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At least 973 records · Page 54

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NASA NTRS2013

Global Response of the Space Shuttle External Tank with the Presence of Intertank Stringer Cracks and Radius Blocks

After propellant was loaded into the external tank (ET), the November 5, 2010 launch of Space Shuttle mission STS-133 was scrubbed due to a gaseous hydrogen leak located in a vent line near the ground umbilical and ET connection. Subsequent visual inspections identified cracks in the sprayed-on foam insulation in the forward end of the ET intertank segment, adjacent to the liquid oxygen (LOX) tank, as shown in Figure 1. These cracks necessitated repair of the foam due to debris concerns that violated launch constraints. As part of the repair process, the affected foam was removed to reveal cracks in the underlying external hat stiffeners on the intertank, as shown in Figure 2. Ultimately, five stiffeners were discovered to be cracked adjacent to the LOX tank. As the managing center for the ET Project, NASA Marshall Space Flight Center (MSFC) coordinated failure investigation and repair activities among multiple organizations, which included the ET prime contractor (Lockheed Martin Space Systems Michoud Operations), the Space Shuttle Program Office at the NASA Johnson Space Center (JSC), the NASA Kennedy Space Center (KSC), and the NASA Engineering and Safety Center (NESC). STS-133 utilized the external tank designated as ET-137. Many aspects of the investigation have been reported previously in Refs. 1-7, which focus on the root cause of the failures, the flight readiness rationale and the local analyses of the stringer failures and repair. This paper summarizes the global analyses that were conducted on ET-137 as part of the NESC effort during the investigation, which was conducted primarily to determine if the repairs that were introduced to the stringers would alter the global response of the ET. In the process of the investigation, a new STAGS tabular input capability was developed to more easily introduce the aerodynamic pressure loads using a method that could easily be extended to incorporate finite element property data such as skin and stiffener thicknesses and beam cross-sectional properties.

Lovejoy, Andrew E.↗

NASA NTRS2010

Launch Pad Flame Trench Refractory Materials

The launch complexes at NASA's John F. Kennedy Space Center (KSC) are critical support facilities for the successful launch of space-based vehicles. These facilities include a flame trench that bisects the pad at ground level. This trench includes a flame deflector system that consists of an inverted, V-shaped steel structure covered with a high temperature concrete material five inches thick that extends across the center of the flame trench. One side of the "V11 receives and deflects the flames from the orbiter main engines; the opposite side deflects the flames from the solid rocket boosters. There are also two movable deflectors at the top of the trench to provide additional protection to shuttle hardware from the solid rocket booster flames. These facilities are over 40 years old and are experiencing constant deterioration from launch heat/blast effects and environmental exposure. The refractory material currently used in launch pad flame deflectors has become susceptible to failure, resulting in large sections of the material breaking away from the steel base structure and creating high-speed projectiles during launch. These projectiles jeopardize the safety of the launch complex, crew, and vehicle. Post launch inspections have revealed that the number and frequency of repairs, as well as the area and size of the damage, is increasing with the number of launches. The Space Shuttle Program has accepted the extensive ground processing costs for post launch repair of damaged areas and investigations of future launch related failures for the remainder of the program. There currently are no long term solutions available for Constellation Program ground operations to address the poor performance and subsequent failures of the refractory materials. Over the last three years, significant liberation of refractory material in the flame trench and fire bricks along the adjacent trench walls following Space Shuttle launches have resulted in extensive investigations of failure mechanisms, load response, ejected material impact evaluation, and repair design analysis (environmental and structural assessment, induced environment from solid rocket booster plume, loads summary, and repair integrity), assessment of risk posture for flame trench debris, and justification of flight readiness rationale. Although the configuration of the launch pad, water and exhaust direction, and location of the Mobile Launcher Platform between the flame trench and the flight hardware should protect the Space Vehicle from debris exposure, loss of material could cause damage to a major element of the ground facility (resulting in temporary usage loss); and damage to other facility elements is possible. These are all significant risks that will impact ground operations for Constellation and development of new refractory material systems is necessary to reduce the likelihood of the foreign object debris hazard during launch. KSC is developing an alternate refractory material for the launch pad flame trench protection system, including flame deflector and flame trench walls, that will withstand launch conditions without the need for repair after every launch, as is currently the case. This paper will present a summary of the results from industry surveys, trade studies, life cycle cost analysis, and preliminary testing that have been performed to support and validate the development, testing, and qualification of new refractory materials.

