Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Repair”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,099 records · Page 61

Aprataxin resolves adenylated RNA–DNA junctions to maintain genome integrity

Faithful maintenance and propagation of eukaryotic genomes is ensured by three-step DNA ligation reactions used by ATP-dependent DNA ligases. Paradoxically, when DNA ligases encounter nicked DNA structures with abnormal DNA termini, DNA ligase catalytic activity can generate and/or exacerbate DNA damage through abortive ligation that produces chemically adducted, toxic 5'-adenylated (5'-AMP) DNA lesions. Aprataxin (APTX) reverses DNA adenylation but the context for deadenylation repair is unclear. Here we examine the importance of APTX to RNase-H2-dependent excision repair (RER) of a lesion that is very frequently introduced into DNA, a ribonucleotide. We show that ligases generate adenylated 5' ends containing a ribose characteristic of RNase H2 incision. APTX efficiently repairs adenylated RNA–DNA, and acting in an RNA–DNA damage response (RDDR), promotes cellular survival and prevents S-phase checkpoint activation in budding yeast undergoing RER. Structure–function studies of human APTX–RNA–DNA–AMP–Zn complexes define a mechanism for detecting and reversing adenylation at RNA–DNA junctions. This involves A-form RNA binding, proper protein folding and conformational changes, all of which are affected by heritable APTX mutations in ataxia with oculomotor apraxia 1. Together, these results indicate that accumulation of adenylated RNA–DNA may contribute to neurological disease.

Tumbale, Percy↗

The topography of mutational processes in breast cancer genomes

Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription, DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Lastly, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.

59 BASIC BIOLOGICAL SCIENCES↗

A mutational signature in gastric cancer suggests therapeutic strategies

Targeting defects in the DNA repair machinery of neoplastic cells, for example, those due to inactivating BRCA1 and/or BRCA2 mutations, has been used for developing new therapies in certain types of breast, ovarian and pancreatic cancers. Recently, a mutational signature was associated with failure of double-strand DNA break repair by homologous recombination based on its high mutational burden in samples harbouring BRCA1 or BRCA2 mutations. In pancreatic cancer, all responders to platinum therapy exhibit this mutational signature including a sample that lacked any defects in BRCA1 or BRCA2. Here, we examine 10,250 cancer genomes across 36 types of cancer and demonstrate that, in addition to breast, ovarian and pancreatic cancers, gastric cancer is another cancer type that exhibits this mutational signature. Furthermore, our results suggest that 7–12% of gastric cancers have defective double-strand DNA break repair by homologous recombination and may benefit from either platinum therapy or PARP inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

Feed-forward alpha particle radiotherapy ablates androgen receptor-addicted prostate cancer

Human kallikrein peptidase 2 (hK2) is a prostate specific enzyme whose expression is governed by the androgen receptor (AR). AR is the central oncogenic driver of prostate cancer (PCa) and is also a key regulator of DNA repair in cancer. We report an innovative therapeutic strategy that exploits the hormone-DNA repair circuit to enable molecularlyspecific alpha particle irradiation of PCa. Alpha-particle irradiation of PCa is prompted by molecularly specific-targeting and internalization of the humanized monoclonal antibody hu11B6 targeting hK2 and further accelerated by inherent DNA-repair that up-regulate hK2 (KLK2) expression in vivo. hu11B6 demonstrates exquisite targeting specificity for KLK2. A single administration of actinium-225 labeled hu11B6 eradicates disease and significantly prolongs survival in animal models. DNA damage arising from alpha particle irradiation induces AR and subsequently KLK2, generating a unique feed-forward mechanism, which increases binding of hu11B6. Imaging data in nonhuman primates support the possibility of utilizing hu11B6 in man.

