Association between daily sitting time and kidney stones based on the National Health and Nutrition Examination Survey (NHANES) 2007-2016: A cross-sectional study.

BACKGROUND: Kidney stones are among the most common urological conditions affecting approximately 9% of the world population. Although some unhealthy diets and unhealthy lifestyles are reportedly risk factors for kidney stone, the association between daily sitting time and kidney stone has not been explored. MATERIALS AND METHODS: This large-scale, cross-sectional study was conducted using data from the National Health and Nutrition Examination Survey (NHANES) database 2007-2016. Kidney stone history and daily sitting time were retrieved from the questionnaire and 24-hour recall interviews. Logistic regression and subgroup analysis were conducted to investigate the association. The analysis was further stratified by vigorous recreational activity. RESULTS: A total of 19188 participants aged ≥20 years with complete information were included in this study. The overall prevalence of kidney stone was 9.6%. Among participants without vigorous recreational activity, a trend towards an increasing prevalence of kidney stone was observed with increased daily sitting time. However, the trend was not observed in individuals who participated in vigorous recreational activity, as they experienced a decreased risk of kidney stone despite having a daily sitting time of 6 to 8 hours (crude model OR=0.659, 95% CI: 0.457 to 0.950, P=0.028), indicating that vigorous recreational activity may partially attenuate the detrimental effect of prolonged sitting time. CONCLUSION: Our study revealed an increasing trend of prevalence of kidney stone with increased daily sitting time among the population not performing vigorous recreational activity despite the difference was nonsignificant. Vigorous recreational activity may modify the association between daily sitting time and kidney stone. More prospective cohort studies are warranted to further examine this association.

Multilevel thresholding with divergence measure and improved particle swarm optimization algorithm for crack image segmentation.

Crack formation is a common phenomenon in engineering structures, which can cause serious damage to the safety and health of these structures. An important method of ensuring the safety and health of engineered structures is the prompt detection of cracks. Image threshold segmentation based on machine vision is a crucial technology for crack detection. Threshold segmentation can separate the crack area from the background, providing convenience for more accurate measurement and evaluation of the crack condition and location. The segmentation of cracks in complex scenes is a challenging task, and this goal can be achieved by means of multilevel thresholding. The arithmetic-geometric divergence combines the advantages of the arithmetic mean and the geometric mean in probability measures, enabling a more precise capture of the local features of an image in image processing. In this paper, a multilevel thresholding method for crack image segmentation based on the minimum arithmetic-geometric divergence is proposed. To address the issue of time complexity in multilevel thresholding, an enhanced particle swarm optimization algorithm with local stochastic perturbation is proposed. In crack detection, the thresholding criterion function based on the minimum arithmetic-geometric divergence can adaptively determine the thresholds according to the distribution characteristics of pixel values in the image. The proposed enhanced particle swarm optimization algorithm can increase the diversity of candidate solutions and enhance the global convergence performance of the algorithm. The proposed method for crack image segmentation is compared with seven state-of-the-art multilevel thresholding methods based on several metrics, including RMSE, PSNR, SSIM, FSIM, and computation time. The experimental results show that the proposed method outperforms several competing methods in terms of these metrics.

UPK3A+ umbrella cell damage mediated by TLR3-NR2F6 triggers programmed destruction of urothelium in Hunner-type interstitial cystitis/painful bladder syndrome.

Urothelial damage and barrier dysfunction emerge as the foremost mechanisms in Hunner-type interstitial cystitis/bladder pain syndrome (HIC). Although treatments aimed at urothelial regeneration and repair have been employed, their therapeutic effectiveness remains limited due to the inadequate understanding of specific cell types involved in damage and the lack of specific molecular targets within these mechanisms. Therefore, we harnessed single-cell RNA sequencing to elucidate the heterogeneity and developmental trajectory of urothelial cells within HIC bladders. Through reclustering, we identified eight distinct clusters of urothelial cells. There was a significant reduction in UPK3A+ umbrella cells and a simultaneous increase in progenitor-like pluripotent cells (PPCs) within the HIC bladder. Pseudotime analysis of the urothelial cells in the HIC bladder revealed that cells faced challenges in differentiating into UPK3A+ umbrella cells, while PPCs exhibited substantial proliferation to compensate for the loss of UPK3A+ umbrella cells. The urothelium in HIC remains unrepaired, despite the substantial proliferation of PPCs. Thus, we propose that inhibiting the pivotal signaling pathways responsible for the injury to UPK3A+ umbrella cells is paramount for restoring the urothelial barrier and alleviating lower urinary tract symptoms in HIC patients. Subsequently, we identified key molecular pathways (TLR3 and NR2F6) associated with the injury of UPK3A+ umbrella cells in HIC urothelium. Finally, we conducted in vitro and in vivo experiments to confirm the potential of the TLR3-NR2F6 axis as a promising therapeutic target for HIC. These findings hold the potential to inhibit urothelial injury, providing promising clues for early diagnosis and functional bladder self-repair strategies for HIC patients. © 2024 The Pathological Society of Great Britain and Ireland.