Calle, Luz M.↗

NASA NTRS2008

Space Transportation System Availability Requirements and Its Influencing Attributes Relationships

It is essential that management and engineering understand the need for an availability requirement for the customer's space transportation system as it enables the meeting of his needs, goal, and objectives. There are three types of availability, e.g., operational availability, achieved availability, or inherent availability. The basic definition of availability is equal to the mean uptime divided by the sum of the mean uptime plus the mean downtime. The major difference is the inclusiveness of the functions within the mean downtime and the mean uptime. This paper will address tIe inherent availability which only addresses the mean downtime as that mean time to repair or the time to determine the failed article, remove it, install a replacement article and verify the functionality of the repaired system. The definitions of operational availability include the replacement hardware supply or maintenance delays and other non-design factors in the mean downtime. Also with inherent availability the mean uptime will only consider the mean time between failures (other availability definitions consider this as mean time between maintenance - preventive and corrective maintenance) that requires the repair of the system to be functional. It is also essential that management and engineering understand all influencing attributes relationships to each other and to the resultant inherent availability requirement. This visibility will provide the decision makers with the understanding necessary to place constraints on the design definition for the major drivers that will determine the inherent availability, safety, reliability, maintainability, and the life cycle cost of the fielded system provided the customer. This inherent availability requirement may be driven by the need to use a multiple launch approach to placing humans on the moon or the desire to control the number of spare parts required to support long stays in either orbit or on the surface of the moon or mars. It is the intent of this paper to provide the visibility of relationships of these major attribute drivers (variables) to each other and the resultant system inherent availability, but also provide the capability to bound the variables providing engineering the insight required to control the system's engineering solution. An example of this visibility will be the need to provide integration of similar discipline functions to allow control of the total parts count of the space transportation system. Also the relationship visibility of selecting a reliability requirement will place a constraint on parts count to achieve a given inherent availability requirement or accepting a larger parts count with the resulting higher reliability requirement. This paper will provide an understanding for the relationship of mean repair time (mean downtime) to maintainability, e.g., accessibility for repair, and both mean time between failure, e.g., reliability of hardware and the system inherent availability. Having an understanding of these relationships and resulting requirements before starting the architectural design concept definition will avoid considerable time and money required to iterate the design to meet the redesign and assessment process required to achieve the results required of the customer's space transportation system. In fact the impact to the schedule to being able to deliver the system that meets the customer's needs, goals, and objectives may cause the customer to compromise his desired operational goal and objectives resulting in considerable increased life cycle cost of the fielded space transportation system.

Rhodes, Russel E.↗

NASA NTRS2013

An Onboard ISS Virtual Reality Trainer

Prior to the retirement of the Space Shuttle, many exterior repairs on the International Space Station (ISS) were carried out by shuttle astronauts, trained on the ground and flown to the Station to perform these specific repairs. With the retirement of the shuttle, this is no longer an available option. As such, the need for ISS crew members to review scenarios while on flight, either for tasks they already trained for on the ground or for contingency operations has become a very critical issue. NASA astronauts prepare for Extra-Vehicular Activities (EVA) or Spacewalks through numerous training media, such as: self-study, part task training, underwater training in the Neutral Buoyancy Laboratory (NBL), hands-on hardware reviews and training at the Virtual Reality Laboratory (VRLab). In many situations, the time between the last session of a training and an EVA task might be 6 to 8 months. EVA tasks are critical for a mission and as time passes the crew members may lose proficiency on previously trained tasks and their options to refresh or learn a new skill while on flight are limited to reading training materials and watching videos. In addition, there is an increased need for unplanned contingency repairs to fix problems arising as the Station ages. In order to help the ISS crew members maintain EVA proficiency or train for contingency repairs during their mission, the Johnson Space Center's VRLab designed an immersive ISS Virtual Reality Trainer (VRT). The VRT incorporates a unique optical system that makes use of the already successful Dynamic On-board Ubiquitous Graphics (DOUG) software to assist crew members with procedure reviews and contingency EVAs while on board the Station. The need to train and re-train crew members for EVAs and contingency scenarios is crucial and extremely demanding. ISS crew members are now asked to perform EVA tasks for which they have not been trained and potentially have never seen before. The Virtual Reality Trainer (VRT) provides an immersive 3D environment similar to the one experienced at the VRLab crew training facility at the NASA Johnson Space Center. VRT bridges the gap by allowing crew members to experience an interactive, 3D environment to reinforce skills already learned and to explore new work sites and repair procedures outside the Station.

