Functional heterogeneity of the UpaH autotransporter protein from uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) are responsible for the majority of urinary tract infections(UTI). To cause UTI, UPEC must adhere to epithelial cells of the urinary tract and overcome the shear flow forces of urine. This function is primarily mediated by fimbrial adhesins, which mediate specific attachment to host cell receptors. Another group of adhesins that contribute to UPEC mediated UTI are autotransporter (AT) proteins. AT proteins possess a range of virulence properties such as adherence, aggregation, invasion and biofilm formation. One recently characterized AT protein of UPEC is UpaH, a large AIDA-I type AT protein that contributes to biofilm formation and bladder colonization. In this study, we have characterized a series of naturally occurring variants of UpaH. We demonstrate that extensive sequence variation exists within the passenger-encoding domain of UpaH variants from different UPEC strains. This sequence variation is associated with functional heterogeneity with respect to the ability of UpaH to mediate biofilm formation. In contrast, all of the UpaH variants examined retained a conserved ability to mediate binding to extracellular matrix (ECM) proteins. Bioinformatic analysis of the UpaH passenger domain identified a conserved region (UpaHCR) and hydrophobic region (UpaHHR). Deletion of these domains reduced biofilm formation but not binding to ECM proteins. Despite variation in upaH sequence, the transcription of upaH was repressed by a conserved mechanism involving the global regulator H-NS, and mutation of the hns gene relieved this repression. Overall, our findings shed new light on the regulation and function of the UpaH AT protein

Alternate trait-based leaf respiration schemes evaluated at ecosystem-scale through carbon optimization modeling and canopy property data

Leaf maintenance respiration (Rleaf,m) is a major but poorly understood component of the terrestrial carbon cycle (C). Earth systems models (ESMs) use simple sub‐models relating Rleaf,m to leaf traits, applied at canopy scale. Rleaf,m models vary depending on which leaf N traits they incorporate (e.g., mass or area based) and the form of relationship (linear or nonlinear). To simulate vegetation responses to global change, some ESMs include ecological optimization to identify canopy structures that maximize net C accumulation. However, the implications for optimization of using alternate leaf‐scale empirical Rleaf,m models are undetermined. Here we combine alternate well‐known empirical models of Rleaf,m with a process model of canopy photosynthesis. We quantify how net canopy exports of C vary with leaf area index (LAI) and total canopy N (TCN). Using data from tropical and arctic canopies, we show that estimates of canopy Rleaf,m vary widely among the three models. Using an optimization framework, we show that the LAI and TCN values maximizing C export depends strongly on the Rleaf,m model used. No single model could match observed arctic and tropical LAI‐TCN patterns with predictions of optimal LAI‐TCN. We recommend caution in using leaf‐scale empirical models for components of ESMs at canopy‐scale. Rleaf,m models may produce reasonable results for a specified LAI, but, due to their varied representations of Rleaf,mfoliar N sensitivity, are associated with different and potentially unrealistic optimization dynamics at canopy scale. We recommend ESMs to be evaluated using response surfaces of canopy C export in LAI‐TCN space to understand and mitigate these risks

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.Fil: Veluchamy, Alaguraj. Institut de Biologie de l'École Normale Supérieure; FranciaFil: Lin, Xin. Institut de Biologie de l'École Normale Supérieure; Francia. Xiamen University; ChinaFil: Maumus, Florian.Fil: Rivarola, Maximo Lisandro.Fil: Bhavsar, Jaysheel.Fil: Creasy, Todd.Fil: O'Brien, Kimberly.Fil: Sengamalay, Naomi A..Fil: Tallon, Luke J..Fil: Smith, Andrew D..Fil: Rayko, Edda.Fil: Ahmed, Ikhlak.Fil: Crom, Stéphane Le.Fil: Farrant, Gregory K..Fil: Sgro, Jean-Yves.Fil: Olson, Sue A..Fil: Bondurant, Sandra Splinter.Fil: Allen, Andrew.Fil: Rabinowicz, Pablo D..Fil: Sussman, Michael R..Fil: Bowler, Chris.Fil: Tirichine, Leïla

Simplifying understory complexity in oil palm plantations is associated with a reduction in the density of a cleptoparasitic spider, Argyrodes miniaceus (Araneae: Theridiidae), in host (Araneae: Nephilinae) webs.

