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Статті в журналах з теми "Repair Assisted Damage Detection"

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Автор: Grafiati

Опубліковано: 10 грудня 2022

Оновлено: 29 січня 2023

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1

Holton, Nathaniel W., Yuval Ebenstein, and Natalie R. Gassman. "Broad spectrum detection of DNA damage by Repair Assisted Damage Detection (RADD)." DNA Repair 66-67 (June 2018): 42–49. http://dx.doi.org/10.1016/j.dnarep.2018.04.007.

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2

Lee, Kevin J., Elise Mann, Luciana Madeira da Silva, Jennifer Scalici, and Natalie R. Gassman. "DNA damage measurements within tissue samples with Repair Assisted Damage Detection (RADD)." Current Research in Biotechnology 1 (November 2019): 78–86. http://dx.doi.org/10.1016/j.crbiot.2019.11.001.

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3

Gilat, Noa, Dmitry Torchinsky, Sapir Margalit, Yael Michaeli, Sigal Avraham, Hila Sharim, Nadav Elkoshi, Carmit Levy, Shahar Zirkin, and Yuval Ebenstein. "Rapid Quantification of Oxidation and UV Induced DNA Damage by Repair Assisted Damage Detection-(Rapid RADD)." Analytical Chemistry 92, no. 14 (June 24, 2020): 9887–94. http://dx.doi.org/10.1021/acs.analchem.0c01393.

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4

Krieger, Kimiko L., Jie H. Gohlke, Kevin J. Lee, Danthasinghe Waduge Badrajee Piyarathna, Patricia D. Castro, Jeffrey A. Jones, Michael M. Ittmann, Natalie R. Gassman, and Arun Sreekumar. "Repair-Assisted Damage Detection Reveals Biological Disparities in Prostate Cancer between African Americans and European Americans." Cancers 14, no. 4 (February 17, 2022): 1012. http://dx.doi.org/10.3390/cancers14041012.

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Анотація:

African Americans (AA) are two times more likely to be diagnosed with and succumb to prostate cancer (PCa) compared to European Americans (EA). There is mounting evidence that biological differences in these tumors contribute to disparities in patient outcomes. Our goal was to examine the differences in DNA damage in AA and EA prostate tissues. Tissue microarrays with matched tumor-benign adjacent pairs from 77 AA and EA PCa patients were analyzed for abasic sites, oxidative lesions, crosslinks, and uracil content using the Repair Assisted Damage Detection (RADD) assay. Our analysis revealed that AA PCa, overall, have more DNA damage than EA PCa. Increased uracil and pyrimidine lesions occurred in AA tumors, while EA tumors had more oxidative lesions. AA PCa have higher levels of UMP and folate cycle metabolites than their EA counterparts. AA PCa showed higher levels of UNG, the uracil-specific glycosylase, than EA, despite uracil lesions being retained within the genome. AA patients also had lower levels of the base excision repair protein XRCC1. These results indicate dysfunction in the base excision repair pathway in AA tumors. Further, these findings reveal how metabolic rewiring in AA PCa drives biological disparities and identifies a targetable axis for cancer therapeutics.

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5

Mann, Elise K., Kevin J. Lee, Dongquan Chen, Luciana Madeira da Silva, Valeria L. Dal Zotto, Jennifer Scalici, and Natalie R. Gassman. "Associations between DNA Damage and PD-L1 Expression in Ovarian Cancer, a Potential Biomarker for Clinical Response." Biology 10, no. 5 (April 29, 2021): 385. http://dx.doi.org/10.3390/biology10050385.

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Programmed death ligand-1 (PD-L1) inhibitors are currently under investigation as a potential treatment option for ovarian cancer. Although this therapy has shown promise, its efficacy is highly variable among patients. Evidence suggests that genomic instability influences the expression of PD-L1, but little is known about this relationship in ovarian cancer. To examine the relationship between PD-L1 expression and genomic instability, we measured DNA damage using Repair Assisted Damage Detection (RADD). We then correlated the presence of persistent DNA damage in the ovarian tumor with protein expression of PD-L1 using immunohistochemistry. Ovarian tumors showed a high prevalence of oxidative DNA damage. As the level of oxidative DNA damage increased, we saw a significant correlation with PD-L1 expression. The highest correlation between DNA damage and PD-L1 expression was observed for mucinous ovarian tumors (r = 0.82), but a strong correlation was also observed for high grade serous and endometrioid tumors (r = 0.67 and 0.69, respectively). These findings link genomic instability to PD-L1 protein expression in ovarian cancer and suggest that persistent DNA damage can be used as a potential biomarker for patient selection for immunotherapy treatment.

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6

Rashki Ghaleno, Leila, AliReza Alizadeh, Joël R. Drevet, Abdolhossein Shahverdi, and Mojtaba Rezazadeh Valojerdi. "Oxidation of Sperm DNA and Male Infertility." Antioxidants 10, no. 1 (January 12, 2021): 97. http://dx.doi.org/10.3390/antiox10010097.