Miralles, Evelyn↗

NASA NTRS2018

Persistence of Gamma-H2AX Foci in Irradiated Bronchial Cells Correlates with Susceptibility to Radiation Associated Lung Cancer in Mice

The risk of developing radiation-induced lung cancer differs between different strains of mice, but the underlying cause of the strain differences is unknown. Strains of mice also differ in their ability to efficiently repair DNA double strand breaks resulting from radiation exposure. We phenotyped mouse strains from the CcS/Dem recombinant congenic strain set for their efficacy in repairing DNA double strand breaks during protracted radiation exposures. We monitored persistent gamma-H2AX radiation induced foci (RIF) 24 hours after exposure to chronic gamma-rays as a surrogate marker for repair deficiency in bronchial epithelial cells for 17 of the CcS/Dem strains and the BALB/cHeN founder strain. We observed a very strong correlation R2 = 79.18%, P < 0.001) between the level of persistent RIF and radiogenic lung cancer percent incidence measured in the same strains. Interestingly, spontaneous levels of foci in non-irradiated strains also showed good correlation with lung cancer incidence (R2=32.74%, P =0.013). These results suggest that genetic differences in DNA repair capacity largely account for differing susceptibilities to radiation-induced lung cancer among CcS/Dem mouse strains and that high levels of spontaneous DNA damage is also a relatively good marker of cancer predisposition. In a smaller pilot study, we found that the repair capacity measured in peripheral blood leucocytes also correlated well with radiogenic lung cancer susceptibility, raising the possibility that such phenotyping assay could be used to detect radiogenic lung cancer susceptibility in humans.

Ochola, Donasian O.↗

NASA NTRSDate not supplied

Individual Variability and Predictive Biomarkers of Human Sensitivity to Ionizing Radiation

High-linear energy transfer (LET) ionizing radiation is a major health hazard for astronauts who will be exposed to galactic cosmic rays during upcoming lunar and Mars missions. Predicting and mitigating personalized health risks from space radiation exposure requires understanding the factors underlying individual radiation sensitivity, which currently remain unknown. We started to address this challenge by identifying the genomic and demographic associations with sensitivity to low and high-LET ionizing radiation in the largest human sample cohort to date and by evaluating baseline DNA damage as a potential predictor of radiation responses. We have collected and irradiated peripheral blood mononuclear cells (PBMCs) from 768 healthy donors of matched ethnicity, 50/50 male/female, 18-70 years old. We have analyzed the responses of 576 donor PBMCs to irradiation with simulated galactic cosmic ray components: 350MeV/n 28Si, 350MeV/n 40Ar and 600MeV/n 56Fe, at 1.1 and 3 particles/100μm2 fluences, as well as 0.1Gy and 1Gy doses of gamma rays, at 4 and 24 hours post irradiation. We quantified post-irradiation DNA repair based on radiation-induced 53BP1+ foci formation, together with oxidative stress and cell death using a flow cytometry-based assay. We also assessed baseline levels of DNA repair in PBMCs at the time of sample collection prior to irradiation experiments. We observed a wide variability of subject- and LET-dependent radiation responses, with radiation-induced DNA repair foci increasing with LET, though oxidative stress being notably reduced by high-LET irradiation, potentially due to a switch between hydrogen peroxide and oxygen radical-based mechanisms. We also identified a relationship between few DNA repair foci at baseline and increased DNA repair after irradiation, accompanied by an alteration in immunoregulatory cytokine secretion, which might be adapted as biomarkers to predict ionizing radiation sensitivity. Among demographic variables, baseline foci levels were positively associated with age and latent cytomegalovirus infection. Finally, we have performed low-throughput whole genome sequencing of all samples and are currently in process of identifying the genes and pathways associated with low and high-LET ionizing radiation sensitivity in humans.