Expansion of oil palm agriculture is currently one of the main drivers of habitat modification in Southeast Asia. Habitat modification can have significant effects on biodiversity, ecosystem function, and interactions between species by altering species abundances or the available resources in an ecosystem. Increasing complexity within modified habitats has the potential to maintain biodiversity and preserve species interactions. We investigated trophic interactions between Argyrodes miniaceus, a cleptoparasitic spider, and its Nephila spp. spider hosts in mature oil palm plantations in Sumatra, Indonesia. A. miniaceus co-occupy the webs of Nephila spp. females and survive by stealing prey items caught in the web. We examined the effects of experimentally manipulated understory vegetation complexity on the density and abundance of A. miniaceus in Nephila spp. webs. Experimental understory treatments included enhanced complexity, standard complexity, and reduced complexity understory vegetation, which had been established as part of the ongoing Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) Project. A. miniaceus density ranged from 14.4 to 31.4 spiders per square meter of web, with significantly lower densities found in reduced vegetation complexity treatments compared with both enhanced and standard treatment plots. A. miniaceus abundance per plot was also significantly lower in reduced complexity than in standard and enhanced complexity plots. Synthesis and applications: Maintenance of understory vegetation complexity contributes to the preservation of spider host-cleptoparasite relationships in oil palm plantations. Understory structural complexity in these simplified agroecosystems therefore helps to support abundant spider populations, a functionally important taxon in agricultural landscapes. In addition, management for more structurally complex agricultural habitats can support more complex trophic interactions in tropical agroecosystems

Expanding lignin thermal property space by fractionation and covalent modification

To fully exploit kraft lignin's potential in material applications, we need to achieve tight control over those key physicochemical lignin parameters that ultimately determine, and serve as proxy for, the properties of lignin-derived materials. Here, we show that fractionation combined with systematic (incremental) modification provides a powerful strategy to expand and controllably tailor lignin property space. In particular, the glass transition temperature (Tg) of a typical kraft lignin could be tuned over a remarkable and unprecedented 213 °C. Remarkably, for all fractions the Tg proved to be highly linearly correlated with the degree of derivatisation by allylation, offering such tight control over the Tg of the lignin and ultimately the ability to ‘dial-in’ this key property. Importantly, such control over this proxy parameter indeed translated well to lignin-based thiol-ene thermosetting films, whose Tgs thus covered a range from 2-124 °C. This proof of concept suggests this approach to be a powerful and generalisable one, allowing a biorefinery or downstream operation to consciously and reliably tailor lignins to predictable specifications which fit their desired application

Rapid Lignin Thermal Property Prediction through Attenuated Total Reflectance-Infrared Spectroscopy and Chemometrics

To expedite the valorisation of lignin as a sustainable component in materials applications, rapid and generally available analytical methods are essential to overcome the bottleneck of lignin characterisation. Where features of a lignin's chemical structure have previously been found to be predicted by Partial Least Squares (PLS) regression models built on Infrared (IR) data, we now show for the first time that this approach can be extended to prediction of the glass transition temperature (Tg), a key physicochemical property. This methodology is shown to be convenient and more robust for prediction of Tg than prediction through empirically derived relationships (e. g., Flory-Fox). The chemometric analysis provided root mean squared errors of prediction (RMSEP) as low as 10.0 °C for a botanically, and a process-diverse set of lignins, and 6.2 °C for kraft-only samples. The PLS models could separately predict both the Tg as well as the degree of allylation (%allyl) for allylated lignin fractions, which were all derived from a single lignin source. The models performed exceptionally well, delivering RMSEP of 6.1 °C, and 5.4 %, respectively, despite the conflicting influences of increasing molecular weight and %allyl on Tg. Finally, the method provided accurate determinations of %allyl with RMSEP of 5.2 %

Reliability Ensemble Averaging of 21st century projections of terrestrial net primary productivity reduces global and regional uncertainties

