Biogeography of prostrate-leaved geophytes in semi-arid South Africa: hypotheses on functionality

Nowhere is the species diversity of geophytes greater than in the five mediterranean-climate ecosystems of the world. Of these, the Cape mediterranean zone of South Africa is the most speciose. While the relative diversity and importance of geophytes of all of the other four mediterranean regions of the world drops off sharply as one moves into adjacent winter-rainfall desert regions, geophytes in the semi-arid to arid Succulent Karoo (including Namaqualand) remain a very important component of the flora, both in terms of abundance and diversity (comprising 13 to 29% of the regional floras in this region). Apart from species richness, there are also a number of interesting geophyte growth forms in this region. One unusual growth form is geophytes with flattened leaves that lie prostrate on the soil surface. At least eight families (Amaryllidaceae, Colchicaceae, Eriospermaceae, Geraniaceae, Hyacinthaceae, Iridaceae, Orchidaceae and Oxalidaceae) exhibit this growth form. While this growth form is relatively common in many geophyte lineages in the Succulent Karoo biome and the Cape mediterranean zone (Fynbos biome), and occurs infrequently through the summer-rainfall temperate regions of Africa, it is virtually absent in other regions worldwide. A null hypothesis is that the prostrate leaved trait is a neutral characteristic, however biogeographical data do not support this. A neutral trait would be unlikely to show such a clear pattern of distribution. Several alternative hypotheses on the adaptive significance of this growth form are discussed. These include: avoidance of herbivory, reduction in competition from neighbors, creation of a CO₂ enriched environment below the leaves, reduction of water loss around the roots, reduction of water loss through transpiration, precipitation of dew on the leaves and maintenance of optimal leaf temperatures for growth.     

Frost and forest stand effects on the population dynamics of Asplenium scolopendrium

Our objective was to analyze which factors are critical for the dynamics of terrestrial Asplenium scolopendrium populations at the northern edge of its distribution. Therefore, a long-term study (1978–1999) on the performance and demography of this fern species has been carried out in three different forest stands (Picea sitchensis with Fagus sylvatica, P. sitchensis with thinning, and Fraxinus excelsior) in the Netherlands. We used the recorded demographic data to parameterize 37 transition matrices. The number of frost days in severe winters correlated closely with frond damage and resulted in increased mortality and retrogression. Landslip on the trench banks and intraspecific competition were also found to increase mortality. In the F. excelsior plot, plants grew faster and bigger, produced more fronds and formed a more closed fern cover than in the P. sitchensis stands, likely due to higher light levels. Life-table response experiments revealed that reproduction contributed greatly to the differences in projected population growth rates: reproduction was importantly higher in the F. excelsior and in the thinned P. sitchensis plots than in the P. sitchensis–F. sylvatica plot. These differences can be attributed to an initial difference in light climate and to the accumulation of F. sylvatica litter which reduced recruitment. Recruitment occurred on bare soil but also in open moss carpets. We expect that the fern Asplenium scolopendrium will profit at its northern distribution edge when severe winters will occur less frequently, which is one of the expectations for global climate change.     

1,5-Anhydro-2-Deoxy-D-Altritol Oligonucleotides as Conformationally Restricted Analogues of Rna

Abstract

As part of a project concerning the investigation of new hexitol nucleic acids (HNA), the 1,5-anhydro-2-deoxy-D-altritol nucleoside building blocks with a uracil, cytosine, adenine and guanine base moiety were synthesized. The uracil analogue was used for the automated synthesis of corresponding oligonucleotides. Hybridization capabilities of these altritol nucleic acids (ANA) are illustrated by the Tm values obtained for the (a ^hU)₁₃/(dA)₁₃ duplex.     

Methods for the Analyses of Case-Cohort Studies

Case-cohort and nested case-control sampling methods have recently been introduced as a means of reducing cost in large cohort studies. The asymptotic distribution theory results for relative rate estimation based on Cox type partial or pseudolikelihoods for case-cohort and nested case-control studies have been accounted for. However, many researchers use (stratified) frequency table methods for a first or primary summarization of the most important evidence on exposure-disease or dose-response relationships, i.e. the classical Mantel-Haenszel analyses, trend tests and tests for heterogeneity of relative rates. These can be followed by exponential failure time regression methods on grouped or individual data to model relationships between several factors and response. In this paper we present the adaptations needed to use these methods with case-cohort designs, illustrating their use with data from a recent case-cohort study on the relationship between diet, life-style and cancer. We assume a very general setup allowing piecewise constant failure rates, possible recurrent events per individual, independent censoring and left truncation.     

