Self-organizing maps: stationary states,metastability and convergence rate

We investigate the effect of various types of neighborhood function on the convergence rates and the presence or absence of metastable stationary states of Kohonen's self-organizing feature map algorithm in one dimension. We demonstrate that the time necessary to form a topographic representation of the unit interval [0, 1] may vary over several orders of magnitude depending on the range and also the shape of the neighborhood function, by which the weight changes of the neurons in the neighborhood of the winning neuron are scaled. We will prove that for neighborhood functions which are convex on an interval given by the length of the Kohonen chain there exist no metastable states. For all other neighborhood functions, metastable states are present and may trap the algorithm during the learning process. For the widely-used Gaussian function there exists a threshold for the width above which metastable states cannot exist. Due to the presence or absence of metastable states, convergence time is very sensitive to slight changes in the shape of the neighborhood function. Fastest convergence is achieved using neighborhood functions which are "convex" over a large range around the winner neuron and yet have large differences in value at neighboring neurons.     

Development and regeneration of the retinotectal map in goldfish: a computational study

We present a simple computational model to study the interplay of activity-dependent and intrinsic processes thought to be involved in the formation of topographic neural projections. Our model consists of two input layers which project to one target layer. The connections between layers are described by a set of synaptic weights. These weights develop according to three interacting developmental rules: (i) an intrinsic fibre-target interaction which generates chemospecific adhesion between afferent fibres and target cells; (ii) an intrinsic fibre-fibre interaction which generates mutual selective adhesion between the afferent fibres; and (iii) an activity-dependent fibre-fibre interaction which implements Hebbian learning. Additionally, constraints are imposed to keep synaptic weights finite. The model is applied to a set of eleven experiments on the regeneration of the retinotectal projection in goldfish. We find that the model is able to reproduce the outcome of an unprecedented range of experiments with the same set of model parameters, including details of the size of receptive and projective fields. We expect this mathematical framework to be a useful tool for the analysis of developmental processes in general. <br>     

Distinct modes of vertebrate hypaxial muscle formation contribute to the teleost body wall musculature

The formation of the body wall musculature in vertebrates is assumed to be initiated by direct ventral extension of the somites/myotomes. This contrasts to the formation of limb muscles and muscles involved in feeding or respiration/ventilation, which are founded by migratory muscle precursors (MMPs) distant to the somites. Here, we present evidence from morphology and expression of molecular markers proposing that the formation of the two muscle layers of the teleost body wall involves both of the above mechanisms: (1) MMPs from somites 5 and 6 found an independent muscle primordium–the so-called posterior hypaxial muscle (PHM)–which subsequently gives rise to the most anterior two segments of the medial obliquus inferioris (OI) muscle. (2) Direct epithelial extension of the hypaxial myotomes generates the OI segments from somite 7 caudalward and the entire lateral obliquus superioris (OS) muscle. The findings are discussed in relation to the evolution of hypaxial myogenic patterning including functional considerations. We hypothesise that the potential of the most anterior somites to generate migratory muscle precursors is a general vertebrate feature that has been differently utilised in the evolution in vertebrate groups.     

Using laser tweezers to measure twitching motility in Neisseria

Dynamic properties of type IV pili are essential for their function in bacterial infection, twitching motility and gene transfer. Laser tweezers are versatile tools to study the molecular mechanism underlying pilus dynamics at the single molecule level. Recently, these optical tweezers have been used to monitor pilus elongation and retraction in vivo at a resolution of several nanometers. The force generated by type IV pili exceeds 100 pN making pili the strongest linear motors characterized to date. The study of pilus dynamics at the single molecule level sheds light on kinetics, force generation, switching and mechanics of the Neisseria gonorrhoeae pilus motor.     

Does genome size in Dasypyrum villosum vary with fruit colour?

Dasypyrum villosum (2n=14), a Mediterranean grass species of the Triticeae, exhibits intraindividual fruit colour polymorphism from pale yellow to almost black. Several studies have reported differences between the plants emerging from pale and dark fruits. They include histone content in root meristem nuclei, cell cycle duration, heterochromatin banding pattern, frequency of a tandemly repeated sequence, and nuclear genome size. In the present study, we examine whether the reports of genome size being up to 1.24-fold larger in seedlings from the lighter caryopses are reproducible. In all, 29 accessions from various countries, totaling 186 plants, were investigated for genome size using flow cytometry with propidium iodide as the DNA stain. Individuals differed 1.12-fold at most and accessions 1.07-fold. The mean genome size (1C-value) was 5.07 pg or 4954 Mbp. Within-accession comparisons of seedlings derived from light and dark caryopses were insignificant (P>0.100). Thus, we found no evidence for a modificatory genome size plasticity in D. villosum. In the light of our data, the previously reported genome size variation, up to 1.66-fold within populations and 1.67-fold between populations, appears unrealistically high. Suboptimal technical procedures for quantitative Feulgen staining are probably responsible for these earlier observations.     

