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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Analysis of ionizing radiation induced DNA damage response in human adult stem cells and differentiated neurons

Findings of neurodegenerative features associated with human radiosensitive syndromes such as Ataxia telangiectasia suggest that DNA repair efficiency is crucial for maintaining the functional integrity of central nervous system. To gain a better understanding of ionizing radiation (IR) induced DNA damage response in undifferentiated and differentiated neural cell types and to evaluate the role of ATM in DNA double strand break (DSB) repair, an in vitro human neural cell differentiation model system was utilized in this study. As compared to adult stem cells, differentiated neurons displayed an attenuated DSB repair response (as judged by the persistence of 53BP1 foci) after IR exposure and the attenuation was even more pronounced in stem cells and neurons after suppression of ATM (Ataxia Telangiectasia Mutated) gene product suggesting the importance of ATM for an optimal DSB repair efficiency in human neural cell types. In corroboration with an attenuated DNA damage response, a sharp decline in the expression levels of several DSB repair genes was observed in neurons. Furthermore, our results suggest that cellular differentiation modulates the expression of several genes thereby compromising the DSB repair fidelity in post mitotic neurons. Further studies are required to verify whether or not ATM mediated exacerbation of DNA repair deficiency in differentiated neurons leads to neurodegeneration.

53 binding protein 1↗
DOE OSTI2023

Identification of recG genetic interactions in Escherichia coli by transposon sequencing

ABSTRACT Maintaining the integrity of the genome is of utmost importance for cell division and propagation. In Escherichia coli , the RecG protein has been implicated in processing branched recombination intermediates during DNA repair processes, but the primary cellular role(s) of RecG and the repair pathways in which it acts have been difficult to define. To gain additional insight into RecG function, we employed transposon sequencing to identify recG genetic interactions and reveal complementary or redundant functions. The strongest hits from the screen were the dam , uvrD , rnhA , radA , and rep genes. The conditional importance of these five genes in cells lacking recG was confirmed using a plasmid-based assay, revealing synthetic lethal interactions for most double deletion strains. Several of the synthetic lethal gene combinations (with uvrD, rep, and radA , but not rnhA or dam ) were suppressed by deletion of recF or recO , indicating that their genetic relationships involved roles in post-replication gap repair. Additionally, loss of the RecG/SSB interaction phenocopied a recG deletion when combined with dam , uvrD , radA , or rnhA deletions but not with rep . The results reinforce the idea of RecG as a general genome guardian. RecG has at least two functions. It plays an important role in the resolution of joint molecules behind the fork, formed during post-replication gap repair. RecG is also required to suppress genome over-replication caused by unscheduled replication initiation at R-loops, at double-strand breaks caused by dam inactivation, and during replication termination. IMPORTANCE DNA damage and subsequent DNA repair processes are mutagenic in nature and an important driver of evolution in prokaryotes, including antibiotic resistance development. Genetic screening approaches, such as transposon sequencing (Tn-seq), have provided important new insights into gene function and genetic relationships. Here, we employed Tn-seq to gain insight into the function of the recG gene, which renders Escherichia coli cells moderately sensitive to a variety of DNA-damaging agents when they are absent. The reported recG genetic interactions can be used in combination with future screens to aid in a more complete reconstruction of DNA repair pathways in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

MLEC-Sim: A Simulator for Evaluating Multi-Level Erasure Coding

We present MLEC-Sim, a sophisticated simulator for Multi-Level Erasure Coding (MLEC), developed in approximately 13 KLOC. The simulator is engineered to analyze the impact of various system configurations and erasure coding policies on system durability and network overhead. It supports a comprehensive range of parameters including disk capacity, disk I/O bandwidth, failure rates, network bandwidth, and system scale, accommodating various erasure coding approaches such as Single-Level Erasure Coding (SLEC), Multi-Level Erasure Coding (MLEC), and Local Reconstruction Codes (LRC). MLEC-Sim provides support for multiple chunk placement policies, including clustered parity and declustered parity, and encompasses a variety of repair methods like Repair-ALL, Repair-FCO, Repair-HYB, and Repair-MIN. It is capable of simulating disk failures through a variety of means, including distribution-based or trace-based mechanisms, and can handle complex multi-level (de)clustered placements and repair processes. A key feature of MLEC-Sim is its adoption of the splitting simulation method for evaluating system durabilities at extremely high levels, which are challenging to assess with traditional simulation approaches. This feature allows for a detailed evaluation of system resilience under a range of conditions, aiding in the selection of appropriate erasure coding solutions for enhancing system durability. MLEC-Sim contributes to the field of data storage and reliability by providing a tool for the detailed evaluation of the durability and efficiency of erasure coding configurations, intended for use by researchers and practitioners in the design and optimization of storage systems.

