Cross-species investigation into the requirement of XPA for nucleotide excision repair.

After reconstitution of nucleotide excision repair (excision repair) with XPA, RPA, XPC, TFIIH, XPF-ERCC1 and XPG, it was concluded that these six factors are the minimal essential components of the excision repair machinery. All six factors are highly conserved across diverse organisms spanning yeast to humans, yet no identifiable homolog of the XPA gene exists in many eukaryotes including green plants. Nevertheless, excision repair is reported to be robust in the XPA-lacking organism, Arabidopsis thaliana, which raises a fundamental question of whether excision repair could occur without XPA in other organisms. Here, we performed a phylogenetic analysis of XPA across all species with annotated genomes and then quantitatively measured excision repair in the absence of XPA using the sensitive whole-genome qXR-Seq method in human cell lines and two model organisms, Caenorhabditis elegans and Drosophila melanogaster. We find that although the absence of XPA results in inefficient excision repair and UV-sensitivity in humans, flies, and worms, excision repair of UV-induced DNA damage is detectable over background. These studies have yielded a significant discovery regarding the evolution of XPA protein and its mechanistic role in nucleotide excision repair.

In vitro DNA repair genomics using XR-seq with Escherichia coli and mammalian cell-free extracts.

The XR-seq (eXcision Repair-sequencing) method has been extensively used to map nucleotide excision repair genome-wide in organisms ranging from Escherichia coli to yeast, Drosophila, Arabidopsis, mice, and humans. The basic feature of the method is to capture the excised oligomers carrying DNA damage, sequence them, and align their sequences to the genome. We wished to perform XR-seq in vitro with cell-free extract supplemented with a damaged DNA substrate so as to have greater flexibility in investigating factors that affect nucleotide excision repair in the cellular context [M. J. Smerdon, J. J. Wyrick, S. Delaney, J. Biol. Chem. 299, 105118 (2023)]. We report here the successful use of ultraviolet light-irradiated plasmids as substrates for repair in vitro and in vivo by E. coli and E. coli cell-free extracts and by mammalian cell-free extract. XR-seq analyses demonstrated common excision product length and sequence characteristics in vitro and in vivo for both the bacterial and mammalian systems. This approach is expected to help understand the effects of epigenetics and other cellular factors and conditions on DNA repair.

Insulin receptor signaling in osteoblasts regulates postnatal bone acquisition and body composition.

Global energy balance in mammals is controlled by the actions of circulating hormones that coordinate fuel production and utilization in metabolically active tissues. Bone-derived osteocalcin, in its undercarboxylated, hormonal form, regulates fat deposition and is a potent insulin secretagogue. Here, we show that insulin receptor (IR) signaling in osteoblasts controls osteoblast development and osteocalcin expression by suppressing the Runx2 inhibitor Twist2. Mice lacking IR in osteoblasts have low circulating undercarboxylated osteocalcin and reduced bone acquisition due to decreased bone formation and deficient numbers of osteoblasts. With age, these mice develop marked peripheral adiposity and hyperglycemia accompanied by severe glucose intolerance and insulin resistance. The metabolic abnormalities in these mice are improved by infusion of undercarboxylated osteocalcin. These results indicate the existence of a bone-pancreas endocrine loop through which insulin signaling in the osteoblast ensures osteoblast differentiation and stimulates osteocalcin production, which in turn regulates insulin sensitivity and pancreatic insulin secretion.

Nucleotide excision repair removes thymidine analog 5-ethynyl-2'-deoxyuridine from the mammalian genome.

Nucleotide excision repair is the principal mechanism for removing bulky DNA adducts from the mammalian genome, including those induced by environmental carcinogens such as UV radiation, and anticancer drugs such as cisplatin. Surprisingly, we found that the widely used thymidine analog EdU is a substrate for excision repair when incorporated into the DNA of replicating cells. A number of thymidine analogs were tested, and only EdU was a substrate for excision repair. EdU excision was absent in repair-deficient cells, and in vitro, DNA duplexes bearing EdU were also substrates for excision by mammalian cell-free extracts. We used the excision repair sequencing (XR-seq) method to map EdU repair in the human genome at single-nucleotide resolution and observed that EdU was excised throughout the genome and was subject to transcription-coupled repair as evidenced by higher repair rates in the transcribed strand (TS) relative to the nontranscribed strand (NTS) in transcriptionally active genes. These properties of EdU, combined with its cellular toxicity and ability to cross the blood-brain barrier, make it a potential candidate for treating cancers of the brain, a tissue that typically demonstrates limited replication in adults.