60 APPLIED LIFE SCIENCES↗

Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells

Clostridium thermocellum forms biofilms adherent to lignocellulosic feedstock in a typical continuous cell-monolayer to efficiently break down and uptake cellulose hydrolysates. The sessile cells of biofilms may revert to non-adherent planktonic cells through generation of offspring cells or microenvironment constraints such as limited surface area. These interdependent cell populations co-exist and have different contributions to culture activity and growth. Here, we developed a novel bioreactor design to rapidly harvest sessile and planktonic cell populations for omics studies. In RNA-seq analyses, within 3299 protein coding genes, 59% (or 1958 genes) were differentially expressed with a minimum two-fold change between the two cell populations isolated simultaneously at high culture activity. Furthermore, sessile cells had definitive greater expression of genes involved in catabolism of carbohydrates by glycolysis and pyruvate fermentation, ATP generation by proton gradient, the anabolism of proteins and lipids and cellular functions critical for cell division; planktonic cells had notably higher gene expression for flagellar motility and chemotaxis, cellulosomal cellulases and anchoring scaffoldins, and a range of stress induced homeostasis mechanisms such as oxidative stress protection by antioxidants and flavoprotein co-factors, methionine repair, Fe-S cluster assembly and repair in redox proteins, cell growth control through tRNA thiolation, recovery of damaged DNA by nucleotide excision repair and removal of terminal proteins by proteases. Our knowledge of these cellular adaptations will aid the engineering of industrially relevant strains for consolidated bioprocessing of solid lignocellulosic biomass

59 BASIC BIOLOGICAL SCIENCES↗

How non-bonding domains affect the active assembly of microtubule spools

We report that structural defects can determine and influence various properties of materials, and many technologies rely on the manipulation of defects ( e.g. , semiconductor industries). In biological systems, management of defects/errors ( e.g. DNA repair) is critical to an organism's survival, which has inspired the design of artificial nanomachines that mimic nature's ability to detect defects and repair damage. Biological motors have captured considerable attention in developing such capabilities due to their ability to convert energy into directed motion in response to environmental stimuli, which maximizes their ability for detection and repair. The objective of the present study was to develop an understanding of how the presence of non-bonding domains, here considered as a “defect”, in microtubule (MT) building blocks affect the kinesin-driven, active assembly of MT spools. The assembly/joining of micron-scale bonding ( i.e. , biotin-containing) and non-bonding ( i.e. , no biotin) MTs resulted in segmented MT building blocks consisting of alternating bonding and non-bonding domains. Here, the introduction of these MT building blocks into a kinesin gliding motility assay along with streptavidin-coated quantum dots resulted in the active assembly of spools with altered morphology but retained functionality. Moreover, it was noted that non-bonding domains were autonomously and preferentially released from the spools over time, representing a mechanism by which defects may be removed from these structures. In conclusion, our findings demonstrate that this active assembly system has an intrinsic ability for quality control, which can be potentially expanded to a wide range of applications such as self-regulation and healing of active materials.

36 MATERIALS SCIENCE↗

Catch bond kinetics are instrumental to cohesion of fire ant rafts under load

Dynamic networks composed of constituents that break and reform bonds reversibly are ubiquitous in nature owing to their modular architectures that enable functions like energy dissipation, self-healing, and even activity. While bond breaking depends only on the current configuration of attachment in these networks, reattachment depends also on the proximity of constituents. Therefore, dynamic networks composed of macroscale constituents (not benefited by the secondary interactions cohering analogous networks composed of molecular-scale constituents) must rely on primary bonds for cohesion and self-repair. Toward understanding how such macroscale networks might adaptively achieve this, we explore the uniaxial tensile response of 2D rafts composed of interlinked fire ants ( S. invicta ). Through experiments and discrete numerical modeling, we find that ant rafts adaptively stabilize their bonded ant-to-ant interactions in response to tensile strains, indicating catch bond dynamics. Consequently, low-strain rates that should theoretically induce creep mechanics of these rafts instead induce elastic-like response. Our results suggest that this force-stabilization delays dissolution of the rafts and improves toughness. Nevertheless, above 35 % strain low cohesion and stress localization cause nucleation and growth of voids whose coalescence patterns result from force-stabilization. These voids mitigate structural repair until initial raft densities are restored and ants can reconnect across defects. However mechanical recovery of ant rafts during cyclic loading suggests that—even upon reinstatement of initial densities—ants exhibit slower repair kinetics if they were recently loaded at faster strain rates. These results exemplify fire ants’ status as active agents capable of memory-driven, stimuli-response for potential inspiration of adaptive structural materials.