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One important reason for male infertility is oxidative stress and its destructive effects on sperm structures and functions. The particular composition of the sperm membrane, rich in polyunsaturated fatty acids, and the easy access of sperm DNA to oxidative damage due to sperm cell specific cytologic and metabolic features (no cytoplasm left and cells unable to mount stress responses) make it the cell type in metazoans most susceptible to oxidative damage. In particular, oxidative damage to the spermatozoa genome is an important issue and a cause of male infertility, usually associated with single- or double-strand paternal DNA breaks. Various methods of detecting sperm DNA fragmentation have become important diagnostic tools in the prognosis of male infertility and such assays are available in research laboratories and andrology clinics. However, to date, there is not a clear consensus in the community as to their respective prognostic value. Nevertheless, it is important to understand that the effects of oxidative stress on the sperm genome go well beyond DNA fragmentation alone. Oxidation of paternal DNA bases, particularly guanine and adenosine residues, the most sensitive residues to oxidative alteration, is the starting point for DNA damage in spermatozoa but is also a danger for the integrity of the embryo genetic material independently of sperm DNA fragmentation. Due to the lack of a spermatozoa DNA repair system and, if the egg is unable to correct the sperm oxidized bases, the risk of de novo mutation transmission to the embryo exists. These will be carried on to every cell of the future individual and its progeny. Thus, in addition to affecting the viability of the pregnancy itself, oxidation of the DNA bases in sperm could be associated with the development of conditions in young and future adults. Despite these important issues, sperm DNA base oxidation has not attracted much interest among clinicians due to the lack of simple, reliable, rapid and consensual methods of assessing this type of damage to the paternal genome. In addition to these technical issues, another reason explaining why the measurement of sperm DNA oxidation is not included in male fertility is likely to be due to the lack of strong evidence for its role in pregnancy outcome. It is, however, becoming clear that the assessment of DNA base oxidation could improve the efficiency of assisted reproductive technologies and provide important information on embryonic developmental failures and pathologies encountered in the offspring. The objective of this work is to review relevant research that has been carried out in the field of sperm DNA base oxidation and its associated genetic and epigenetic consequences.

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7

Huston, Dryver, David Hurley, Kenneth Gollins, Anthony Gervais, and Tim Ziegler. "Damage Detection and Autonomous Repair System Coordination." Advances in Structural Engineering 14, no. 1 (February 2011): 41–45. http://dx.doi.org/10.1260/1369-4332.14.1.41.

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8

Cooke, Marcus S., Ian D. Podmore, Nalini Mistry, Mark D. Evans, Karl E. Herbert, Helen R. Griffiths, and Joseph Lunec. "Immunochemical detection of UV-induced DNA damage and repair." Journal of Immunological Methods 280, no. 1-2 (September 2003): 125–33. http://dx.doi.org/10.1016/s0022-1759(03)00269-2.

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9

Helleday, Thomas, Fredrik Johansson, and Dag Jenssen. "The DRAG Test: An Assay for Detection of Genotoxic Damage." Alternatives to Laboratory Animals 29, no. 3 (May 2001): 233–41. http://dx.doi.org/10.1177/026119290102900309.

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A high throughput assay (the DRAG test) is described, which could be a useful tool for the detection of repairable DNA adducts, and which is based on the inhibition of the growth of DNA repair-deficient Chinese hamster ovary (CHO) cells. The cytotoxicity of a test substance towards DNA repair-deficient CHO cell lines is compared with the corresponding cytotoxicity in the parental wild-type CHO cell line (AA8). A more pronounced toxicity toward a DNA repair-deficient cell line is interpreted as being the consequence of its inability to repair the DNA adduct induced by the compound. (+)-7β,8α-Dihydroxy-9α,10α-epoxy-7,8,9,10-tetrahydrobenzo[ a]pyrene, camptothecin, ethyl methanesulphonate and mitomycin C were used as reference substances, and the overall results indicate that the DRAG test could be useful in the screening of compounds for the production of repairable DNA adducts. The main advantages with the DRAG test are that it provides a relevant endpoint, it is rapid, it requires small amounts of the test item, and it permits a large number of compounds to be tested.

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10

Rouse, J. "Interfaces Between the Detection, Signaling, and Repair of DNA Damage." Science 297, no. 5581 (July 26, 2002): 547–51. http://dx.doi.org/10.1126/science.1074740.

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11

Malik, Rayaz A. "Early detection of nerve damage and repair in diabetic neuropathy." Nature Clinical Practice Neurology 4, no. 12 (November 18, 2008): 646–47. http://dx.doi.org/10.1038/ncpneuro0938.

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12

Prof. A. Zingoni, Alphose. "Advances in damage detection, repair and rehabilitation of engineering structures." Engineering Structures 24, no. 7 (July 2002): 841–42. http://dx.doi.org/10.1016/s0141-0296(02)00022-6.

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13

Yang, Cai-Guang, Kristel Garcia, and Chuan He. "Damage Detection and Base Flipping in Direct DNA Alkylation Repair." ChemBioChem 10, no. 3 (February 13, 2009): 417–23. http://dx.doi.org/10.1002/cbic.200800580.

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14

Chang, Hanjui, Guangyi Zhang, Yue Sun, and Shuzhou Lu. "A Node Detection Method Based on Johnson–Cook and Thin-Film IMD Characteristic Model Armor Damage Detection Repair and Subsequent Optimization." Polymers 14, no. 21 (October 26, 2022): 4540. http://dx.doi.org/10.3390/polym14214540.

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In this paper, a node detection method is proposed for the detection of battle damage to armor. This experiment uses the special nature of the film to virtualize the surface of the armor IMD film coverage. The die index is a large area and is easy to damage, but with the use of a unique IMD film stamping die, the possibility of damage decreases, which provides a damage prediction function for the armor. In addition, for the damaged armor, the same method can be used to detect because the damaged part more easily causes the surface film to rupture after being impacted, so it is possible to optimize the design of the armor and the molding through the die index. The die index can also detect the degree of damage to the damaged part of the damaged armor. Therefore, the IMD die index is introduced to quantify the data, and the degree of damage is judged by the IMD die index. The novelty of this work is that each node can efficiently detect the vulnerable damage position of the armor using the die index and then pass through the COMSOL. The Johnson–Cook stress model simulates the battle loss, obtains the stress deformation that occurs after the battle loss, and verifies the experiment by comparing the results obtained. Finally, the repair method is used to repair all the predicted battle damage parts based on additive manufacturing to ensure that they can be used again after repair.

