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Abstract The engineered TadA variants used in cytosine base editors (CBEs) present distinctive advantages, including a smaller size and fewer off-target effects compared to cytosine base editors that rely on natural deaminases. However, the current TadA variants demonstrate a preference for base editing in DNA with specific motif sequences and possess dual deaminase activity, acting on both cytosine and adenosine in adjacent positions, limiting their application scope. To address these issues, we employ TadA orthologs screening and multi sequence alignment (MSA)-guided protein engineering techniques to create a highly effective cytosine base editor (aTdCBE) without motif and adenosine deaminase activity limitations. Notably, the delivery of aTdCBE to a humanized mouse model of Duchenne muscular dystrophy (DMD) mice achieves robust exon 55 skipping and restoration of dystrophin expression. Our advancement in engineering TadA ortholog for cytosine editing enriches the base editing toolkits for gene-editing therapy and other potential applications.

Abstract Duchenne muscular dystrophy (DMD) affecting 1 in 3500–5000 live male newborns is the frequently fatal genetic disease resulted from various mutations in DMD gene encoding dystrophin protein. About 70% of DMD-causing mutations are exon deletion leading to frameshift of open reading frame and dystrophin deficiency. To facilitate translating human DMD-targeting CRISPR therapeutics into patients, we herein establish a genetically humanized mouse model of DMD by replacing exon 50 and 51 of mouse Dmd gene with human exon 50 sequence. This humanized mouse model recapitulats patient’s DMD phenotypes of dystrophin deficiency and muscle dysfunction. Furthermore, we target splicing sites in human exon 50 with adenine base editor to induce exon skipping and robustly restored dystrophin expression in heart, tibialis anterior and diaphragm muscles. Importantly, systemic delivery of base editor via adeno-associated virus in the humanized male mouse model improves the muscle function of DMD mice to the similar level of wildtype ones, indicating the therapeutic efficacy of base editing strategy in treating most of DMD types with exon deletion or point mutations via exon-skipping induction.

Abstract R-loop-triggered collateral single-stranded DNA (ssDNA) nuclease activity within Class 1 Type I CRISPR-Cas systems holds immense potential for nucleic acid detection. However, the hyperactive ssDNase activity of Cas3 introduces unwanted noise and false-positive results. In this study, we identified a novel Type I-A Cas3 variant derived from Thermococcus siculi, which remains in an auto-inhibited state until it is triggered by Cascade complex and R-loop formation. This Type I-A CRISPR-Cas3 system not only exhibits an expanded protospacer adjacent motif (PAM) recognition capability but also demonstrates remarkable intolerance towards mismatched sequences. Furthermore, it exhibits dual activation modes—responding to both DNA and RNA targets. The culmination of our research efforts has led to the development of the Hyper-Active-Verification Establishment (HAVE, 惠父). This innovation enables swift and precise human papillomavirus (HPV) diagnosis in clinical samples, providing a robust molecular diagnostic tool based on the Type I-A CRISPR-Cas3 system. Our findings contribute to understanding type I-A CRISPR-Cas3 system regulation and facilitate the creation of advanced diagnostic solutions with broad clinical applicability.

Duchenne muscular dystrophy (DMD) is the most prevalent herediatry disease in men, characterized by dystrophin deficiency, progressive muscle wasting, cardiac insufficiency, and premature mortality, with no effective therapeutic options. Here, we investigated whether adenine base editing can correct pathological nonsense point mutations leading to premature stop codons in the dystrophin gene. We identified 27 causative nonsense mutations in our DMD patient cohort. Treatment with adenine base editor (ABE) could restore dystrophin expression by direct A-to-G editing of pathological nonsense mutations in cardiomyocytes generated from DMD patient-derived induced pluripotent stem cells. We also generated two humanized mouse models of DMD expressing mutation-bearing exons 23 or 30 of human dystrophin gene. Intramuscular administration of ABE, driven by ubiquitous or muscle-specific promoters could correct these nonsense mutations in vivo, albeit with higher efficiency in exon 30, restoring dystrophin expression in skeletal fibers of humanized DMD mice. Moreover, a single systemic delivery of ABE with human single guide RNA (sgRNA) could induce body-wide dystrophin expression and improve muscle function in rotarod tests of humanized DMD mice. These findings demonstrate that ABE with human sgRNAs can confer therapeutic alleviation of DMD in mice, providing a basis for development of adenine base editing therapies in monogenic diseases.