Science & Technology - Other Topics↗

ATM–dependent phosphorylation of CHD7 regulates morphogenesis-coupled DSB stress response in fetal radiation exposure

Following radiation exposure, unrepaired DNA double-strand breaks (DSBs) persist to some extent in a subset of cells as residual damage; they can exert adverse effects, including late-onset diseases. In search of the factor(s) that characterize(s) cells bearing such damage, we discovered ataxia-telangiectasia mutated (ATM)-dependent phosphorylation of the transcription factor chromodomain helicase DNA binding protein 7 (CHD7). CHD7 controls the morphogenesis of cell populations derived from neural crest cells during vertebrate early development. Indeed, malformations in various fetal bodies are attributable to CHD7 haploinsufficiency. Following radiation exposure, CHD7 becomes phosphorylated, ceases promoter/enhancer binding to target genes, and relocates to the DSB-repair protein complex, where it remains until the damage is repaired. Thus, ATM-dependent CHD7 phosphorylation appears to act as a functional switch. As such stress responses contribute to improved cell survival and canonical nonhomologous end joining, we conclude that CHD7 is involved in both morphogenetic and DSB-response functions. Thus, we propose that higher vertebrates have evolved intrinsic mechanisms underlying the morphogenesis-coupled DSB stress response. In fetal exposure, if the function of CHD7 becomes primarily shifted toward DNA repair, morphogenic activity is reduced, resulting in malformations.

59 BASIC BIOLOGICAL SCIENCES↗

Preventive Power Outage Estimation Based on a Novel Scenario Clustering Strategy

The increasing occurrence of extreme weather events is challenging power grid operation. For extreme weather events, the system operator is responsible for estimating the power outages and scheduling the restoration resources. This paper proposes an outage evaluation framework to identify the possible unserved load profiles, vulnerable areas, and mobile energy adequacy. The outputs of an outage prediction model tool are used to generate numerous faulted line scenarios. Next, each scenario's nodal unserved load profile is obtained by solving a three-phase restoration model that considers repair crews and mobile energy resources (MERs). Then, a novel scenario clustering strategy is developed to cluster the unserved load profiles into multiple representative profiles which the system operator can focus on. Finally, case studies on a distribution system evaluate the damage caused by an extreme weather event and verify the effectiveness of the proposed scenario clustering strategy.

MATHEMATICS AND COMPUTING,POWER TRANSMISSION AND D↗

Prediction of Substrate Distortion in Powder DED Using Finite Element Model

Abstract Leveraging the capabilities of both additive and subtractive manufacturing to repair tooling and other high value items can result in significant cost and time saving opportunities. However, when dimensional accuracy of the repaired component must be held within a specified tolerance, distortion of the component induced during repair can lead to an out of specification final component. This work presents simulation of a novel method to mitigate part distortion using sacrificial support structures. A blown powder directed energy deposition system was utilized for deposition of sacrificial support structures and clad surface depositions. Sacrificial support structures were deposited on the underside of the substrate with varying geometries prior to clad surface depositions. A finite element model was developed and verified using experimental results. The simulation and experimental control results were found to match within 6%. It has been shown that simulation can be used to predict effects of sacrificial support structures on substrate distortion in a blown powder directed energy deposition process.

