In Silico Fatigue Optimization of TAVR Stent Designs with Physiological Motion in a Beating Heart Model

The rapid expansion of TAVR to younger, low-risk patients raises concerns regarding device durability. Necessarily, extended stent lifetime will become more critical for new generation devices. In vitro methods commonly used for TAVR stent fatigue testing exclude the effects of the beating heart. We present a more realistic in silico stent fatigue analysis utilizing a beating heart model in which TAVR stents experience complex, nonuniform dynamic loading. Virtual TAVR deployments were simulated in the SIMULIA Living Heart Human Model of a beating heart using stent models of the self-expandable nitinol 26-mm CoreValve and Evolut R devices, and a 27-mm PolyV-2. Stent deformation was monitored over three cardiac cycles, and fatigue resistance was evaluated for the nitinol stents using finite element analysis via ABAQUS/Explicit. In all models, there were elements in which strains exceeded fatigue failure. The PolyV-2 stent had far fewer failing elements since its struts were optimized to reduce the strain in stent joints, achieving better fatigue resistance in the stent crown and waist elements. Different stent sections showed markedly different fatigue resistance due to the varying loading conditions. This study demonstrates the utility of advanced in silico analysis of devices deployed within a beating heart that mimics in vivo loading, offering a cost-effective alternative to human or animal trials and establishing a platform to assess the impact of device design on device durability. The limited fatigue life of TAVR stents indicated here highlights a clinical complication that may eventually develop as younger, lower-risk TAVR patients, age.Comment: 24 pages, 13 figures, 2 table

Accelerated search kinetics mediated by redox reactions of DNA repair enzymes

A Charge Transport (CT) mechanism has been proposed in several papers (e.g., Yavin, et al. PNAS, v102 3546 (2005)) to explain the localization of Base Excision Repair (BER) enzymes to lesions on DNA. The CT mechanism relies on redox reactions of iron-sulfur cofactors that modify the enzyme's binding affinity. These redox reactions are mediated by the DNA strand and involve the exchange of electrons between BER enzymes along DNA. We propose a mathematical model that incorporates enzyme binding/unbinding, electron transport, and enzyme diffusion along DNA. Analysis of our model within a range of parameter values suggests that the redox reactions can increase desorption of BER enzymes not already bound to their targets, allowing the enzymes to be recycled, thus accelerating the overall search process. This acceleration mechanism is most effective when enzyme copy numbers and enzyme diffusivity along the DNA are small. Under such conditions, we find that CT BER enzymes find their targets more quickly than simple "passive" enzymes that simply attach to the DNA without desorbing.Comment: 17 pages, 8 figure

Photooxidants from brown carbon and other chromophores in illuminated particle extracts

While photooxidants are important in atmospheric condensed phases, there are very few measurements in particulate matter (PM). Here we measure light absorption and the concentrations of three photooxidants – hydroxyl radical (⚫OH), singlet molecular oxygen (1O2*), and oxidizing triplet excited states of organic matter (3C*) – in illuminated aqueous extracts of wintertime particles from Davis, California. 1O2* and 3C*, which are formed from photoexcitation of brown carbon (BrC), have not been previously measured in PM. In the extracts, mass absorption coefficients for dissolved organic compounds (MACDOC) at 300&thinsp;nm range between 13&thinsp;000 and 30&thinsp;000&thinsp;cm2&thinsp;(g&thinsp;C)−1 are approximately twice as high as previous values in Davis fogs. The average (±1σ)⚫OH steady-state concentration in particle extracts is 4.4(±2.3)×10-16&thinsp;M, which is very similar to previous values in fog, cloud, and rain: although our particle extracts are more concentrated, the resulting enhancement in the rate of ⚫OH photoproduction is essentially canceled out by a corresponding enhancement in concentrations of natural sinks for ⚫OH. In contrast, concentrations of the two oxidants formed primarily from brown carbon (i.e., 1O2* and 3C*) are both enhanced in the particle extracts compared to Davis fogs, a result of higher concentrations of dissolved organic carbon and faster rates of light absorption in the extracts. The average 1O2* concentration in the PM extracts is 1.6(±0.5)×10-12&thinsp;M, 7 times higher than past fog measurements, while the average concentration of oxidizing triplets is 1.0(±0.4)×10-13&thinsp;M, nearly double the average Davis fog value. Additionally, the rates of 1O2* and 3C* photoproduction are both well correlated with the rate of sunlight absorption. Since we cannot experimentally measure photooxidants under ambient particle water conditions, we measured the effect of PM dilution on oxidant concentrations and then extrapolated to ambient particle conditions. As the particle mass concentration in the extracts increases, measured concentrations of ⚫OH remain relatively unchanged, 1O2* increases linearly, and 3C* concentrations increase less than linearly, likely due to quenching by dissolved organics. Based on our measurements, and accounting for additional sources and sinks that should be important under PM conditions, we estimate that [⚫OH] in particles is somewhat lower than in dilute cloud/fog drops, while [3C*] is 30 to 2000 times higher in PM than in drops, and [1O2*] is enhanced by a factor of roughly 2400 in PM compared to drops. Because of these enhancements in 1O2* and 3C* concentrations, the lifetimes of some highly soluble organics appear to be much shorter in particle liquid water than under foggy/cloudy conditions. Based on extrapolating our measured rates of formation in PM extracts, BrC-derived singlet molecular oxygen and triplet excited states are overall the dominant sinks for organic compounds in particle liquid water, with an aggregate rate of reaction for each oxidant that is approximately 200–300 times higher than the aggregate rate of reactions for organics with ⚫OH. For individual, highly soluble reactive organic compounds it appears that 1O2* is often the major sink in particle water, which is a new finding. Triplet excited states are likely also important in the fate of individual particulate organics, but assessing this requires additional measurements of triplet interactions with dissolved organic carbon in natural samples.</p