Abstract Transposon-associated ribonucleoprotein TnpB is known to be the ancestry endonuclease of diverse Cas12 effector proteins from type-V CRISPR system. Given its small size (408 aa), it is of interest to examine whether engineered TnpB could be used for efficient mammalian genome editing. Here, we showed that the gene editing activity of native TnpB from Deinococcus radiodurans (ISDra2 TnpB) in mouse embryos was already higher than previously identified small-sized Cas12f1. Further stepwise engineering of noncoding RNA (ωRNA or reRNA) component of TnpB significantly elevated the nuclease activity of TnpB. Notably, an optimized TnpB-ωRNA system could be efficiently delivered in vivo with single adeno-associated virus (AAV) and corrected the disease phenotype in a tyrosinaemia mouse model. Thus, the engineered miniature TnpB system represents a new addition to the current genome editing toolbox, with the unique feature of the smallest effector size that facilitate efficient AAV delivery for editing of cells and tissues.

Mutations in Rhodopsin (RHO) gene commonly cause autosomal dominant retinitis pigmentosa (adRP) without effective therapeutic treatment so far. Compared with genomic DNA-targeting CRISPR-Cas9 system, Cas13 edits RNA for therapeutic applications, avoiding the risk of causing permanent changes in the genome. In particular, a compact and high-fidelity Cas13X (hfCas13X) recently has been developed to degrade targeted RNA with minimal collateral effects and could also be packaged in a single adeno-associated virus for efficient in vivo delivery. In this study, we engineered single-guide RNA for hfCas13X to specifically knock down human mutant Rhodopsin transcripts RHO-P23H with minimal effect on wild-type transcripts. Moreover, treatment with hfCas13X alleviated the adRP progression in both RHO-P23H overexpression-induced and humanized hRHOP23H/WT mouse models. Our study indicates the potential of hfCas13X in treating adRP caused by RHO mutations and other genetic diseases.

Abstract Mitochondrial base editing with DddA‐derived cytosine base editor (DdCBE) is limited in the accessible target sequences and modest activity. Here, the optimized DdCBE tools is presented with improved editing activity and expanded C‐to‐T targeting scope by fusing DddA11 variant with different cytosine deaminases with single‐strand DNA activity. Compared to previous DdCBE based on DddA11 variant alone, fusion of the activation‐induced cytidine deaminase (AID) from Xenopus laevis not only permits cytosine editing of 5′‐GC‐3′ sequence, but also elevates editing efficiency at 5′‐TC‐3′, 5′‐CC‐3′, and 5′‐GC‐3′ targets by up to 25‐, 10‐, and 6‐fold, respectively. Furthermore, the A‐to‐G editing efficiency is significantly improved by fusing the evolved DddA6 variant with TALE‐linked deoxyadenosine deaminase (TALED). Notably, the authors introduce the reported high‐fidelity mutations in DddA and add nuclear export signal (NES) sequences in DdCBE and TALED to reduce off‐target editing in the nuclear and mitochondrial genome while improving on‐target editing efficiency in mitochondrial DNA (mtDNA). Finally, these engineered mitochondrial base editors are shown to be efficient in installing mtDNA mutations in human cells or mouse embryos for disease modeling. Collectively, the study shows broad implications for the basic study and therapeutic applications of optimized DdCBE and TALED.