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15

Sosa, Edward D., Erica S. Worthy, and Thomas K. Darlington. "Microwave Assisted Manufacturing and Repair of Carbon Reinforced Nanocomposites." Journal of Composites 2016 (October 13, 2016): 1–9. http://dx.doi.org/10.1155/2016/7058649.

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We report a composite capable of advanced manufacturing and damage repair. Microwave energy is used to induce thermal reversible polymerization of the matrix allowing for microwave assisted composite welding and repair. Composites can be bonded together in just a few minutes through microwave welding. Lap shear testing demonstrates that microwave welded composites exhibit 40% bond strength relative to composites bonded with epoxy resin. Double cantilever beam testing shows 60% recovery in delamination strength after microwave assisted composite repair. The interfacial adhesion and composite repair after microwave exposure are examined by X-ray computed tomography. The microwave processing is shown to be reproducible and consistent. The ability to perform scalable manufacturing is demonstrated by the construction of a large structure from smaller components.

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16

Apelt, Katja, Hannes Lans, Orlando D. Schärer, and Martijn S. Luijsterburg. "Nucleotide excision repair leaves a mark on chromatin: DNA damage detection in nucleosomes." Cellular and Molecular Life Sciences 78, no. 24 (November 3, 2021): 7925–42. http://dx.doi.org/10.1007/s00018-021-03984-7.

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AbstractGlobal genome nucleotide excision repair (GG-NER) eliminates a broad spectrum of DNA lesions from genomic DNA. Genomic DNA is tightly wrapped around histones creating a barrier for DNA repair proteins to access DNA lesions buried in nucleosomal DNA. The DNA-damage sensors XPC and DDB2 recognize DNA lesions in nucleosomal DNA and initiate repair. The emerging view is that a tight interplay between XPC and DDB2 is regulated by post-translational modifications on the damage sensors themselves as well as on chromatin containing DNA lesions. The choreography between XPC and DDB2, their interconnection with post-translational modifications such as ubiquitylation, SUMOylation, methylation, poly(ADP-ribos)ylation, acetylation, and the functional links with chromatin remodelling activities regulate not only the initial recognition of DNA lesions in nucleosomes, but also the downstream recruitment and necessary displacement of GG-NER factors as repair progresses. In this review, we highlight how nucleotide excision repair leaves a mark on chromatin to enable DNA damage detection in nucleosomes.

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17

Kumar, Shreya, and Marxa Figueiredo. "556 Chemo-immunotherapy to treat bone-metastatic prostate cancer." Journal for ImmunoTherapy of Cancer 9, Suppl 2 (November 2021): A586. http://dx.doi.org/10.1136/jitc-2021-sitc2021.556.

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BackgroundProstate cancer is the second most common cancer and is one of the leading causes of cancer-related death among American men.1 Prostate cancer exhibits significant tropism for the bone and once metastasis occurs, survival rates fall rapidly compared to primary tumors.2 Bone metastasis can lead to bone loss and fractures which can severely compromise the patient‘s quality of life. Current treatment options are limited and focused on symptom management. Immune-based treatments are rapidly emerging as a possible therapeutic option for a variety of cancers including prostate cancer, however, patient sensitivity remains a concern. Chemotherapies such as cabozantinib have been shown to have immune-priming effects which can sensitize tumors to immunotherapies.3 Additionally, lower doses of chemotherapy can be used in this context which can reduce side effects. For this project, we hypothesized that a combination of chemotherapy (cabozantinib) and immunotherapy (Interleukin-27) could be effective in treating bone-metastatic prostate cancer and can help reverse some of the bone damage caused by the tumor. IL-27 is a multi-functional cytokine, which recruits immune cells to the tumor site, and promotes bone repair.4MethodsTo test our hypothesis, we performed an in vivo experiment where syngeneic C57BL/6J mice were implanted with intratibial (cortical bone) TRAMP-C2ras tumors (TRAMP-C2 cells were infected with Lv-HrasG12V to make them more aggressive and gain the ability to grow in bone, and marked with Lv-Luc to follow tumor growth). Immunotherapy was administered in the form of sonoporation-assisted intramuscular gene delivery,4 with control (empty) vectors or vectors expressing mouse IL-27. Following immunotherapy, the animals received either cabozantinib (60 mg/kg) or vehicle control by oral gavage daily for two weeks. Bioluminescence imaging (BLI) was used to monitor Luc-expressing tumor size twice a week. Upon reaching a humane endpoint, the animals were euthanized, and tumor samples were harvested.ResultsBLI showed that mice treated with a combination of IL-27 and cabozantinib had smaller tumor sizes compared to mice treated with individual treatments. The combination group had a significantly lower tumor burden compared to the control group. RNA sequencing was used to characterize changes in gene expression relating to the impact of therapeutics in signaling and cellular composition in the tumor microenvironment.ConclusionsWe envision that chemo-immunotherapy approaches will emerge as a novel therapeutic strategy for treating bone-metastatic prostate cancer while reducing chemotherapy-associated toxicity, improving sensitivity to immunotherapy, and promoting healthy musculoskeletal tissue repair.AcknowledgementsSource of research support: R01CA196947ReferencesProstate Cancer Statistics | CDC 2021.[https://www.cdc.gov/cancer/prostate/statistics/index.htm.]Survival Rates for Prostate Cancer. [https://www.cancer.org/cancer/prostate-cancer/detection-diagnosis-staging/survival-rates.html.].Kwilas AR, Ardiani A, Donahue RN, Aftab DT, Hodge JW. Dual effects of a targeted small-molecule inhibitor (cabozantinib) on immune-mediated killing of tumor cells and immune tumor microenvironment permissiveness when combined with a cancer vaccine. J Transl Med 2014;12(1):1–15.Figueiredo ML, Neto MF, Salameh JW, Decker RE, Letteri R, Chan-Seng D, Emrick T. Ligand-Mediated Targeting of Cytokine Interleukin-27 Enhances Its Bioactivity In Vivo. Mol Ther Methods Clin Dev 2020;17:739–751.