Multi-model averaging techniques provide opportunities to extract additional information from large ensembles of simulations. In particular, present-day model skill can be used to evaluate their potential performance in future climate simulations. Multi-model averaging methods have been used extensively in climate and hydrological sciences, but they have not been used to constrain projected plant productivity responses to climate change, which is a major uncertainty in Earth system modelling. Here, we use three global observationally orientated estimates of current net primary productivity (NPP) to perform a reliability ensemble averaging (REA) method using 30 global simulations of the 21st century change in NPP based on the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) <q>business as usual</q> emissions scenario. We find that the three REA methods support an increase in global NPP by the end of the 21st century (2095–2099) compared to 2001–2005, which is 2–3 % stronger than the ensemble ISIMIP mean value of 24.2 Pg C y⁻¹. Using REA also leads to a 45–68 % reduction in the global uncertainty of 21st century NPP projection, which strengthens confidence in the resilience of the CO₂ fertilization effect to climate change. This reduction in uncertainty is especially clear for boreal ecosystems although it may be an artefact due to the lack of representation of nutrient limitations on NPP in most models. Conversely, the large uncertainty that remains on the sign of the response of NPP in semi-arid regions points to the need for better observations and model development in these regions

Trastuzumab-associated cardiac events in the Persephone trial.

BACKGROUND: We report cardiac events in the Persephone trial which compares 6-12 months of adjuvant trastuzumab in women with confirmed HER2-positive, early-stage breast cancer. METHODS: Clinical cardiac events were defined as any of the following: symptoms and/or signs of congestive heart failure (CHF) and new or altered CHF medication. In addition, left ventricular ejection fraction (LVEF) was measured at baseline and then 3 monthly for 12 months. RESULTS: A total of 2500 patients, aged 22-82, were included: 1251 randomised to 12 months and 1249 to 6 months of trastuzumab treatment. A total of 93% (2335/2500) received anthracyclines, 49% of these (1136/2335) with taxanes. Cardiotoxicity delayed treatment in 6% of 12-month and 4% of 6-month patients (P=0.01), and stopped treatment early in 8% (96/1214) of 12-month and 4% (45/1216) of 6-month patients (P3 cycles of anthracycline was associated with higher risk of cardiac events only for 12-month patients (OR 1.41 (1.04-1.90)), and not for 6-month patients (OR 1.28 (0.91-1.79)). CONCLUSIONS: We demonstrate significantly fewer cardiac events from 6 months of adjuvant trastuzumab compared with that from 12 months. This cardiac signal adds importance to the question of the optimum duration of adjuvant trastuzumab treatment. If 6 months is proven to have non-inferior outcomes to 12 months treatment, these data would support 6 months as the standard of care.National Institute of Health Research Health Technology Assessment (NIHR HTA) Programme UK. Funding reference number - 06/303/98This is the author accepted manuscript. The final version is available from Nature Publishing Group via https://doi.org/10.1038/bjc.2016.35

Staphylococcus aureus infections following knee and hip prosthesis insertion procedures

BackgroundStaphylococcus aureus is the most common and most important pathogen following knee and hip arthroplasty procedures. Understanding the epidemiology of invasive S. aureus infections is important to quantify this serious complication.MethodsThis nested retrospective cohort analysis included adult patients who had undergone insertion of knee or hip prostheses with clean or clean-contaminated wound class at 11 hospitals between 2003&ndash;2006. Invasive S. aureus infections, non-superficial incisional surgical site infections (SSIs) and blood stream infections (BSIs), were prospectively identified following each procedure. Prevalence rates, per 100 procedures, were estimated.Results13,719 prosthetic knee (62%) and hip (38%) insertion procedures were performed. Of 92 invasive S. aureus infections identified, SSIs were more common (80%) than SSI and BSI (10%) or BSI alone (10%). The rate of invasive S. aureus infection/100 procedures was 0.57 [95% CI: 0.43-0.73] for knee insertion and 0.83 [95% CI: 0.61-1.08] for hip insertion. More than half (53%) were methicillin-resistant. Median time-to-onset of infection was 34 and 26 days for knee and hip insertion, respectively. Infection was associated with higher National Healthcare Safety Network risk index (p&thinsp;&le;&thinsp;0.0001).ConclusionsPost-operative invasive S. aureus infections were rare, but difficult-to-treat methicillin-resistant infections were relatively common. Optimizing preventative efforts may greatly reduce the healthcare burden associated with S. aureus infections