CSB-independent, XPC-dependent transcription-coupled repair in Drosophila.

Drosophila melanogaster has been extensively used as a model system to study ionizing radiation and chemical-induced mutagenesis, double-strand break repair, and recombination. However, there are only limited studies on nucleotide excision repair in this important model organism. An early study reported that Drosophila lacks the transcription-coupled repair (TCR) form of nucleotide excision repair. This conclusion was seemingly supported by the Drosophila genome sequencing project, which revealed that Drosophila lacks a homolog to CSB, which is known to be required for TCR in mammals and yeasts. However, by using excision repair sequencing (XR-seq) genome-wide repair mapping technology, we recently found that the Drosophila S2 cell line performs TCR comparable to human cells. Here, we have extended this work to Drosophila at all its developmental stages. We find TCR takes place throughout the life cycle of the organism. Moreover, we find that in contrast to humans and other multicellular organisms previously studied, the XPC repair factor is required for both global and transcription-coupled repair in Drosophila.

Analysis of mammalian circadian clock protein complexes over a circadian cycle.

Circadian rhythmicity is maintained by a set of core clock proteins including the transcriptional activators CLOCK and BMAL1, and the repressors PER (PER1, PER2, and PER3), CRY (CRY1 and CRY2), and CK1δ. In mice, peak expression of the repressors in the early morning reduces CLOCK- and BMAL1-mediated transcription/translation of the repressors themselves. By late afternoon the repressors are largely depleted by degradation, and thereby their expression is reactivated in a cycle repeated every 24 h. Studies have characterized a variety of possible protein interactions and complexes associated with the function of this transcription-translation feedback loop. Our prior investigation suggested there were two circadian complexes responsible for rhythmicity, one containing CLOCK-BMAL and the other containing PER2, CRY1, and CK1δ. In this investigation, we acquired data from glycerol gradient centrifugation and gel filtration chromatography of mouse liver extracts obtained at different circadian times to further characterize circadian complexes. In addition, anti-PER2 and anti-CRY1 immunoprecipitates obtained from the same extracts were analyzed by liquid chromatography-tandem mass spectrometry to identify components of circadian complexes. Our results confirm the presence of discrete CLOCK-BMAL1 and PER-CRY-CK1δ complexes at the different circadian time points, provide masses of 255 and 707 kDa, respectively, for these complexes, and indicate that these complexes are composed principally of the core circadian proteins.

Molecular mechanism of the repressive phase of the mammalian circadian clock.

The mammalian circadian clock consists of a transcription-translation feedback loop (TTFL) composed of CLOCK-BMAL1 transcriptional activators and CRY-PER transcriptional repressors. Previous work showed that CRY inhibits CLOCK-BMAL1-activated transcription by a "blocking"-type mechanism and that CRY-PER inhibits CLOCK-BMAL1 by a "displacement"-type mechanism. While the mechanism of CRY-mediated repression was explained by both in vitro and in vivo experiments, the CRY-PER-mediated repression in vivo seemed in conflict with the in vitro data demonstrating PER removes CRY from the CLOCK-BMAL1-E-box complex. Here, we show that CRY-PER participates in the displacement-type repression by recruiting CK1δ to the nucleus and mediating an increased local concentration of CK1δ at CLOCK-BMAL1-bound promoters/enhancers and thus promoting the phosphorylation of CLOCK and dissociation of CLOCK-BMAL1 along with CRY from the E-box. Our findings bring clarity to the role of PER in the dynamic nature of the repressive phase of the TTFL.

Differential miR-195-5p and its potential role during the development of carotid artery stenosis.

OBJECTIVES: Carotid artery stenosis (CAS) is a leading cause of cerebral ischemic events (CIE). Timely detection and risk assessment can aid in managing CAS patients and improving their prognosis. The aim of the current study is to identify a new biomarker for CAS and to further investigate the impact of miR-195-5p on cellular processes in vascular smooth muscle cells (VSMCs). METHODS: This study involved 112 CAS patients and 65 healthy individuals. Serum miR-195-5p levels were measured using RT-qPCR. The ROC curve was then plotted to evaluate the diagnostic potential of miR-195-5p for CAS. The Kaplan-Meier curve and Cox regression were employed to determine miR-195-5p's prognostic significance. In vitro, the effects of miR-195-5p mimic or inhibitor on VSMC proliferation and migration were assessed using CCK-8 and Transwell assays. RESULTS: In CAS patients, serum miR-195-5p levels were elevated and correlated with the degree of CAS. The ROC curve had an AUC value of 0.897, with sensitivity of 71.4% and specificity of 95.4%. Higher levels of miR-195-5p indicated a higher risk of CIE occurrence and may serve as an independent predictor of CIE. The upregulation of miR-195-5p promoted VSMC proliferation and migration, while downregulation had the opposite effect. CONCLUSIONS: miR-195-5p was demonstrated to have diagnostic and prognostic significance in CAS and may serve as a potential biomarker. It may contribute to the progression of CAS by promoting the proliferation and migration of VSMCs.

