An apparatus for studying the thermal transition of nucleic acids at high resolution

A fully automatized apparatus for studying the spectrophotometer-monitored thermal transition of nucleic acids is described.Measurements are made with improved accuracy over standard methods, under thermodynamically well-defined conditions (thermal and phase equilibrium). Examples of highly resolved melting profiles of DNA are presented along with the general procedures for the computer treatment of experimental data.     

A Matched Pairs Selection method for the analysis of abundance data with many zero values

Abstract. A simple method is described to analyze plant species abundance data with many zero values. To investigate the impact of an environmental factor on rare species, two subsets of sampling plots are selected pair-wise from the original data set. They differ in the value of the particular factor under consideration but are similar with respect to all other factors. Subsequently, the botanical composition of these subsets, including rare species, is compared using non-parametric tests. An example is given from a study on ditch bank vegetation. Some limitations, and a method for taking into account the dependence of the statistical tests, are discussed.     

The problems of evaluating the automatized and exploratory intellectual actions of man]

On the basis of psychological testing two groups of subjects have been formed: "automatizators" and "searchers". The incompatibility in the individual structure of the ability to automatized and searching actions, according to the data, are connected with the presence of the complex of alternative signs of cognitive styles. The neurophysiological organization of searching and automatized intellectual actions was studied by a method of computer toposcopy of the synchronous electrical processes. It has been shown that there are spatial-frequency interactions of electrical processes of the cerebral cortex, characteristic for each of the two above mentioned individuals groups, which are probably based on the functioning of neuronal networks with different lability levels.     

Seed bank assembly in an unmanaged ruderal grassland recovering from long-term exposure to industrial emissions

The main aim of this 3-year study was to relate the temporal patterns in seed bank composition of a ruderal grassland previously subjected to industrial pollution with the successional patterns in the above-ground vegetation. In particular, we tested whether the observed changes conformed to a paradigm of declining seed numbers and diversity and decreasing similarity between seed bank and vegetation, as previously formulated for secondary successions. We found that seed numbers and the number of species per soil sample increased during the 3 years of the study. The compositional similarity between seed bank and vegetation did increase for the 0–2 cm surface layer, and remained roughly constant for deeper soil layers. Thus, the patterns found differed from those of other secondary successional communities and do not support the tested paradigm. Rather, our findings resemble those from a number of primary successional ecosystems. We suggest that temporal patterns of similarity between seed bank and vegetation should be interpreted in terms of the factors that determine the relative rates of compositional change in vegetation and seed bank at different stages of succession. Our study also provides information about the seed bank persistence of 22 species, including several species for which such knowledge previously was scarce. In particular, this study indicates the extreme longevity of the seeds of the halophytic grass Puccinellia distans. Several years after its rapid decline in the vegetation, this species dominated the seed bank, and no measurable decline in seed density was detected during this study.     

Seed bank assembly in an unmanaged ruderal grassland recovering from long-term exposure to industrial emissions

The main aim of this 3-year study was to relate the temporal patterns in seed bank composition of a ruderal grassland previously subjected to industrial pollution with the successional patterns in the above-ground vegetation. In particular, we tested whether the observed changes conformed to a paradigm of declining seed numbers and diversity and decreasing similarity between seed bank and vegetation, as previously formulated for secondary successions. We found that seed numbers and the number of species per soil sample increased during the 3 years of the study. The compositional similarity between seed bank and vegetation did increase for the 0–2 cm surface layer, and remained roughly constant for deeper soil layers. Thus, the patterns found differed from those of other secondary successional communities and do not support the tested paradigm. Rather, our findings resemble those from a number of primary successional ecosystems. We suggest that temporal patterns of similarity between seed bank and vegetation should be interpreted in terms of the factors that determine the relative rates of compositional change in vegetation and seed bank at different stages of succession. Our study also provides information about the seed bank persistence of 22 species, including several species for which such knowledge previously was scarce. In particular, this study indicates the extreme longevity of the seeds of the halophytic grass Puccinellia distans. Several years after its rapid decline in the vegetation, this species dominated the seed bank, and no measurable decline in seed density was detected during this study.     