Approximately 10% of monogenic diseases are caused by nonsense point mutations that generate premature termination codons (PTCs), resulting in a truncated protein and nonsense-mediated decay of the mutant mRNAs. Here, we demonstrate a mini-dCas13X–mediated RNA adenine base editing (mxABE) strategy to treat nonsense mutation–related monogenic diseases via A-to-G editing in a genetically humanized mouse model of Duchenne muscular dystrophy (DMD). Initially, we identified a nonsense point mutation (c.4174C>T, p.Gln1392*) in the DMD gene of a patient and validated its pathogenicity in humanized mice. In this model, mxABE packaged in a single adeno-associated virus (AAV) reached A-to-G editing rates up to 84% in vivo, at least 20-fold greater than rates reported in previous studies using other RNA editing modalities. Furthermore, mxABE restored robust expression of dystrophin protein to over 50% of WT levels by enabling PTC read-through in multiple muscle tissues. Importantly, systemic delivery of mxABE by AAV also rescued dystrophin expression to averages of 37%, 6%, and 54% of WT levels in the diaphragm, tibialis anterior, and heart muscle, respectively, as well as rescued muscle function. Our data strongly suggest that mxABE-based strategies may be a viable new treatment modality for DMD and other monogenic diseases.

Abstract Fuel cavitation can cause damage to the structure of an injector control valve, which can further affect the service life of the injector. Therefore, it is of great importance to carry out research on the mechanism of cavitation in injector control valves. In this study, the dynamic evolution of the cavitation and fuel flow characteristics during the opening of a ball valve in a high‐pressure common rail injector control valve were studied. First, a transient CFD simulation of the cavitation during the opening of the control valve was performed using dynamic mesh technology to analyze the evolution and formation mechanism of the cavitation. The cavitation was influenced by the fuel flow velocity, which was affected by the sealing cone angle and the ball valve movement. Additionally, the fuel reflux could effectively inhibit the development of cavitation. By comparing with the pressure, velocity, and mass flow rate of the fuel under conditions without cavitation, it was found that the cavitation had a remarkable effect on reducing the hydraulic shock to the ball valve and sealing cone as well as stabilizing the fluctuation of the fuel velocity in the control chamber. In addition, the cavitation noticeably decreased the fuel mass flow rate (by up to 32% at 0.015 ms) and increased the average pressure in the chamber (by up to 29.1% at 0.01 ms), ultimately leading to a slower response of the control valve. The analysis of different inlet pressures of the control valve indicated that the increase in the inlet pressure caused the cavitation to extend upward along the sealing cone, and that the cavitation ring area and the cavitation strength increased.

Interfacial polarization is generally a major cause of dielectric loss, but its exact contribution to the electromagnetic wave (EMW) absorption capacity of absorbers remains to be elucidated. In this work, SnO2@rGO composite (S2) with tight interfaces formed by chemical bonds and SnO2/rGO mixture (S3) were synthesized by a simple chemical route followed by further calcined in argon, respectively. Compared with pure SnO2 (S1) and S3, S2 exhibits much better EMW-dissipation ability, with a smaller minimum reflection loss (RLmin) value of −20.5 dB at a matched thickness of 5 mm and a larger effective absorption bandwidth (fe) value of 5.8 GHz (from 11 GHz to 16.8 GHz) at 3.2 mm. By comprehensively comparing the defects, dipoles, and interfaces in S2 and S3, it is concluded that the excellent EMW absorption capacity of S2 is mainly caused by strong dielectric loss dominated by interfacial polarization as well as suitable impedance matching. This study provides an insight into the exact contribution of interfacial polarization to the EMW-dissipation ability of absorbers, showing that the EMW absorption of graphene-based composites can be effectively promoted by constructing well-connected interfaces between graphene and absorbers.

Common rail injector response characteristics depend on the control chamber pressure change rate, the outlet throttle diameter by manufacturing errors, or wear-induced deviations that affect the rate of pressure change in the control chamber, so the accuracy of the outlet throttle diameter directly affects the control valve response consistency. This paper presents a computational fluid dynamics (CFD) simulation of the effect of the deviation of the outlet throttle diameter on the average mass flow rate of the outlet throttle during the opening of the spherical valve in order to reduce this difference and ensure uniform injection characteristics. The results illustrate that with the increase in outlet throttle diameter deviation, the volume of gas phase in the control valve increases and the rate of pressure reduction in the control chamber accelerates, and the sensitivity coefficient of the average mass flow rate of the outlet throttle to the outlet throttle diameter deviation remains unchanged at 24.77. Cavitation occurs in the area of the outlet throttle when the spherical valve lift is 0.045 mm. The increase in rail pressure not only leads to an increase in the low-pressure area on the inner wall of the outlet throttle, an increase in the volume share of the gas phase, and an increase in the hydraulic impact on the sealing wall but also makes the average mass flow rate of the outlet throttle and the rate of change of the control chamber pressure during the opening of the spherical valve more sensitive to the deviation of the outlet throttle diameter.