Burl, Alan G.↗

FRICTION STIR WELDING AND PRELIMINARY CHARACTERIZATION OF IRRADIATED 304 STAINLESS STEEL

The mitigation of helium induced cracking in the heat affected zone (HAZ), a transition metallurgical zone between the weld zone and base metal, during repair welding is a great challenge in nuclear industry. Successful traditional fusion welding repairs are limited to metals with a maximum of a couple of atomic parts per million (appm) helium, and structural materials helium levels in operating nuclear power plants are generally exceed a couple of appm after years of operations. Therefore, fusion welding is very limited in nuclear power plants structural materials repairing. Friction stir welding (FSW) is a solid-state joining technology that reduces the drivers (temperature and tensile residual stress) for helium-induced cracking. This paper will detail initial procedural development of FSW weld trials on irradiated 304L stainless steel (304L SS) coupons utilizing a unique welding facility located at one of Oak Ridge National Laboratory’s hot cell facilities. The successful early results of FSW of an irradiated 304L SS coupon containing high helium are discussed. Helium induced cracking was not observed by scanning electron microscopy in the friction stir weld zone and the metallurgical zones between the weld zone and base metal, i.e. thermal mechanical affected zone (TMAZ) and HAZ. Characterization of the weld, TMAZ and HAZ regions are detailed in this paper.

Tang, Wei↗

WE-AB-204-02: Molecular-Imaging Based Assessment of Liver Complications for Yttrium-90 Microsphere Treatments: Can Existing NTCP Models Explain Clinical Outcomes?

Purpose: To evaluate weather the current radiobiological models can predict the normal liver complications of radioactive Yttrium-90 ({sup 90}Y) selective-internal-radiation-treatment (SIRT) for metastatic liver lesions based on the post-infusion {sup 90}Y PET images. Methods: A total of 20 patients with metastatic liver tumors treated with SIRT that received a post-infusion {sup 90}Y-PET/CT scan were analyzed in this work. The 3D activity distribution of the PET images was converted into a 3D dose distribution via a kernel convolution process. The physical dose distribution was converted into the equivalent dose (EQ2) delivered at 2 Gy based on the linear-quadratic (LQ) model considering the dose rate effect. The biological endpoint of this work was radiation-induce liver disease (RILD). The NTCPs were calculated with four different repair-times (T1/2-Liver-Repair= 0,0.5,1.0,2.0 hr) and three published NTCP models (Lyman-external-RT, Lyman 90Y-HCC-SIRT, parallel model) were compared to the incidence of RILD of the recruited patients to evaluate their ability of outcome prediction. Results: The mean normal liver physical dose (avg. 51.9 Gy, range 31.9–69.8 Gy) is higher than the suggested liver dose constraint for external beam treatment (∼30 Gy). However, none of the patients in our study developed RILD after the SIRT. The estimated probability of ‘no patient developing RILD’ obtained from the two Lyman models are 46.3% to 48.3% (T1/2-Liver-Repair= 0hr) and <1% for all other repair times. For the parallel model, the estimated probability is 97.3% (0hr), 51.7% (0.5hr), 2.0% (1.0hr) and <1% (2.0hr). Conclusion: Molecular-images providing the distribution of {sup 90}Y enable the dose-volume based dose/outcome analysis for SIRT. Current NTCP models fail to predict RILD complications in our patient population, unless a very short repair-time for the liver is assumed. The discrepancy between the Lyman {sup 90}Y-HCC-SIRT model predicted and the clinically observed outcomes further demonstrates the need of an NTCP model specific to the metastatic liver SIRT.

60 APPLIED LIFE SCIENCES↗

NEIL2 Protects against Oxidative DNA Damage Induced by Sidestream Smoke in Human Cells

