Chromosome condensation in mitosis and meiosis of rye (Secale cereale L.)

Structural investigation and morphometry of meiotic chromosomes by scanning electron microscopy (in comparison to light microscopy) of all stages of condensation of meiosis I + II show remarkable differences during chromosome condensation in mitosis and meiosis I of rye (Secale cereale) with respect to initiation, mode and degree of condensation. Mitotic chromosomes condense in a linear fashion, shorten in length and increase moderately in diameter. In contrast, in meiosis I, condensation of chromosomes in length and diameter is a sigmoidal process with a retardation in zygotene and pachytene and an acceleration from diplotene to diakinesis. The basic structural components of mitotic chromosomes of rye are ``parallel fibers{''} and ``chromomeres{''} which become highly compacted in metaphase. Although chromosome architecture in early prophase of meiosis seems similar to mitosis in principle, there is no equivalent stage during transition to metaphase I when chromosomes condense to a much higher degree and show a characteristic ``smooth{''} surface. No indication was found for helical winding of chromosomes either in mitosis or in meiosis. Based on measurements, we propose a mechanism for chromosome dynamics in mitosis and meiosis, which involves three individual processes: (i) aggregation of chromatin subdomains into a chromosome filament, (ii) condensation in length, which involves a progressive increase in diameter and (iii) separation of chromatids. Copyright (C) 2003 S. Karger AG, Basel

Ultrastructural analysis of chromatin in meiosis I plus II of rye (Secale cereale L.)

Scanning electron microscopy (SEM) proves to be an appropriate technique for imaging chromatin organization in meiosis I and II of rye (Secale cereale) down to a resolution of a few nanometers. It could be shown for the first time that organization of basic structural elements (coiled and parallel fibers, chromomeres) changes dramatically during the progression to metaphase I and II. Controlled loosening with proteinase K (after fixation with glutaraldehyde) provides an enhanced insight into chromosome architecture even of highly condensed stages of meiosis. By selective staining with platinum blue, DNA content and distribution can be visualized within compact chromosomes as well as in a complex arrangement of fibers. Chromatin interconnecting threads, which are typically observed in prophase I between homologous and non-homologous chromosomes, stain clearly for DNA. In zygotene transversion of chromatid strands to their homologous counterparts becomes evident. In pachytene segments of synapsed and non-synapsed homologs alternate. At synapsed regions pairing is so intimate that homologous chromosomes form one filament of structural entity. Chiasmata are characterized by chromatid strands which traverse from one homolog to its counterpart. Bivalents are characteristically fused at their telomeric regions. In metaphase I and II there is no structural evidence for primary and secondary constrictions. Copyright (C) 2003 S. Karger AG, Basel

Origin of multiple periodicities in the Fourier power spectra of the Plasmodium falciparum genome

<p>Abstract</p> <p>Background</p> <p>Fourier transforms and their associated power spectra are used for detecting periodicities and protein-coding genes and is generally regarded as a well established technique. Many of the periodicities which have been found with this method are quite well understood such as the periodicity of 3 nt which is associated to codon usage. But what is the origin of the peculiar frequency multiples <it>k</it>/21 which were reported for a tiny section of chromosome 2 in <it>P. falciparum</it>? Are these present in other chromosomes and perhaps in related organisms? And how should we interpret fractional periodicities in genomes?</p> <p>Results</p> <p>We applied the binary indicator power spectrum to all chromosomes of <it>P. falciparum</it>, and found that the frequency overtones <it>k</it>/21 are present only in non-coding sections. We did not find such frequency overtones in any other related genomes. Furthermore, the frequency overtones were identified as artifacts of the way the genome is encoded into a numerical sequence, that is, they are frequency aliases. By choosing a different way to encode the sequence the overtones do not appear. In view of these results, we revisited early applications of this technique to proteins where frequency overtones were reported.</p> <p>Conclusions</p> <p>Some authors hinted recently at the possibility of mapping artifacts and frequency aliases in power spectra. However, in the case of <it>P. falciparum</it> the frequency aliases are particularly strong and can mask the 1/3 frequency which is used for gene detecting. This shows that albeit being a well known technique, with a long history of application in proteins, few researchers seem to be aware of the problems represented by frequency aliases.</p

