e.g.A. albida andA. rovumae).     

Plant O-methyltransferases: molecular analysis,common signature and classification

Comparative analysis of the predicted amino acid sequences of a number of plant O-methyltransferase cDNA clones show that they share some 32–71% sequence identity, and can be grouped according to the different compounds they utilise as substrates. Five highly conserved regions are proposed as a signature for plant O-methyltransferases, two of which (regions I and IV) are believed to be involved in S-adenosyl-L-methionine and metal binding, respectively. The glycine-rich signature regions include a 36 amino acid domain which is located in the mid-terminal section of the carboxy terminus of most O-methyltransferase sequences. Cladistic analysis of the amino acid sequences suggests that plant O-methyltransferases may have arisen from common ancestral genes that were driven by different structural and/or functional requirements, and whose descendants segregated into different biochemical species. A comprehensive classification of plant O-methyltransferases is proposed following the guidelines of the Commission of Plant Gene Nomenclature.     

Classification and ordination of cryptogamic communities in Wilkes Land,Continental Antarctica

The entirely cryptogamic vegetation of Bailey and Clark Peninsulas, Windmill Islands, Budd Coast, Wilkes Land, Antarctica, is described for the first time. The vegetation of this area is exceptionally well developed and diverse and represents one of the most important botanical sites on the continent. The macroflora comprises three species of moss, one liverwort, three fruticose lichens, four foliose and over 20 crustose lichens; several macroalgae also occur. Seventy stands of relatively homogeneous vegetation were analysed and the percentage cover afforded by every species within 20 quadrats per site was recorded. A subjective classification was developed by visual ordering of the data sets and a hierarchical system erected which incorporates one moss- and one lichen-dominated sub-formation; the former includes two associations and seven sociations, while the latter comprises one association which includes four sociations. The data were then arranged by centroid linkage analysis to produce and objective classification, and subsequently ordinated by principal components analysis to generate groups of stands, the inter-relations of which were interpreted in ecological and environmental terms. The objective classification and ordination strongly support the subjectively derived groupings or sociations. Examples of plant interactions are qualitatively described.     

Fidelity Estimation for a Hierarchical Classifier

To estimate the correct classification rate of a classifier, many different methods exist (test sample, bootstrap, cross validation). The test sample is a method with very small expense. Sometimes, only a small number of objects is available (seldom diseases, high costs for experiments). When we split the sample in training set and test set, we get good or bad fidelity estimations but, unfortunately, vice versa a big or small confidence interval for the estimation. Overcoming this dilemma is only possible for simple classifiers. Such a simple classifier is investigated and a direct fidelity estimation is proposed.     

Systematic distribution of bioluminescence in living organisms

A list of the genera of living organisms known or believed to contain luminous species is provided in the Appendix, in a systematic context. The constraints on the accuracy of such a list and some aspects of the apparent distribution of bioluminescence are discussed.