Integration of pharmacometabolomics with pharmacokinetics and pharmacodynamics: towards personalized drug therapy

Personalized medicine, in modern drug therapy, aims at a tailored drug treatment accounting for inter-individual variations in drug pharmacology to treat individuals effectively and safely. The inter-individual variability in drug response upon drug administration is caused by the interplay between drug pharmacology and the patients’ (patho)physiological status. Individual variations in (patho)physiological status may result from genetic polymorphisms, environmental factors (including current/past treatments), demographic characteristics, and disease related factors. Identification and quantification of predictors of inter-individual variability in drug pharmacology is necessary to achieve personalized medicine. Here, we highlight the potential of pharmacometabolomics in prospectively informing on the inter-individual differences in drug pharmacology, including both pharmacokinetic (PK) and pharmacodynamic (PD) processes, and thereby guiding drug selection and drug dosing. This review focusses on the pharmacometabolomics studies that have additional value on top of the conventional covariates in predicting drug PK. Additionally, employing pharmacometabolomics to predict drug PD is highlighted, and we suggest not only considering the endogenous metabolites as static variables but to include also drug dose and temporal changes in drug concentration in these studies. Although there are many endogenous metabolite biomarkers identified to predict PK and more often to predict PD, validation of these biomarkers in terms of specificity, sensitivity, reproducibility and clinical relevance is highly important. Furthermore, the application of these identified biomarkers in routine clinical practice deserves notable attention to truly personalize drug treatment in the near future.     

Rapid Generation of Replication-Deficient Monovalent and Multivalent Vaccines for Bluetongue Virus: Protection against Virulent Virus Challenge in Cattle and Sheep

Since 1998, 9 of the 26 serotypes of bluetongue virus (BTV) have spread throughout Europe, and serotype 8 has suddenly emerged in northern Europe, causing considerable economic losses, direct (mortality and morbidity) but also indirect, due to restriction in animal movements. Therefore, many new types of vaccines, particularly subunit vaccines, with improved safety and efficacy for a broad range of BTV serotypes are currently being developed by different laboratories. Here we exploited a reverse genetics-based replication-deficient BTV serotype 1 (BTV-1) (disabled infectious single cycle [DISC]) strain to generate a series of DISC vaccine strains. Cattle and sheep were vaccinated with these viruses either singly or in cocktail form as a multivalent vaccine candidate. All vaccinated animals were seroconverted and developed neutralizing antibody responses to their respective serotypes. After challenge with the virulent strains at 21 days postvaccination, vaccinated animals showed neither any clinical reaction nor viremia. Further, there was no interference with protection with a multivalent preparation of six distinct DISC viruses. These data indicate that a very-rapid-response vaccine could be developed based on which serotypes are circulating in the population at the time of an outbreak.     

Crystallographic Refinement and Structure-Factor Time-Averaging by Molecular Dynamics in the Absence of a Physical Force Field

Abstract

The application of Molecular-Dynamics simulation in protein-crystallographic structure refinement has become common practice. In this paper, structure optimizations are described where the driving force is derived only from the crystallographic data and not from any physical potential energy function. Under this extreme condition ab initio structure refinement and the application of structure-factor time averaging was investigated using a small 9 atom test system. Success in ab initio refinement, where the starting atomic positions are randomly distributed, depends on the resolution of the crystallographic data used in the optimization. The presence of high resolution data introduces false minima in the X-ray energy profile, enhancing the search problem significantly. On the same system, we also tested the method of time-averaged crystallographically restrained Molecular Dynamics, again in the absence of a physical force field. In this method, the diffraction data is modelled by an ensemble of structures instead of one single structure. In comparison to conventional single-structure refinement, more reflections were required to determine a correct atomic distribution. A time-averaging simulation at 0.2 nm resolution (40 reflections) yielded an incorrect distribution, although a low R-factor was obtained. Simulations at 0.1 nm resolution (248 reflections) gave both low R-factors, 3 to 4%, and correct atomic distributions. The scale factor between the observed and time-averaged calculated structure factor amplitudes appeared to be unstable, when optimized during a time-averaging simulation. Tests of time-averaged restrained simulations with noise added to the observed structure-factor amplitudes, indicated that noise is modelled when no information in the form of constraints or restraints is available to distinguish it from real data.