Damage Verification Research Articles

Elf1 promotes transcription-coupled repair in yeast by using its C-terminal domain to bind TFIIH

Transcription coupled-nucleotide excision repair (TC-NER) removes DNA lesions that block RNA polymerase II (Pol II) transcription. A key step in TC-NER is the recruitment of the TFIIH complex, which initiates DNA unwinding and damage verification; however, the mechanism by which TFIIH is recruited during TC-NER, particularly in yeast, remains unclear. Here, we show that the C-terminal domain (CTD) of elongation factor-1 (Elf1) plays a critical role in TC-NER in yeast by binding TFIIH. Analysis of genome-wide repair of UV-induced cyclobutane pyrimidine dimers (CPDs) using CPD-seq indicates that the Elf1 CTD in yeast is required for efficient TC-NER. We show that the Elf1 CTD binds to the pleckstrin homology (PH) domain of the p62 subunit of TFIIH in vitro, and identify a putative TFIIH-interaction region (TIR) in the Elf1 CTD that is important for PH binding and TC-NER. The Elf1 TIR shows functional, structural, and sequence similarities to a conserved TIR in the mammalian UV sensitivity syndrome A (UVSSA) protein, which recruits TFIIH during TC-NER in mammalian cells. These findings suggest that the Elf1 CTD acts as a functional counterpart to mammalian UVSSA in TC-NER by recruiting TFIIH in response to Pol II stalling at DNA lesions.

Sustainable Geoinformatic Approaches to Insurance for Small-Scale Farmers in Colombia

This article presents a low-cost insurance system developed for smallholder farms in disaster-prone regions, primarily using free Earth observation (EO) data and free open source software’s (FOSS), collectively termed “sustainable geoinformatics.” The study examined 30 farms in Risaralda Department, Colombia. A digital elevation model (12.5 m pixels) from the ALOS PALSAR satellite sensor was used with a geographic information system (GIS) to map the terrain, drainage, and geohazards of each farming district. Google Earth Engine (GEE) was used to carry out time-series analysis of 15 EO and weather datasets for 1998 to 2020. This analysis enabled the levels of risk from hydrometeorological hazards to be determined for each farm of the study, providing key data for the setting of insurance premiums. A parametric insurance product was developed using a proprietary mobile phone app that collected GPS-tagged, time-stamped mobile phone photos to verify crop damage, with further verification of crop health also provided by daily near-real-time satellite imagery (e.g., PlanetScope with 3 m pixels). Machine learning was used for feature identification with the photos and the satellite imagery. Key features of this insurance system are its low operational cost and rapid damage verification relative to conventional approaches to farm insurance. This relatively fast, low-cost, and affordable approach to insurance for small-scale farming enhances sustainable development by enabling policyholder farmers to recover more quickly from disasters.

XPD stalled on cross-linked DNA provides insight into damage verification.

The superfamily 2 helicase XPD is a central component of the general transcription factor II H (TFIIH), which is essential for transcription and nucleotide excision DNA repair (NER). Within these two processes, the helicase function of XPD is vital for NER but not for transcription initiation, where XPD acts only as a scaffold for other factors. Using cryo-EM, we deciphered one of the most enigmatic steps in XPD helicase action: the active separation of double-stranded DNA (dsDNA) and its stalling upon approaching a DNA interstrand cross-link, a highly toxic form of DNA damage. The structure shows how dsDNA is separated and reveals a highly unusual involvement of the Arch domain in active dsDNA separation. Combined with mutagenesis and biochemical analyses, we identified distinct functional regions important for helicase activity. Surprisingly, those areas also affect core TFIIH translocase activity, revealing a yet unencountered function of XPD within the TFIIH scaffold. In summary, our data provide a universal basis for NER bubble formation, XPD damage verification and XPG incision.