Ginkgo biloba L. exocarp petroleum ether extract inhibits methicillin-resistant Staphylococcus aureus by modulating ion transport, virulence, and biofilm formation in vitro and in vivo.

ETHNOPHARMACOLOGICAL RELEVANCE: As reported in the Ancient Chinese Medicinal Books, Ginkgo biloba L. fruit has been used as a traditional Chinese medicine for the treatment asthma and cough or as a disinfectant. Our previous study demonstrated that G. biloba exocarp extract (GBEE), an extract of a traditional Chinese herb, inhibits the formation of methicillin-resistant Staphylococcus aureus (MRSA) biofilms. However, GBEE is a crude extract that contains many components, and the underlying mechanisms of purified GBEE fractions extracted with solvents of different polarities are unknown. AIM OF THE STUDY: This study aimed to investigate the different components in GBEE fractions extracted with solvents of different polarities and their antibacterial effects and mechanisms against MRSA and Staphylococcus haemolyticus biofilms both in vitro and in vivo. METHODS: The components in different fractions were detected by high-performance liquid chromatography-high resolution mass spectrometry (HPLC-HRMS). Microbroth dilution assays and time growth curves were used to determine the antibacterial effects of the fractions on 15 clinical bacterial isolates. Crystal violet staining, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were utilized to identify the fractions that affected bacterial biofilm formation. The potential MRSA targets of the GBEE fraction obtained with petroleum ether (PE), denoted GBEE-PE, were screened by transcriptome sequencing, and the gene expression profile was verified by quantitative polymerase chain reaction (qPCR). RESULTS: HPLC-HRMS analysis revealed that the four GBEE fractions (extracted with petroleum ether, ethyl acetate, n-butanol, and water) contained different ginkgo components, and the antibacterial effects decreased as the polarity of the extraction solvent increased. The antibacterial activity of GBEE-PE was greater than that of the GBEE fraction extracted with ethyl acetate (EA). GBEE-PE improved H. illucens survival and reduced MRSA colonization in model mouse organs. Crystal violet staining and SEM and TEM analyses revealed that GBEE-PE inhibited MRSA and S. haemolyticus biofilm formation. Transcriptional analysis revealed that GBEE-PE inhibits MRSA biofilms by altering ion transport, cell wall metabolism and virulence-related gene expression. In addition, the LO2 cell viability and H. illucens toxicity assay data showed that GBEE-PE at 20 mg/kg was nontoxic. CONCLUSION: The GBEE fractions contained different components, and their antibacterial effects decreased with increases in the polarity of the extraction solvent. GBEE-PE limited MRSA growth and biofilm formation by affecting ion transport, cell wall synthesis, and virulence-related pathways. This research provides a more detailed overview of the mechanism by which GBEE-PE inhibits MRSA both in vitro and in vivo and suggests that GBEE-PE is a new prospective antimicrobial with the potential to be used in MRSA therapeutics in the future.

The design and evaluation of a quick checklist for urodynamic quality control: A prospective single-center small sample study.

PURPOSE: To design a quick checklist for urodynamic study (UDS), aiming to reduce the occurrence of errors in the process, which may help to increase the quality of UDS. And further to analyze the effectiveness of this quick checklist for UDS quality control. METHODS: First, a quick checklist for uroflow study and pressure-flow study was developed, based on the International Continence Society-Good Urodynamic Practice standards, our previous studies, and recent literature, as well as expert suggestions. Then, patients who underwent UDS between January 2023 to February 2023 were randomly assigned to a study group or a control group. For the study group, the quick checklist was used throughout the UDS process, while the control group did not. The main artefacts were chosen to verify the effectiveness of the quick checklist for improving the UDS quality. RESULTS: The quick checklist comprised three subtypes: checklist for patients, checklist for environment and device, and checklist for UDS test process. 38 UDS traces per group were included. The incidence of missing the standard cough test decreased significantly from 18.4% to 0 (p = 0.012), with the checklist implementation. The baseline drift frequency rate also declined significantly from 39.5% to 5.3% (p < 0.05). Volume < 150 mL on uroflow study occurred in 68.4% of cases and its frequency rate decreased significantly with checklist implementation (p < 0.05). CONCLUSION: A quick checklist for quality control of UDS was developed. The quick checklist as a convenient, quick, and easy used urodynamic quality control method, may help to reduce the technical artefacts and improve fundamental urodynamic quality control. Future research with a larger sample size is needed to confirm the effectiveness of the checklist.