Controlling defects and interfaces in composite absorbers can effectively regulate electromagnetic (EM) parameters and enhance the electromagnetic wave (EMW) absorption ability, but the mechanism still needs to be further elucidated. In this study, ZnFe2O4/ZnO/C composite was synthesized via the hydrothermal method followed by post-annealing in different atmospheres. Defects and interfaces were characterized by Raman, PL spectroscopy, XPS and TEM, and their relationship with dielectric loss and EMW absorption performance was discussed in detail. Results show that the N2-annealed ZnFe2O4/ZnO/C composite with abundant defects and interfaces as well as an optimized composition exhibits excellent EMW dissipation ability, with a RLmin value of −17.4 dB and an fe of 3.85 GHz at a thickness of 2.28 mm. The excellent EMW absorption performance originates from suitable impedance matching, significant conduction loss and strong dielectric loss (interfacial polarization, diploe polarization and defect polarization) dominated by lattice defects and interfaces. This study provides a view into the relationship between defects, interfaces, EM parameters and EMW absorption ability, and also suggests an effective way to promote EMW dissipation ability of the absorbers by controlling defects and interfaces.

Abstract Base editing installs a precise nucleotide change in specific gene loci without causing a double-strand break. Its efficiency in human embryos is generally low, limiting its utility in functional genetic studies. Here, we report that injecting base editors into human cleaving two-cell and four-cell embryos results in much higher (up to 13-fold) homozygotic nucleotide substitution efficiency as opposed to MII oocytes or zygotes. Furthermore, as a proof-of-principle study, a point mutation can be efficiently corrected by our method. Our study indicates that human cleaving embryos provide an efficient base editing window for robust gene disruption and correction.

Summary: MicroRNAs (miRNAs) are the effectors of a conserved gene-silencing system with broad roles in post-transcriptional regulation. Due to functional overlaps, assigning specific functions to individual miRNAs has been challenging. DICER1 cleaves pre-miRNA hairpins into mature miRNAs, and previously Dicer1 knockout mouse embryonic stem cells have been generated to study miRNA function in early mouse development. Here we report an essential requirement of DICER1 for the self-renewal of human embryonic stem cells (hESCs). Utilizing a conditional knockout approach, we found that DICER1 deletion led to increased death receptor-mediated apoptosis and failure of hESC self-renewal. We further devised a targeted miRNA screening strategy and uncovered essential pro-survival roles of members of the mir-302-367 and mir-371-373 clusters that bear the seed sequence AAGUGC. This platform is uniquely suitable for dissecting the roles of individual miRNAs in hESC self-renewal and differentiation, which may help us better understand the early development of human embryos. : Huangfu and colleagues report an unexpected requirement for DICER1 in preventing death-receptor-mediated apoptosis in hESCs. This essential pro-survival role is largely mediated by mir-302-367 and mir-371-373 cluster members that bear the seed sequence “AAGUGC” shared by the ESC-specific cell-cycle-regulating family of miRNAs. This work provides a robust platform for interrogating miRNA function in hESC pluripotency and differentiation. Keywords: human embryonic stem cells (hESCs), human pluripotent stem cells (hPSCs), DICER1, microRNAs (miRNAs), self-renewal, apoptosis, ESCC miRNAs