The evolutionary history of the white-rayed species of Melampodium (Asteraceae) involved multiple cycles of hybridization and polyploidization

? Premise of the study: Polyploidy plays an important role in race differentiation and eventually speciation. Underlying mechanisms include chromosomal and genomic changes facilitating reproductive isolation and/or stabilization of hybrids. A prerequisite for studying these processes is a sound knowledge on the origin of polyploids. A well-suited group for studying polyploid evolution consists of the three species of Melampodium ser. Leucantha (Asteraceae): M. argophyllum, M. cinereum, and M. leucanthum. ? Methods: The origin of polyploids was inferred using network and tree-based phylogenetic analyses of several plastid and nuclear DNA sequences and of fingerprint data (AFLP). Genome evolution was assessed via genome size measurements, karyotype analysis, and in situ hybridization of ribosomal DNA. ? Key results: Tetraploid cytotypes of the phylogenetically distinct M. cinereum and M. leucanthum had, compared to the diploid cytotypes, doubled genome sizes and no evidence of gross chromosomal rearrangements. Hexaploid M. argophyllum constituted a separate lineage with limited intermixing with the other species, except in analyses from nuclear ITS. Its genome size was lower than expected if M. cinereum and/or M. leucanthum were involved in its origin, and no chromosomal rearrangements were evident. ? Conclusions: Polyploids in M. cinereum and M. leucanthum are of recent autopolyploid origin in line with the lack of significant genomic changes. Hexaploid M. argophyllum also appears to be of autopolyploid origin against the previous hypothesis of an allopolyploid origin involving the other two species, but some gene flow with the other species in early phases of differentiation cannot be excluded.     

Impact of adaptation currents on synchronization of coupled exponential integrate-and-fire neurons

The ability of spiking neurons to synchronize their activity in a network depends on the response behavior of these neurons as quantified by the phase response curve (PRC) and on coupling properties. The PRC characterizes the effects of transient inputs on spike timing and can be measured experimentally. Here we use the adaptive exponential integrate-and-fire (aEIF) neuron model to determine how subthreshold and spike-triggered slow adaptation currents shape the PRC. Based on that, we predict how synchrony and phase locked states of coupled neurons change in presence of synaptic delays and unequal coupling strengths. We find that increased subthreshold adaptation currents cause a transition of the PRC from only phase advances to phase advances and delays in response to excitatory perturbations. Increased spike-triggered adaptation currents on the other hand predominantly skew the PRC to the right. Both adaptation induced changes of the PRC are modulated by spike frequency, being more prominent at lower frequencies. Applying phase reduction theory, we show that subthreshold adaptation stabilizes synchrony for pairs of coupled excitatory neurons, while spike-triggered adaptation causes locking with a small phase difference, as long as synaptic heterogeneities are negligible. For inhibitory pairs synchrony is stable and robust against conduction delays, and adaptation can mediate bistability of in-phase and anti-phase locking. We further demonstrate that stable synchrony and bistable in/anti-phase locking of pairs carry over to synchronization and clustering of larger networks. The effects of adaptation in aEIF neurons on PRCs and network dynamics qualitatively reflect those of biophysical adaptation currents in detailed Hodgkin-Huxley-based neurons, which underscores the utility of the aEIF model for investigating the dynamical behavior of networks. Our results suggest neuronal spike frequency adaptation as a mechanism synchronizing low frequency oscillations in local excitatory networks, but indicate that inhibition rather than excitation generates coherent rhythms at higher frequencies.     

Cryptopolyploidy revisited: the case of Vinca (Apocynaceae)

This investigation presents a look back to ancient times of karyology with modern optical instruments. `Cryptopolyploidy', i.e. an intrinsically polyploid but numerically non-polyploid structure of chromosome complements, today is an obsolete concept of chromosome architecture and evolution, but was actively discussed up to the mid-seventies of the past century. We focus here at a hypothesis of cryptooctoploidy in Vinca difformis (2n = 46), which was based on a measured four-fold chromosome volume compared with V. minor (2n = 46), the proposed diploid. We used DNA flow cytometry and Feulgen densitometry to see, if the postulate of cryptooctoploidy in V. difformis in the retrospect could be justified. It was found not defendable, because V. difformis differed only about 1.55-fold in C-value from V. minor, which is far from a regular multiple and much less than the 4-fold. C-values are given also for V. major, V. herbacea and V. rosea.