Internal iliac artery ligation as a damage control method in hemodynamically unstable pelvic fractures: A systematic review of the literature.

PURPOSE: Internal iliac artery ligation (IIAL) has been used as a damage control procedure to treat hemodynamically unstable pelvic fracture for many years. However, there is ongoing debate regarding the effectiveness and safety of this hemostatic method. Therefore, we performed a systematic literature review to assess the efficacy and safety of IIAL for pelvic fracture hemostasis. METHODS: Three major databases, PubMed, Embase, and Google Scholar, were searched to screen eligible original studies published in English journals. Two reviewers independently read the titles, abstracts, and full texts of all literature. Articles were included if they reported the use and effects of IIAL. RESULTS: A total of 171 articles were initially identified, with 22 fully meeting the inclusion criteria. Among the analyzed cases, up to 66.7% of patients had associated abdominal and pelvic organ injuries, with the urethra being the most frequently injured organ, followed by the bowel. The outcomes of IIAL for achieving hemostasis in pelvic fractures were found to be satisfactory, with an effective rate of 80%. Hemorrhagic shock was the leading cause of death, followed by craniocerebral injury. Notably, no reports of ischemic complications involving the pelvic organs due to IIAL were found. CONCLUSION: IIAL has a good effect in treating hemodynamically unstable pelvic fracture without the risk of pelvic organ ischemia. This procedure should be considered a priority for hemodynamically unstable pelvic fracture patients with abdominal organ injuries.

Increasing positive rate of IgG against hepatitis E virus with steady IgM positivity and clinical incidence: A retrospective seroprevalence time series analysis of HEV from 2012 to 2021 in Chongqing, China.

China is an epidemic area of hepatitis E, and the serum prevalence data is very important for formulating prevention and control strategies. However, almost all related research in the past decade are cross-sectional studies. In this study, we analyzed the serological data from 2012 to 2021 in Chongqing for 10 consecutive years. We found that the positive rate of hepatitis E IgG antibody increased gradually, from 1.61% in January 2012 to 50.63% in December 2021. The autoregressive integrated moving average model was used to predict the trend, and it was found that it will continue to show an upward trend in the recent future. In contrast, the positive rate of IgM and clinical incidence of hepatitis E showed a relatively stable trend. Although the positive rate of antibodies gradually increased with age, there was no significant difference in the age distribution of the subjects each year. Therefore, these results suggest that the accumulated infection of hepatitis E in Chongqing may be gradually increasing, but the clinical incidence rate remains unchanged, which provides a new concern for formulating prevention and control strategies.

Acalculous cholecystitis is a common extrahepatic manifestation of hepatitis E and suggests a more serious condition.

BACKGROUND: This study aimed to understand the incidence and clinical significance of acalculous cholecystitis in patients with acute hepatitis E (HE). PATIENTS AND METHODS: A single center enrolled 114 patients with acute HE. All patients underwent imaging of the gallbladder, and patients with gallstones and cholecystectomy were excluded. RESULTS: Acalculous cholecystitis was found in 66 patients (57.89%) with acute HE. The incidence in males was 63.95%, which was significantly higher than in females (39.29%) (P = 0.022). The mean length of hospital stay and the incidence of spontaneous peritonitis in patients with cholecystitis (20.12 ± 9.43 days and 9.09%, respectively) were significantly higher than those in patients without cholecystitis (12.98 ± 7.26 days and 0%, respectively) (P < 0.001 and P = 0.032). Albumin, total bile acid, bilirubin, cholinesterase, and prothrombin activity in patients with cholecystitis were significantly inferior to those in patients without cholecystitis (P < 0.001, P < 0.001, P < 0.001, P < 0.001 and P = 0.003, respectively). After correction by multivariate analysis, albumin and total bile acid were found to be closely related to acalculous cholecystitis in HE. CONCLUSION: Acalculous cholecystitis is very common in patients with acute HE, and may serve as a predictor of increased peritonitis, synthetic decompensation, and longer hospital stay.

