Physics of intense, high energy radiation effects.

This document summarizes the work done in our three-year LDRD project titled 'Physics of Intense, High Energy Radiation Effects.' This LDRD is focused on electrical effects of ionizing radiation at high dose-rates. One major thrust throughout the project has been the radiation-induced conductivity (RIC) produced by the ionizing radiation. Another important consideration has been the electrical effect of dose-enhanced radiation. This transient effect can produce an electromagnetic pulse (EMP). The unifying theme of the project has been the dielectric function. This quantity contains much of the physics covered in this project. For example, the work on transient electrical effects in radiation-induced conductivity (RIC) has been a key focus for the work on the EMP effects. This physics in contained in the dielectric function, which can also be expressed as a conductivity. The transient defects created during a radiation event are also contained, in principle. The energy loss lead the hot electrons and holes is given by the stopping power of ionizing radiation. This information is given by the inverse dielectric function. Finally, the short time atomistic phenomena caused by ionizing radiation can also be considered to be contained within the dielectric function. During the LDRD, meetings about the work were held every week. These discussions involved theorists, experimentalists and engineers. These discussions branched out into the work done in other projects. For example, the work on EMP effects had influence on another project focused on such phenomena in gases. Furthermore, the physics of radiation detectors and radiation dosimeters was often discussed, and these discussions had impact on related projects. Some LDRD-related documents are now stored on a sharepoint site (https://sharepoint.sandia.gov/sites/LDRD-REMS/default.aspx). In the remainder of this document the work is described in catergories but there is much overlap between the atomistic calculations, the continuum calculations and the experiments

Molecular dynamics of membrane proteins.

Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins

Substructured multibody molecular dynamics.

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics

The interfacial bioscience grand challenge.

This report is broken down into the following 3 sections: (1) Chemical Cross-linking and Mass Spectrometry Applied to Determination of Protein Structure and Dynamics; (2) Computational Modeling of Membrane Protein Structure and Dynamics; and (3) Studies of Toxin-Membrane Interactions using Single Molecule Biophysical Methods

Basic science232. Certolizumab pegol prevents pro-inflammatory alterations in endothelial cell function

Background: Cardiovascular disease is a major comorbidity of rheumatoid arthritis (RA) and a leading cause of death. Chronic systemic inflammation involving tumour necrosis factor alpha (TNF) could contribute to endothelial activation and atherogenesis. A number of anti-TNF therapies are in current use for the treatment of RA, including certolizumab pegol (CZP), (Cimzia ®; UCB, Belgium). Anti-TNF therapy has been associated with reduced clinical cardiovascular disease risk and ameliorated vascular function in RA patients. However, the specific effects of TNF inhibitors on endothelial cell function are largely unknown. Our aim was to investigate the mechanisms underpinning CZP effects on TNF-activated human endothelial cells. Methods: Human aortic endothelial cells (HAoECs) were cultured in vitro and exposed to a) TNF alone, b) TNF plus CZP, or c) neither agent. Microarray analysis was used to examine the transcriptional profile of cells treated for 6 hrs and quantitative polymerase chain reaction (qPCR) analysed gene expression at 1, 3, 6 and 24 hrs. NF-κB localization and IκB degradation were investigated using immunocytochemistry, high content analysis and western blotting. Flow cytometry was conducted to detect microparticle release from HAoECs. Results: Transcriptional profiling revealed that while TNF alone had strong effects on endothelial gene expression, TNF and CZP in combination produced a global gene expression pattern similar to untreated control. The two most highly up-regulated genes in response to TNF treatment were adhesion molecules E-selectin and VCAM-1 (q 0.2 compared to control; p > 0.05 compared to TNF alone). The NF-κB pathway was confirmed as a downstream target of TNF-induced HAoEC activation, via nuclear translocation of NF-κB and degradation of IκB, effects which were abolished by treatment with CZP. In addition, flow cytometry detected an increased production of endothelial microparticles in TNF-activated HAoECs, which was prevented by treatment with CZP. Conclusions: We have found at a cellular level that a clinically available TNF inhibitor, CZP reduces the expression of adhesion molecule expression, and prevents TNF-induced activation of the NF-κB pathway. Furthermore, CZP prevents the production of microparticles by activated endothelial cells. This could be central to the prevention of inflammatory environments underlying these conditions and measurement of microparticles has potential as a novel prognostic marker for future cardiovascular events in this patient group. Disclosure statement: Y.A. received a research grant from UCB. I.B. received a research grant from UCB. S.H. received a research grant from UCB. All other authors have declared no conflicts of interes