Secondhand smoke (SHS) is a confirmed lung carcinogen that introduces thousands of toxic chemicals into the lungs. SHS contains chemicals that have been implicated in causing oxidative DNA damage in the airway epithelium. Although DNA repair is considered a key defensive mechanism against various environmental attacks, such as cigarette smoking, the associations of individual repair enzymes with susceptibility to lung cancer are largely unknown. This study investigated the role of NEIL2, a DNA glycosylase excising oxidative base lesions, in human lung cells treated with side-stream smoke (SSS), the main component of SHS. To do so, we generated NEIL2 knockdown cells using siRNA-technology and exposed them to SSS-laden medium. Representative SSS chemical compounds in the medium were analyzed by mass spectrometry. An increased production of reactive oxygen species (ROS) in SSS-exposed cells was detected through the fluorescent detection and the induction of HIF-1a. The long amplicon–quantitative PCR (LA-QPCR) assay detected significant dose-dependent increases of oxidative DNA damage in the HPRT gene of cultured human pulmonary fibroblasts (hPF) and BEAS-2B epithelial cells exposed to SSS for 24 h. These data suggest that SSS exposure increased oxidative stress, which could contribute to SSS-mediated toxicity. siRNA knockdown of NEIL2 in hPF and HEK 293 cells exposed to SSS for 24 h resulted in significantly more oxidative DNA damage in HPRT and POLB than in cells with control siRNA. Taken together, our data strongly suggest that decreased repair of oxidative DNA base lesions due to an impaired NEIL2 expression in non-smokers exposed to SSS would lead to accumulation of mutations in genomic DNA of lung cells over time, thus contributing to the onset of SSS induced lung cancer.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular Dissection of Induced Platinum Resistance through Functional and Gene Expression Analysis in a Cell Culture Model of Bladder Cancer

Here, we report the development, functional and molecular characterization of an isogenic, paired bladder cancer cell culture model system for studying platinum drug resistance. The 5637 human bladder cancer cell line was cultured over ten months with stepwise increases in oxaliplatin concentration to generate a drug resistant 5637R sub cell line. The MTT assay was used to measure the cytotoxicity of several bladder cancer drugs. Liquid scintillation counting allowed quantification of cellular drug uptake and efflux of radiolabeled oxaliplatin and carboplatin. The impact of intracellular drug inactivation was assessed by chemical modulation of glutathione levels. Oxaliplatin- and carboplatin-DNA adduct formation and repair was measured using accelerator mass spectrometry. Resistance factors including apoptosis, growth factor signaling and others were assessed with RNAseq of both cell lines and included confirmation of selected transcripts by RT-PCR. Oxaliplatin, carboplatin, cisplatin and gemcitabine were significantly less cytotoxic to 5637R cells compared to the 5637 cells. In contrast, doxorubicin, methotrexate and vinblastine had no cell line dependent difference in cytotoxicity. Upon exposure to therapeutically relevant doses of oxaliplatin, 5637R cells had lower drug-DNA adduct levels than 5637 cells. This difference was partially accounted for by pre-DNA damage mechanisms such as drug uptake and intracellular inactivation by glutathione, as well as faster oxaliplatin-DNA adduct repair. In contrast, both cell lines had no significant differences in carboplatin cell uptake, efflux and drug-DNA adduct formation and repair, suggesting distinct resistance mechanisms for these two closely related drugs. The functional studies were augmented by RNAseq analysis, which demonstrated a significant change in expression of 83 transcripts, including 50 known genes and 22 novel transcripts. Most of the transcripts were not previously associated with bladder cancer chemoresistance. This model system and the associated phenotypic and genotypic data has the potential to identify some novel details of resistance mechanisms of clinical importance to bladder cancer.

59 BASIC BIOLOGICAL SCIENCES↗

Replication stress induced site-specific phosphorylation targets WRN to the ubiquitin-proteasome pathway

Faithful and complete genome replication in human cells is essential for preventing the accumulation of cancer-promoting mutations. WRN, the protein defective in Werner syndrome, plays critical roles in preventing replication stress, chromosome instability, and tumorigenesis. Herein, we report that ATR-mediated WRN phosphorylation is needed for DNA replication and repair upon replication stress. A serine residue, S1141, in WRN is phosphorylated in vivo by the ATR kinase in response to replication stress. ATR-mediated WRN S1141 phosphorylation leads to ubiquitination of WRN, facilitating the reversible interaction of WRN with perturbed replication forks and subsequent degradation of WRN. The dynamic interaction between WRN and DNA is required for the suppression of new origin firing and Rad51-dependent double-stranded DNA break repair. Significantly, ATR-mediated WRN phosphorylation is critical for the suppression of chromosome breakage during replication stress. These findings reveal a unique role for WRN as a modulator of DNA repair, replication, and recombination, and link ATR-WRN signaling to the maintenance of genome stability.