Analysis of clinical and anatomical characteristics of road transport injuries in the conditions of a rural location. Anatomical verification of damage

Analysis of clinical and anatomical characteristics of road transport injuries in the conditions of a rural location. Anatomical verification of damage

Modified Model and Simulation Verification of Rock-Fatigue Damage Considering Repeated Discharge Impact

The existing rock-fatigue-damage constitutive model fails to consider the influence of discharge energy and discharge times on the effect of rock damage under discharge impact. In this regard, the impact load test of sandstone was carried out. Based on the test results, the quantitative characterization formula of different discharge parameters on the weakening degree of rock compressive strength was established. Based on the TCK (Taylor–Chen–Kuszmaul) model, a constitutive model considering the mechanical properties of rock and the dynamic hange of micro-crack geometric size is established, and the cohesive model is proposed to calculate the crack size. The constitutive model includes the relationship between crack width, crack number, and rock compressive strength, and the change of damage factor D is used to consider the fatigue-damage effect of discharge shock on the rock. The results show that the modified model can quantitatively and accurately reflect the dynamic damage and failure process of rock and that the weakening of rock mechanical properties and the development of micro-cracks can be controlled by designing different discharge parameters.

Digital twin-driven fatigue life prediction framework of mechanical structures using a power density theory: Application to off-road vehicle front axle housing

Accurate fatigue life prediction is beneficial for fatigue maintenance of complex mechanical structures of off-road vehicles. For fatigue life prediction of mechanical structures subjected to non-stationary random loads during operation, this paper proposes a digital twin-driven fatigue life prediction method for mechanical structures. The core consists of improved fatigue theory, stress online measurement, and fatigue damage verification. In this study, a digital twin (DT) prediction framework containing multiple correction factors is established, in which the actual stress values in the physical world and the stress predictions of the estimated twin model can be obtained in real time. The remaining strength degradation of the structure and material can be compared to correct the prediction accuracy of fatigue analysis. In addition, based on the power density theory, combined with the short-time Fourier transform, a fatigue life analysis method that can comprehensively calculate the effect of load amplitude and frequency on fatigue is proposed. A test case has been demonstrated using a front axle housing of the off-road vehicle. The difference between the results predicted by the method in this paper and the actual fatigue results in failure time is only 2.65 h, with a relative error of only 3.95 %. In terms of failure location, the relative error is only 3.15 %.

ASH1L-MRG15 methyltransferase deposits H3K4me3 and FACT for damage verification in nucleotide excision repair

To recognize DNA adducts, nucleotide excision repair (NER) deploys the XPC sensor, which detects damage-induced helical distortions, followed by engagement of TFIIH for lesion verification. Accessory players ensure that this factor handover takes place in chromatin where DNA is tightly wrapped around histones. Here, we describe how the histone methyltransferase ASH1L, once activated by MRG15, helps XPC and TFIIH to navigate through chromatin and induce global-genome NER hotspots. Upon UV irradiation, ASH1L adds H3K4me3 all over the genome (except in active gene promoters), thus priming chromatin for XPC relocations from native to damaged DNA. The ASH1L-MRG15 complex further recruits the histone chaperone FACT to DNA lesions. In the absence of ASH1L, MRG15 or FACT, XPC is misplaced and persists on damaged DNA without being able to deliver the lesions to TFIIH. We conclude that ASH1L-MRG15 makes damage verifiable by the NER machinery through the sequential deposition of H3K4me3 and FACT.

Probing the damage-sensing mechanism(s) of a DNA repair helicase.

XPD (xeroderma pigmentosum group D) helicase serves as a prototype for 5’-3’ superfamily 2 helicases and has homologs in archaea, bacteria, and all eukaryotes. The helicase activity of eukaryotic XPD is vital to nucleotide excision repair (NER). In addition, some variants of XPD have been shown to have damage-sensing capabilities. In particular, mutation of specific residues in human XPD and in XPD from the archaeon Ferroplasma acidarmanus (FacXPD) compromises recognition of DNA damage in vivo and in vitro, respectively. However, many questions remain on XPD damage verification. Despite a number of studies, there is a lack of consensus on the mechanism by which XPD responds to different types of lesions or modifications and to the DNA strand they reside on. One study has suggested that distinct types of lesions are sensed through different mechanisms.