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18

Torchinsky, Dmitry, Yael Michaeli, Natalie R. Gassman, and Yuval Ebenstein. "Simultaneous detection of multiple DNA damage types by multi-colour fluorescent labelling." Chemical Communications 55, no. 76 (2019): 11414–17. http://dx.doi.org/10.1039/c9cc05198h.

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Specific and simultaneous quantitation of DNA adducts is a major obstacle. Using repair enzymes, we present a protocol to quantify two types of DNA lesions simultaneously on the same DNA molecule and examine repair dynamics by single-molecule imaging.

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19

Zhang, Jiangmei, Xiang Gao, Kunpeng Wang, Youyong Liu, Xiuhong Yang, and Yihui Ao. "Detection of the damage threshold of fused silica components and morphologies of repaired damage sites based on the beam deflection method." Open Physics 16, no. 1 (August 20, 2018): 539–43. http://dx.doi.org/10.1515/phys-2018-0070.

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Abstract This article proposes a method to quickly detect the damage threshold of the fused silica components and the characteristics of the repair point damage. With a device detecting the beam deflection, the laser damage threshold is detected, quickly and effectively. Then, based on the beam deflection though mitigated sites, the beam deflection signals of the damage repair points are measured and the morphologies of mitigated sites are analyzed. This method is helpful in the online assessment of the damage resistance of the downstream optics and provides the guidance of the repair process.

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20

PANG, J., and I. BOND. "‘Bleeding composites’—damage detection and self-repair using a biomimetic approach." Composites Part A: Applied Science and Manufacturing 36, no. 2 (February 2005): 183–88. http://dx.doi.org/10.1016/s1359-835x(04)00166-6.

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21

Bassal, Sahar, and Assam El‐Osta. "DNA damage detection and repair, and the involvement of epigenetic states." Human Mutation 25, no. 2 (January 10, 2005): 101–9. http://dx.doi.org/10.1002/humu.20130.

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22

Sosa, Edward D., Thomas K. Darlington, Brian A. Hanos, and Mary Jane E. O’Rourke. "Microwave Assisted Healing of Thermally Mendable Composites." Smart Materials Research 2015 (February 4, 2015): 1–8. http://dx.doi.org/10.1155/2015/248490.

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Polymer matrix composites offer high specific strength; however, their potential weight savings have been limited by the concern of damage tolerance. If microcracking and similar incurred damage could be autonomously sealed, composite structures could be built thinner and lighter while still addressing damage tolerance, thus achieving the weight savings they promise. Various self-healing mechanisms have been proposed to this end. Herein, a method of thermally reversible polymerization is investigated. To date, thermally activated repair of composites have been accomplished typically through resistive heating, which has certain inherent complexities. An alternate heating method, via microwave exposure of carbon nanotubes incorporated throughout a thermal reversible polymer matrix, is demonstrated. Carbon nanotube-doped composites exhibit enhanced microwave absorption over an undoped control sample. Furthermore, it is shown that these composites can be heated locally by a focused microwave source. The particular composite formulation and layup studied could be uniformly heated to the targeted healing temperature of 100°C in as little as 20 seconds, followed by a healing time on the scale of minutes with total time depending upon the extent of damage.

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23

Sharafutdinov, D. M., R. R. Shavaleev, I. R. Kabirov, and V. N. Pavlov. "Preventing postoperative complications after robot-assisted transabdominal preperetoneal repair: clinical case." Creative surgery and oncology 12, no. 4 (January 5, 2023): 345–49. http://dx.doi.org/10.24060/2076-3093-2022-12-4-345-349.

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Introduction. Inguinal hernia repair is one of the most common elective surgeries today. In our clinic, the majority of inguinal hernia repairs are performed laparoscopically. The most frequent complication after transabdominal preperitoneal inguinal hernia repair is postoperative seroma.Materials and methods. A 35-year-old patient C. with a right-sided inguinal hernia sought medical care in our clinic. He underwent robot-assisted TAPP with fluorescence lymphography using indocyanine green (ICG).Results and discussion. The present paper describes the possible relationship between intraoperative damage of the lymphatic vessels within the spermatic cord induced by robot-assisted transabdominal preperitoneal inguinal hernia repair and postoperative development of inguinal seroma. 5 mg/ml of indocyanine green was injected into the testicle on the side with the hernial bulge to visualize the lymphatic vessels. In this case such procedure is safe and feasible. Due to the tight fusion of the hernia sac with two visualized lymphatic vessels, they were excised during surgery. In the early postoperative period, an ultrasound scan revealed a subclinical seroma in the inguinal region of approximately 10 ml.Conclusion. A case series of ICG fluorescence lymphography during robot-assisted TAPP should be performed further to elucidate the relationship between lymphatic vessel damage and hydrocele.

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24

Itsumi, Manabu, Masahiko Maeda, Hideaki Takeuchi, and Takashi Morie. "Water-assisted repair of plasma-induced damage in the silicon/silicon-dioxide system." Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures 18, no. 3 (2000): 1268. http://dx.doi.org/10.1116/1.591373.

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25

Kuokkanen, Hannu. "Tissue Expander-Assisted Ventral Hernia Repair for the Skin-Grafted Damage Control Abdomen." World Journal of Surgery 38, no. 4 (December 4, 2013): 788–89. http://dx.doi.org/10.1007/s00268-013-2354-5.

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26

Carr, John Alfred. "Tissue Expander-Assisted Ventral Hernia Repair for the Skin-Grafted Damage Control Abdomen." World Journal of Surgery 38, no. 4 (November 26, 2013): 782–87. http://dx.doi.org/10.1007/s00268-013-2377-y.