Cell Biology↗

Development of volume deposition on cast iron by additive manufacturing

ORNL partnered with Cummins to demonstrate the feasibility of using additive manufacturing techniques to help develop repair techniques for refurbished cast iron engine blocks. Cummins is interested in the refurbished engine business due to the increased cost savings and reduced emissions. It is expected that by refurbishing engines could help reduce the green house gas emissions by as much as 85%. Though such repair techniques are possible in principle there has been no major industry in the automotive sector that has deployed this technology. Therefore phase-1 would seek to evaluate the feasibility of using the laser directed energy deposition technique to repair cast iron engine blocks. The objective of the phase-1 would be to explore various strategies and understand the challenges involved. During phase-1 deposits were made using Inconel-718, Nickel, Nr-Cr-B braze filler. Inconel 718 builds showed significant cracking in the heat-affected zone in the cast iron. Nickel was used to reduce the cracking in the cast iron substrate, however the Ni builds did not wet the substrate sufficiently resulting in poor dimensional tolerance. In order to increase wetting the Ni was alloyed with the Ni-Cr-B braze to decrease the surface tension of Ni. This however resulted in significant cracks in the build due to shrinkage stresses associated with multiple thermal cycling. Hence to reduce the residual stresses in the builds the DMD-103D equipment was modified and the cast iron block was pre heated using cartridge heaters. Inconel-718 alloyed with Ni was deposited on the engine block. The pre-heated deposits showed a reduced susceptibility to cracking. If awarded the phase-2 of the project would aim to develop process parameters to achieve a crack free deposit engine block.

36 MATERIALS SCIENCE↗

Report on the Progress of Weld Development of Irradiated Materials at the Oak Ridge National Laboratory

This report summarizes recent welding activities on irradiated alloys in the advanced welding facility at the Radiochemical Engineering Development Center of Oak Ridge National Laboratory and the development of post-weld characterization capabilities and procedures that will be critical for assessing the ability of the advanced welding processes housed within the facility to make successful repairs on irradiated alloys. This facility and its capabilities were developed jointly by the U.S. Department of Energy, Office of Nuclear Energy, Light Water Reactor Sustainability Program and the Electric Power Research Institute, Long Term Operations Program (and the Welding and Repair Technology Center), with additional support from Oak Ridge National Laboratory. The significant, on-going effort to weld irradiated alloys with high Helium concentrations and comprehensively analyze the results will eventually yield validated repair techniques and guidelines for use by the nuclear industry in extending the operational lifetimes of nuclear power plants.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Malleable Thermosets (Vitrimers) from CO 2 and Plants

Fiber-reinforced composite materials are increasingly used to replace heavy metal components in transportation applications for lightweighting purposes. Polymer matrix materials used in automotive parts, such as epoxies, nylons, and polypropylenes, are almost all produced from fossil fuels. Higher performance thermoset composites are generally not repairable and lower-cost thermoplastic composites do not have enough performance to replace steel. Vitrimers are a new class of polymer materials with long shelf life, low waste in production, ease of processing, and repairability that have the potential to break through the high-cost thermoset/low-performance thermoplastic barrier to vehicle light-weighting. Vitrimers also exhibit easier chemical recyclability than conventional thermosets with reversible chemical crosslinking that enables reprocessing of scrap from production and end of life components. Vitrimers are a new class of engineered plastics that are weldable, repairable and recyclable like thermoplastics but have high mechanical properties like thermosets. Bio-based vitrimers have only recently been reported in the academic and patent literature. These materials represent an unusual opportunity to meet both VTO light-weighting targets for low-density, high performance materials and BETO sustainability targets for value-added high-volume applications of bio-fuel byproducts. Also, PNNL researchers have previously demonstrated a process to convert CO 2 into potential vitrimer precursors. Washington State University (WSU) success in demonstration of bio-based vitrimers and recent steps toward commercialization of petroleum-based vitrimers support the opportunity for PNNL success in development of sustainable vitrimer materials for recyclable, high-performance fiber-reinforced composites for the transportation sectors.

36 MATERIALS SCIENCE↗