Enterotoxic potential of dietary cholesterol autoxidation products

Background In both Western and Westernized diets, together with a relatively high amount of cholesterol, variable amountsof its oxidized metabolites, oxysterols, are consistently consumed. These oxysterols, mostly of non-enzymatic origin, are produced during sterol autoxidation in foodstuff manufacturing and storage. Objective This study aimed to analyze the potential enterotoxic effects of all main oxysterols of non-enzymatic origin so far identified in a variety of foods. Experimental plan Differentiated human intestinal cell monolayers (CaCo-2) were incubated up to 48 h in the presence or absence of 0.5, 1 or 5 µM with one out of seven non-enzymatic oxysterols, prior to the verification of minimal irreversible cell damage within the chosen concentration range. Results All tested oxysterols were proven to exert damaging effects on cell monolayers in vitro. The inflammatory interleukin-8 and monocyte chemotactic protein-1 were mostly upregulated by 7-ketocholesterol and 7β-hydroxycholesterol, respectively, then to a lower extent by 5α,6α-epoxycholesterol, 7α-hydroxycholesterol and 5β,6β-epoxycholesterol. 7-Ketocholesterol and 7β-hydroxycholesterol also appeared to be most effective in impairing claudin-1, occludin and E-cadherin proteins, followed by 25-hydroxycholesterol and triol. Conclusions The oxysterols consistently derived by food autoxidation were tested; they potentially impaired the integrity of the intestinal epithelial barrier and triggered an inflammatory response within 0.5–5 µM concentrations, easily reachable in a single Western meal. Significance Statement This comprehensive analysis focused on the potential impairment of the intestinal barrier by the main dietary non-enzymatic oxysterols, should guide further nutrition research aiming at defining a threshold amount of these cholesterol derivatives in order not to derange the physiological gut–brain axis.

Comparative Analysis of Ultrasonic NDT Techniques for the Detection and Characterisation of Hydrogen-Induced Cracking.

The article is devoted to the investigation of ultrasonic inspection techniques suitable for detecting hydrogen-induced cracking (HIC) and a high-temperature hydrogen attack (HTHA), which are of great importance in petrochemical and refinery industries. Four techniques were investigated: total focusing method (TFM), advanced velocity ratio (AVR) measurement, advanced ultrasonic backscatter technique (AUBT) and time of flight diffraction method using ultra low angle ultrasonic transducers (TULA). The experimental investigation has been carried out on two carbon steel samples cut off from a heat exchanger of an oil refinery and potentially affected by HIC. It was shown that the AVR technique did not reveal any damage and was not effective in the case of the investigated samples due to a thin damage zone with respect to the total thickness of the samples. The AUBT method enabled us to indicate and classify the presence of the hydrogen-induced damage; however, it is complicated to use in practise due to the need perform measurements exactly at the same position using two transducers of different frequencies. The method is more suitable for the verification of damage at a particular position, rather than for scanning. Both other methods—TFM and TULA—enabled us to identify the presence of HIC in large areas of samples. The obtained results have been verified using a metallographic analysis of the section cut from the side of the sample. The results of metallographic examinations have been compared with indications observed using above mentioned techniques and a good correspondence was obtained. It was demonstrated, that the TFM method can detect cracks with dimensions close to 200 µm, while larger cracks of 2 mm were observed very evidently using a 7.5 MHz phased array. Overall, the results suggested that the TULA method is the most suitable method for the primary detection of hydrogen-induced cracking, while the TFM is recommended for the precise assessment of the extent of the detected cracking.

Mechanism of lesion verification by the human XPD helicase in nucleotide excision repair.

In nucleotide excision repair (NER), the xeroderma pigmentosum D helicase (XPD) scans DNA searching for bulky lesions, stalls when encountering such damage to verify its presence, and allows repair to proceed. Structural studies have shown XPD bound to its single-stranded DNA substrate, but molecular and dynamic characterization of how XPD translocates on undamaged DNA and how it stalls to verify lesions remains poorly understood. Here, we have performed extensive all-atom MD simulations of human XPD bound to undamaged and damaged ssDNA, containing a mutagenic pyrimidine (6−4) pyrimidone UV photoproduct (6−4PP), near the XPD pore entrance. We characterize how XPD responds to the presence of the DNA lesion, delineating the atomistic-scale mechanism that it utilizes to discriminate between damaged and undamaged nucleotides. We identify key amino acid residues, including FeS residues R112, R196, H135, K128, Arch residues E377 and R380, and ATPase lobe 1 residues 215−221, that are involved in damage verification and show how movements of Arch and ATPase lobe 1 domains relative to the FeS domain modulate these interactions. These structural and dynamic molecular depictions of XPD helicase activity with unmodified DNA and its inhibition by the lesion elucidate how the lesion is verified by inducing XPD stalling.