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27

Thompson, Ruth, Rachel Gatenby, and Samuel Sidi. "How Cells Handle DNA Breaks during Mitosis: Detection, Signaling, Repair, and Fate Choice." Cells 8, no. 9 (September 7, 2019): 1049. http://dx.doi.org/10.3390/cells8091049.

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Mitosis is controlled by a complex series of signaling pathways but mitotic control following DNA damage remains poorly understood. Effective DNA damage sensing and repair is integral to survival but is largely thought to occur primarily in interphase and be repressed during mitosis due to the risk of telomere fusion. There is, however, increasing evidence to suggest tight control of mitotic progression in the incidence of DNA damage, whether induced in mitotic cells or having progressed from failed interphase checkpoints. Here we will discuss what is known to date about signaling pathways controlling mitotic progression and resulting cell fate in the incidence of mitotic DNA damage.

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28

Uhlmann, Eckart, and Florian Heitmüller. "Improving Efficiency in Robot Assisted Belt Grinding of High Performance Materials." Advanced Materials Research 907 (April 2014): 139–49. http://dx.doi.org/10.4028/www.scientific.net/amr.907.139.

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In gas turbines and turbo jet engines, high performance materials such as nickel-based alloys are widely used for blades and vanes. In the case of repair, finishing of complex turbine blades made of high performance materials is carried out predominantly manually. The repair process is therefore quite time consuming. And the costs of presently available repair strategies, especially for integrated parts, are high, due to the individual process planning and great amount of manually performed work steps. Moreover, there are severe risks of partial damage during manually conducted repair. All that leads to the fact that economy of scale effects remain widely unused for repair tasks, although the piece number of components to be repaired is increasing significantly. In the future, a persistent automation of the repair process chain should be achieved by developing adaptive robot assisted finishing strategies. The goal of this research is to use the automation potential for repair tasks by developing a technology that enables industrial robots to re-contour turbine blades via force controlled belt grinding.

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29

Fabbrizi, Maria Rita, Jonathan R. Hughes, and Jason L. Parsons. "The Enzyme-Modified Neutral Comet (EMNC) Assay for Complex DNA Damage Detection." Methods and Protocols 4, no. 1 (February 16, 2021): 14. http://dx.doi.org/10.3390/mps4010014.

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The comet assay is a versatile, simple, and sensitive gel electrophoresis–based method that can be used to measure and accurately quantify DNA damage, particularly single and double DNA strand breaks, in single cells. While generally this is used to measure variation in DNA strand break levels and repair capacity within a population of cells, the technique has more recently been adapted and evolved into more complex analysis and detection of specific DNA lesions, such as oxidized purines and pyrimidines, achieved through the utilization of damage-specific DNA repair enzymes following cell lysis. Here, we detail a version of the enzyme-modified neutral comet (EMNC) assay for the specific detection of complex DNA damage (CDD), defined as two or more DNA damage lesions within 1–2 helical turns of the DNA. CDD induction is specifically relevant to ionizing radiation (IR), particularly of increasing linear energy transfer (LET), and is known to contribute to the cell-killing effects of IR due to the difficult nature of its repair. Consequently, the EMNC assay reveals important details regarding the extent and complexity of DNA damage induced by IR, but also has potential for the study of other genotoxic agents that may induce CDD.

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30

Brown, Jessica S., and Stephen P. Jackson. "Ubiquitylation, neddylation and the DNA damage response." Open Biology 5, no. 4 (April 2015): 150018. http://dx.doi.org/10.1098/rsob.150018.

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Failure of accurate DNA damage sensing and repair mechanisms manifests as a variety of human diseases, including neurodegenerative disorders, immunodeficiency, infertility and cancer. The accuracy and efficiency of DNA damage detection and repair, collectively termed the DNA damage response (DDR), requires the recruitment and subsequent post-translational modification (PTM) of a complex network of proteins. Ubiquitin and the ubiquitin-like protein (UBL) SUMO have established roles in regulating the cellular response to DNA double-strand breaks (DSBs). A role for other UBLs, such as NEDD8, is also now emerging. This article provides an overview of the DDR, discusses our current understanding of the process and function of PTM by ubiquitin and NEDD8, and reviews the literature surrounding the role of ubiquitylation and neddylation in DNA repair processes, focusing particularly on DNA DSB repair.

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31

Singh, Gyanesh, U. C. Pachouri, Devika Chanu Khaidem, Aman Kundu, Chirag Chopra, and Pushplata Singh. "Mitochondrial DNA Damage and Diseases." F1000Research 4 (July 1, 2015): 176. http://dx.doi.org/10.12688/f1000research.6665.1.

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Various endogenous and environmental factors can cause mitochondrial DNA (mtDNA) damage. One of the reasons for enhanced mtDNA damage could be its proximity to the source of oxidants, and lack of histone-like protective proteins. Moreover, mitochondria contain inadequate DNA repair pathways, and, diminished DNA repair capacity may be one of the factors responsible for high mutation frequency of the mtDNA. mtDNA damage might cause impaired mitochondrial function, and, unrepaired mtDNA damage has been frequently linked with several diseases. Exploration of mitochondrial perspective of diseases might lead to a better understanding of several diseases, and will certainly open new avenues for detection, cure, and prevention of ailments.

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32

Rohwer, Forest, and Farooq Azam. "Detection of DNA Damage in Prokaryotes by Terminal Deoxyribonucleotide Transferase-Mediated dUTP Nick End Labeling." Applied and Environmental Microbiology 66, no. 3 (March 1, 2000): 1001–6. http://dx.doi.org/10.1128/aem.66.3.1001-1006.2000.