Wang, Meng↗
DOE OSTI2023

Quantifying Uncertainty of Deep Reinforcement Learning Based Decision Making for Operations and Maintenance of Nuclear Power Plant

This paper summarizes research that integrates condition monitoring and prognostics with decision making for nuclear power plant operations and maintenance. As part of this research, we have developed an online asset management tool to help reduce life-cycle maintenance and repair costs. Using the latest advancements in condition monitoring, supply chain analytics, and deep reinforcement learning, we have created a predictive maintenance tool that can optimize the maintenance and spare-part management of a repairable nuclear system. To demonstrate these methods, preliminary studies were conducted on a simple, representative maintenance system undergoing a stochastic degradation process that requires repairs or replacement to continue operation. Through Monte Carlo simulations, we were able to reduce maintenance spending by approximately 50% compared to optimized, time-based maintenance strategies. Not only does the decision maker reduce the average life-cycle costs, it also minimizes the chance of high cost scenarios, lowering the variance of the expected cost distributions, and reducing overall financial risk. Furthermore, this work also studies the ability of the decision maker to handle various levels of noise from observation uncertainty. By introducing uncertainty into the decision-making process, we have quantified the robustness and resiliency of the decision maker, as well as identified necessary levels of observability to demonstrate cost effectiveness.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Nondestructive Evaluation of Carbon Fiber Reinforced Polymers

The American Society of Mechanical Engineers Boiler and Pressure Vessel Code requires repair and replacement of safety-related piping materials to meet the original Construction Code; however, no construction criteria currently exist for carbon fiber reinforced polymer (CFRP) materials in the nuclear industry. Although nondestructive examination (NDE) techniques for cast and wrought ferritic and austenitic steels are well established, licensees are increasingly deploying novel materials such as CFRP for which assessment of the use of NDE is required, as the inspectability of such materials and the influence of manufacturing processes on inspectability remain insufficiently understood. To address these gaps, Pacific Northwest National Laboratory (PNNL) evaluated the fabrication of several CFRP repair mockups and the effectiveness of NDE methods to support regulatory review of CFRP repairs in nuclear power plant applications. Representative flat-plate mockups containing realistic fabrication defects were manufactured and inspected using manual and automated tap testing, dynamic response spectroscopy (DRS), and ultrasonic testing (UT). The study identified significant fabrication variability, particularly in controlling defect size and epoxy thickness, which strongly influenced defect detectability by NDE methods. Tap testing was effective for shallow defects in thin epoxy configurations but unreliable for thicker repairs and deeper flaws. DRS demonstrated higher sensitivity to dry spots but produced unconfirmed indications for thicker plates, requiring further validation. Conventional UT, particularly at 1.0 MHz, showed the strongest overall capability for detecting a range of defects, although performance degraded with increasing repair thickness and complexity. The results highlight the need to better define critical defect sizes, develop reliable mockup fabrication methods, and validate NDE methods needed to support CFRP repairs.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Mitigation for Removal of Building 01-103 in the Area 1 Subdock, Nevada National Security Site, Nye County, Nevada