Schaftoside reduces inflammation in Aspergillus fumigatus keratitis through the inhibition of the TLR4/MyD88 pathway.

PURPOSE: The purpose of this research study was to investigate the impact of schaftoside on Aspergillus fumigatus (A. fumigatus) keratitis and elucidate its underlying mechanisms. METHODS: In order to establish safe experimental concentrations of schaftoside in human corneal epithelial cells (HCECs), RAW264.7 cells, and mouse models, various techniques were employed including cytotoxicity assay (CCK-8) assay, cell scratch assay, and Draize test. The therapeutic effect of schaftoside was assessed using slit-lamp biomicroscopy, clinical scores, as well as determination of neutrophil infiltration through hematoxylin and eosin (HE) staining, immunofluorescence (IF) staining, and myeloperoxidase (MPO) assay. The levels of Toll-like receptor 4 (TLR4), myeloid differentiation primary response 88 (MyD88), pro-inflammatory mediators interleukin (IL)-1ß, tumor necrosis factor (TNF)-α, and IL-6 were determined using quantitative real-time polymerase chain reaction (qRT-PCR), western blotting, and IF techniques. RESULTS: Schaftoside at a concentration of 160 µM displayed no harmful side effects on HCECs, RAW cells, and mouse corneas, rendering it suitable for further experiments. In a murine fungal keratitis model, schaftoside mitigated the severity of fungal keratitis by inhibiting neutrophil infiltration and reducing MPO activity. Both in vitro and in vivo experiments demonstrated that schaftoside treatment suppressed the upregulation of IL-1ß, TNF-α, and IL-6 expression, while also downregulating the expressions of TLR4 as well as MyD88 at both mRNA and protein levels. CONCLUSIONS: Schaftoside demonstrated a protective effect against A. fumigatus keratitis by reducing corneal damage through inhibition of neutrophil recruitment and downstream inflammatory cytokines. The anti-inflammatory properties of schaftoside in A. fumigatus keratitis may involve modulation of the TLR4/MyD88 pathway.

Identification of circRNA-miRNA-mRNA network as biomarkers for interstitial cystitis/bladder pain syndrome.

Interstitial cystitis/bladder pain syndrome (IC/BPS) is a long-lasting and incapacitating disease, and the exact factors that affect its onset and advancement are still uncertain. Thus, the main aim was to explore new biomarkers and possible therapeutic targets for IC/BPS. Next-generation high-throughput sequencing experiments were performed on bladder tissues. Based on the interactions between circRNA and miRNA, as well as miRNA and mRNA, candidates were selected to build a network of circRNA-miRNA-mRNA. The STRING database and Cytoscape software were utilized to build a protein-protein interaction (PPI) network to pinpoint the hub genes associated with IC/BPS. The expression levels of circRNA and miRNA in the network were confirmed through quantitative polymerase chain reaction. Western blot was applied to confirm the stability of the lipopolysaccharide-induced IC/BPS model, and the effect of overexpression of circ.5863 by lentivirus on inflammation. Ten circRNA-miRNA interactions involving three circRNAs and six miRNAs were identified, and IFIT3 and RSAD2 were identified as hub genes in the resulting PPI network with 19 nodes. Circ.5863 showed a statistically significant decrease in the constructed model, which is consistent with the sequencing results, and overexpression via lentiviral transfection of circ.5863 was found to alleviate inflammation damage. In this study, a circRNA-miRNA-mRNA network was successfully constructed, and IFIT3 and RSAD2 were identified as hub genes. Our findings suggest that circ.5863 can mitigate inflammation damage in IC/BPS. The identified marker genes may serve as valuable targets for future research aimed at developing diagnostic tools and more effective therapies for IC/BPS.

Experimental and theoretic mechanism of successive adsorption of oppositely charged Cu(II) and Cr(VI) onto amine-rich cellulose adsorbent.