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ABSTRACT Numerous agents can damage the DNA of prokaryotes in the environment (e.g., reactive oxygen species, irradiation, and secondary metabolites such as antibiotics, enzymes, starvation, etc.). The large number of potential DNA-damaging agents, as well as their diverse modes of action, precludes a simple test of DNA damage based on detection of nucleic acid breakdown products. In this study, free 3′-OH DNA ends, produced by either direct damage or excision DNA repair, were used to assess DNA damage. Terminal deoxyribonucleotide transferase (TdT)-mediated dUTP nick end labeling (TUNEL) is a procedure in which 3′-OH DNA ends are enzymatically labeled with dUTP-fluorescein isothiocyanate using TdT. Cells labeled by this method can be detected using fluorescence microscopy or flow cytometry. TUNEL was used to measure hydrogen peroxide-induced DNA damage in the archaeonHaloferax volcanii and the bacterium Escherichia coli. DNA repair systems were implicated in the hydrogen peroxide-dependent generation of 3′-OH DNA ends by the finding that the protein synthesis inhibitors chloramphenicol and diphtheria toxin blocked TUNEL labeling of E. coli and H. volcanii, respectively. DNA damage induced by UV light and bacteriophage infection was also measured using TUNEL. This methodology should be useful in applications where DNA damage and repair are of interest, including mutant screening and monitoring of DNA damage in the environment.

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33

Bradbury, J. M., and S. P. Jackson. "The complex matter of DNA double-strand break detection." Biochemical Society Transactions 31, no. 1 (February 1, 2003): 40–44. http://dx.doi.org/10.1042/bst0310040.

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To maintain genomic stability, despite constant exposure to agents that damage DNA, eukaryotic cells have developed elaborate and highly conserved pathways of DNA damage sensing, signalling and repair. In this review, we concentrate mainly on what we know about DNA damage sensing with particular reference to Lcd1p, a yeast protein that functions early in DNA damage signalling, and MDC1 (mediator of DNA damage checkpoint 1), a recently identified human protein that may be involved in recruiting the MRE11 complex to radiation-induced nuclear foci. We describe a model for the DNA damage response in which factors are recruited sequentially to sites of DNA damage to form complexes that can amplify the original signal and propagate it to the multitude of response pathways necessary for genome stability.

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34

Lambinet, Florian, and Zahra Sharif Khodaei. "Damage detection & localization on composite patch repair under different environmental effects." Engineering Research Express 2, no. 4 (December 16, 2020): 045032. http://dx.doi.org/10.1088/2631-8695/abd0d3.

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35

Munzer, J. S., S. K. Jones, J. P. O'Neill, J. N. Hartshorn, and S. H. Robison. "Detection of DNA damage and repair by alkaline elution using human lymphocytes." Mutation Research/DNA Repair Reports 194, no. 2 (September 1988): 101–8. http://dx.doi.org/10.1016/0167-8817(88)90012-0.

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36

Yin, Zhenhua, Cheng Li, Ying Tie, and Yuechen Duan. "Impact Damage Detection in Patch-Repaired CFRP Laminates Using Nonlinear Lamb Waves." Sensors 21, no. 1 (December 31, 2020): 219. http://dx.doi.org/10.3390/s21010219.

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Carbon fiber-reinforced polymer (CFRP) laminates, a key composite material, are widely used in aircraft structures and are susceptible to low-velocity impact (LVI) damage from bird strikes, lightning strikes, hail impacts and other situations. Therefore, finding a method that repairs the damaged structure and detects the effect of these repairs under LVI is a very important goal. In this work, the repair effect of LVI damage in CFRP laminates repaired with patches of various sizes is investigated via experimental and numerical nonlinear Lamb wave analyses. An integrated numerical procedure that combines LVI with nonlinear Lamb wave detection is developed to predict the nonlinear Lamb wave behavior in LVI-damaged patch-repaired CFRP laminates. The CFRP laminate damage in the nonlinear Lamb wave simulation is evaluated based on relative acoustic nonlinearity parameters (RANPs). As a result, the integrated numerical procedure is validated with drop-weight impact tests and RAM-5000 SNAP nonlinear ultrasonic detection system. An optimal patch design is established via interpolation to optimize the absorbed energy, delamination surface area, second RANP and third RANP with different patch repair sizes. These parameters exhibit consistent curve fitting trends, indicating that they can be used as important indicators of impact damage. The optimal circular patch design with a radius of 2.5 r has better impact resistance behavior and repair performance.

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37

Kanyó, Katalin, J. Konc, L. Solti, and S. Cseh. "Assisted reproductive research: Laser assisted hatching and spindle detection (spindle view technique)." Acta Veterinaria Hungarica 52, no. 1 (January 1, 2004): 113–23. http://dx.doi.org/10.1556/avet.52.2004.1.11.

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Animal experiments are very important for the development of new assisted reproductive techniques (ART) for use in human and animal reproductive medicine. Most technical aspects of reproductive manipulation of humans and animals are very similar, and many components of successful human ART used nowadays have been derived from animal studies. In this study we examined (1) the use of 'non-contact' laser for assisted hatching, (2) whether spindles in living mouse oocytes could safely be imaged/examined by polarisation microscope (polscope) and (3) the influence of environment (e.g. temperature, in vitro culture, etc.) on spindle detection/visualisation. The data of the study presented here show that (1) laser assisted hatching (AH) is a fast, very accurate and safe procedure without any harmful effect on embryo development and it can support very effectively the implantation of embryos, (2) the use of polscope facilitates the evaluation of oocyte quality and the selection of oocytes with spindle, (3) by monitoring the spindle position during intracytoplasmic sperm injection (ICSI), we can reduce spindle damage and increase the chance of fertilisation. Further studies are underway to test the hypothesised connection between spindle birefringence and developmental capacity of oocytes/embryos.

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Dang, Wenya, Chunyi Tong, Yupei Yang, Yongbei Liu, Bin Liu, Hongyan Zhou, and Wei Wang. "A cascade amplification platform assisted with DNAzyme for activity analysis, kinetic study and effector screening of Fpg in vitro." Analyst 144, no. 5 (2019): 1731–40. http://dx.doi.org/10.1039/c8an02253d.

