TERRA and RAD51AP1 promote alternative lengthening of telomeres through an R- to D-loop switch.

Alternative lengthening of telomeres (ALT), a telomerase-independent process maintaining telomeres, is mediated by break-induced replication (BIR). RAD52 promotes ALT by facilitating D-loop formation, but ALT also occurs through a RAD52-independent BIR pathway. Here, we show that the telomere non-coding RNA TERRA forms dynamic telomeric R-loops and contributes to ALT activity in RAD52 knockout cells. TERRA forms R-loops in vitro and at telomeres in a RAD51AP1-dependent manner. The formation of R-loops by TERRA increases G-quadruplexes (G4s) at telomeres. G4 stabilization enhances ALT even when TERRA is depleted, suggesting that G4s act downstream of R-loops to promote BIR. In vitro, the telomeric R-loops assembled by TERRA and RAD51AP1 generate G4s, which persist after R-loop resolution and allow formation of telomeric D-loops without RAD52. Thus, the dynamic telomeric R-loops formed by TERRA and RAD51AP1 enable the RAD52-independent ALT pathway, and G4s orchestrate an R- to D-loop switch at telomeres to stimulate BIR.

Alternative lengthening of telomeres is a self-perpetuating process in ALT-associated PML bodies.

Alternative lengthening of telomeres (ALT) is mediated by break-induced replication (BIR), but how BIR is regulated at telomeres is poorly understood. Here, we show that telomeric BIR is a self-perpetuating process. By tethering PML-IV to telomeres, we induced telomere clustering in ALT-associated PML bodies (APBs) and a POLD3-dependent ATR response at telomeres, showing that BIR generates replication stress. Ablation of BLM helicase activity in APBs abolishes telomere synthesis but causes multiple chromosome bridges between telomeres, revealing a function of BLM in processing inter-telomere BIR intermediates. Interestingly, the accumulation of BLM in APBs requires its own helicase activity and POLD3, suggesting that BIR triggers a feedforward loop to further recruit BLM. Enhancing BIR induces PIAS4-mediated TRF2 SUMOylation, and PIAS4 loss deprives APBs of repair proteins and compromises ALT telomere synthesis. Thus, a BLM-driven and PIAS4-mediated feedforward loop operates in APBs to perpetuate BIR, providing a critical mechanism to extend ALT telomeres.

NR4A1 regulates expression of immediate early genes, suppressing replication stress in cancer.

Deregulation of oncogenic signals in cancer triggers replication stress. Immediate early genes (IEGs) are rapidly and transiently expressed following stressful signals, contributing to an integrated response. Here, we find that the orphan nuclear receptor NR4A1 localizes across the gene body and 3' UTR of IEGs, where it inhibits transcriptional elongation by RNA Pol II, generating R-loops and accessible chromatin domains. Acute replication stress causes immediate dissociation of NR4A1 and a burst of transcriptionally poised IEG expression. Ectopic expression of NR4A1 enhances tumorigenesis by breast cancer cells, while its deletion leads to massive chromosomal instability and proliferative failure, driven by deregulated expression of its IEG target, FOS. Approximately half of breast and other primary cancers exhibit accessible chromatin domains at IEG gene bodies, consistent with this stress-regulatory pathway. Cancers that have retained this mechanism in adapting to oncogenic replication stress may be dependent on NR4A1 for their proliferation.

ATR Protects the Genome against R Loops through a MUS81-Triggered Feedback Loop.

R loops arising during transcription induce genomic instability, but how cells respond to the R loop-associated genomic stress is still poorly understood. Here, we show that cells harboring high levels of R loops rely on the ATR kinase for survival. In response to aberrant R loop accumulation, the ataxia telangiectasia and Rad3-related (ATR)-Chk1 pathway is activated by R loop-induced reversed replication forks. In contrast to the activation of ATR by replication inhibitors, R loop-induced ATR activation requires the MUS81 endonuclease. ATR protects the genome from R loops by suppressing transcription-replication collisions, promoting replication fork recovery, and enforcing a G2/M cell-cycle arrest. Furthermore, ATR prevents excessive cleavage of reversed forks by MUS81, revealing a MUS81-triggered and ATR-mediated feedback loop that fine-tunes MUS81 activity at replication forks. These results suggest that ATR is a key sensor and suppressor of R loop-induced genomic instability, uncovering a signaling circuitry that safeguards the genome against R loops.