A novel layer-by-layer adsorption was proposed and used for adsorption of Cu(II) and Cr(VI) on the pre-bleached sawdust cellulose coated with polyethylenimine (PSC-PEI). It was found that PSC-PEI loaded with Cu(II) cations was favorable for Cr(VI) anions adsorption. The maximum adsorption capacities estimated by Langmuir model for Cu(II) and Cr(VI) were 80.0 and 93.5 mg/g, respectively. The kinetic regression results, as fitted by the pseudo-second order model, revealed that the rate constant (k2) for Cr(VI) at 0.07 g/mg/min is significantly greater than that observed for Cu(II) at 0.02 g/mg/min, indicating that PSC-PEI exhibited a stronger affinity towards Cr(VI). The first-layer adsorption mechanism for Cu(II) involved the formation of copper-amine complex. Zeta potential and XPS results revealed that the second-layer adsorption of Cr(VI) mainly involved electrostatic attraction and redox reaction. The simulated results for dynamic column test showed good agreement between the theoretical values and the experimental values. The mass transfer mechanism indicated that Cu(II) adsorption was dependent on external mass transfer process, while the internal mass transfer is the rate-determining step for Cr(VI) adsorption. The saturated adsorbent was regenerated by washing with 5% NaOH and 5% H2SO4 solutions and the adsorption ability of more than 70% was sustained after three cycles of regeneration. This study demonstrated that the oppositely charged Cu(II) cations and Cr(VI) anions could be effectively removed by amine-rich cellulose adsorbent from wastewater through layer-by-layer adsorption.

Diagnostic value of transperineal ultrasound in patients with stress urinary incontinence (SUI): a systematic review and meta-analysis.

PURPOSE: We aimed to analyze the diagnostic value of transperineal ultrasound in patients with stress urinary incontinence (SUI) using evidence-based methods. METHODS: A comprehensive search of the studies on the diagnosis of SUI by transperineal ultrasound in PubMed, EMBASE, MEDLINE, Cochrane library, Medicine, Web of Science, and clinicaltrials.gov databases on August 1, 2022. Studies were included if they met the inclusion criteria and were evaluated by different quality evaluation methods according to study types. Various ultrasound parameters were collected and counted to analyze and judge the diagnostic value of transperineal ultrasound in SUI patients. RESULTS: A total of 13 studies with 1563 participants were finally included. The combined statistics showed no significant difference in age and parity among the included patients, and the BMI of the SUI group was slightly higher than that of the normal population (MD 1.20, 95%CI 0.68-1.72). The results indicated that compared with the normal population, the α angle (MD 15.56, 95%CI 9.93-21.90), ß angle (at rest: MD 10.02 mm, 95%CI 1.95-18.09; at Valsalva: MD 22.40 mm, 95%CI 13.79-31.01), bladder neck descent (MD 6.82 mm, 95%CI 4.49-9.14), area of hiatus (MD 2.83 cm2, 95%CI 0.71-4.94) and bladder neck funneling (RR 4.71, 95%CI 1.08-20.62) of SUI patients were significantly different, which illustrated the potential value of transperineal ultrasound in diagnosing SUI. CONCLUSION: Evidence-based medicine was applied to statistically analyze published articles on the diagnostic value of transperineal ultrasound in SUI. The results suggested that transperineal ultrasound had application value in the diagnosis of SUI and had the potential to become a routine examination method to assist clinical decision-making.

The Production of Pyruvate in Biological Technology: A Critical Review.

Pyruvic acid has numerous applications in the food, chemical, and pharmaceutical industries. The high costs of chemical synthesis have prevented the extensive use of pyruvate for many applications. Metabolic engineering and traditional strategies for mutation and selection have been applied to microorganisms to enhance their ability to produce pyruvate. In the past decades, different microbial strains were generated to enhance their pyruvate production capability. In addition to the development of genetic engineering and metabolic engineering in recent years, the metabolic transformation of wild-type yeast, E. coli, and so on to produce high-yielding pyruvate strains has become a hot spot. The strategy and the understanding of the central metabolism directly related to pyruvate production could provide valuable information for improvements in fermentation products. One of the goals of this review was to collect information regarding metabolically engineered strains and the microbial fermentation processes used to produce pyruvate in high yield and productivity.

Comprehensive assessment of miniature CRISPR-Cas12f nucleases for gene disruption.