Building 01-103, the Drill Bit Repair Building was originally recorded as SHPO Resource No. B18848 in 2020 during an architectural survey of the Area 1 Subdock (Collins et al. 2022). It was recommended individually eligible for listing in the NRHP under Criteria A and C and contributing to the significance of the Area 1 Subdock Historic District. The SHPO concurred with these determinations in a letter dated April 29, 2022 (Reed 2022). The Drill Bit Repair Building retains all seven aspects of integrity. The location, materials, workmanship, feeling, and association have not changed since its original construction. The design was modified slightly in 1996 with the addition of a removable and non-destructive chain-link fence. Nearby buildings 01-101 and 01-102 were removed (Collins and Menocal 2020) but the other buildings and storage yards remain. Therefore, the integrity of setting has been changed, but not to the degree that the building no longer conveys its significance (see Figures 4 and 5 for comparison). Building 01-103 was constructed in 1985 to coincide with the relocation of the Area 3 Subdock to Area 1. The design for the new Subdock provided a centralized cluster of buildings surrounded by two large storage yards. The buildings included administrative and engineering office space, warehouses, a radiograph building, and Building 01-103 as the drill bit maintenance and repair building, among others. The Drill Bit Repair Building was critical to the success of underground nuclear testing and is eligible under Criterion A for its contribution to broad patterns of history by maintaining specially designed equipment for underground nuclear testing at the NNSS. It is also eligible under Criterion C as it is the only recorded example of a facility built specifically for the maintenance of big-hole drill bits on the NNSS. As it retains both significance and integrity, it remains individually eligible under Criteria A and C. In addition to its individual significance, the Drill Bit Repair Building also contributes to the significance of the Area 1 Subdock Historic District as a representative of a big-hole drilling support facility necessary for underground nuclear testing. The building and the equipment therein were designed specifically for testing at the NNSS, where much of the early technology and methods for big-hole drilling were developed. Its removal will result in not only the demolition of a contributing element but also a change in the physical features of the district’s setting that contribute to its historic significance. The change in setting will diminish the district’s integrity. However, the district still contains numerous examples of other buildings constructed for the purpose of supporting big-hole drilling and remains eligible under Criteria A and C.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Cas9-induced large deletions and small indels are controlled in a convergent fashion

Repair of Cas9-induced double-stranded breaks results primarily in formation of small insertions and deletions (indels), but can also cause potentially harmful large deletions. While mechanisms leading to the creation of small indels are relatively well understood, very little is known about the origins of large deletions. Using a library of clonal NGS-validated mouse embryonic stem cells deficient for 32 DNA repair genes, we have shown that large deletion frequency increases in cells impaired for non-homologous end joining and decreases in cells deficient for the central resection gene Nbn and the microhomology-mediated end joining gene Polq. Across deficient clones, increase in large deletion frequency was closely correlated with the increase in the extent of microhomology and the size of small indels, implying a continuity of repair processes across different genomic scales. Furthermore, by targeting diverse genomic sites, we identified examples of repair processes that were highly locus-specific, discovering a role for exonuclease Trex1. Finally, we present evidence that indel sizes increase with the overall efficiency of Cas9 mutagenesis. These findings may have impact on both basic research and clinical use of CRISPR-Cas9, in particular in conjunction with repair pathway modulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

DNA double-strand break movement in heterochromatin depends on the histone acetyltransferase dGcn5

Abstract Cells employ diverse strategies to repair double-strand breaks (DSBs), a dangerous form of DNA damage that threatens genome integrity. Eukaryotic nuclei consist of different chromatin environments, each displaying distinct molecular and biophysical properties that can significantly influence the DSB-repair process. DSBs arising in the compact and silenced heterochromatin domains have been found to move to the heterochromatin periphery in mouse and Drosophila to prevent aberrant recombination events. However, it is poorly understood how chromatin components, such as histone post-translational modifications, contribute to these DSB movements within heterochromatin. Using irradiation as well as locus-specific DSB induction in Drosophila tissues and cultured cells, we find enrichment of histone H3 lysine 9 acetylation (H3K9ac) at DSBs in heterochromatin but not euchromatin. We find this increase is mediated by the histone acetyltransferase dGcn5, which rapidly localizes to heterochromatic DSBs. Moreover, we demonstrate that in the absence of dGcn5, heterochromatic DSBs display impaired recruitment of the SUMO E3 ligase Nse2/Qjt and fail to relocate to the heterochromatin periphery to complete repair. In summary, our results reveal a previously unidentified role for dGcn5 and H3K9ac in heterochromatic DSB repair and underscore the importance of differential chromatin responses at heterochromatic and euchromatic DSBs to promote safe repair.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Abstract Background Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost. Results Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26–120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost. Conclusions Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars.

54 ENVIRONMENTAL SCIENCES↗