RNA transcripts stimulate homologous recombination by forming DR-loops.

Homologous recombination (HR) repairs DNA double-strand breaks (DSBs) in the S and G2 phases of the cell cycle1-3. Several HR proteins are preferentially recruited to DSBs at transcriptionally active loci4-10, but how transcription promotes HR is poorly understood. Here we develop an assay to assess the effect of local transcription on HR. Using this assay, we find that transcription stimulates HR to a substantial extent. Tethering RNA transcripts to the vicinity of DSBs recapitulates the effects of local transcription, which suggests that transcription enhances HR through RNA transcripts. Tethered RNA transcripts stimulate HR in a sequence- and orientation-dependent manner, indicating that they function by forming DNA-RNA hybrids. In contrast to most HR proteins, RAD51-associated protein 1 (RAD51AP1) only promotes HR when local transcription is active. RAD51AP1 drives the formation of R-loops in vitro and is required for tethered RNAs to stimulate HR in cells. Notably, RAD51AP1 is necessary for the DSB-induced formation of DNA-RNA hybrids in donor DNA, linking R-loops to D-loops. In vitro, RAD51AP1-generated R-loops enhance the RAD51-mediated formation of D-loops locally and give rise to intermediates that we term 'DR-loops', which contain both DNA-DNA and DNA-RNA hybrids and favour RAD51 function. Thus, at DSBs in transcribed regions, RAD51AP1 promotes the invasion of RNA transcripts into donor DNA, and stimulates HR through the formation of DR-loops.

Localized protein biotinylation at DNA damage sites identifies ZPET, a repressor of homologous recombination.

Numerous DNA repair and signaling proteins function at DNA damage sites to protect the genome. Here, we show that fusion of the promiscuous biotin ligase BirAR118G with RAD18 leads to localized protein biotinylation at DNA damage sites, allowing identification of ZPET (zinc finger protein proximal to RAD eighteen)/ZNF280C as a potential DNA damage response (DDR) protein. ZPET binds ssDNA and localizes to DNA double-strand breaks (DSBs) and stalled replication forks. In vitro, ZPET inhibits MRE11 binding to ssDNA. In cells, ZPET delays MRE11 binding to chromatin after DSB formation and slows DNA end resection through binding ssDNA. ZPET hinders resection independently of 53BP1 and HELB. Cells lacking ZPET displayed enhanced homologous recombination (HR), accelerated replication forks under stress, and increased resistance to DSBs and PARP inhibition. These results not only reveal ZPET as an HR repressor but also suggest that localized protein biotinylation at DNA damage sites is a useful strategy to identify DDR proteins.

Membrane-Based Preparation Process and Antioxidant and Anti-AGEs Activities of a Novel Propolis Ultrafiltrate.

Propolis is one functional supplement with hundreds of years of usage. However, it's rarely consumed directly for its resinous property. Herein, a pre-treated process which can remove the impurity while preserve its bioactivities is needed to maximise its therapeutic opportunities. In the present study, a membrane-based ultrafiltration process was developed on a KM1812-NF experimental instrument. Using Brazilian green propolis as testing material, all experimental steps and parameters were sequentially optimized. In addition, a mathematical model was developed to fit the process. As a result, the optimum solvent was 60 % ethanol adjusted to pH 8-9, while the optimum MWCO (molecular weight cut-off) value of membrane was 30 KDa. The membrane filtration dynamic model fitted with the function y=(ax+b)/(1+cx+dx2 ). The resulting propolis ultrafiltrate from Brazilian green propolis, termed P30K, contains the similar profile of flavonoids and phenolic acids as raw propolis. Meanwhile, the ORAC (oxygen radical absorbance capacity) value of P30K is 11429.45±1557.58 µM TE/g and the IC50 value of inhibition of fluorescent AGEs (advanced glycation end products) formation is 0.064 mg/mL. Our work provides an innovative alternative process for extraction of active compounds from propolis and reveals P30K as an efficient therapeutic antioxidant.

Dual Proton/Silver-Catalyzed Serial (5 + 2)-Cycloaddition and Nazarov Cyclization of (E)-2-Arylidene-3-hydroxyindanones with Conjugated Eneynes: Synthesis of Indanone-Fused Benzo[cd]azulenes.

