Mechanism of substrate hydrolysis by a thermophilic endoglucanase from Thermotoga maritima†

A cellulase from the thermophile, Thermotoga maritima, hydrolyzed oligosaccharide substrates by an exoglucanase mode of action but acted as an endoglucanase to rapidly reduce the viscosity of the soluble polysaccharides carboxymethylcellulose and barley -glucan. The V _max for hydrolysis of the substrate, p-nitrophenyl -d-cellobioside, was 42 mol min^–1 (mg protein)^–1, while that for barley -glucan was 637. The enzyme had little activity on crystalline cellulose.     

The cellulase complex of Neurospora crassa: activity, stability and release

The temperature and pH optima, and the temperature and pH stability, of crude and purified enzymes of the cellulase complex of the cellulolytic ascomycete fungus Neurospora crassa were investigated. The effects of some non-ionic surfactants and fatty acids on the production/release of enzymes of cellulase complex were also examined. For the different enzymes of the complex, activity maxima occurred between pH 4.0 and 7.0, with pH 5.0 being close to optimal for stability of all. Temperature optima for activity ranged between 45 and 65 degrees C, with the stability optimum between 45 and 50 degrees C. The presence of C18 fatty acids and surfactants resulted in increased production of both endoglucanase and exoglucanase in the medium. Oleic acid was the most effective fatty acid tested, and Tween 80 the most effective surfactant. Oleic acid had no detectable effect on production of beta-glucosidase, and Tween 80 actually reduced its production.     

Gene expression profiles of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum

Inflammatory breast cancer (IBC) is a highly aggressive breast cancer that metastasizes largely via tumor emboli, and has a 5-year survival rate of less than 30%. No unique genomic signature has yet been identified for IBC nor has any specific molecular therapeutic been developed to manage the disease. Thus, identifying gene expression signatures specific to IBC remains crucial. Here, we compare various gene lists that have been proposed as molecular footprints of IBC using different clinical samples as training and validation sets and using independent training algorithms, and determine their accuracy in identifying IBC samples in three independent datasets. We show that these gene lists have little to no mutual overlap, and have limited predictive accuracy in identifying IBC samples. Despite this inconsistency, single-sample gene set enrichment analysis (ssGSEA) of IBC samples correlate with their position on the epithelial-hybrid-mesenchymal spectrum. This positioning, together with ssGSEA scores, improves the accuracy of IBC identification across the three independent datasets. Finally, we observed that IBC samples robustly displayed a higher coefficient of variation in terms of EMT scores, as compared to non-IBC samples. Pending verification that this patient-to-patient variability extends to intratumor heterogeneity within a single patient, these results suggest that higher heterogeneity along the epithelial-hybrid-mesenchymal spectrum can be regarded to be a hallmark of IBC and a possibly useful biomarker.     

Comparing benthic biogeochemistry at a sandy and a muddy site in the Celtic Sea using a model and observations

Results from a 1D setup of the European Regional Seas Ecosystem Model (ERSEM) biogeochemical model were compared with new observations collected under the UK Shelf Seas Biogeochemistry (SSB) programme to assess model performance and clarify elements of shelf-sea benthic biogeochemistry and carbon cycling. Observations from two contrasting sites (muddy and sandy) in the Celtic Sea in otherwise comparable hydrographic conditions were considered, with the focus on the benthic system. A standard model parameterisation with site-specific light and nutrient adjustments was used, along with modifications to the within-seabed diffusivity to accommodate the modelling of permeable (sandy) sediments. Differences between modelled and observed quantities of organic carbon in the bed were interpreted to suggest that a large part (>90%) of the observed benthic organic carbon is biologically relatively inactive. Evidence on the rate at which this inactive fraction is produced will constitute important information to quantify offshore carbon sequestration. Total oxygen uptake and oxic layer depths were within the range of the measured values. Modelled depth average pore water concentrations of ammonium, phosphate and silicate were typically 5–20% of observed values at the muddy site due to an underestimate of concentrations associated with the deeper sediment layers. Model agreement for these nutrients was better at the sandy site, which had lower pore water concentrations, especially deeper in the sediment. Comparison of pore water nitrate with observations had added uncertainty, as the results from process studies at the sites indicated the dominance of the anammox pathway for nitrogen removal; a pathway that is not included in the model. Macrofaunal biomasses were overestimated, although a model run with increased macrofaunal background mortality rates decreased macrofaunal biomass and improved agreement with observations. The decrease in macrofaunal biomass was compensated by an increase in meiofaunal biomass such that total oxygen demand remained within the observed range. The permeable sediment modification reproduced some of the observed behaviour of oxygen penetration depth at the sandy site. It is suggested that future development in ERSEM benthic modelling should focus on: (1) mixing and degradation rates of benthic organic matter, (2) validation of benthic faunal biomass against large scale spatial datasets, (3) incorporation of anammox in the benthic nitrogen cycle, and (4) further developments to represent permeable sediment processes.     