Space radiation, human spaceflight, DNA damage↗

DOE OSTI2013

Repopulation of interacting tumor cells during fractionated radiotherapy: Stochastic modeling of the tumor control probability

Purpose: Optimal treatment planning for fractionated external beam radiation therapy requires inputs from radiobiology based on recent thinking about the “five Rs” (repopulation, radiosensitivity, reoxygenation, redistribution, and repair). The need is especially acute for the newer, often individualized, protocols made feasible by progress in image guided radiation therapy and dose conformity. Current stochastic tumor control probability (TCP) models incorporating tumor repopulation effects consider “stem-like cancer cells” (SLCC) to be independent, but the authors here propose that SLCC-SLCC interactions may be significant. The authors present a new stochastic TCP model for repopulating SLCC interacting within microenvironmental niches. Our approach is meant mainly for comparing similar protocols. It aims at practical generalizations of previous mathematical models. Methods: The authors consider protocols with complete sublethal damage repair between fractions. The authors use customized open-source software and recent mathematical approaches from stochastic process theory for calculating the time-dependent SLCC number and thereby estimating SLCC eradication probabilities. As specific numerical examples, the authors consider predicted TCP results for a 2 Gy per fraction, 60 Gy protocol compared to 64 Gy protocols involving early or late boosts in a limited volume to some fractions. Results: In sample calculations with linear quadratic parameters α = 0.3 per Gy, α/β = 10 Gy, boosting is predicted to raise TCP from a dismal 14.5% observed in some older protocols for advanced NSCLC to above 70%. This prediction is robust as regards: (a) the assumed values of parameters other than α and (b) the choice of models for intraniche SLCC-SLCC interactions. However, α = 0.03 per Gy leads to a prediction of almost no improvement when boosting. Conclusions: The predicted efficacy of moderate boosts depends sensitively on α. Presumably, the larger values of α are the ones appropriate for individualized treatment protocols, with the smaller values relevant only to protocols for a heterogeneous patient population. On that assumption, boosting is predicted to be highly effective. Front boosting, apart from practical advantages and a possible advantage as regards iatrogenic second cancers, also probably gives a slightly higher TCP than back boosting. If the total number of SLCC at the start of treatment can be measured even roughly, it will provide a highly sensitive way of discriminating between various models and parameter choices. Updated mathematical methods for calculating repopulation allow credible generalizations of earlier results.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2018

Numerical Modeling of RBMK-1000 Graphite Stack Distortion

Engineering and detailed three-dimensional models of the RBMK-1000 graphite stack for modeling of its distortions caused by the appearance of longitudinal cracks in the blocks owing to the nonuniformity of the temperature and fluence distributions are described. As the neutron fluence accumulates and the limit longitudinal deflection of the graphite columns is reached, the graphite stack is repaired by cutting the graphite blocks. The developed models make it possible to evaluate the accumulation of deflection of the columns before and after repairs and the effectiveness of various repair schemes. The developed models are used to calculate the maximum deflection of the stack columns in the No. 1 unit of the Leningradskaya NPP for different operating conditions after repairs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2018

Insulin-like growth factor I receptor regulates the radiation-induced G2/M checkpoint in HeLa cells

Highlights: • Inhibition of IGF-IR elongated radiation-induced G2 arrest in HeLa cells. • Inhibition of PI3K or AKT, but not MEK, induced the same effect. • IGF-IR inhibition did not essentially affect DSB repair kinetics. • Radiation-induced CHK1 nuclear localization lasted longer in IGF-IR-inhibited cells. • IGF-IR may regulate G2/M checkpoint in part via CHK1 shuttling within the cell. Insulin-like growth factor I receptor (IGF-IR) plays pivotal roles in various biological events, including cell growth, transformation, survival, and DNA repair. In this study, we explored its possible involvement in cell cycle checkpoints, using HeLa cells expressing the fluorescent ubiquitination-based cell cycle indicator (Fucci). We found that IGF-IR inhibitor delayed release from radiation-induced G2 arrest, as demonstrated by FACS and pedigree analysis of Fucci fluorescence. Elongated G2 arrest was also induced by inhibitors of phosphatidylinositol-3 kinase (PI3K) and AKT, but not by inhibitor of MEK, which are two major IGF-IR downstream signaling pathways. Double-strand break (DSB) repair kinetics were not affected by IGF-IR inhibitor. CHK1 inhibitor abrogated radiation-induced G2 arrest, whereas radiation-induced phosphorylation of CHK1 at Ser 345 or Ser 296 was decreased by the IGF-IR inhibitor. However, radiation-induced nuclear localization of CHK1 was prolonged in IGF-IR inhibitor–treated cells in comparison with cells that received radiation alone; in the latter, CHK1 returned to the original diffuse distribution in conjunction with release from G2 arrest. We conclude that IGF-IR directly regulates the G2/M checkpoint via the PI3K/AKT pathway without influencing DSB repair, in part by controlling CHK1 localization between the nucleus and cytoplasm.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Involvement of the Artemis Protein in the Relative Biological Efficiency Observed With the 76-MeV Proton Beam Used at the Institut Curie Proton Therapy Center in Orsay