Because of their small size, the recently developed CRISPR-Cas12f nucleases can be effectively packaged into adeno-associated viruses for gene therapy. However, a systematic evaluation of the editing outcomes of CRISPR-Cas12f is lacking. In this study, we apply a high-throughput sequencing method to comprehensively assess the editing efficiency, specificity, and safety of four Cas12f proteins in parallel with that of Cas9 and two Cas12a proteins at multiple genomic sites. Cas12f nucleases achieve robust cleavage at most of the tested sites and mainly produce deletional fragments. In contrast, Cas9 and Cas12a show relatively higher editing efficiency at the vast majority of the tested sites. However, the off-target hotspots identified in the Cas9- and Cas12a-edited cells are negligibly detected in the Cas12f-edited cells. Moreover, compared to Cas9 and Cas12a nucleases, Cas12f nucleases reduce the levels of chromosomal translocations, large deletions, and integrated vectors by 2- to 3-fold. Therefore, our findings confirm the editing capacity of Cas12f and reveal the ability of this nuclease family to preserve genome integrity during genome editing.

Construction of OH-functionalized MWCNT/solid waste composites with tubular/spherical heterostructures for enhanced electromagnetic wave absorption property.

Electromagnetic wave (EMW) absorption materials with high efficiency and simple preparation process are highly desirable for practical applications. However, there are still many obstacles to simultaneously satisfy the practical requirements. Herein, fly ash cenospheres (FACs), solid waste from power plants, were selected as a framework to prepare OH-functionalized multi-walled carbon nanotube (MWCNT)/FAC hybrids with multilayer, connected and porous architectures via a facile physical mixing process for the first time. Accordingly, a novel tubular/spherical model for EMW absorption materials was established. The effect of the unique heterostructure, which possessed multiple interfaces, on the EMW absorption property was studied. The results indicated that this structure is conducive to extending the transmission route, adjusting the conductivity and improving the dielectric loss. Thus, the composite showed an excellent EMW absorption performance. The minimum reflection loss of -44.67 dB occurs at 4.9 GHz and the effective bandwidth below -10 dB (90% attenuation of EMW) could shift from 4.1 to 19.2 GHz with a thickness in the range of 1.5-5.5 mm. The superior absorption property is mostly attributed to the synergistic effect of good impedance matching, multiple loss mechanisms, and multiple reflections and scatterings. Thus, this product meets the requirement of high absorption performance and simple preparation, which greatly enhance its applicability.

PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair.

The repair products of double-stranded DNA breaks (DSBs) are crucial for investigating the mechanism underlying DNA damage repair as well as evaluating the safety and efficiency of gene-editing; however, a comprehensively quantitative assay remains to be established. Here, we describe the step-by-step instructions of the primer extension-mediated sequencing (PEM-seq), followed by the framework of data processing and statistical analysis. PEM-seq presents a full spectrum of repair outcomes for both genome-editing-induced and endogenous DSBs in mouse and human cells. For complete details on the use and execution of this profile, please refer to Gan et al. (2021), Yin et al. (2019), Liu et al. (2021a), and Zhang et al. (2021).

Engineering of Yarrowia lipolytica for producing pyruvate from glycerol.

The present study aims to increase pyruvate production by engineering Yarrowia lipolytica through modifying the glycerol metabolic pathway. Results: Wild-type Yarrowia lipolytica (Po1d) was engineered to produce six different strains, namely ZS099 (by over-expressing PYK1), ZS100 (by deleting DGA2), ZS101 (by over-expressing DAK1, DAK2, and GCY1), ZS102 (by over-expressing GUT1 and GUT2), ZS103 (by over-expressing GUT1) and ZSGP (by over-expressing POS5 and deleting GPD2). Production of pyruvate from engineered and control strains was determined using high-performance liquid chromatography (HPLC). Subsequently, the fermentation conditions for producing pyruvate were optimized, including the amount of initial inoculation, the addition of calcium carbonate (CaCO3), thiamine and glycerol. Finally, for scaled-up purposes, a 20-L fermentor was used. It was observed that pyruvate production increased by 136% (8.55 g/L) in ZSGP strain compared to control (3.62 g/L). Furthermore, pyruvate production by ZSGP reached up to 110.4 g/L in 96 h in the scaled-up process. We conclude that ZSGP strain of Y. lipolytica can be effectively used for pyruvate production at the industrial level. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03158-7.

Cas9 exo-endonuclease eliminates chromosomal translocations during genome editing.