Verification of Damage Caused by the Genroku Earthquake and Tsunami from Tomb Stones

The Genroku earthquake and tsunami were the largest disaster in Japan during the Edo period. The earthquake occurred late at night on November 23, 1703, and widespread house collapses and fires in cities in Kanto region, including Edo (the old name of Tokyo) and Odawara. Following this, a huge tsunami hit the Pacific coast, which killed tens of thousands of people who lived there. This paper discusses a part of the actual situation of the tsunami disaster based on the tomb erected for the victims, as well as of the Buddhist memorial services held, such as kaimyo (posthumous Buddhist names), written on the tomb stones, ihai (Buddhist spirit tables), and kuyo-tou (memorial pagodas).

Миокардит на фоне COVID-19: клинические особенности и медикаментозное лечение

Myocarditis associated with the novel coronavirus infection (COVID-19) is a challenging diagnosis. Clinical presentations of this disease are either non-specific or occult. Meanwhile, long-term outcomes are unknown. Diagnostic approaches are challenging and virtually impossible to be applied in the COVID-19 hospitals. In addition, therapy for the COVID-19 infection is potentially harmful to the myocardium. This review article summarizes currently available published data on the clinical aspects and medical treatment for inflammatory myocardial damage in the COVID-19 infection. More than 300 publications were analyzed. This paper addresses the most relevant information. International published data provide strong evidence of the potential development of myocarditis secondary to the COVID-19 infection. Histological verification of myocardial damage is associated with significant differences since endomyocardial biopsy is not always possible in the setting of severe infection course. As a result, statistical data do not fully represent the prevalence of COVID-19-associated myocarditis. Pharmacotherapeutic strategies are generally empirical due to the understudied pathogenesis of inflammatory myocardial damage. Further studies are needed, given a controversial prognosis of COVID-19-associated myocarditis. KEYWORDS: COVID-19, SARS-CoV-2, myocarditis, myocardial damage, cardiovascular system, clinical presentations, treatment, drug effects. FOR CITATION: Sergeeva V.A., Lipatova T.E. COVID-19-associated myocarditis: clinical pattern and medical treatment. Russian Medical Inquiry. 2022;6(1):26–32 (in Russ.). DOI: 10.32364/2587-6821-2022-6-1-26-32

Verification of Fatigue Damage and Prognosis Related to Degradation of Polymer-Ceramic.

Statistically, road accidents involving pedestrians occur in the autumn and winter months, when outdoor temperatures reach −30 °C. The research presented in this paper investigates the impact of a pedestrian’s head on laminated windscreen, taking into account the effects of external temperature, heating of the windscreen from the inside, and fatigue of the glass. The automotive laminated windscreen under study is made from two layers of glass and a Polyvinyl Butyral (PVB) resin bonding them together. PVB significantly changes its properties with temperature. The Finite Element Method (FEM) simulations of a pedestrian’s head hitting the windscreen of an Opel Astra II at <−30 °C, +20 °C> were performed. The obtained Head Injury Criterion (HIC) results revealed an almost twofold decrease in safety between +20 °C and −20 °C. The same test was then performed taking into account the heating of the windscreen from the inside and the fatigue of the glass layers. Surprisingly, the highest HIC value of all the cases studied was obtained at −30 °C and heating the windscreen. The nature of safety changes with temperature variation is different for the cases of heating, non-heating, and fatigue of glass layers. Glass fatigue increases pedestrian safety throughout the temperature range analysed.

