Detection of Native-State Nonadditivity in Double Mutant Cycles via Hydrogen Exchange

Proteins have evolved to exploit long-range structural and dynamic effects as a means of regulating function. Understanding communication between sites in proteins is therefore vital to our comprehension of such phenomena as allostery, catalysis, and ligand binding/ejection. Double mutant cycle analysis has long been used to determine the existence of communication between pairs of sites—proximal or distal—in proteins. Typically, non-additivity (or “thermodynamic coupling”) is measured from global transitions in concert with a single probe. Here, we have applied the atomic resolution of NMR in tandem with native-state hydrogen exchange (HX) to probe the structure/energy landscape for information transduction between a large number of distal sites in a protein. Considering the event of amide proton exchange as an energetically quantifiable structural perturbation, m n-dimensional cycles can be constructed from mutation of n-1 residues, where m is the number of residues for which HX data is available. Thus, efficient mapping of a large number of couplings is made possible. We have applied this technique to one additive and two non-additive double mutant cycles in a model system, eglin c. We find heterogeneity of HX-monitored couplings for each cycle, yet, averaging results in strong agreement with traditionally measured values. Furthermore, long-range couplings observed at locally exchanging residues indicate that the basis for communication can occur within the native state ensemble, a conclusion which is not apparent from traditional measurements. We propose that higher-order couplings can be obtained and show that such couplings provide a mechanistic basis for understanding lower-order couplings, via “spheres of perturbation”. The method is presented as an additional tool for identifying a large number of couplings with greater coverage of the protein of interest

Escherichia coli α-Hemolysin Counteracts the Anti-Virulence Innate Immune Response Triggered by the Rho GTPase Activating Toxin CNF1 during Bacteremia

International audienceThe detection of the activities of pathogen-encoded virulence factors by the innate immune system has emerged as a new paradigm of pathogen recognition. Much remains to be determined with regard to the molecular and cellular components contributing to this defense mechanism in mammals and importance during infection. Here, we reveal the central role of the IL-1 beta signaling axis and Gr1+ cells in controlling the Escherichia coli burden in the blood in response to the sensing of the Rho GTPase-activating toxin CNF1. Consistently, this innate immune response is abrogated in caspase-1/11-impaired mice or following the treatment of infected mice with an IL-1 beta antagonist. In vitro experiments further revealed the synergistic effects of CNF1 and LPS in promoting the maturation/secretion of IL-1 beta and establishing the roles of Rac, ASC and caspase-1 in this pathway. Furthermore, we found that the Phi-hemolysin toxin inhibits IL-1 beta secretion without affecting the recruitment of Gr1+ cells. Here, we report the first example of anti-virulence-triggered immunity counteracted by a pore-forming toxin during bacteremia

Functionality and feedback: a realist synthesis of the collation, interpretation and utilisation of patient-reported outcome measures data to improve patient care

Background: The feedback of patient-reported outcome measures (PROMs) data is intended to support the care of individual patients and to act as a quality improvement (QI) strategy. Objectives: To (1) identify the ideas and assumptions underlying how individual and aggregated PROMs data are intended to improve patient care, and (2) review the evidence to examine the circumstances in which and processes through which PROMs feedback improves patient care. Design: Two separate but related realist syntheses: (1) feedback of aggregate PROMs and performance data to improve patient care, and (2) feedback of individual PROMs data to improve patient care. Interventions: Aggregate – feedback and public reporting of PROMs, patient experience data and performance data to hospital providers and primary care organisations. Individual – feedback of PROMs in oncology, palliative care and the care of people with mental health problems in primary and secondary care settings. Main outcome measures: Aggregate – providers’ responses, attitudes and experiences of using PROMs and performance data to improve patient care. Individual – providers’ and patients’ experiences of using PROMs data to raise issues with clinicians, change clinicians’ communication practices, change patient management and improve patient well-being. Data sources: Searches of electronic databases and forwards and backwards citation tracking. Review methods: Realist synthesis to identify, test and refine programme theories about when, how and why PROMs feedback leads to improvements in patient care. Results: Providers were more likely to take steps to improve patient care in response to the feedback and public reporting of aggregate PROMs and performance data if they perceived that these data were credible, were aimed at improving patient care, and were timely and provided a clear indication of the source of the problem. However, implementing substantial and sustainable improvement to patient care required system-wide approaches. In the care of individual patients, PROMs function more as a tool to support patients in raising issues with clinicians than they do in substantially changing clinicians’ communication practices with patients. Patients valued both standardised and individualised PROMs as a tool to raise issues, but thought is required as to which patients may benefit and which may not. In settings such as palliative care and psychotherapy, clinicians viewed individualised PROMs as useful to build rapport and support the therapeutic process. PROMs feedback did not substantially shift clinicians’ communication practices or focus discussion on psychosocial issues; this required a shift in clinicians’ perceptions of their remit. Strengths and limitations: There was a paucity of research examining the feedback of aggregate PROMs data to providers, and we drew on evidence from interventions with similar programme theories (other forms of performance data) to test our theories. Conclusions: PROMs data act as ‘tin openers’ rather than ‘dials’. Providers need more support and guidance on how to collect their own internal data, how to rule out alternative explanations for their outlier status and how to explore the possible causes of their outlier status. There is also tension between PROMs as a QI strategy versus their use in the care of individual patients; PROMs that clinicians find useful in assessing patients, such as individualised measures, are not useful as indicators of service quality. Future work: Future research should (1) explore how differently performing providers have responded to aggregate PROMs feedback, and how organisations have collected PROMs data both for individual patient care and to improve service quality; and (2) explore whether or not and how incorporating PROMs into patients’ electronic records allows multiple different clinicians to receive PROMs feedback, discuss it with patients and act on the data to improve patient care