The mechanism underlying unwanted structural variations induced by CRISPR-Cas9 remains poorly understood, and no effective strategy is available to inhibit the generation of these byproducts. Here we find that the generation of a high level of translocations is dependent on repeated cleavage at the Cas9-targeting sites. Therefore, we employ a strategy in which Cas9 is fused with optimized TREX2 to generate Cas9TX, a Cas9 exo-endonuclease, which prevents perfect DNA repair and thereby avoids repeated cleavage. In comparison with CRISPR-Cas9, CRISPR-Cas9TX greatly suppressed translocation levels and enhanced the editing efficiency of single-site editing. The number of large deletions associated with Cas9TX was also reduced to very low level. The application of CRISPR-Cas9TX for multiplex gene editing in chimeric antigen receptor T cells nearly eliminated deleterious chromosomal translocations. We report the mechanism underlying translocations induced by Cas9, and propose a general strategy for reducing chromosomal abnormalities induced by CRISPR-RNA-guided endonucleases.

Quantifying impacts of climate dynamics and land-use changes on water yield service in the agro-pastoral ecotone of northern China.

Large-scale revegetation practices have lasted approximately two decades in the agro-pastoral ecotone of northern China (AENC), and their impacts on hydrological and ecological effects remain poorly understood. Previous studies largely focused on assessing water yield service (WYs) based on several fixed time points, whereas time series information-continuous WYs dynamics were more reliable and valuable in decision-making about water sustainability goals. This study analyzed the interannual WYs trend and relative roles of its drivers in the last 20 years based on a newly proposed approach, and revealed the past, present and future impacts of revegetation on WYs. The final results indicated that the annual WYs averaged approximately 97 mm and exhibited an increasing trend of 1.96 mm year-1 (p = 0.086) during 2000-2019, in which climate and land-use changes were responsible for 88% and 12% of WYs variations, respectively. From 2000 to 2019, WYs was pronouncedly 1.47 mm year-1 (p = 0.119) lower in the afforestation area than in the nonafforestation area, but the precipitation in the two regions had a statistically insignificant difference (p = 0.97). Future revegetation scenarios showed great potential for the shrinkage of WYs provision, even approaching a maximum of 50 mm at a local scale. Even so, the afforestation-induced reductions in blue water and benefits in green water both should receive equal attention. Specifically, any attempts to assess WYs or other climate-driven ecosystem services using discontinuous years as the study period must be taken with extreme caution.

Global detection of DNA repair outcomes induced by CRISPR-Cas9.

CRISPR-Cas9 generates double-stranded DNA breaks (DSBs) to activate cellular DNA repair pathways for genome editing. The repair of DSBs leads to small insertions or deletions (indels) and other complex byproducts, including large deletions and chromosomal translocations. Indels are well understood to disrupt target genes, while the other deleterious byproducts remain elusive. We developed a new in silico analysis pipeline for the previously described primer-extension-mediated sequencing assay to comprehensively characterize CRISPR-Cas9-induced DSB repair outcomes in human or mouse cells. We identified tremendous deleterious DSB repair byproducts of CRISPR-Cas9 editing, including large deletions, vector integrations, and chromosomal translocations. We further elucidated the important roles of microhomology, chromosomal interaction, recurrent DSBs, and DSB repair pathways in the generation of these byproducts. Our findings provide an extra dimension for genome editing safety besides off-targets. And caution should be exercised to avoid not only off-target damages but also deleterious DSB repair byproducts during genome editing.

In-depth assessment of the PAM compatibility and editing activities of Cas9 variants.

A series of Cas9 variants have been developed to improve the editing fidelity or targeting range of CRISPR-Cas9. Here, we employ a high-throughput sequencing approach primer-extension-mediated sequencing to analyze the editing efficiency, specificity and protospacer adjacent motif (PAM) compatibility of a dozen of SpCas9 variants at multiple target sites in depth, and our findings validate the high fidelity or broad editing range of these SpCas9 variants. With regard to the PAM-flexible SpCas9 variants, we detect significantly increased levels of off-target activity and propose a trade-off between targeting range and editing specificity for them, especially for the near-PAM-less SpRY. Moreover, we use a deep learning model to verify the consistency and predictability of SpRY off-target sites. Furthermore, we combine high-fidelity SpCas9 variants with SpRY to generate three new SpCas9 variants with both high fidelity and broad editing range. Finally, we also find that the existing SpCas9 variants are not effective in suppressing genome instability elicited by CRISPR-Cas9 editing, raising an urgent issue to be addressed.