공익사업시행지구 밖의 어업손실보상에 관한 연구 『공익사업을 위한 토지 등의 취득 및 보상에 관한 법률 시행규칙』 제63조의 해석을 중심으로

The regulation on 'the Compensation for Fishery outside Zones where Public Works are Performed' not only can cause arbitrary interpretation and judgment of its contents, but also contains considerable problems, such as irrationally stipulating the contents of the regulation itself. In order to solve these problems, the significance and legal basis (II), requirements (III), methods, procedures and contents (IV) of indirect loss compensation in fishery were reviewed sequentially. First, 'the Compensation for Fishery outside Zones where Public Works are Performed' can be defined as &quot;Where the performance of public works causes damage to fishery in the vicinity of the relevant zone where public works are performed, Compensation for such damages&quot;. Such compensation is based on Article 23(3) of the Constitution, Article 79(2) of the Land Compensation Act, and Article 63 of the Enforcement Rules of the Land Compensation Act. Second, regarding the 'compensation requirements', it is contemplated that 'performance' should include 'operation', 'degree of damage' does not need to be considered in the requirements, and it is necessary to revise the regulations 'after the date of an announcement of approval of a project', and 'date of completion of construction of the project' needs to be interpreted as 'the date of occurrence of damage' or 'the date of completion of operation of the project'. In particular, 'verification of the actual damage' should be viewed as a matter of 'compensation content' rather than 'compensation requirements'. Third, with respect to the 'compensation method', it has a characteristic that it is carried out ex post 'when damage has occurred' or 'when the actual damage can be verified'. Regarding the 'compensation procedure', a 'Adjudication' is required. Regarding the 'compensation content', 'actual damage' is compensated to the extent that it does not exceed 'cancellation compensation'.

Instrumental Non-Invasive Diagnostics of the Depth of Skin Burn:&#x0D; Current Opportunities and Unsolved Problems

Introduction. Burns of various etiologies are on the 3-4 place in frequency among all injuries, they are associated with a high percentage of complications, disability and mortality. Currently, a single algorithm for objective verification of the depth of skin damage has not been developed. Numerous diagnostic technologies used to solve this problem require systemic analysis.The aim of study was to analyze current literature data on technologies for instrumental diagnostics of the depth of thermal damage to the skin.Materials and methods. A search for literary sources in databases was conducted using eLIBRARY.RU, PubMed, Cyberleninka databases. The period of publications was limited to 2011-2020.Results. The method of objective "gold standard" verification of thermal damage to the skin remains a biopsy followed by morphological examination, but the method's traumaticity does not allow it to be used for monitoring the course of the process in dynamics, for multi-focal studies. Among non-invasive methods, dermatoscopy and video microscopy are noted, but the small imaging area and the need for direct contact of the device with the skin surface limit the use of these methods. Laser Doppler flowmetry and imaging are fairly accurate non-contact methods that allow assessing the condition of a burn wound in real time. The method is not applicable to wounds with blisters, insufficient sanitation. Laser speckle contrast imaging is used to evaluate blood flow and is based on the analysis of speckle structure fluctuations. The method allows determining the degree of burn damage depending on changes in the blood flow. However, the method is difficult to apply with a vessel diameter sized 40 microns. The method is sensitive to movement and internal factors. Infrared and Raman spectroscopy are technique for evaluating vibrational patterns in a particular spectrum, these can be used to identify a molecule or determine its structure. Simultaneous use of spatial frequency visualization and speckle imaging demonstrated a high level of correlation with the results of histological research, which makes the use of these methods promising. Ultrasound also provides a proper correlation with histological data, but it is an imperfect method due to inaccuracies in determining the thickness of the epidermis, dermis, and scar condition. Optical coherence tomography (OCT) is a non-invasive optical method that allows obtaining high-resolution images of skin architecture in real time. The high level of compliance of the visualized structures, in particular, layers, appendages and vessels of the skin, with histological findings, gave this method a name "optical biopsy". Anatomical congruence of normal and damaged skin was established in an experiment between histology and OCT.Conclusion. Early assessment of the depth of thermal damage to the skin is crucial for choosing a personalized treatment strategy for the burned. None of the modern diagnostic methods is universal. Multimodal approaches to diagnostics are the most effective.

The Interaction Efficiency of XPD-p44 With Bulky DNA Damages Depends on the Structure of the Damage.