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39

Luo, Dong, Shangwei Wang, Xiaohong Du, Peng Zhao, Tian Lu, Hangting Yang, and Y. Frank Chen. "Health detection techniques for historic structures." Materials Testing 63, no. 9 (September 1, 2021): 855–64. http://dx.doi.org/10.1515/mt-2021-0013.

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Abstract The protection of historic buildings has drawn increasing attention and usually requires a sound nondestructive testing (NDT) technique. This paper first describes the significance of and the status on the protection of historic structures followed by a summary of common damage and repair measures for such structures. Lastly, the principles, characteristics, and applications of NDT techniques for historic wooden and masonry structures, including ultra-CT testing, stress wave testing, micro-drilling resistance meter, radar detection, and X-ray diffraction, are described and compared. This study concludes by providing a guide for studying the structural damage of historic structures and for the selection of a detection technique.

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40

Wilkinson, Emma A., Tong Wu, Gayoung Park, Yan-Hong Cui, Chuan He, and Yu-Ying He. "Abstract 227: Kethoxal-assisted single-stranded DNA sequencing (KAS-seq) reveals dynamic and temporal changes in transcription in response to UVB exposure." Cancer Research 82, no. 12_Supplement (June 15, 2022): 227. http://dx.doi.org/10.1158/1538-7445.am2022-227.

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Abstract Skin cancer is the most common form of cancer, with over 5 million cases reported in 2021. UVB exposure derived from sunlight is the major carcinogenic driver of skin cancer and poses a major public health risk. In response to UVB exposure, keratinocytes must activate DNA repair pathways to avoid mutagenesis. In addition to DNA repair pathways, cells initiate well-coordinated DNA damage response pathways to facilitate the repair process, including arresting global transcription. Here we report the use of kethoxal-assisted single-strand DNA-Sequencing (KAS-Seq) technology to profile the transcriptional dynamics that underlie the DNA damage response upon UVB exposure. Mechanistically, KAS-Seq involves the addition of an azide-tagged kethoxal group (N3-kethoxal) to DNA samples, which then reacts with guanines on single-stranded DNA (ssDNA). A “KAS signal” is therefore only obtained when DNA is unwound, allowing the N3-kethoxal reaction with accessible guanines to occur. Accordingly, in response to DNA damage, DNA can form ssDNA bubbles in order to facilitate DNA damage recognition and repair processes. KAS-Seq is therefore a suitable method to profile the transcriptional dynamics that occur in response to UVB-induced DNA damage. Here we show that UVB exposure in normal human keratinocytes (NHEK) cells induces a temporal and dynamic reprogramming in transcription using KAS-Seq. In terms of global transcription, our data show that the greatest loss of KAS signal occurs rapidly between 30mins and 3hrs post-UVB exposure, signifying transcriptional arrest. Interestingly, KAS signal is regained between 6-24hrs post-UVB, which is representative of a transition towards transcriptional recovery and induction of DNA damage processes. Furthermore, a more discrete and targeted analysis shows that the gain and loss of KAS signals primarily occur within the gene body, followed by promoter and intergenic regions. Overall, our data shows that transcriptional control in response to UVB-induced DNA damage is both dynamic and temporal. Further analysis is required to identify which transcriptional phenotype (transcriptional arrest or transcriptional recovery) is the most deleterious to the cell and DNA damage repair processes when disrupted. Additionally, we aim to further elucidate the molecular mechanisms that underlie these global changes in transcription, which will provide expanded insights into the wide-ranging oncogenic mechanisms that underlie UVB exposure. Citation Format: Emma A. Wilkinson, Tong Wu, Gayoung Park, Yan-Hong Cui, Chuan He, Yu-Ying He. Kethoxal-assisted single-stranded DNA sequencing (KAS-seq) reveals dynamic and temporal changes in transcription in response to UVB exposure [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 227.

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Tay, Ian J., James J. H. Park, Anna L. Price, Bevin P. Engelward, and Scott R. Floyd. "HTS-Compatible CometChip Enables Genetic Screening for Modulators of Apoptosis and DNA Double-Strand Break Repair." SLAS DISCOVERY: Advancing the Science of Drug Discovery 25, no. 8 (May 26, 2020): 906–22. http://dx.doi.org/10.1177/2472555220918367.

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Dysfunction of apoptosis and DNA damage response pathways often drive cancer, and so a better understanding of these pathways can contribute to new cancer therapeutic strategies. Diverse discovery approaches have identified many apoptosis regulators, DNA damage response, and DNA damage repair proteins; however, many of these approaches rely on indirect detection of DNA damage. Here, we describe a novel discovery platform based on the comet assay that leverages previous technical advances in assay precision by incorporating high-throughput robotics. The high-throughput screening (HTS) CometChip is the first high-throughput-compatible assay that can directly detect physical damage in DNA. We focused on DNA double-strand breaks (DSBs) and utilized our HTS CometChip technology to perform a first-of-its-kind screen using an shRNA library targeting 2564 cancer-relevant genes. Conditions of the assay enable detection of DNA fragmentation from both exogenous (ionizing radiation) and endogenous (apoptosis) sources. Using this approach, we identified LATS2 as a novel DNA repair factor as well as a modulator of apoptosis. We conclude that the HTS CometChip is an effective assay for HTS to identify modulators of physical DNA damage and repair.

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42

Feng, Tianyi, and M. H. Ferri Aliabadi. "Smart Patch for Structural Health Monitoring of Composite Repair." Applied Sciences 12, no. 10 (May 12, 2022): 4916. http://dx.doi.org/10.3390/app12104916.

