Severe liver disease resembling PSC in mice with K5-Cre mediated deletion of Krüppel-like factor 5 (Klf5)

Transgenic Research - Chronic cholestatic liver diseases including primary sclerosing cholangitis (PSC) present a complex spectrum with regards to the cause, age of manifestation and...     

Effects of nitrogen enrichment on zooplankton biomass and N:P recycling ratios across a DOC gradient in northern-latitude lakes

We used data from whole-lake studies to assess how changes in food quantity (phytoplankton biomass) and quality (phytoplankton community composition, seston C:P and N:P) with N fertilization affect zooplankton biomass, community composition and C:N:P stoichiometry, and their N:P recycling ratio along a gradient in lake DOC concentrations. We found that despite major differences in phytoplankton biomass with DOC (unimodal distributions, especially with N fertilization), no major differences in zooplankton biomass were detectable. Instead, phytoplankton to zooplankton biomass ratios were high, especially at intermediate DOC and after N fertilization, implying low trophic transfer efficiencies. An explanation for the observed low phytoplankton resource use, and biomass responses in zooplankton, was dominance of colony forming chlorophytes of reduced edibility at intermediate lake DOC, combined with reduced phytoplankton mineral quality (enhanced seston N:P) with N fertilization. N fertilization, however, increased zooplankton N:P recycling ratios, with largest impact at low DOC where phytoplankton benefitted from light sufficiently to cause enhanced seston N:P. Our results suggest that although N enrichment and increased phytoplankton biomass do not necessarily increase zooplankton biomass, bottom-up effects may still impact zooplankton and their N:P recycling ratio through promotion of phytoplankton species of low edibility and altered mineral quality.

     

Variable shrimp in variable environments: reproductive investment within Palaemon varians

The maternal environment may influence the quantity and quality of resources invested in offspring (per-offspring provisioning) and this trait, in turn, affects larval fitness and may carry-over into early juvenile life. Here, per-offspring investment was measured across three consecutive breeding seasons for the caridean shrimp, Palaemon varians. Egg and hatchling larval dry weight as well as hatchling larval biochemical composition were measured. Results indicate that egg volume is positively correlated with dry weight, but egg volume as a proxy for dry weight should be used with caution. Correlations were identified between per-offspring investment and average breeding season temperature, but the period over which temperature was averaged was important to whether these correlations were positive or negative, highlighting the complexity of identifying environmental influence on phenotypic traits. The most important factor determining offspring size and per-offspring investment was maternal size, which may be influenced by the environment as carapace length varied significantly between breeding seasons. These data demonstrate variation in egg and larval composition, related to maternal size, which will affect early life traits and survivorship for P. varians.

     

Interactions between cover crops and soil microorganisms increase phosphorus availability in conservation agriculture

Plant and Soil - An essential task of agricultural systems is to improve internal phosphorus (P) recycling. Cover crops and tillage reduction can increase sustainability, but it is not known...     

Can differences in microbial abundances help explain enhanced N2O emissions in a permanent grassland under elevated atmospheric CO2?

Long‐term effects of elevated atmospheric CO₂ on the ammonia‐oxidizing and denitrifying bacteria in a grassland soil were investigated to test whether a shift in abundance of these N‐cycling microorganisms was responsible for enhanced N₂O emissions under elevated atmospheric CO₂. Soil samples (7.5 cm increments to 45 cm depth) were collected in 2008 from the University of Giessen Free Air Carbon dioxide Enrichment (GiFACE), a permanent grassland exposed to moderately elevated atmospheric CO₂ (+20%) since 1998. GiFACE plots lay on a soil moisture gradient because of gradually changing depth to the underlying water table and labeled as the DRY block (furthest from water table), MED block (intermediate to water table), and WET block (nearest to water table). Mean N₂O emissions measured since 1998 have been significantly higher under elevated CO₂. This study sought to identify microbial and biochemical parameters that might explain higher N₂O emissions under elevated CO₂. Soil biochemical parameters [extractable organic carbon (EOC), dissolved organic nitrogen (DON), NH₄⁺, NO₃^?], and abundances of genes encoding the key enzymes involved in ammonia oxidation (amoA) and denitrification (nirK, nirS, nosZ) depended more on soil depth and block (underlying soil moisture gradient) than on elevated CO₂. Ammonia oxidation and denitrification gene abundances, relative abundances (ratios) of nirS to nirK, of nosZ to both nirS and to nirK, and of the measured soil biochemical properties DON and NO₃^? tended to be lower in elevated CO₂ plots as compared with ambient plots in the MED and WET blocks while the DRY block exhibited an opposite trend. High N₂O emissions under elevated CO₂ in the MED and WET blocks correlated with lower nosZ to nirK ratios, suggesting that increased N₂O emissions under elevated CO₂ might be caused by a higher proportion of N₂O‐producing rather than N₂O consuming (N₂ producing) denitrifiers.     

Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study

For the last 2 decades, supertree reconstruction has been an active field of research and has seen the development of a large number of major algorithms. Because of the growing popularity of the supertree methods, it has become necessary to evaluate the performance of these algorithms to determine which are the best options (especially with regard to the supermatrix approach that is widely used). In this study, seven of the most commonly used supertree methods are investigated by using a large empirical data set (in terms of number of taxa and molecular markers) from the worldwide flowering plant family Sapindaceae. Supertree methods were evaluated using several criteria: similarity of the supertrees with the input trees, similarity between the supertrees and the total evidence tree, level of resolution of the supertree and computational time required by the algorithm. Additional analyses were also conducted on a reduced data set to test if the performance levels were affected by the heuristic searches rather than the algorithms themselves. Based on our results, two main groups of supertree methods were identified: on one hand, the matrix representation with parsimony (MRP), MinFlip, and MinCut methods performed well according to our criteria, whereas the average consensus, split fit, and most similar supertree methods showed a poorer performance or at least did not behave the same way as the total evidence tree. Results for the super distance matrix, that is, the most recent approach tested here, were promising with at least one derived method performing as well as MRP, MinFlip, and MinCut. The output of each method was only slightly improved when applied to the reduced data set, suggesting a correct behavior of the heuristic searches and a relatively low sensitivity of the algorithms to data set sizes and missing data. Results also showed that the MRP analyses could reach a high level of quality even when using a simple heuristic search strategy, with the exception of MRP with Purvis coding scheme and reversible parsimony. The future of supertrees lies in the implementation of a standardized heuristic search for all methods and the increase in computing power to handle large data sets. The latter would prove to be particularly useful for promising approaches such as the maximum quartet fit method that yet requires substantial computing power.     

Solute and particle retention in the digestive tract of the Phillip's dikdik (Madoqua saltiana phillipsi), a very small browsing ruminant: biological and methodological implications

Morphological characteristics of the forestomach, as well as reports of a natural diet that mostly excludes monocots, suggest that dikdiks (Madoqua spp.), among smallest extant ruminants, should have a 'moose-type' forestomach physiology characterised by a low degree of selective particle retention. We tested this assumption in a series of feeding experiments with 12 adult Phillip's dikdiks (Madoqua saltiana phillipsi) on three different intake levels per animal, using cobalt-EDTA as a solute marker and a 'conventional' chromium-mordanted fibre (<2 mm; mean particle size 0.63 mm) marker for the particle phase. Body mass had no influence on retention measurements, whereas food intake level clearly had. Drinking water intake was not related to the retention of the solute marker. In contrast to our expectations, the particle marker was retained distinctively longer than the solute marker. Comparisons with results in larger ruminants and with faecal particle sizes measured in dikdiks suggested that in these small animals, the chosen particle marker was above the critical size threshold, above which particle delay in the forestomach is not only due to selective particle retention (as compared to fluids), but additionally due to the ruminal particle sorting mechanism that retains particles above this threshold longer than particles below this threshold. A second study with a similar marker of a lower mean particle size (0.17 mm, which is below the faecal particle size reported for dikdiks) resulted in particle and fluid retention patterns similar to those documented in other 'moose-type' ruminants. Nevertheless, even this smaller particle marker yielded retention times that were longer than those predicted by allometric equations based on quarter-power scaling, providing further support for observations that small ruminants generally achieve longer retention times and higher digestive efficiencies than expected based on their body size.