A one-pot step-economic tandem process involving (5 + 2)-cycloaddition and Nazarov cyclization reactions has been reported for the facile synthesis of indanone-fused benzo[cd]azulenes from (E)-2-arylidene-3-hydroxyindanones and conjugated eneynes. This highly regio- and stereoselective bisannulation reaction is enabled by dual silver and Brønsted acid catalysis and opens up a new avenue for the construction of important bicyclo[5.3.0]decane skeletons.

CRL4Cdt2 ubiquitin ligase regulates Dna2 and Rad16 (XPF) nucleases by targeting Pxd1 for degradation.

Structure-specific endonucleases (SSEs) play key roles in DNA replication, recombination, and repair. SSEs must be tightly regulated to ensure genome stability but their regulatory mechanisms remain incompletely understood. Here, we show that in the fission yeast Schizosaccharomyces pombe, the activities of two SSEs, Dna2 and Rad16 (ortholog of human XPF), are temporally controlled during the cell cycle by the CRL4Cdt2 ubiquitin ligase. CRL4Cdt2 targets Pxd1, an inhibitor of Dna2 and an activator of Rad16, for degradation in S phase. The ubiquitination and degradation of Pxd1 is dependent on CRL4Cdt2, PCNA, and a PCNA-binding degron motif on Pxd1. CRL4Cdt2-mediated Pxd1 degradation prevents Pxd1 from interfering with the normal S-phase functions of Dna2. Moreover, Pxd1 degradation leads to a reduction of Rad16 nuclease activity in S phase, and restrains Rad16-mediated single-strand annealing, a hazardous pathway of repairing double-strand breaks. These results demonstrate a new role of the CRL4Cdt2 ubiquitin ligase in genome stability maintenance and shed new light on how SSE activities are regulated during the cell cycle.

Spatial-temporal Distribution and Influencing Factors of Helicobacter pylori Infection in Chinese Mainland, 2001-2020: A Systematic Review and Meta-Analysis.

BACKGROUND: The spatial-temporal distribution of Helicobacter pylori infection in China is poorly understood. We aimed to study the spatial-temporal distribution of H. pylori infection in Chinese mainland and to explore its influencing factors. MATERIALS AND METHODS: We searched the relevant literature from 2001 to 2021 and applied meta-analysis to obtain the pooled prevalence estimates of all studies and subgroups. Then, we used the pooled prevalence as the dependent variable for the following analysis, including time series analysis, statistical mapping, spatial autocorrelation analysis, and influencing factor analysis based on generalized additive model and panel data model. RESULTS: A total of 726 articles and 3,407,392 people were included. The pooled prevalence was 43.7% (95% confidence interval: 42.7%-44.8%). The prevalence decreased in the past 20 years, with high in the eastern and western regions and low in the central region. Qinghai Tibet Plateau and Guizhou Plateau were the high incidence areas of this disease. The intake of vegetable oil, aquatic products, meat, milk, per capita gross domestic product, and annual average humidity were significantly correlated with H. pylori. CONCLUSIONS: The prevalence of H. pylori is decreasing in Chinese mainland, but still high in underdeveloped areas. Appropriate strategies for the prevention need greater attention.

An R-loop-initiated CSB-RAD52-POLD3 pathway suppresses ROS-induced telomeric DNA breaks.

Reactive oxygen species (ROS) inflict multiple types of lesions in DNA, threatening genomic integrity. How cells respond to ROS-induced DNA damage at telomeres is still largely unknown. Here, we show that ROS-induced DNA damage at telomeres triggers R-loop accumulation in a TERRA- and TRF2-dependent manner. Both ROS-induced single- and double-strand DNA breaks (SSBs and DSBs) contribute to R-loop induction, promoting the localization of CSB and RAD52 to damaged telomeres. RAD52 is recruited to telomeric R-loops through its interactions with both CSB and DNA:RNA hybrids. Both CSB and RAD52 are required for the efficient repair of ROS-induced telomeric DSBs. The function of RAD52 in telomere repair is dependent on its ability to bind and recruit POLD3, a protein critical for break-induced DNA replication (BIR). Thus, ROS-induced telomeric R-loops promote repair of telomeric DSBs through CSB-RAD52-POLD3-mediated BIR, a previously unknown pathway protecting telomeres from ROS. ROS-induced telomeric SSBs may not only give rise to DSBs indirectly, but also promote DSB repair by inducing R-loops, revealing an unexpected interplay between distinct ROS-induced DNA lesions.

