Introducing the Multivariate Dale Model in Population‐Based Genetic Association Studies

Until recently, the most common parametric approaches to study the combined effects of several genetic polymorphisms located within a gene or in a small genomic region are, at the genotype level, logistic regressions and at the haplotype level, haplotype analyses. An alternative modeling approach, based on the case/control principle, is to regard exposures (e.g., genetic data such as derived from Single Nucleotide Polymorphisms – SNPs) as random and disease status as fixed and to use a marginal multivariate model that accounts for inter‐relationships between exposures. One such model is the multivariate Dale model. This model is based on multiple logistic regressions. That is why the model, applied in a case/control setting, leads to straightforward interpretations that are similar to those drawn in a classical logistic modeling framework. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Release of dormancy during after-ripening of Agrostemma githago seeds

Freshly harvested seeds of Agrostemma githago L. do not germinate when they are imbibed at 20°C. The block is located in the embryo and is relased by dry storage at 20°C (after-ripening). Freshly harvested seeds complete only a small part of the processes that occur in after-ripened seeds during the lag phase prior to germination (radicle protrusion). After-ripening removed the block on lag phase processes much faster than the block on germination. This was shown both by direct determinations of the completion of lag phase processes and by measurements of the rate of axial protein synthesis, which approximately doubles when seeds are progressing through the lag phase. It is concluded that the percentage germination does not adequately reflect the extent to which the dormancy mechanism has been overcome.     

Measurement of Acetylcholine Release in Freely Moving Rats by Means of Automated Intracerebral Dialysis

The present study demonstrates the feasibility of measuring acetylcholine in perfusion samples collected by means of in vivo brain dialysis in the striata of freely moving rats. The output of the dialysis device was directly connected to an automated sample valve of a HPLC-assay system that comprises a cation exchanger, a post-column enzyme reactor, and an electrochemical detector. The presence of an acetylcholinesterase inhibitor (neostigmine) in the perfusion fluid was required for the detection of acetylcholine in the perfusate. Increasing concentrations of neostigmine induced increasing amounts of acetylcholine. Continuous perfusion with a fixed concentration (2 microM) of neostigmine resulted in gradually increasing amounts of collected acetylcholine over time although a considerable variation between successive samples exists. The brain dialysis technique was further validated by studying the effect of various drugs. Systemically administered atropine increased the output of acetylcholine, whereas the addition of tetrodotoxin to the perfusion fluid resulted in a complete disappearance of the neurotransmitter.     

Mutations in the FAD-binding fold of alcohol oxidase from Hansenula polymorpha.

Alcohol oxidase of methylotrophic yeast is an FAD-containing enzyme. When in its active form, the enzyme is an octamer and located in the peroxisomes. To study the importance of FAD-binding on the activity, octamerization and intracellular localization of the enzyme, alcohol oxidase of Hansenula polymorpha was mutated in its presumed nucleotide-binding domain, which is formed by the N-terminal sequence. Whereas mutations of a glutamic acid residue (E42) reduced the stability of the octamer, it hardly affected enzyme activity and expression. However, replacements of three conserved glycines (G13, G15 and G18) and a conserved glutamic acid (E39) within the fold had severe effects. The mutations not only resulted in loss of enzyme activity but in reduced protein levels as well, probably due to decreased stability of the mutant alcohol oxidase. However, octamerization of the protein still occurred. The existence of inactive octameric proteins provides information about the formation pathway of this octameric flavoprotein.     

Biomechanical interactions of cancer cells with the microvasculature during metastasis

Metastasis is a major, life-threatening complication of cancer. The bloodstream is the most important disseminative route for cancer cells liberated from their parent tumors. Single circulating cancer cells are arrested in the microvasculature, where the vast majority are killed by rapid or slow processes, and the relatively few survivors grow into micrometastases. We review the underlying causes of one type of rapid cancer cell death in the microcirculation, namely, that caused by biomechanical interactions of cancer cells with microvessel walls, which may result in cell surface membrane expansion and lethal rupture. These lethal interactions appear to be important rate-regulators in hematogenous metastasis, and to dictate some aspects of metastatic patterns. Although these are not the only interactions involving cancer cells, in contrast to others involving cellular and humoral defense mechanisms, they have received comparatively little attention.     