The successful elimination of bulky DNA damages via the nucleotide excision repair (NER) system is largely determined by the damage recognition step. This step consists of primary recognition and verification of the damage. The TFIIH helicase XPD plays a key role in the verification step during NER. To date, the mechanism of damage verification is not sufficiently understood and requires further detailed research. This study is a systematic investigation of the interaction of ctXPD (Chaetomium thermophilum) as well as ctXPD-ctp44 with model DNAs, which contain structurally different bulky lesions with previously estimated NER repair efficiencies. We have used ATPase and DNA binding studies to assess the interaction of ctXPD with damaged DNA. The result of the analysis of ctXPD-ctp44 binding to DNA containing fluorescent and photoactivatable lesions demonstrates the relationship between the affinity of XPD for DNAs containing bulky damages and the ability of the NER system to eliminate the damage. Photo-cross-linking of ctXPD with DNA probes containing repairable and unrepairable photoactivatable damages reveals differences in the DNA interaction efficiency in the presence and absence of ctp44. In general, the results obtained indicate the ability of ctXPD-ctp44 to interact with a damage and suggest a significant role for ctp44 subunit in the verification process.

Chaperones for dancing on chromatin: Role of post-translational modifications in dynamic damage detection hand-offs during nucleotide excision repair.

We highlight a recent study exploring the hand-off of UV damage to several key nucleotide excision repair (NER) proteins in the cascade: UV-DDB, XPC and TFIIH. The delicate dance of DNA repair proteins is choreographed by the dynamic hand-off of DNA damage from one recognition complex to another damage verification protein or set of proteins. These DNA transactions on chromatin are strictly chaperoned by post-translational modifications (PTM). This new study examines the role that ubiquitylation and subsequent DDB2 degradation has during this process. In total, this study suggests an intricate cellular timer mechanism that under normal conditions DDB2 helps recruit and ubiquitylate XPC, stabilizing XPC at damaged sites. If DDB2 persists at damaged sites too long, it is turned over by auto-ubiquitylation and removed from DNA by the action of VCP/p97 for degradation in the 26S proteosome.

Ubiquitin and TFIIH-stimulated DDB2 dissociation drives DNA damage handover in nucleotide excision repair

DNA damage sensors DDB2 and XPC initiate global genome nucleotide excision repair (NER) to protect DNA from mutagenesis caused by helix-distorting lesions. XPC recognizes helical distortions by binding to unpaired ssDNA opposite DNA lesions. DDB2 binds to UV-induced lesions directly and facilitates efficient recognition by XPC. We show that not only lesion-binding but also timely DDB2 dissociation is required for DNA damage handover to XPC and swift progression of the multistep repair reaction. DNA-binding-induced DDB2 ubiquitylation and ensuing degradation regulate its homeostasis to prevent excessive lesion (re)binding. Additionally, damage handover from DDB2 to XPC coincides with the arrival of the TFIIH complex, which further promotes DDB2 dissociation and formation of a stable XPC-TFIIH damage verification complex. Our results reveal a reciprocal coordination between DNA damage recognition and verification within NER and illustrate that timely repair factor dissociation is vital for correct spatiotemporal control of a multistep repair process.

XPA: DNA Repair Protein of Significant Clinical Importance.

The nucleotide excision repair (NER) pathway is activated in response to a broad spectrum of DNA lesions, including bulky lesions induced by platinum-based chemotherapeutic agents. Expression levels of NER factors and resistance to chemotherapy has been examined with some suggestion that NER plays a role in tumour resistance; however, there is a great degree of variability in these studies. Nevertheless, recent clinical studies have suggested Xeroderma Pigmentosum group A (XPA) protein, a key regulator of the NER pathway that is essential for the repair of DNA damage induced by platinum-based chemotherapeutics, as a potential prognostic and predictive biomarker for response to treatment. XPA functions in damage verification step in NER, as well as a molecular scaffold to assemble other NER core factors around the DNA damage site, mediated by protein–protein interactions. In this review, we focus on the interacting partners and mechanisms of regulation of the XPA protein. We summarize clinical oncology data related to this DNA repair factor, particularly its relationship with treatment outcome, and examine the potential of XPA as a target for small molecule inhibitors.