Structure of Human DNA Polymerase κ Inserting dATP Opposite an 8-OxoG DNA Lesion

Background: Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase κ (Polκ) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polκ\u27s preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polκ in ternary complex with a template-primer presenting 8-oxoG in the active site and with dATP as the incoming nucleotide. Methodology and Principal Findings: We show that the Polκ active site is well-adapted to accommodate 8-oxoG in the syn conformation. That is, the polymerase and the bound template-primer are almost identical in their conformations to that in the ternary complex with undamaged DNA. There is no steric hindrance to accommodating 8-oxoG in the syn conformation for Hoogsteen base-paring with incoming dATP. Conclusions and Significance: The structure we present here is the first for a eukaryotic translesion synthesis (TLS) DNA polymerase with an 8-oxoG:A base pair in the active site. The structure shows why Polκ is more efficient at inserting an A opposite the 8-oxoG lesion than a C. The structure also provides a basis for why Polκ is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases

KRIT1 Regulates the Homeostasis of Intracellular Reactive Oxygen Species

KRIT1 is a gene responsible for Cerebral Cavernous Malformations (CCM), a major cerebrovascular disease characterized by abnormally enlarged and leaky capillaries that predispose to seizures, focal neurological deficits, and fatal intracerebral hemorrhage. Comprehensive analysis of the KRIT1 gene in CCM patients has suggested that KRIT1 functions need to be severely impaired for pathogenesis. However, the molecular and cellular functions of KRIT1 as well as CCM pathogenesis mechanisms are still research challenges. We found that KRIT1 plays an important role in molecular mechanisms involved in the maintenance of the intracellular Reactive Oxygen Species (ROS) homeostasis to prevent oxidative cellular damage. In particular, we demonstrate that KRIT1 loss/down-regulation is associated with a significant increase in intracellular ROS levels. Conversely, ROS levels in KRIT1−/− cells are significantly and dose-dependently reduced after restoration of KRIT1 expression. Moreover, we show that the modulation of intracellular ROS levels by KRIT1 loss/restoration is strictly correlated with the modulation of the expression of the antioxidant protein SOD2 as well as of the transcriptional factor FoxO1, a master regulator of cell responses to oxidative stress and a modulator of SOD2 levels. Furthermore, we show that the KRIT1-dependent maintenance of low ROS levels facilitates the downregulation of cyclin D1 expression required for cell transition from proliferative growth to quiescence. Finally, we demonstrate that the enhanced ROS levels in KRIT1−/− cells are associated with an increased cell susceptibility to oxidative DNA damage and a marked induction of the DNA damage sensor and repair gene Gadd45α, as well as with a decline of mitochondrial energy metabolism. Taken together, our results point to a new model where KRIT1 limits the accumulation of intracellular oxidants and prevents oxidative stress-mediated cellular dysfunction and DNA damage by enhancing the cell capacity to scavenge intracellular ROS through an antioxidant pathway involving FoxO1 and SOD2, thus providing novel and useful insights into the understanding of KRIT1 molecular and cellular functions

The Causes of American Presidents\u27 Immigration Decisions: A Preliminary Logit Analysis

Although the office of the American Presidency would seem to wield enormous power over immigration policy, very few scholars have rigorously examined the roots of Presidents\u27 policy-making in this area. Throughout my preliminary research, I cataloged 91 immigration statutes passed between 1864 and 2001 according to whether the law was pro- or anti-immigration. This data then became the basis for a Logit regression model of whether Presidents supported or opposed immigration. My tentative results suggest that a President\u27s religious identification, ancestry, and racial ideology have affected their actions on immigration. In contrast, the partisanship of the President or Congress, wartime conditions, election years, nativity of his parents, and the year the law was passed, had no statistically significant effect