Purpose: Previously we showed that the relative biological efficiency for induced cell killing by the 76-MeV beam used at the Institut Curie Proton Therapy Center in Orsay increased with depth throughout the spread-out Bragg peak (SOBP). To investigate the repair pathways underlying this increase, we used an isogenic human cell model in which individual DNA repair proteins have been depleted, and techniques dedicated to precise measurements of radiation-induced DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). Methods and Materials: The 3-Gy surviving fractions of HeLa cells individually depleted of Ogg1, XRCC1, and PARP1 (the base excision repair/SSB repair pathway) or of ATM, DNA-PKcs, XRCC4, and Artemis (nonhomologous end-joining pathway) were determined at the 3 positions previously defined in the SOBP. Quantification of incident SSBs and DSBs by the alkaline elution technique and 3-dimensional (3D) immunofluorescence of γ-H2AX foci, respectively, was performed in SQ20 B cells. Results: We showed that the amount of SSBs and DSBs depends directly on the particle fluence and that the increase in relative biological efficiency observed in the distal part of the SOBP is due to a subset of lesions generated under these conditions, leading to cell death via a pathway in which the Artemis protein plays a central role. Conclusions: Because therapies like proton or carbon beams are now being used to treat cancer, it is even more important to dissect the mechanisms implicated in the repair of the lesions generated by these particles. Additionally, alteration of the expression or activity of the Artemis protein could be a novel therapeutic tool before high linear energy transfer irradiation treatment.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2021

Preclinical Risk Evaluation of Normal Tissue Injury With Novel Radiosensitizers

Genotoxic damage induced by radiation triggers a highly coordinated DNA damage response, and molecular inhibitors of key nodes within this complex response network can profoundly enhance the antitumor efficacy of radiation. This is especially true for drugs targeting the catalytic subunit of DNA-dependent protein kinase, which is a core component of the nonhomologous end-joining DNA repair pathway, and ataxia telangiectasia mutated, which coordinates cell cycle arrest, apoptosis, and DNA repair functionalities after radiation exposure. Unlike the more modest in vitro radiosensitizing effects seen with classic sensitizing agents such as cisplatin, 5-fluorouracil, or taxanes, DNA-dependent protein kinase or ataxia telangiectasia mutated inhibitors provide much more robust sensitizing effects in vitro, as might be anticipated from targeting these key DNA repair modulators. However, patients with homozygous inactivating mutations of ataxia telangiectasia mutated or mice with homozygous defects in DNA-dependent protein kinase (severe combined immunodeficiency) have profoundly enhanced acute normal tissue radiation reactions. Therefore, there is significant potential that the combination of small molecule inhibitors of these kinases with radiation could cause similar dose-limiting acute normal tissue toxicities. Similarly, although less understood, inhibition of these DNA repair response pathways could markedly increase the risk of late radiation toxicities. Because these potent radiosensitizers could be highly useful to improve local control of otherwise radiation-resistant tumors, understanding the potential for elevated risks of radiation injury is essential for optimizing therapeutic ratio and developing safe and informative clinical trials. In this review, we will discuss 2 straightforward models to assess the potential for enhanced mucosal toxicity in the oral cavity and small intestine established in our laboratories. We also will discuss similar strategies for evaluating potential drug–radiation interactions with regard to increased risks of debilitating late effects.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2016

Bifunctional alkylating agent-mediated MGMT-DNA cross-linking and its proteolytic cleavage in 16HBE cells