Analysis of hippocampal participation in organizing animal behavior

Based on some properties of hippocampal circuitry, an attempt has been made to interpret behavioural changes in hippocampectomized animals. The regulation of cortically initiated information flow through the hippocampus by the unspecific inhibitory blocking, selective depression or potentiation of intrinsic hippocampal chains has been analyzed at different levels of reticulo-septal input, characteristic of different behavioural patterns. By the first mode of hippocampal regulation the ignorance of irrelevant stimuli during an automatized behaviour is achieved; temporary selective depression or strengthening of influence of certain relevant stimuli takes places in the two other modes.     

Computerization of specimen data from the Edward Lee Greene Herbarium (ND-G) at Notre Dame

Computerization of the Edward Lee Greene Herbarium at Notre Dame is described. Reasons for the justification of such a project and the steps involved in data accumulation and data processing are presented. Results are or will be available in two forms: 1) formal publications containing summary information, including information on the more than 4400 taxa that Greene named; and 2) a computerized data bank that today can provide answers to questions from individual systematists about the 65,000 specimens. Problems in automation are discussed, as are the relation of this project to similar ones. Finally, an invitation is extended to readers to query the data bank without cost.     

SASBDB: Towards an automatically curated and validated repository for biological scattering data

Small‐angle scattering (SAS) of X‐rays and neutrons is a fundamental tool to study the nanostructural properties, and in particular, biological macromolecules in solution. In structural biology, SAS recently transformed from a specialization into a general technique leading to a dramatic increase in the number of publications reporting structural models. The growing amount of data recorded and published has led to an urgent need for a global SAS repository that includes both primary data and models. In response to this, a small‐angle scattering biological data bank (SASBDB) was designed in 2014 and is available for public access at www.sasbdb.org . SASBDB is a comprehensive, free and searchable repository of SAS experimental data and models deposited together with the relevant experimental conditions, sample details and instrument characteristics. SASBDB is rapidly growing, and presently has over 1,000 entries containing more than 1,600 models. We describe here the overall organization and procedures of SASBDB paying most attention to user‐relevant information during submission. Perspectives of further developments, in particular, with OneDep system of the Protein Data Bank, and also widening of SASBDB including new types of data/models are discussed.     

A rapid method for quantitative determination of L-tryptophan

Summary A modified colorimetric technique automatized by an Alpkem micro-continuous flow analyser was described for estimating the concentration of L-tryptophan in fermentation broth. This approach provided a convenient alternative to HPLC for L-tryptophan estimation and may help to avoid the time-consuming and laborious screening work encountered in the strain improvement programme.     

Structure and mechanisms of function of visual system proteins

Recent progress in understanding visual signal transduction in retinal cells is summarized. The roles of particular proteins in activation, amplification and termination of the photoresponse are described. Detailed information on the structure and function of the photoreceptor protein rhodopsin is presented. The latest data on visual pigment sequences, rhodopsin mutations in the autosomal-dominant retinitis pigmentosa, and the results of site-directed mutagenesis of the rhodopsin molecule are summarized.     

双重条形码技术在临床组织样本库标准化管理中的应用

双重条形码的应用改变了临床组织样本库传统的记录模式,具有信息录入、储存、浏览、检索以及数据维护、管理等功能,并具有安全、高效、操作方便等优点。可准确、动态地反映储存于组织样本库中的样本信息,从而大大提高组织样本库的样本管理效率和质量。     

Spatial patterns produced by a reaction-diffusion system in primary hair follicles

This paper is the third in a series examining the role of a reaction-diffusion (RD) system as the principal mechanism providing spatial information for cell differentiation during hair follicle initiation and development and hair fibre formation. A theoretical mechanism is described by which the RD system supplies positional information during hair follicle development. Solutions of the RD system within the primordial follicle are described as well as the sequence of spatial patterns provides the follicle/epidermis boundary conditions required to account for the density and grouping of follicles during initiation. At the same time the spatial patterns are also shown to be capable of providing the positional information which determines various geometrical aspects of follicle development; in particular the development of follicles at an angle to the skin surface and the initiation and location of sweat glands and sebaceous glands on the follicle.     