Circadian regulation of c-MYC in mice.

The circadian clock is a global regulatory mechanism that controls the expression of 50 to 80% of transcripts in mammals. Some of the genes controlled by the circadian clock are oncogenes or tumor suppressors. Among these Myc has been the focus of several studies which have investigated the effect of clock genes and proteins on Myc transcription and MYC protein stability. Other studies have focused on effects of Myc mutation or overproduction on the circadian clock in comparison to their effects on cell cycle progression and tumorigenesis. Here we have used mice with mutations in the essential clock genes Bmal1, Cry1, and Cry2 to gain further insight into the effect of the circadian clock on this important oncogene/oncoprotein and tumorigenesis. We find that mutation of both Cry1 and Cry2, which abolishes the negative arm of the clock transcription-translation feedback loop (TTFL), causes down-regulation of c-MYC, and mutation of Bmal1, which abolishes the positive arm of TTFL, causes up-regulation of the c-MYC protein level in mouse spleen. These findings must be taken into account in models of the clock disruption-cancer connection.

Circadian clock, carcinogenesis, chronochemotherapy connections.

The circadian clock controls the expression of nearly 50% of protein coding genes in mice and most likely in humans as well. Therefore, disruption of the circadian clock is presumed to have serious pathological effects including cancer. However, epidemiological studies on individuals with circadian disruption because of night shift or rotating shift work have produced contradictory data not conducive to scientific consensus as to whether circadian disruption increases the incidence of breast, ovarian, prostate, or colorectal cancers. Similarly, genetically engineered mice with clock disruption do not exhibit spontaneous or radiation-induced cancers at higher incidence than wild-type controls. Because many cellular functions including the cell cycle and cell division are, at least in part, controlled by the molecular clock components (CLOCK, BMAL1, CRYs, PERs), it has also been expected that appropriate timing of chemotherapy may increase the efficacy of chemotherapeutic drugs and ameliorate their side effect. However, empirical attempts at chronochemotherapy have not produced beneficial outcomes. Using mice without and with human tumor xenografts, sites of DNA damage and repair following treatment with the anticancer drug cisplatin have been mapped genome-wide at single nucleotide resolution and as a function of circadian time. The data indicate that mechanism-based studies such as these may provide information necessary for devising rational chronochemotherapy regimens.

Transcription factor CBF-1 is critical for circadian gene expression by modulating WHITE COLLAR complex recruitment to the frq locus.

Transcription of the Neurospora crassa circadian clock gene frequency (frq) is an essential process in the negative feedback loop that controls circadian rhythms. WHITE COLLAR 1 (WC-1) and WHITE COLLAR 2 (WC-2) forms the WC complex (WCC) that is the main activator of frq transcription by binding to its promoter. Here, we show that Centromere Binding Factor 1 (CBF-1) is a critical component of the N. crassa circadian clock by regulating frq transcription. Deletion of cbf-1 resulted in long period and low amplitude rhythms, whereas overexpression of CBF-1 abolished the circadian rhythms. Loss of CBF-1 resulted in WC-independent FRQ expression and suppression of WCC activity. As WCC, CBF-1 also binds to the C-box at the frq promoter. Overexpression of CBF-1 impaired WCC binding to the C-box to suppress frq transcription. Together, our results suggest that the proper level of CBF-1 is critical for circadian clock function by suppressing WC-independent FRQ expression and by regulating WCC binding to the frq promoter.

Transcriptional repression of frequency by the IEC-1-INO80 complex is required for normal Neurospora circadian clock function.

Rhythmic activation and repression of the frequency (frq) gene are essential for normal function of the Neurospora circadian clock. WHITE COLLAR (WC) complex, the positive element of the Neurospora circadian system, is responsible for stimulation of frq transcription. We report that a C2H2 finger domain-containing protein IEC-1 and its associated chromatin remodeling complex INO80 play important roles in normal Neurospora circadian clock function. In iec-1KO strains, circadian rhythms are abolished, and the frq transcript levels are increased compared to that of the wild-type strain. Similar results are observed in mutant strains of the INO80 subunits. Furthermore, ChIP data show that recruitment of the INO80 complex to the frq promoter is IEC-1-dependent. WC-mediated transcription of frq contributes to the rhythmic binding of the INO80 complex at the frq promoter. As demonstrated by ChIP analysis, the INO80 complex is required for the re-establishment of the dense chromatin environment at the frq promoter. In addition, WC-independent frq transcription is present in ino80 mutants. Altogether, our data indicate that the INO80 complex suppresses frq transcription by re-assembling the suppressive mechanisms at the frq promoter after transcription of frq.

