Lessons from practice: assessing early progress and success in river rehabilitation

This article comprises a literature analysis of 41 river rehabilitation projects to assess the short-term (5 years) ability of indicator groups to demonstrate progress towards river rehabilitation goals. Positive indications were compared to land-use, river size, rehabilitation intervention and time. A questionnaire was developed to investigate river manager’s interpretation of rehabilitation success and to assess their level of adherence to recommendations in the literature with regard to rehabilitation assessment on a conceptual level. A total of 54 responses were received from respondents based in Germany, The Netherlands and the United Kingdom. The results indicate that macroinvertebrate indicators, while widely used in assessing river rehabilitation efforts, exhibited a lower frequency of positive responses than most other indicator types in the short term. Conversely, terrestrial floodplain indicators exhibited the most frequent level of positive response for all ecological type indicators leading to recommendations for further investigations into their use for short-term monitoring. Assessment procedures recommended in literature are largely followed, illustrating the advances that have been made with regard to assessment planning. Indicator responses are influenced by scale factors, for example, land-use and river size, that are often not considered by rehabilitation managers. While an emphasis is placed on ecological, hydrological and morphological indicators in monitoring schemes, the socioeconomic perspective (emphasized in the literature as forming an integral part of the river system) is neglected.     

Sugar-induced increases in trehalose 6-phosphate are correlated with redox activation of ADPglucose pyrophosphorylase and higher rates of starch synthesis in Arabidopsis thaliana

Tre6P (trehalose 6-phosphate) is implicated in sugar-signalling pathways in plants, but its exact functions in vivo are uncertain. One of the main obstacles to discovering these functions is the difficulty of measuring the amount of Tre6P in plant tissues. We have developed a highly specific assay, using liquid chromatography coupled to MS-Q3 (triple quadrupole MS), to measure Tre6P in the femto-picomole range. The Tre6P content of sucrose-starved Arabidopsis thaliana seedlings in axenic culture increased from 18 to 482 pmol x g(-1) FW (fresh weight) after adding sucrose. Leaves from soil-grown plants contained 67 pmol x g(-1) FW at the end of the night, which rose to 108 pmol x g(-1)FW after 4 h of illumination. Even greater changes in Tre6P content were seen after a 6 h extension of the dark period, and in the starchless mutant, pgm. The intracellular concentration of Tre6P in wild-type leaves was estimated to range from 1 to 15 microM. It has recently been reported that the addition of Tre6P to isolated chloroplasts leads to redox activation of AGPase (ADPglucose pyrophosphorylase) [Kolbe, Tiessen, Schluepmann, Paul, Ulrich and Geigenberger (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 11118-11123]. Using the new assay for Tre6P, we found that rising sugar levels in plants are accompanied by increases in the level of Tre6P, redox activation of AGPase and the stimulation of starch synthesis in vivo. These results indicate that Tre6P acts as a signalling metabolite of sugar status in plants, and support the proposal that Tre6P mediates sucrose-induced changes in the rate of starch synthesis.     

Plasticity as a plastic response: how submergence-induced leaf elongation in Rumex palustris depends on light and nutrient availability in its early life stage

Plants may experience different environmental cues throughout their development which interact in determining their phenotype. This paper tests the hypothesis that environmental conditions experienced early during ontogeny affect the phenotypic response to subsequent environmental cues. This hypothesis was tested by exposing different accessions of Rumex palustris to different light and nutrient conditions, followed by subsequent complete submergence. Final leaf length and submergence-induced plasticity were affected by the environmental conditions experienced at early developmental stages. In developmentally older leaves, submergence-induced elongation was lower in plants previously subjected to high-light conditions. Submergence-induced elongation of developmentally younger leaves, however, was larger when pregrown in high light. High-light and low-nutrient conditions led to an increase of nonstructural carbohydrates in the plants. There was a positive correlation between submergence-induced leaf elongation and carbohydrate concentration and content in roots and shoots, but not with root and shoot biomass before submergence. These results show that conditions experienced by young plants modulate the responses to subsequent environmental conditions, in both magnitude and direction. Internal resource status interacts with cues perceived at different developmental stages in determining plastic responses to the environment.     