Stability of dissolved and soluble Fe(II) in shelf sediment pore waters and release to an oxic water column

Shelf sediments underlying temperate and oxic waters of the Celtic Sea (NW European Shelf) were found to have shallow oxygen penetrations depths from late spring to late summer (2.2–5.8 mm below seafloor) with the shallowest during/after the spring-bloom (mid-April to mid-May) when the organic carbon content was highest. Sediment porewater dissolved iron (dFe, <0.15 µm) mainly (>85%) consisted of Fe(II) and gradually increased from 0.4 to 15 μM at the sediment surface to ~100–170 µM at about 6 cm depth. During the late spring this Fe(II) was found to be mainly present as soluble Fe(II) (>85% sFe, <0.02 µm). Sub-surface dFe(II) maxima were enriched in light isotopes (δ⁵⁶Fe ?2.0 to ?1.5‰), which is attributed to dissimilatory iron reduction (DIR) during the bacterial decomposition of organic matter. As porewater Fe(II) was oxidised to insoluble Fe(III) in the surface sediment layer, residual Fe(II) was further enriched in light isotopes (down to ?3.0‰). Ferrozine-reactive Fe(II) was found in surface porewaters and in overlying core top waters, and was highest in the late spring period. Shipboard experiments showed that depletion of bottom water oxygen in late spring can lead to a substantial release of Fe(II). Reoxygenation of bottom water caused this Fe(II) to be rapidly lost from solution, but residual dFe(II) and dFe(III) remained (12 and 33 nM) after >7 h. Iron(II) oxidation experiments in core top and bottom waters also showed removal from solution but at rates up to 5-times slower than predicted from theoretical reaction kinetics. These data imply the presence of ligands capable of complexing Fe(II) and supressing oxidation. The lower oxidation rate allows more time for the diffusion of Fe(II) from the sediments into the overlying water column. Modelling indicates significant diffusive fluxes of Fe(II) (on the order of 23–31 µmol m^?2 day^?1) are possible during late spring when oxygen penetration depths are shallow, and pore water Fe(II) concentrations are highest. In the water column this stabilised Fe(II) will gradually be oxidised and become part of the dFe(III) pool. Thus oxic continental shelves can supply dFe to the water column, which is enhanced during a small period of the year after phytoplankton bloom events when organic matter is transferred to the seafloor. This input is based on conservative assumptions for solute exchange (diffusion-reaction), whereas (bio)physical advection and resuspension events are likely to accelerate these solute exchanges in shelf-seas.     

Management of Meloidogyne incognita with Chemicals and Cultivars in Cotton in a Semi-Arid Environment