On the mechanisms governing gas penetration into a tokamak plasma during a massive gas injection

A new 1D radial fluid code, IMAGINE, is used to simulate the penetration of gas into a tokamak plasma during a massive gas injection (MGI). The main result is that the gas is in general strongly braked as it reaches the plasma, due to mechanisms related to charge exchange and (to a smaller extent) recombination. As a result, only a fraction of the gas penetrates into the plasma. Also, a shock wave is created in the gas which propagates away from the plasma, braking and compressing the incoming gas. Simulation results are quantitatively consistent, at least in terms of orders of magnitude, with experimental data for a D 2 MGI into a JET Ohmic plasma. Simulations of MGI into the background plasma surrounding a runaway electron beam show that if the background electron density is too high, the gas may not penetrate, suggesting a possible explanation for the recent results of Reux et al in JET (2015 Nucl. Fusion 55 093013)

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR

Modelling of the effect of ELMs on fuel retention at the bulk W divertor of JET

Effect of ELMs on fuel retention at the bulk W target of JET ITER-Like Wall was studied with multi-scale calculations. Plasma input parameters were taken from ELMy H-mode plasma experiment. The energetic intra-ELM fuel particles get implanted and create near-surface defects up to depths of few tens of nm, which act as the main fuel trapping sites during ELMs. Clustering of implantation-induced vacancies were found to take place. The incoming flux of inter-ELM plasma particles increases the different filling levels of trapped fuel in defects. The temperature increase of the W target during the pulse increases the fuel detrapping rate. The inter-ELM fuel particle flux refills the partially emptied trapping sites and fills new sites. This leads to a competing effect on the retention and release rates of the implanted particles. At high temperatures the main retention appeared in larger vacancy clusters due to increased clustering rate

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Impact of fast ions on density peaking in JET: fluid and gyrokinetic modeling

The effect of fast ions on turbulent particle transport, driven by ion temperature gradient (ITG)/ trapped electron mode turbulence, is studied. Two neutral beam injection (NBI) heated JET discharges in different regimes are analyzed at the radial position ρ$_{t}$=0.6, one of them an L-mode and the other one an H-mode discharge. Results obtained from the computationally efficient fluid model EDWM and the gyro-fluid model TGLF are compared to linear and nonlinear gyrokinetic GENE simulations as well as the experimentally obtained density peaking. In these models, the fast ions are treated as a dynamic species with a Maxwellian background distribution. The dependence of the zero particle flux density gradient (peaking factor) on fast ion density, temperature and corresponding gradients, is investigated. The simulations show that the inclusion of a fast ion species has a stabilizing influence on the ITG mode and reduces the peaking of the main ion and electron density profiles in the absence of sources. The models mostly reproduce the experimentally obtained density peaking for the L-mode discharge whereas the H-mode density peaking is significantly underpredicted, indicating the importance of the NBI particle source for the H-mode density profile

Current Research into Applications of Tomography for Fusion Diagnostics

Retrieving spatial distribution of plasma emissivity from line integrated measurements on tokamaks presents a challenging task due to ill-posedness of the tomography problem and limited number of the lines of sight. Modern methods of plasma tomography therefore implement a-priori information as well as constraints, in particular some form of penalisation of complexity. In this contribution, the current tomography methods under development (Tikhonov regularisation, Bayesian methods and neural networks) are briefly explained taking into account their potential for integration into the fusion reactor diagnostics. In particular, current development of the Minimum Fisher Regularisation method is exemplified with respect to real-time reconstruction capability, combination with spectral unfolding and other prospective tasks