Nitrogen mustard (NM), a bifunctional alkylating agent (BAA), contains two alkyl arms and can act as a cross-linking bridge between DNA and protein to form a DNA-protein cross-link (DPC). O{sup 6}-methylguanine–DNA methyltransferase (MGMT), a DNA repair enzyme for alkyl adducts removal, is found to enhance cell sensitivity to BAAs and to promote damage, possibly due to its stable covalent cross-linking with DNA mediated by BAAs. To investigate MGMT-DNA cross-link (mDPC) formation and its possible dual roles in NM exposure, human bronchial epithelial cell line 16HBE was subjected to different concentrations of HN2, a kind of NM, and we found mDPC was induced by HN2 in a concentration-dependent manner, but the mRNA and total protein of MGMT were suppressed. As early as 1 h after HN2 treatment, high mDPC was achieved and the level maintained for up to 24 h. Quick total DPC (tDPC) and γ-H2AX accumulation were observed. To evaluate the effect of newly predicted protease DVC1 on DPC cleavage, we applied siRNA of MGMT and DVC1, MG132 (proteasome inhibitor), and NMS-873 (p97 inhibitor) and found that proteolysis plays a role. DVC1 was proven to be more important in the cleavage of mDPC than tDPC in a p97-dependent manner. HN2 exposure induced DVC1 upregulation, which was at least partially contributed to MGMT cleavage by proteolysis because HN2-induced mDPC level and DNA damage was closely related with DVC1 expression. Homologous recombination (HR) was also activated. Our findings demonstrated that MGMT might turn into a DNA damage promoter by forming DPC when exposed to HN2. Proteolysis, especially DVC1, plays a crucial role in mDPC repair. - Highlights: • Nitrogen mustard-induced MGMT-DNA cross-linking was detected in a living cell. • Concentration- and time-dependent manners of MGMT-DNA cross-linking were revealed. • Proteolysis played an important role in protein (MGMT)-DNA cross-linking repair. • DVC1 acts as a proteolytic enzyme in cross-linking repair in a p97-dependent manner.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

MiR-26a enhances the radiosensitivity of glioblastoma multiforme cells through targeting of ataxia–telangiectasia mutated

Glioblastoma multiforme (GBM) is notoriously resistant to radiation, and consequently, new radiosensitizers are urgently needed. MicroRNAs are a class of endogenous gene modulators with emerging roles in DNA repair. We found that overexpression of miR-26a can enhance radiosensitivity and reduce the DNA repair ability of U87 cells. However, knockdown miR-26a in U87 cells could act the converse manner. Mechanistically, this effect is mediated by direct targeting of miR-26a to the 3′UTR of ATM, which leads to reduced ATM levels and consequent inhibition of the homologous recombination repair pathway. These results suggest that miR-26a may act as a new radiosensitizer of GBM. - Highlights: ●miR-26a directly target ATM in GBM cells. ●miR-26a enhances the radiosensitivity of GBM cells. ●miR-26a could reduce the DNA repair capacity of GBM cells.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Structural basis for $\mathrm{APE1}$ processing $\mathrm{DNA}$ damage in the nucleosome

Genomic DNA is continually exposed to endogenous and exogenous factors that promote DNA damage. Eukaryotic genomic DNA is packaged into nucleosomes, which present a barrier to accessing and effectively repairing DNA damage. The mechanisms by which DNA repair proteins overcome this barrier to repair DNA damage in the nucleosome and protect genomic stability is unknown. Here, we determine how the base excision repair (BER) endonuclease AP-endonuclease 1 (APE1) recognizes and cleaves DNA damage in the nucleosome. Kinetic assays determine that APE1 cleaves solvent-exposed AP sites in the nucleosome with 3-6 orders of magnitude higher efficiency than occluded AP sites. A cryo-electron microscopy structure of APE1 bound to a nucleosome containing a solvent-exposed AP site reveal that APE1 uses a DNA sculpting mechanism for AP site recognition, where APE1 bends the nucleosomal DNA to access the AP site. Notably, additional biochemical and structural characterization of occluded AP sites identify contacts between the nucleosomal DNA and histone octamer that prevent efficient processing of the AP site by APE1. These findings provide a rationale for the position-dependent activity of BER proteins in the nucleosome and suggests the ability of BER proteins to sculpt nucleosomal DNA drives efficient BER in chromatin.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Structure of a DNA glycosylase that unhooks interstrand cross-links