Lyapunov design of a simple step-size adaptation strategy based on success

A simple success-based step-size adaptation rule for singleparent Evolution Strategies is formulated, and the setting of the corresponding parameters is considered. Theoretical convergence on the class of strictly unimodal functions of one variable that are symmetric around the optimum is investigated using a stochastic Lyapunov function method developed by Semenov and Terkel [5] in the context of martingale theory. General expressions for the conditional expectations of the next values of step size and distance to the optimum under (1 +, λ)-selection are analytically derived, and an appropriate Lyapunov function is constructed. Convergence rate upper bounds, as well as adaptation parameter values, are obtained through numerical optimization for increasing values of λ. By selecting the number of offspring that minimizes the bound on the convergence rate with respect to the number of function evaluations, all strategy parameter values result from the analysis

How Does the Choice of the Lower Boundary Conditions in Large-Eddy Simulations Affect the Development of Dispersive Fluxes Near the Surface?

Large-eddy simulations (LES) are an important tool for investigating the longstanding energy-balance-closure problem, as they provide continuous, spatially-distributed information about turbulent flow at a high temporal resolution. Former LES studies reproduced an energy-balance gap similar to the observations in the field typically amounting to 10–30% for heights on the order of 100 m in convective boundary layers even above homogeneous surfaces. The underestimation is caused by dispersive fluxes associated with large-scale turbulent organized structures that are not captured by single-tower measurements. However, the gap typically vanishes near the surface, i.e. at typical eddy-covariance measurement heights below 20 m, contrary to the findings from field measurements. In this study, we aim to find a LES set-up that can represent the correct magnitude of the energy-balance gap close to the surface. Therefore, we use a nested two-way coupled LES, with a fine grid that allows us to resolve fluxes and atmospheric structures at typical eddy-covariance measurement heights of 20 m. Under different stability regimes we compare three different options for lower boundary conditions featuring grassland and forest surfaces, i.e. (1) prescribed surface fluxes, (2) a land-surface model, and (3) a land-surface model in combination with a resolved canopy. We show that the use of prescribed surface fluxes and a land-surface model yields similar dispersive heat fluxes that are very small near the vegetation top for both grassland and forest surfaces. However, with the resolved forest canopy, dispersive heat fluxes are clearly larger, which we explain by a clear impact of the resolved canopy on the relationship between variance and flux–variance similarity functions

Optimizing the parameters for hydro-jet dissection in fatty tissue — A morphological Ex Vivo analysis

Summary: Background: The advantage of water-jet dissection is the preservation of vessels and nerves. Especially in liver surgery, blood loss can be significantly decreased. The use of water-jet dissectors in other fields of surgery is currently under investigation. The preparation of vessels in fatty tissue is of special interest for plastic surgeons. The optimal technical parameters were investigated. Methods: Abdominal fat tissue of fresh cadavers was cut under standardized conditions with different parameters of the water-jet dissector. Results: One single pass at a cutting pressure between 20 and 60 Bar makes an incision of 8 mm. Deeper cuts can be achieved by repeated application on the same cut. Five passes at 40 Bar results in a depth of 1.7 cm without vessel damage. If the applied pressure is 50 or 60 Bar, up to 7% damaged vessels can be found. The water-jet dissection leads to a water uptake of the cut tissue. Conclusions: The optimal pressure for water-jet dissection of fatty tissue lies between 30 and 40 Bar. The effect of the mechanical irritation of the vessels has to be investigatedin vivo before using the water-jet dissector for preparation of blood vessels in humans, e.g. for flap dissectio

Good Learning and Implicit Model Enumeration

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation