Computational Chemistry Modelling of the Oxidation of Highly Oriented Pyrolitic Graphite (HOPG)

Under high heat flux, carbon based Thermal Protection Systems (TPS) are observed to rapidly ablate and an accurate characterization is essential to their design. Dissociated oxygen atoms (from the gas phase) striking the surface of TPS could lead to several possibilites. The O atom could adsorb on the surface, recombine with another O atom to form O2 and oxidize the surface to produce CO or CO2 resulting in recession of the surface (ablation). The goal is to predict finite rate models for these reactions which could be incorporated into CFD and DSMC solvers. Our efforts are to predict the rates through large scale Molecular Dynamics (MD) simulations using the ReaxFF potential which enables accurate simulation of large chemically reacting systems of molecules. In this work, we simulate the collision of hyperthermal (5eV) O atoms on Highly Oriented Pyrolitic Graphite (HOPG) at 525K. The simulations are compared to molecular beam experiments performed by Minton and co-workers

Is mitochondrial DNA turnover slower than commonly assumed?

Mutations arise during DNA replication due to oxidative lesions and intrinsic polymerase errors. Mitochondrial DNA (mtDNA) mutation rate is therefore closely linked to the mitochondrial DNA turnover process, especially in post mitotic cells. This makes the mitochondrial DNA turnover rate critical for understanding the origin and dynamics of mtDNA mutagenesis in post mitotic cells. Experimental mitochondrial turnover quantification has been based on different mitochondrial macromolecules, such as mitochondrial proteins, lipids and DNA, and the experimental data suggested highly divergent turnover rates, ranging from over 2days to about 1year. In this article we argue that mtDNA turnover rate cannot be as fast as is often envisaged. Using a stochastic model based on the chemical master equation, we show that a turnover rate corresponding to mtDNA half-life in the order of months is the most consistent with published mtDNA mutation level

SYSTEMS BIOLOGY OF AGING: MODELING & ANALYSIS OF MITOCHONDRIAL GENOME INTEGRITY

Ph.DDOCTOR OF PHILOSOPH

Prognostication of Bell’s palsy: a new perspective

Background: Bell’s palsy is considered as the most frequent cranial neuropathy. Early and adequate risk stratification may help both the patients and the treating physicians in taking informed decisions regarding treatment and understanding their outcomes. We aimed to formulate accessible and sensitive methods of risk stratification in Bell’s palsy by utilizing electrophysiological and hematological parameters. Methods: We prospectively followed up 101 patients with Bell’s palsy over a period of 18 months. Electrophysiological parameters were measured thrice i.e., on the first evaluation and after the first week and first month. The N/L, P/L ratio, erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) were documented in steroid naïve cases. Patients were graded in severity based on the Sunnybrook and House Brackmann systems. Results: The mean SB and HB grades at admission were 53.89±24.725 and 3.92±1.04 indicating moderate severity. The mean N/L, P/L ratios and ESR on the first day was 3.46±3.45, 145.42±162.84 and 22.51±21.105 respectively. There was no statistical correlation with severity at any time point. The mean CMAP indices on the 1st day, 1st week and 1st month were 0.585±0.31,0.43±0.26 and 0.45±0.23 respectively. The CMAP index at 1 month was correlating with severity. Blink amplitude ratios were correlating with the HB scores at 1 week and 1 month (p<0.0001 both) and the SB score at 1 month (p<0.0001). Conclusions: Hematological parameters were not correlated to disease severity. However, electrophysiological parameters are correlated to disease severity at one week and one month. Blink amplitude ratio may be a useful indicator for risk stratification of Bell’s palsy patients

Maximizing signal-to-noise ratio in the random mutation capture assay

The ‘Random Mutation Capture' assay allows for the sensitive quantitation of DNA mutations at extremely low mutation frequencies. This method is based on PCR detection of mutations that render the mutated target sequence resistant to restriction enzyme digestion. The original protocol prescribes an end-point dilution to about 0.1 mutant DNA molecules per PCR well, such that the mutation burden can be simply calculated by counting the number of amplified PCR wells. However, the statistical aspects associated with the single molecular nature of this protocol and several other molecular approaches relying on binary (on/off) output can significantly affect the quantification accuracy, and this issue has so far been ignored. The present work proposes a design of experiment (DoE) using statistical modeling and Monte Carlo simulations to obtain a statistically optimal sampling protocol, one that minimizes the coefficient of variance in the measurement estimates. Here, the DoE prescribed a dilution factor at about 1.6 mutant molecules per well. Theoretical results and experimental validation revealed an up to 10-fold improvement in the information obtained per PCR well, i.e. the optimal protocol achieves the same coefficient of variation using one-tenth the number of wells used in the original assay. Additionally, this optimization equally applies to any method that relies on binary detection of a small number of template

Instrumentation Design and Placement for KRUPS Re-Entry Capsules

Atmospheric re-entry flight tests are one of the best ways to evaluate the performance of new Thermal Protection System (TPS) materials. The flight proven Kentucky Re-Entry Payload System (KRUPS) project provides a low cost, quick turnaround platform for these evaluative missions. Following the success of the first KREPE mission, the Krups Flight Computer (KFC) and the instrumentation suite were redesigned for the next mission, KREPE-2. The original suite contained only four thermocouoples. The new design contains six thermocouples, five pressure sensors, a mini-spectrometer, an IMU and an accelerometer