18F-2-deoxy-2-fluoro-D-glucose positron emission tomography, computed tomography, and magnetic resonance imaging for the detection of experimental colorectal liver metastases

During the treatment of colorectal liver metastases, evaluation of treatment efficacy is of the utmost importance for decision making. The aim of the present study was to explore the ability of preclinical imaging modalities to detect experimental liver metastases. Nine male Wag/Rij rats underwent a laparotomy with intraportal injection of CC531 tumor cells. On days 7, 10, and 14 after tumor induction, sequential positron emission tomography (PET), computed tomography (CT), and magnetic resonance imaging (MRI) scans were acquired of each rat. At each time point, three rats were euthanized and the metastases in the liver were documented histologically. Topographically, the liver was divided into eight segments and the image findings were compared on a segment-by-segment basis with the histopathologic findings. Sixty-four liver segments were analyzed, 20 of which contained tumor deposits. The overall sensitivity of PET, CT, and MRI was 30%, 25%, and 20%, respectively. For the detection of tumors with a histologic diameter exceeding 1 mm (n = 8), the sensitivity of PET, CT, and MRI was 63%, 38%, and 38%, respectively. The overall specificity of PET, CT, and MRI was 98%, 100%, and 93%, respectively. This study showed encouraging detectability and sensitivity for preclinical imaging of small liver tumors and provides valuable information on the imaging techniques for designing future protocols.     

Inferring differences in the distribution of reaction rates across conditions

Elucidating changes in the distribution of reaction rates in metabolic pathways under different conditions is a central challenge in systems biology. Here we present a method for inferring regulation mechanisms responsible for changes in the distribution of reaction rates across conditions from correlations in time-resolved data. A reversal of correlations between conditions reveals information about regulation mechanisms. With the use of a small in silico hypothetical network, based on only the topology and directionality of a known pathway, several regulation scenarios can be formulated. Confronting these scenarios with experimental data results in a short list of possible pathway regulation mechanisms associated with the reversal of correlations between conditions. This procedure allows for the formulation of regulation scenarios without detailed prior knowledge of kinetics and for the inference of reaction rate changes without rate information. The method was applied to experimental time-resolved metabolomics data from multiple short-term perturbation-response experiments in S. cerevisiae across aerobic and anaerobic conditions. The method's output was validated against a detailed kinetic model of glycolysis in S. cerevisiae, which showed that the method can indeed infer the correct regulation scenario.     

Scaling of offspring number and mass to plant and animal size: model and meta-analysis

The scaling of reproductive parameters to body size is important for understanding ecological and evolutionary patterns. Here, we derived allometric relationships for the number and mass of seeds, eggs and neonates from an existing model on population production. In a separate meta-analysis, we collected 79 empirical regressions on offspring mass and number covering different taxa and various habitats. The literature review served as a validation of the model, whereas, vice versa, consistency of isolated regressions with each other and related ecological quantities was checked with the model. The total offspring mass delivered in a reproductive event scaled to adult size with slopes in the range of about 3/4 to 1. Exponents for individual seed, egg and neonate mass varied around 1/2 for most heterotherms and between 3/4 and 1 for most homeotherms. The scaling of the progeny number released in a sowing, clutch or litter was opposite to that of their size. The linear regressions fitted into a triangular envelope where maximum offspring mass is limited by the size of the adult. Minimum seed and egg size scaled with weight exponents of approximately 0 up to 1/4. These patterns can be explained by the influence of parents on the fate of their offspring, covering the continuum of r-strategists (pelagic–aquatic, arial, most invertebrates, heterotherms) and K-strategists (littoral–terrestrial, some invertebrates, homeotherms).     

Protein tyrosine phosphatases: functional inferences from mouse models and human diseases

Some 40-odd genes in mammals encode phosphotyrosine-specific, 'classical' protein tyrosine phosphatases. The generation of animal model systems and the study of various human disease states have begun to elucidate the important and diverse roles of protein tyrosine phosphatases in cellular signalling pathways, development and disease. Here, we provide an overview of those findings from mice and men, and indicate several novel approaches that are now being exploited to further our knowledge of this fascinating enzyme family.