A prenylated dsRNA sensor protects against severe COVID-19

Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that OAS1, through RNase L, potently inhibits SARS-CoV-2. We show that a common splice-acceptor SNP (Rs10774671) governs whether people express prenylated OAS1 isoforms that are membrane-associated and sense specific regions of SARS-CoV-2 RNAs, or only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. Importantly, in hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting this antiviral defense is a major component of a protective antiviral response

Outcomes following small bowel obstruction due to malignancy in the national audit of small bowel obstruction

Introduction Patients with cancer who develop small bowel obstruction are at high risk of malnutrition and morbidity following compromise of gastrointestinal tract continuity. This study aimed to characterise current management and outcomes following malignant small bowel obstruction. Methods A prospective, multicentre cohort study of patients with small bowel obstruction who presented to UK hospitals between 16th January and 13th March 2017. Patients who presented with small bowel obstruction due to primary tumours of the intestine (excluding left-sided colonic tumours) or disseminated intra-abdominal malignancy were included. Outcomes included 30-day mortality and in-hospital complications. Cox-proportional hazards models were used to generate adjusted effects estimates, which are presented as hazard ratios (HR) alongside the corresponding 95% confidence interval (95% CI). The threshold for statistical significance was set at the level of P ≤ 0.05 a-priori. Results 205 patients with malignant small bowel obstruction presented to emergency surgery services during the study period. Of these patients, 50 had obstruction due to right sided colon cancer, 143 due to disseminated intraabdominal malignancy, 10 had primary tumours of the small bowel and 2 patients had gastrointestinal stromal tumours. In total 100 out of 205 patients underwent a surgical intervention for obstruction. 30-day in-hospital mortality rate was 11.3% for those with primary tumours and 19.6% for those with disseminated malignancy. Severe risk of malnutrition was an independent predictor for poor mortality in this cohort (adjusted HR 16.18, 95% CI 1.86 to 140.84, p = 0.012). Patients with right-sided colon cancer had high rates of morbidity. Conclusions Mortality rates were high in patients with disseminated malignancy and in those with right sided colon cancer. Further research should identify optimal management strategy to reduce morbidity for these patient groups

Physics of intense, high energy radiation effects.

This document summarizes the work done in our three-year LDRD project titled 'Physics of Intense, High Energy Radiation Effects.' This LDRD is focused on electrical effects of ionizing radiation at high dose-rates. One major thrust throughout the project has been the radiation-induced conductivity (RIC) produced by the ionizing radiation. Another important consideration has been the electrical effect of dose-enhanced radiation. This transient effect can produce an electromagnetic pulse (EMP). The unifying theme of the project has been the dielectric function. This quantity contains much of the physics covered in this project. For example, the work on transient electrical effects in radiation-induced conductivity (RIC) has been a key focus for the work on the EMP effects. This physics in contained in the dielectric function, which can also be expressed as a conductivity. The transient defects created during a radiation event are also contained, in principle. The energy loss lead the hot electrons and holes is given by the stopping power of ionizing radiation. This information is given by the inverse dielectric function. Finally, the short time atomistic phenomena caused by ionizing radiation can also be considered to be contained within the dielectric function. During the LDRD, meetings about the work were held every week. These discussions involved theorists, experimentalists and engineers. These discussions branched out into the work done in other projects. For example, the work on EMP effects had influence on another project focused on such phenomena in gases. Furthermore, the physics of radiation detectors and radiation dosimeters was often discussed, and these discussions had impact on related projects. Some LDRD-related documents are now stored on a sharepoint site (https://sharepoint.sandia.gov/sites/LDRD-REMS/default.aspx). In the remainder of this document the work is described in catergories but there is much overlap between the atomistic calculations, the continuum calculations and the experiments