Interfacial Charging-Decharging Strategy for Efficient and Selective Aerobic NO Oxidation on Oxygen Vacancy.

Intelligent defect engineering to harness surface molecular processes is at the core of selective oxidation catalysis. Here, we demonstrate that the two-electron-trapped oxygen vacancy (VO) of BiOCl, a prototypical F center (VŐ''), is a superb site to confine O2 toward efficient and selective NO oxidation to nitrate. Stimulated by solar light, VŐ'' accomplishes NO oxidation through a two-electron charging (VŐ'' + O2 → VŐ''-O22-) and subsequent one-electron decharging process (VŐ''-O22- + NO → VO-NO3- + e-). The back-donated electron is retrapped by VO to produce a new single-electron-trapped VO (VO'), simultaneously triggering a second round of NO oxidation (VO'-O2 + NO → VO-NO3-). This unprecedented interfacial charging-decharging scheme alters the peroxide-associated NO oxidation selectivity from NO2 to NO3- with a high efficiency and thus hold great promise for the treatment of risky NO x species in indoor air.

Oxygen Vacancies Mediated Complete Visible Light NO Oxidation via Side-On Bridging Superoxide Radicals.

It is of a great challenge to seek for semiconductor photocatalysts with prominent reactivity to remove kinetically inert dilute NO without NO2 emission. In this study, complete visible light NO oxidation mediated by O2 is achieved over a defect-engineered BiOCl with selectivity exceeding 99%. Well-designed oxygen vacancies on the prototypical (001) surface of BiOCl favored the possible formation of geometric-favorable superoxide radicals (•O2-) in a side-on bridging mode under ambient condition, which thermodynamically suppressed the terminal end-on •O2- associated NO2 emission in case of higher temperatures, and thus selectively oxidized NO to nitrate. These findings can help us to understand the intriguing surface chemistry of photocatalytic NO oxidation and design highly efficient NO x removal systems.

Aberration analyses for improving the frontal projection three-dimensional display.

The crosstalk severely affects the viewing experience for the auto-stereoscopic 3D displays based on frontal projection lenticular sheet. To suppress unclear stereo vision and ghosts are observed in marginal viewing zones(MVZs), aberration of the lenticular sheet combining with the frontal projector is analyzed and designed. Theoretical and experimental results show that increasing radius of curvature (ROC) or decreasing aperture of the lenticular sheet can suppress the aberration and reduce the crosstalk. A projector array with 20 micro-projectors is used to frontally project 20 parallax images one lenticular sheet with the ROC of 10 mm and the size of 1.9 m × 1.2 m. The 3D image with the high quality is experimentally demonstrated in both the mid-viewing zone and MVZs in the optimal viewing plane. The 3D clear depth of 1.2m can be perceived. To provide an excellent 3D image and enlarge the field of view at the same time, a novel structure of lenticular sheet is presented to reduce aberration, and the crosstalk is well suppressed.

Mitochondrial genetic background modulates bioenergetics and susceptibility to acute cardiac volume overload.

Dysfunctional bioenergetics has emerged as a key feature in many chronic pathologies such as diabetes and cardiovascular disease. This has led to the mitochondrial paradigm in which it has been proposed that mtDNA sequence variation contributes to disease susceptibility. In the present study we show a novel animal model of mtDNA polymorphisms, the MNX (mitochondrial-nuclear exchange) mouse, in which the mtDNA from the C3H/HeN mouse has been inserted on to the C57/BL6 nuclear background and vice versa to test this concept. Our data show a major contribution of the C57/BL6 mtDNA to the susceptibility to the pathological stress of cardiac volume overload which is independent of the nuclear background. Mitochondria harbouring the C57/BL6J mtDNA generate more ROS (reactive oxygen species) and have a higher mitochondrial membrane potential relative to those with C3H/HeN mtDNA, independent of nuclear background. We propose this is the primary mechanism associated with increased bioenergetic dysfunction in response to volume overload. In summary, these studies support the 'mitochondrial paradigm' for the development of disease susceptibility, and show that the mtDNA modulates cellular bioenergetics, mitochondrial ROS generation and susceptibility to cardiac stress.