Management of Meloidogyne incognita (root-knot nematode) in cotton in the United States was substantially affected by the decision to stop production of aldicarb by its principle manufacturer in 2011. The remaining commercially available tools to manage M. incognita included soil fumigation, nematicide seed treatments, postemergence nematicide application, and cultivars partially resistant to M. incognita. Small plot field studies were conducted on a total of nine sites from 2011–2013 to examine the effects of each of these tools alone or in combinations, on early season galling, late-season nematode density in soil, yield, and value ($/ha = lint value minus chemical costs/ha). The use of a partially resistant cultivar resulted in fewer galls/root system at 35 d after planting in eight of nine tests, lower root-knot nematode density late in the growing season for all test sites, higher lint yield in eight of nine sites, and higher value/ha in six of nine sites. Galls per root were reduced by aldicarb in three of nine sites and by 1,3-dichloropropene (1,3-D) in two of eight sites, relative to the nontreated control (no insecticide or nematicide treatment). Soil fumigation reduced M. incognita density late in the season in three of nine sites. Value/ha was not affected by chemical treatment in four of nine sites, but there was a cultivar × chemical interaction in four of nine sites. When value/ha was affected by chemical treatment, the nontreated control had a similar value to the treatment with the highest value/ha in seven of eight cultivar-site combinations. The next “best” value/ha were associated with seed treatment insecticide (STI) + oxamyl and aldicarb (similar value to the highest value/ha in six of eight cultivar-site combinations). The lowest valued treatment was STI + 1,3-D. In a semi-arid region, where rainfall was low during the spring for all three years, cultivars with partial resistance to M. incognita was the most profitable method of managing root-knot nematode in cotton.     

Temperature effects on fish production across a natural thermal gradient

Global warming is widely predicted to reduce the biomass production of top predators, or even result in species loss. Several exceptions to this expectation have been identified, however, and it is vital that we understand the underlying mechanisms if we are to improve our ability to predict future trends. Here, we used a natural warming experiment in Iceland and quantitative theoretical predictions to investigate the success of brown trout as top predators across a stream temperature gradient (4–25 °C). Brown trout are at the northern limit of their geographic distribution in this system, with ambient stream temperatures below their optimum for maximal growth, and above it in the warmest streams. A five‐month mark‐recapture study revealed that population abundance, biomass, growth rate, and production of trout all increased with stream temperature. We identified two mechanisms that contributed to these responses: (1) trout became more selective in their diet as stream temperature increased, feeding higher in the food web and increasing in trophic position; and (2) trophic transfer through the food web was more efficient in the warmer streams. We found little evidence to support a third potential mechanism: that external subsidies would play a more important role in the diet of trout with increasing stream temperature. Resource availability was also amplified through the trophic levels with warming, as predicted by metabolic theory in nutrient‐replete systems. These results highlight circumstances in which top predators can thrive in warmer environments and contribute to our knowledge of warming impacts on natural communities and ecosystem functioning.     

What factors influence primary care physicians' charges for their services? An exploratory study using standardized patients

OBJECTIVE: To determine the extent of variation in physicians'' charges for health care encounters with unannounced standardized patients and factors associated with the variation. DESIGN: Cross-sectional study. SETTING: Family practices open to new patients within 1 hour''s drive of Hamilton, Ont. PARTICIPANTS: A stratified random sample of 125 physicians who had responded to an earlier survey regarding preventive care were invited to participate. Of the 125, 44 (35.2%) declined to participate, and an additional 19 (15.2%) initially consented but later withdrew because they closed their practices to new patients. Sixty-two physicians thus participated in the study. INTERVENTION: Unannounced standardized patients posing as new patients to the practice visited study physicians'' practices between September 1994 and August 1995, portraying 4 scenarios: 28-year-old woman, 52-year-old woman, 48-year-old man and 70-year-old man. OUTCOME MEASURES: Physician characteristics, encounter characteristics and charges made for services. RESULTS: The 62 physicians had 246 encounters with the standardized patients. Charges were made to the health insurance plan for services by 59 physicians for up to 4 encounters (215 encounters in all). Charges varied considerably both within and across patient scenarios. Time spent with the patient was an important factor predicting charges made (p < 0.01), although the effect of time spent on charges varied across scenarios (p < 0.01). Fee-for-service physicians charged more for their services than physicians who usually had alternative billing arrangements (p < 0.01). Female physicians charged more for their services than their male colleagues (p = 0.03). No relation was found between quality of preventive care and charges made (p = 0.15). CONCLUSIONS: Physician-related factors are better able to account for the variability in charges for their services than patient-related factors. Physicians seeing comparable patients may earn much more or less than their colleagues because of differences in the services they provide and the way they apply the fee schedule. Quality-assurance techniques are likely needed to reduce the variability in charges seen and increase value for money spent in health care.