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The bondline integrity of a repair patch to the parent composite laminate is considered the most important factor in the repair design. A smart repair patch is proposed here to allow for real-time ultrasonic guided wave monitoring of repaired composites. A diagnostic film with lead zirconate titanate (PZT) transducers and inkjet-printed wires is embedded into the repair patch using a cut-out method. The electro-mechanical impedance (EMI) method is used to verify the integrity of the embedded PZT transducers. The performance of the smart repair patch is assessed on the external panel with artificial bondline delamination and surface-mounted artificial damage. The damage index correlation coefficient and delay-and-sum (DAS) algorithm are used for damage detection and localization. The results show that the developed repair patch can successfully detect and locate damages.

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43

Hoogstraten, D., S. Bergink, V. H. M. Verbiest, M. S. Luijsterburg, B. Geverts, A. Raams, C. Dinant, J. H. J. Hoeijmakers, W. Vermeulen, and A. B. Houtsmuller. "Versatile DNA damage detection by the global genome nucleotide excision repair protein XPC." Journal of Cell Science 121, no. 17 (September 1, 2008): 2972. http://dx.doi.org/10.1242/jcs.03502.

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44

Hoogstraten, D., S. Bergink, J. M. Y. Ng, V. H. M. Verbiest, M. S. Luijsterburg, B. Geverts, A. Raams, et al. "Versatile DNA damage detection by the global genome nucleotide excision repair protein XPC." Journal of Cell Science 121, no. 23 (November 19, 2008): 3991. http://dx.doi.org/10.1242/jcs.03503.

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45

Hoogstraten, D., S. Bergink, J. M. Y. Ng, V. H. M. Verbiest, M. S. Luijsterburg, B. Geverts, A. Raams, et al. "Versatile DNA damage detection by the global genome nucleotide excision repair protein XPC." Journal of Cell Science 121, no. 17 (September 1, 2008): 2850–59. http://dx.doi.org/10.1242/jcs.031708.

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46

Salles, Bernard, Gregory Rodrigo, Ruo Ya Li, and Patrick Calsou. "DNA damage excision repair in microplate wells with chemiluminescence detection: Development and perspectives." Biochimie 81, no. 1-2 (January 1999): 53–58. http://dx.doi.org/10.1016/s0300-9084(99)80038-8.

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47

Helt, Christopher E., Wensheng Wang, Peter C. Keng, and Robert A. Bambara. "9-1-1 Complex Involvement in DNA Repair: Evidence that DNA Damage Detection Machinery Participates in DNA Repair." Cell Cycle 4, no. 4 (January 28, 2005): 529–32. http://dx.doi.org/10.4161/cc.4.4.1598.

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48

Farkash, Evan A., and Eline T. Luning Prak. "DNA Damage and L1 Retrotransposition." Journal of Biomedicine and Biotechnology 2006 (2006): 1–8. http://dx.doi.org/10.1155/jbb/2006/37285.

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Barbara McClintock was the first to suggest that transposons are a source of genome instability and that genotoxic stress assisted in their mobilization. The generation of double-stranded DNA breaks (DSBs) is a severe form of genotoxic stress that threatens the integrity of the genome, activates cell cycle checkpoints, and, in some cases, causes cell death. Applying McClintock's stress hypothesis to humans, are L1 retrotransposons, the most active autonomous mobile elements in the modern day human genome, mobilized by DSBs? Here, evidence that transposable elements, particularly retrotransposons, are mobilized by genotoxic stress is reviewed. In the setting of DSB formation, L1 mobility may be affected by changes in the substrate for L1 integration, the DNA repair machinery, or the L1 element itself. The review concludes with a discussion of the potential consequences of L1 mobilization in the setting of genotoxic stress.

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Et.al, Hesti Susilawati ,. "Sistem Pendeteksian Kerusakan Mesin Sepeda Motor 4-Langkah Berbasis Suara Menggunakan Support Vector Machine (SVM)." Semesta Teknika 14, no. 1 (December 16, 2015): 52–57. http://dx.doi.org/10.18196/st.v14i1.584.

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Detection process early towards motorcycle engine condition will be important matter especially for common user motorcycle. This detection can be used to estimate motorcycle engine condition (normal or damage), damage kind, how big damage influence towards motorcycle continuance, motorcycle duration can survive with damage and cost estimate that taked suppose will repair damage. In this research is built 4-stroke motorcycle engine damage detection system based on voice uses Support Vector Machine (SVM) multi class. In system that proposed, motorcycle engine voice is recorded and then cultivated so that produce feature shaped coefficient Linear Predictive Coding (LPC). Coefficient LPC that extracted from this motorcycle engine voice then become an input for SVM. Furthermore SVM will determine motorcycle engine condition. Engine condition detection system based on SVM this meant to detect three engine conditions that is normal condition, damage cham chain and damage ignition system. System applications that proposed show that motorcycle engine condition detection system based on voice uses SVM has good accuracy that is 100%.

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Vadivel Gnanasundram, Sivakumar, Ondrej Bonczek, Lixiao Wang, Sa Chen, and Robin Fahraeus. "p53 mRNA Metabolism Links with the DNA Damage Response." Genes 12, no. 9 (September 20, 2021): 1446. http://dx.doi.org/10.3390/genes12091446.

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Human cells are subjected to continuous challenges by different genotoxic stress attacks. DNA damage leads to erroneous mutations, which can alter the function of oncogenes or tumor suppressors, resulting in cancer development. To circumvent this, cells activate the DNA damage response (DDR), which mainly involves cell cycle regulation and DNA repair processes. The tumor suppressor p53 plays a pivotal role in the DDR by halting the cell cycle and facilitating the DNA repair processes. Various pathways and factors participating in the detection and repair of DNA have been described, including scores of RNA-binding proteins (RBPs) and RNAs. It has become increasingly clear that p53’s role is multitasking, and p53 mRNA regulation plays a prominent part in the DDR. This review is aimed at covering the p53 RNA metabolism linked to the DDR and highlights the recent findings.

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