DNA glycosylases are important editing enzymes that protect genomic stability by excising chemically modified nucleobases that alter normal DNA metabolism. Here, these enzymes have been known only to initiate base excision repair of small adducts by extrusion from the DNA helix. However, recent reports have described both vertebrate and microbial DNA glycosylases capable of unhooking highly toxic interstrand cross-links (ICLs) and bulky minor groove adducts normally recognized by Fanconi anemia and nucleotide excision repair machinery, although the mechanisms of these activities are unknown. Here we report the crystal structure of Streptomyces sahachiroi AlkZ (previously Orf1), a bacterial DNA glycosylase that protects its host by excising ICLs derived from azinomycin B (AZB), a potent antimicrobial and antitumor genotoxin. AlkZ adopts a unique fold in which three tandem winged helix-turn-helix motifs scaffold a positively charged concave surface perfectly shaped for duplex DNA. Through mutational analysis, we identified two glutamine residues and a β-hairpin within this putative DNA-binding cleft that are essential for catalytic activity. Additionally, we present a molecular docking model for how this active site can unhook either or both sides of an AZB ICL, providing a basis for understanding the mechanisms of base excision repair of ICLs. Given the prevalence of this protein fold in pathogenic bacteria, this work also lays the foundation for an emerging role of DNA repair in bacteria-host pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Stable hypermutators revealed by the genomic landscape of genes involved in genome stability among yeast species

Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can undergo prolonged accelerated evolution after losing genes involved in DNA repair. Here, we surveyed 1,154 yeast genomes representing nearly all known yeast species of the subphylum Saccharomycotina (phylum Ascomycota) to examine the relationship between reduced gene repertoires broadly associated with genome stability functions (e.g., DNA repair, cell cycle) and elevated evolutionary rates. We identified three distantly related lineages—encompassing 12% of species—that had both the most streamlined sets of genes involved in genome stability (specifically DNA repair) and the highest evolutionary rates in the entire subphylum. Two of these “faster-evolving lineages” (FELs)—a subclade within the order Pichiales and the Wickerhamiella/Starmerella (W/S) clade (order Dipodascales)—are described here for the first time, while the third corresponds to a previously documented Hanseniaspora FEL. Examination of genome stability gene repertoires revealed a set of genes predominantly absent in these three FELs, suggesting a potential role in the observed acceleration of evolutionary rates. In the W/S clade, genomic signatures are consistent with a substantial mutational burden, including pronounced A|T bias and endogenous DNA damage. Interestingly, we found that the W/S clade also contains DNA repair genes possibly acquired through horizontal gene transfer, including a photolyase of bacterial origin. These findings highlight how hypermutators can persist across macroevolutionary timescales, potentially linked to the loss of genes related with genome stability, with horizontal gene transfer as a possible avenue for partial functional compensation.

DNA repair↗

DOE OSTI2014

SU-F-19A-08: Optimal Time Release Schedule of In-Situ Drug Release During Permanent Prostate Brachytherapy

Purpose: Permanent prostate brachytherapy spacers can be used to deliver sustained doses of radiosentitizing drug directly to the target, in order to enhance the radiation effect. Implantable nanoplatforms for chemo-radiation therapy (INCeRTs) have a maximum drug capacity and can be engineered to control the drug release schedule. The optimal schedule for sensitization during continuous low dose rate irradiation is unknown. This work studies the optimal release schedule of drug for both traditional sensitizers, and those that work by suppressing DNA repair processes. Methods: Six brachytherapy treatment plans were used to model the anatomy, implant geometry and calculate the spatial distribution of radiation dose and drug concentrations for a range of drug diffusion parameters. Three state partial differential equations (cells healthy, damaged or dead) modeled the effect of continuous radiation (radiosensitivities α,β) and cellular repair (time tr) on a cell population. Radiosensitization was modeled as concentration dependent change in α,β or tr which with variable duration under the constraint of fixed total drug release. Average cell kill was used to measure effectiveness. Sensitization by means of both enhanced damage and reduced repair were studied. Results: Optimal release duration is dependent on the concentration of radiosensitizer compared to the saturation concentration (csat) above which additional sensitization does not occur. Long duration drug release when enhancing α or β maximizes cell death when drug concentrations are generally over csat. Short term release is optimal for concentrations below saturation. Sensitization by suppressing repair has a similar though less distinct trend that is more affected by the radiation dose distribution. Conclusion: Models of sustained local radiosensitization show potential to increase the effectiveness of radiation in permanent prostate brachytherapy. INCeRTs with high drug capacity produce the greatest benefit with drug release over weeks. If in-vivo drug concentrations are not able to approach saturation concentration, durations of days is optimal. DOD 1R21CA16977501; A. David Mazzone Awards Program 2012PD164.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

WE-DE-202-00: Connecting Radiation Physics with Computational Biology

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

60 APPLIED LIFE SCIENCES↗