Effect of cooking methods on the edible, nutritive qualities and volatile flavor compounds of rabbit meat.

BACKGROUND: Rabbit meat is a good edible meat source with high nutritional values. Cooking has a significant impact on the edible properties, nutritional qualities and flavor characteristics of meat. Studying the effect of cooking methods on rabbit meat qualities could encourage more understanding and acceptance of rabbit meat by consumers, and could also provide some reference for rabbit meat processing. Therefore, the effects of boiling, sous-vide cooking, steaming, microwaving, roasting, frying and pressure cooking on the edible, nutritive and volatile qualities of rabbit meat were investigated. RESULTS: The sous-vide cooked rabbit meat sample showed higher moisture content, water-holding capacity and lower cooking losses than other samples, but the results of roasted rabbit meat sample were the opposite, and scanning electron microscopy observations also verified the results. There was no significant difference in 2-thiobarbituric acid reactive substance (TBARS) value in the cooked samples except for roasting. Microwaving, roasting and frying exhibited stronger antioxidant activity than the other cooked samples after in vitro digestion. A total of 38 volatiles were identified in the cooked meat samples, and the samples were well divided into four groups by principal component analysis, and 13 volatiles were considered discriminatory variables for the cooked rabbit meat. CONCLUSION: The physicochemical characteristics of cooked meat differed significantly between the processing methods. Roasted meat showed lower TBARS value and stronger antioxidant activity after simulated digestion compared to the other meats. However, pressure cooked meat detected the most volatile components while roasting the least. © 2022 Society of Chemical Industry.

Simultaneous directed evolution of coupled enzymes for efficient asymmetric synthesis of l-phosphinothricin.

The traditional strategy to improve the efficiency of an entire coupled enzyme system relies on separate direction of the evolution of enzymes involved in their respective enzymatic reactions. This strategy can lead to enhanced single-enzyme catalytic efficiency but may also lead to loss of coordination among enzymes. This study aimed to overcome such shortcomings by executing a directed evolution strategy on multiple enzymes in one combined group that catalyzes the asymmetric biosynthesis of l-phosphinothricin. The genes of a glutamate dehydrogenase from Pseudomonas moorei (PmGluDH) and a glucose dehydrogenase from Exiguobacterium sibiricum (EsGDH), along with other gene parts (promoters, ribosomal binding sites (RBSs), and terminators) were simultaneously evolved. The catalytic efficiency of PmGluDH was boosted by introducing the beneficial mutation A164G (from 1.29 s-1mM-1 to 183.52 s-1mM-1), and the EsGDH expression level was improved by optimizing the linker length between the RBS and the start codon of gdh. The total turnover numbers of the bioreaction increased from 115 (GluDH WTNADPH) to 5846 (A164GNADPH coupled with low expression of EsGDH), and to 33950 (A164GNADPH coupled with high expression of EsGDH). The coupling efficiency was increased from ∼30% (GluDH_WT with low expression of GDH) to 83.3% (GluDH_A164G with high expression of GDH). In the batch production of l-phosphinothricin utilizing whole-cell catalysis, the strongest biocatalytic reaction exhibited a high space-time yield (6410 g·L-1·d-1) with strict stereoselectivity (>99% enantiomeric excess).Importance: The traditional strategy to improve multienzyme-catalyzed reaction efficiency may lead to enhanced single-enzyme catalytic efficiency but may also result in loss of coordination among enzymes. We describe a directed evolution strategy of an entire coupled enzyme system to simultaneously enhance enzyme coordination and catalytic efficiency. The simultaneous evolution strategy was applied to a multienzyme-catalyzed reaction for the asymmetric synthesis of l-phosphinothricin, which not only enhanced the catalytic efficiency of GluDH but also improved the coordination between GluDH and GDH. Since this strategy is enzyme-independent, it may be applicable to other coupled enzyme systems for chiral chemical synthesis.

DPEP1 expression promotes proliferation and survival of leukaemia cells and correlates with relapse in adults with common B cell acute lymphoblastic leukaemia.