A telescopic method for photographing within 8×8 cm minirhizotrons

The volatile organic compounds produced during a sequence of soil incubations under controlled conditions, with either added NH₄ ⁺-N or NO₃ ^--N, were collected and identified. The nature and relative amounts of the volatile organic compounds produced by the microorganisms in the soils were remarkably reproducible and consistent.     

Study of the influence of plasmids on the arbitrary primer polymerase chain reaction fingerprint of Escherichia coli strains

Abstract To study the effect of plasmids on the arbitrary primer-polymerase chain reaction fingerprint of bacterial strains, the Escherichia coli strains DH5, Top10, and W3110 were transformed with plasmids of different sizes: respectively, pUC19, pCEP and two clinically important plasmids carrying resistance to several antibiotics. Total DNA, i.e. both chromosomal and plasmid DNA, was prepared from transformed cells by boiling the cell suspensions and by phenol-chloroform extraction; chromosomal DNA was prepared by the same methods from the non-transformed, plasmid-free strains; plasmid DNA of pUC19 was purchased; plasmid DNA of pCEP was purified from the transformed strains by caesium chloride density gradient centrifugation. Arbitrarily primed polymerase chain reaction was carried out for all of these preparations. Amplification carried out independently with three different primers resulted in similar patterns for the chromosomal preparations whether or not plasmid was present. Amplification of plasmid DNA gave different patterns, characterized by fragments larger than those obtained when total or chromosomal DNA were used as the target. These data illustrate that the plasmids studied here do not influence the chromosomal arbitrarily primed PCR fingerprint, although plasmids alone are amplified in the absence of chromosomal DNA. Experiments comparing different relative concentrations of plasmid and chromosomal DNA indicate that under natural conditions the amount of chromosomal DNA per cell is sufficient to inhibit observable amplification of the plasmid(s) present.     

An ecosystems approach to base-rich freshwater wetlands,with special reference to fenlands

A survey of base-rich wetlands in The Netherlands is presented. The main area of their occurrence is the low-lying Holocene part of the country, until some thousand years ago a large and coherent wetland landscape: the Holland wetland. The development of various parts of the Holland wetland into marshes, fens and bogs can be understood from hydrological relations in mire basins, as recognized in the distinction of primary, secondary and tertiary mire basin stages. Presently, the remnants of the Holland wetland are separate base-rich wetlands. The succession of their vegetation reflects various abiotic conditions and human influences. Three main developmental periods are distinguished as regards these factors. The first, geological period of mire development is seen as a post-glacial relaxation, with the inertia due to the considerable mass of wetland as a stabilizing factor. Biological “grazing” influences, as an aspect of utilization by humans, converted base-rich wetlands to whole new types in the second, historical period. Presently, mass and harvesting have decreased in importance, and actual successions in terrestrializing turbaries seem to reflect rapidly changing environmental conditions. Human control could well become the most important factor in the future development of wetland nature. The present value of open fen vegetation strongly depends on the continuation of the historical harvesting. The development of wooded fen may help to increase the mass of wetland in the future. Best results in terms of biodiversity are expected when their base state is maintained through water management. The vegetation and hydrology of floating fens in terrestrializing turbaries is treated in some more detail. Various lines and phases in the succession are distinguished. Open fen vegetation at base-rich, yet nutrient-poor sites is very rich in species threatened elsewhere. The fast acidification of certain such fens is attributed to hydrological and management factors. This acidification is illustrated in the profile of a floating raft sample. At the scale of these small fens, the elemental structure comprising base-rich fen, transitional fen and bog vegetation, is not as stable as it was in the large Holland wetland. A critical role seems to be played by the supply of bases with the water influx. The changing base state is supposed to change the nutrient cycling to such an extent that it would be correct to call this trophic excitation of the ecosystem, rather than just eutrophication. Eutrophication indicates a quantitative reaction to an increased nutrient supply, the internal system being unaltered. The drainage of fens, resulting in an increased productivity of the vegetation, provides another example of excitation, to the effect that the functional system is dramatically changed internally.