Genome-wide profiling of promoter recognition by the two-component response regulator CpxR-P in Escherichia coli

In Escherichia coli, the two-component Cpx system comprising the CpxA sensor kinase and the CpxR response regulator modulates gene expression in response to a variety of stresses including membrane-protein damage, starvation, and high osmolarity. To date, the few known CpxR-P target operons were mostly identified by genetic screens. To facilitate the discovery of all target operons, we derived a 15-bp weighted matrix for CpxR-P recognition that takes into account the relative base frequency at each nucleotide position. This matrix essentially consists of two tandem 5'-GTAAA-3' motifs separated by a 5-bp linker. All of the 15-bp stretches on both strands of the E. coli MG1655 genome were then scored for their degree of matching with the matrix and classified in statistical deviation groups. The effectiveness of this screening is indicated by the identification of eight new target operons (ung, ompC, psd, mviA, aroK, rpoErseABC, secA, and aer) among eleven candidates tested. Moreover, the matrix score correlates with the likelihood that a site is a true target and with the relative site affinity for CpxR-P in vitro. Our data indicate that some 100 operons are under direct CpxR-P control and that the signal transduction pathway interacts with several other control circuits in manners hitherto unanticipated.     

Effect of polydimethylsiloxane oxygen carriers on the biological bleaching of hardwood kraft pulp by Trametes versicolor

Summary Improving the availability of oxygen by adding polydimethylsiloxanes (PDMS) oxygen carriers to Trametes versicolor cultures increased pulp brightening. The presence of the oxygen carriers in cultures of T. versicolor with hardwood kraft pulp increased the growth rate of the fungus, but not the ultimate biomass yield. The PDMS also stimulated brightening of hardwood kraft pulp by it T. versicolor immobilized in polyurethane foam. A threefold increase in the oxygen uptake rate in T. versicolor cultures with PDMS was observed. This increase can be explained by elevated oxygen transfer rate and attributed to the surfactant properties of PDMS. Offprint requests to: E. ZiomekIssued as NRCC 32760     

Tropical soils degraded by slash‐and‐burn cultivation can be recultivated when amended with ashes and compost

In many tropical regions, slash‐and‐burn agriculture is considered as a driver of deforestation; the forest is converted into agricultural land by cutting and burning the trees. However, the fields are abandoned after few years because of yield decrease and weed invasion. Consequently, new surfaces are regularly cleared from the primary forest. We propose a reclamation strategy for abandoned fields allowing and sustaining re‐cultivation. In the dry region of south‐western Madagascar, we tested, according to a split‐plot design, an alternative selective slash‐and‐burn cultivation technique coupled with compost amendment on 30–year‐old abandoned fields. Corn plants (Zea mays L.) were grown on four different types of soil amendments: no amendment (control), compost, ashes (as in traditional slash‐and‐burn cultivation), and compost + ashes additions. Furthermore, two tree cover treatments were applied: 0% tree cover (as in traditional slash‐and‐burn cultivation) and 50% tree cover (selective slash‐and‐burn). Both corn growth and soil fertility parameters were monitored during the growing season 2015 up to final harvest. The amendment compost + ashes strongly increased corn yield, which was multiplied by 4–5 in comparison with ashes or compost alone, reaching 1.5 t/ha compared to 0.25 and 0.35 t/ha for ashes and compost, respectively. On control plots, yield was negligible as expected on these degraded soils. Structural equation modeling evidenced that compost and ashes were complementary fertilizing pathways promoting soil fertility through positive effects on soil moisture, pH, organic matter, and microbial activity. Concerning the tree cover treatment, yield was reduced on shaded plots (50% tree cover) compared to sunny plots (0% tree cover) for all soil amendments, except ashes. To conclude, our results provide empirical evidence on the potential of recultivating tropical degraded soils with compost and ashes. This would help mitigating deforestation of the primary forest by increasing lifespan of agricultural lands.     

Appraisal Tools for Clinical Practice Guidelines: A Systematic Review

Introduction

Clinical practice guidelines can improve healthcare processes and patient outcomes, but are often of low quality. Guideline appraisal tools aim to help potential guideline users in assessing guideline quality. We conducted a systematic review of publications describing guideline appraisal tools in order to identify and compare existing tools.

Methods

Among others we searched MEDLINE, EMBASE and the Cochrane Database of Systematic Reviews from 1995 to May 2011 for relevant primary and secondary publications. We also handsearched the reference lists of relevant publications.On the basis of the available literature we firstly generated 34 items to be used in the comparison of appraisal tools and grouped them into thirteen quality dimensions. We then extracted formal characteristics as well as questions and statements of the appraisal tools and assigned them to the items.

Results

We identified 40 different appraisal tools. They covered between three and thirteen of the thirteen possible quality dimensions and between three and 29 of the possible 34 items. The main focus of the appraisal tools were the quality dimensions “evaluation of evidence” (mentioned in 35 tools; 88%), “presentation of guideline content” (34 tools; 85%), “transferability” (33 tools; 83%), “independence” (32 tools; 80%), “scope” (30 tools; 75%), and “information retrieval” (29 tools; 73%). The quality dimensions “consideration of different perspectives” and “dissemination, implementation and evaluation of the guideline” were covered by only twenty (50%) and eighteen tools (45%) respectively.

Conclusions

Most guideline appraisal tools assess whether the literature search and the evaluation, synthesis and presentation of the evidence in guidelines follow the principles of evidence-based medicine. Although conflicts of interest and norms and values of guideline developers, as well as patient involvement, affect the trustworthiness of guidelines, they are currently insufficiently considered. Greater focus should be placed on these issues in the further development of guideline appraisal tools.     

Subtidal macrozoobenthic community resilience to change following natural mouth breaching of the temporarily open/closed East Kleinemonde Estuary,South Africa

The East Kleinemonde Estuary, on the south-east coast of South Africa, typically opens for only short periods, usually <10 days. During a nine-month study in 2006, marine influence persisted for a near-continuous period of three months. This provided an opportunity to explore potential changes in the structure and pattern of the subtidal estuarine macrozoobenthic community. Salinity changes were minimal after mouth opening, decreasing by c. 4 and 8 in the lower and upper estuary, respectively. Salinity decrease was due to river dominance over tidal influence. Two biotic assemblages, structured by sediment characteristics, typified the community throughout the study: a sand-associated group near the mouth and a mud-associated group upstream. Amphipods were proportionally the most abundant group within each assemblage and on each sampling occasion. At the species level, high variability typified the community, with no trends or patterns observed. However, species richness declined from 27–30 to 23 after mouth opening. The number of species returned to former levels at the time of the final survey and just before final mouth closure. An analysis of the subtidal macrozoobenthos in the East Kleinemonde and other temporarily open/closed estuaries (TOCEs) of similar size in the bioregion indicated that communities were typically composed of relatively few, broadly tolerant euryhaline species with no species unique to TOCEs.