Dehydropeptidase-1 (DPEP1) is a zinc-dependent metalloproteinase abnormally expressed in many cancers. However, its potential role in adults with B cell acute lymphoblastic leukaemia (ALL) is unknown. We found that in adults with common B cell ALL high DPEP1, transcript levels at diagnosis were independently associated with an increased cumulative incidence of relapse (CIR) and worse relapse-free survival (RFS) compared with subjects with low transcript levels. We show an increased proliferation and prosurvival role of DPEP1 in B cell ALL cells via regulation of phosphCREB and p53, which may be the biological basis of the clinical correlation we report. Our data implicate DPEP1 expression in the biology of common B cell ALL in adults. We report clinical correlates and provide a potential biological basis for these correlations. If confirmed, analysing DPEP1 transcript levels at diagnosis could help predict therapy outcomes. Moreover, regulation of DPEP1 expression could be a therapy target in B cell ALL.

Lipoxin A4 inhibited the activation of hepatic stellate cells -T6 cells by modulating profibrotic cytokines and NF-κB signaling pathway.

BACKGROUND: The deposition of extracellular matrix (ECM) during hepatic fibrosis is an intermediate process in the progression of multiple chronic liver diseases to cirrhosis. Because activated hepatic stellate cells (HSCs) are the main source of ECM, HSCs activation is the central link in the formation of liver fibrosis. It was reported that the analogs of lipoxin A4 (LXA4) had anti-fibrotic effects, but the mechanisms are still not clear. This study was conducted to explore the possible mechanisms involved in the process of LXA4-mediated inhibition of HSCs activation. METHODS: Rat HSC-T6 cells were activated by LPS and treated with LXA4 and/or BOC-2. The levels of ECM were assessed by hydroxyproline (Hyp) kit. The protein levels of α-SMA, Collagen I and III, MMP-2, MMP-9, TGF-ß1, PDGF A and B, NF-κB P65, phosphorylated NF-κB P65 (P-P65) and NF-κB inhibitor α (I-κBα) were measured via western blot. The mRNA levels of MMP-2 and MMP-9 were observed by real-time PCR. The contents of TGF-ß1 and PDGF were assessed by ELISA kits. Nuclear transfer assay kit was used to assess the activation and translation of NF-κB P65. RESULTS: (1) LPS activated HSC-T6 cells and up-regulated α-SMA, but LXA4 decreased LPS-induced α-SMA in HSC-T6 cells. (2) LXA4 inhibited LPS-induced Hyp production, meanwhile down-regulated LPS-induced Collagen I, Collagen III, MMP-2, and MMP-9 in HSC-T6 cells. (3) LXA4 decreased LPS-induced TGF-ß1 and PDGF in HSC-T6 cells. (4) LXA4 repressed LPS-activated NF-κB signaling pathway, causing a reduction of I-κBα degradation, NF-κB phosphorylation, and NF-κB p65 transposition in HSC-T6 cells. (4) BOC-2, the blocker of LXA4 receptor, inhibited all the effects of LXA4. CONCLUSION: LXA4 inhibited HSCs activation through down-regulation TGF-ß1/PDGF, and repression NF-κB signal pathway.

Comparative review and the recent progress in detection technologies of meat product adulteration.

Meat adulteration, mainly for the purpose of economic pursuit, is widespread and leads to serious public health risks, religious violations, and moral loss. Rapid, effective, accurate, and reliable detection technologies are keys to effectively supervising meat adulteration. Considering the importance and rapid advances in meat adulteration detection technologies, a comprehensive review to summarize the recent progress in this area and to suggest directions for future progress is beneficial. In this review, destructive meat adulteration technologies based on DNA, protein, and metabolite analyses and nondestructive technologies based on spectroscopy were comparatively analyzed. The advantages and disadvantages, application situations of these technologies were discussed. In the future, determining suitable indicators or markers is particularly important for destructive methods. To improve sensitivity and save time, new interdisciplinary technologies, such as biochips and biosensors, are promising for application in the future. For nondestructive techniques, convenient and effective chemometric models are crucial, and the development of portable devices based on these technologies for onsite monitoring is a future trend. Moreover, omics technologies, especially proteomics, are important methods in laboratory detection because they enable multispecies detection and unknown target screening by using mass spectrometry databases.