Problems and pitfalls in a clinical research data management system

The problems and pitfalls encountered in the computerized data bank for the Netherlands Coronary Surgery (NCS) study are reviewed. This study involved 848 patients seen before coronary artery surgery and at 1 and 3 yr after surgery. Nineteen data forms were used resulting in maximally 1142 variables per patient. The importance of quality control is emphasized as well as the efficient transfer of information from data bank to statistical processing.     

Problems and pitfalls in a clinical resarch data management system

The problems and pitfalls encountered in the computerized data bank for the Netherlands Coronary Surgery (NCS) study are reviewed. This study involved 848 patients seen before coronary artery surgery and at 1 and 3 yr after surgery. Nineteen data forms were used resulting in maximally 1142 variables per patient. The importance of quality control is emphasized as well as the efficient transfer of information from data bank to statistical processing.     

VANTED: A system for advanced data analysis and visualization in the context of biological networks

Background  

Recent advances with high-throughput methods in life-science research have increased the need for automatized data analysis and visual exploration techniques. Sophisticated bioinformatics tools are essential to deduct biologically meaningful interpretations from the large amount of experimental data, and help to understand biological processes.     

Simultaneous modelling of metabolic, genetic and product-interaction networks

The creation of cell models from annotated genome information, as well as additional data from other databases, requires both a format and medium for its distribution. Standards are described for the representation of the data in the form of Document Type Definitions (DTDs) for XML files. Separate DTDs are detailed for genetic, metabolic and gene product-interaction networks, which can be used to hold information on individual subsystems, or which may be combined to create a whole cell DTD. In the execution of this work, a fifth DTD was also created for a metabolite thesaurus, which allows incorporation of metabolite synonyms and generic nomenclature data into the models. A gene-regulation classification scheme was also created, to facilitate incorporation of gene regulatory information in an efficient manner. The work is described with particular reference to the metabolic network of Escherichia coli, which contains 808 individual enzymes. The assignment of confidence levels to these data, through the use of Gene Ontology evidence codes, is highlighted. In silico investigations may now be performed using the mathematical simulation workbench, DBsolve, which incorporates the facility to introduce data directly from XML.     

Time-related shape control modifications during erythrocyte storage with additive solutions

To obtain more detailed information on the reversibility of shape alterations in blood bank stored erythrocytes, we have studied shape recovery after chemical crenation and rheological properties in 8 PAGGS-sorbitol preserved erythrocyte concentrates during a five week storage period under blood bank conditions. Our results show that red cell capability to regain a normal discoid shape after chemical crenation decreases during storage but is not lost over a five week period. Moreover there is a significant but weak correlation between red cell ATP content and both shape recovery capability and viscosity. Our results confirm suspicious that red cell shape perturbations following blood bank storage are widely reversible. Two different mechanisms may be involved in reducing shape recovery capability during storage, namely an ATP-dependent mechanism and an energy-independent one. The energy dependent mechanism may be preserved by the previous addition of solutions which maintain higher energy levels during storage.     

Quantitative measure of sexual selection with respect to the operational sex ratio: a comparison of selection indices

Despite numerous indices proposed to predict the evolution of mating systems, a unified measure of sexual selection has remained elusive. Three previous studies have compared indices of sexual selection under laboratory conditions. Here, we use a genetic study to compare the most widely used measures of sexual selection in natural populations. We explored the mating and reproductive successes of male and female bank voles, Clethrionomys glareolus, across manipulated operational sex ratios (OSRs) by genotyping all adult and pup bank voles on 13 islands using six microsatellite loci. We used Bateman's principles (Is and I and Bateman gradients) and selection coefficients (s' and beta') to evaluate, for the first time, the genetic mating system of bank voles and compared these measures with alternative indices of sexual selection (index of monopolization and Morisita's index) across the OSRs. We found that all the sexual selection indices show significant positive intercorrelations for both males and females, suggesting that Bateman's principles are an accurate and a valid measure of the mating system. The Bateman gradient, in particular, provides information over and above that of other sexual selection indices. Male bank voles show a greater potential for sexual selection than females, and Bateman gradients indicate a polygynandrous mating system. Selection coefficients reveal strong selection gradients on male bank vole plasma testosterone level rather than body size.