Investigation of the High-Energy Oxidation of FiberForm from DSMC Analysis of Molecular Beam Experiments

A collaborative effort between the University of Illinois at Urbana-Champaign (UIUC), NASA Ames Research Center (ARC) and Montana State University (MSU) succeeded at developing a new finite-rate carbon oxidation model from molecular beam scattering experiments on vitreous carbon (VC). We now aim to use the direct simulation Monte Carlo (DSMC) code SPARTA to apply the model to each fiber of the porous fibrous Thermal Protection Systems (TPS) material FiberForm (FF). The detailed micro-structure of FF was obtained from X-ray micro-tomography and then used in DSMC. Both experiments and simulations show that the CO/O products ratio increased at all temperatures from VC to FF. We postulate this is due to the larger number of collisions an O atom encounters inside the porous FF material compared to the flat surface of VC. For the simulations, we particularly focused on the lowest and highest temperatures studied experimentally, 1023 K and 1823 K, and found good agreement between the finite-rate DSMC simulations and experiments

Molecular and cognitive signatures of ageing partially restored through synthetic delivery of IL2 to the brain

Cognitive decline is a common pathological outcome during aging, with an ill-defined molecular and cellular basis. In recent years, the concept of inflammaging, defined as a low-grade inflammation increasing with age, has emerged. Infiltrating T cells accumulate in the brain with age and may contribute to the amplification of inflammatory cascades and disruptions to the neurogenic niche observed with age. Recently, a small resident population of regulatory T cells has been identified in the brain, and the capacity of IL2-mediated expansion of this population to counter neuroinflammatory disease has been demonstrated. Here, we test a brain-specific IL2 delivery system for the prevention of neurological decline in aging mice. We identify the molecular hallmarks of aging in the brain glial compartments and identify partial restoration of this signature through IL2 treatment. At a behavioral level, brain IL2 delivery prevented the age-induced defect in spatial learning, without improving the general decline in motor skill or arousal. These results identify immune modulation as a potential path to preserving cognitive function for healthy aging.The work was supported by the Wellcome Trust (222442/Z/21/Z to AL), anERC Consolidator Grant TissueTreg (to A.L.), an ERC Proof of Concept GrantTreatBrainDamage (to A.L.), FWO Research Grant1503420N (to E.P.), anSAO-FRA pilot grant (20190032, to E.P.), an ERC Starting Grant AstroFunc(to M.G.H.), ERC Proof of Concept Grant AD-VIP (to M.G.H.), ERA ChairNCBio (to M.G.H.), and the Biotechnology and Biological Sciences ResearchCouncil through Institute Strategic Program Grant funding BBS/E/B/000C0427and BBS/E/B/000C0428, and the Biotechnology and BiologicalSciences Research Council Core Capability Grant to the BabrahamInstitute. E.P. was supported by a fellowship from the FWO. The authorsacknowledge the important contributions of Jeason Haughton (VIB) formouse husbandry, Pier-Andr ee Penttila and the KUL FACS Core, and theVIB Single Cell Sequencing Core. The visual abstract was created with BioRender.com

Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans

Single-nucleus RNA sequencing (snRNA-seq) is used as an alternative to single-cell RNA-seq, as it allows transcriptomic profiling of frozen tissue. However, it is unclear whether snRNA-seq is able to detect cellular state in human tissue. Indeed, snRNA-seq analyses of human brain samples have failed to detect a consistent microglial activation signature in Alzheimer's disease. Our comparison of microglia from single cells and single nuclei of four human subjects reveals that, although most genes show similar relative abundances in cells and nuclei, a small population of genes (∼1%) is depleted in nuclei compared to whole cells. This population is enriched for genes previously implicated in microglial activation, including APOE, CST3, SPP1, and CD74, comprising 18% of previously identified microglial-disease-associated genes. Given the low sensitivity of snRNA-seq to detect many activation genes, we conclude that snRNA-seq is not suited for detecting cellular activation in microglia in human disease

Stochastic modelling, Bayesian inference, and new in vivo measurements elucidate the debated mtDNA bottleneck mechanism

Dangerous damage to mitochondrial DNA (mtDNA) can be ameliorated during mammalian development through a highly debated mechanism called the mtDNA bottleneck. Uncertainty surrounding this process limits our ability to address inherited mtDNA diseases. We produce a new, physically motivated, generalisable theoretical model for mtDNA populations during development, allowing the first statistical comparison of proposed bottleneck mechanisms. Using approximate Bayesian computation and mouse data, we find most statistical support for a combination of binomial partitioning of mtDNAs at cell divisions and random mtDNA turnover, meaning that the debated exact magnitude of mtDNA copy number depletion is flexible. New experimental measurements from a wild-derived mtDNA pairing in mice confirm the theoretical predictions of this model. We analytically solve a mathematical description of this mechanism, computing probabilities of mtDNA disease onset, efficacy of clinical sampling strategies, and effects of potential dynamic interventions, thus developing a quantitative and experimentally-supported stochastic theory of the bottleneck.Comment: Main text: 14 pages, 5 figures; Supplement: 17 pages, 4 figures; Total: 31 pages, 9 figure