ß-Elemene suppresses the proliferation of human airway granulation fibroblasts via attenuation of TGF-ß/Smad signaling pathway.

BACKGROUND: Benign airway stenosis is easily to recur as a result of hyperplastic airway granulation tissues. Our previous study proved that a Chinese drug, ß-elemene, could inhibit the proliferation of fibroblasts cultured from these tissues, which could decrease the recurrence rate of this disease. METHODS: To find out the mechanism for this effect, we first cultured normal human airway fibroblasts and human airway granulation fibroblasts with different concentrations of ß-elemene for the same time or the same dose of ß-elemene for different times to explore the dose/time-effect relationship between the drug and these cells. Then we used gene microarray to screen out the most important pathway by which the drug influenced human airway granulation fibroblasts. At last, we assessed the condition of this pathway in human airway granulation fibroblasts and verified the effect of this drug on this pathway. RESULTS: ß-Elemene inhibited the proliferation of human airway granulation fibroblasts in a dose but no time-dependent manner and did not affect normal human airway fibroblasts. Affecting the expression of transforming growth factor ß (TGF-ß)/Smad pathway may be the key mechanism for this effect. This pathway was activated in human airway granulation fibroblasts and ß-elemene inhibited it in a dose-dependent manner. This effect was similar to the pathway inhibitor, SB431542, and exogenous TGF-ß could attenuate this effect. CONCLUSION: These results indicated that suppressing TGF-ß/Smad pathway was possibly the key mechanism by which ß-elemene inhibits the proliferation of human airway granulation fibroblasts. This pathway may be a promising target to treat benign airway stenosis.

S100A16 suppresses the growth and survival of leukaemia cells and correlates with relapse and relapse free survival in adults with Philadelphia chromosome-negative B-cell acute lymphoblastic leukaemia.

Refinement of risk stratification in Philadelphia chromosome (Ph)-negative B-cell acute lymphoblastic leukaemia (ALL) might aid the identification of patients who are likely to relapse. Abnormal S100 calcium binding protein A16 (S100A16) has been implicated in various cancers, but its function remains unclear. We found S100A16 transcript levels were higher in 130 adults with newly-diagnosed Ph-negative B-cell ALL compared with 33 healthy controls. In 115 of 130 patients who achieved first complete remission, those with high S100A16 transcript levels displayed a lower 3-year cumulative incidence of relapse (CIR; 34% [21, 47%] vs. 40% [48, 72%]; P = 0·012) and higher 3-year relapse-free survival (RFS; 65% [53, 78%] vs. 35% [23, 46%]; P = 0·012), especially when receiving chemotherapy only. In multivariate analysis a low S100A16 transcript level was independently-associated with a higher CIR (Hazard ratio [HR] = 3·74 [1·01-13·82]; P = 0·048) and inferior RFS (HR = 5·78 [1·91, 17·84]; P < 0·001). Function analysis indicated that knockdown of S100A16 promoted proliferation and anti-apoptosis and reduced chemosensitivity. S100A16 over-expression revealed an opposite trend, especially in a xeno-transplant mouse model. Western blotting analysis showed upregulation of PI3K/AKT and ERK1/2 in S100A16-knockdown and S100A16-overexpression B-cell ALL cell lines respectively. Inhibition assays suggested these two signalling pathways participated in the S100A16-mediated proliferation and survival effects in B-cell ALL cell lines. Trial Registration: Registered in the Chinese Clinical Trial Registry [ChiCTR-OCH-10000940]; http://www.chictr.org.cn.

Single-Pixel Imaging and Its Application in Three-Dimensional Reconstruction: A Brief Review.

Whereas modern digital cameras use a pixelated detector array to capture images, single-pixel imaging reconstructs images by sampling a scene with a series of masks and associating the knowledge of these masks with the corresponding intensity measured with a single-pixel detector. Though not performing as well as digital cameras in conventional visible imaging, single-pixel imaging has been demonstrated to be advantageous in unconventional applications, such as multi-wavelength imaging, terahertz imaging, X-ray imaging, and three-dimensional imaging. The developments and working principles of single-pixel imaging are reviewed, a mathematical interpretation is given, and the key elements are analyzed. The research works of three-dimensional single-pixel imaging and their potential applications are further reviewed and discussed.