The global incidence of cancer is rapidly rising, and despite an improved understanding of cancer molecular biology, immune landscapes, and advancements in cytotoxic, biologic, and immunologic anti-cancer therapeutics, cancer remains a leading cause of death worldwide. Cancer is caused by the accumulation of a series of gene mutations called driver mutations that confer selective growth advantages to tumor cells. As cancer therapies move toward personalized medicine, predictive modeling of the role driver mutations play in tumorigenesis and therapeutic susceptibility will become essential. The development of next-generation sequencing technology has made the evaluation of mutated genes possible in clinical practice, allowing for identification of driver mutations underlying cancer development in individual patients. This, combined with recent advances in gene editing technologies such as CRISPR-Cas9 enables development of personalized tumor models for prediction of treatment responses for mutational profiles observed clinically. Pigs represent an ideal animal model for development of personalized tumor models due to their similar size, anatomy, physiology, metabolism, immunity, and genetics compared to humans. Such models would support new initiatives in precision medicine, provide approaches to create disease site tumor models with designated spatial and temporal clinical outcomes, and create standardized tumor models analogous to human tumors to enable therapeutic studies. In this review, we discuss the process of utilizing genomic sequencing approaches, gene editing technologies, and transgenic porcine cancer models to develop clinically relevant, personalized large animal cancer models for use in co-clinical trials, ultimately improving treatment stratification and translation of novel therapeutic approaches to clinical practice.

Large steel storage tanks designed with long-span structures, employed for storing oil and fuel, have been widely used in many countries over the past twenty years. Most of these tanks are thin-walled cylindrical shells. Owing to the high risk of gas explosions and the resulting deaths, injuries, and economic losses, more thorough damage analyses of these large structures should be conducted. This study examines the structural response of a simplified steel storage tank under a blast impact, as calculated by the LS-DYNA software package. The numerical results are then compared with a scale-model experiment. On that basis, the simplified storage tank prototype, which has a 15 × 104 m3 capacity, is analyzed using numerical simulation. In this study, we address issues around the variation in structural responses—particularly of the failure mode, resultant displacement, structural energy, and dynamic strain under the impact. In addition, we also discuss the effects of varying the internal liquid level, constraint conditions, and blast intensity.

The sensitivity of key structural parameters to the hydraulic response characteristics in an electronic fuel injector is investigated. First, the hydraulic response characteristic is defined in detail (the opening/closing delay and the opening/closing time). Second, the key structural parameters influencing the hydraulic response characteristics are derived. Finally, the importance and effects of key structural parameters on hydraulic response characteristics are examined, by using the design of experiments method and the range analysis. Results show that the fuel inlet passage diameter is the primary influencing factor to the opening delay and closing delay, while the control piston diameter has the dominant effect on opening time and closing time. A small opening delay and a small opening time prefer a little fuel inlet passage diameter and control piston diameter; however, they contribute to a large closing time and closing delay. The fuel outlet passage diameter is the secondary influencing factor in opening delay, but the second factor that affects the opening time is the diameter of needle.

Induced pluripotent stem cells (iPSCs) generated from somatic cells by ectopic expression of reprogramming factors, e.g., POU5F1 (OCT4), KLF4, and SOX2, have great potential for regenerative medicine. However, before they can be used in a clinical setting, the mechanism of reprogramming needs to be better understood. Here, by engineering reprogramming factors to a destabilizing protein domain, we achieved inducible generation of mouse and pig iPSCs. Stability of the fusion protein was precisely regulated by the addition of the cell-permeable small molecule trimethoprim (TMP) in a dose-dependent manner. With these tools, we found that during the early and middle stages of reprogramming, exogenous OCT4 or KLF4 could be omitted, whereas exogenous SOX2 expression at early and middle stages was required for successful reprogramming. Our TMP reprogramming system is useful for defining the stoichiometry and temporal requirements of transcription factors for reprogramming.

A stochastic material point method is proposed for stochastic analysis in non-linear dynamics of metals with varying random material properties. The basic random variables are parameters of equation of state and those of constitutive equation. In conjunction with the material point method, the Taylor series expansion is employed to predict first- and second-moment characteristics of structural response. Unlike the traditional grid methods, the stochastic material point method does not require structured mesh; instead, only a scattered cluster of nodes is required in the computational domain. In addition, there is no need for fixed connectivity between nodes. Hence, the stochastic material point method is more suitable than the stochastic method based on grids, when solving dynamics problems of metals involving large deformations and strong nonlinearity. Numerical examples show good agreement between the results of the stochastic material point method and Monte Carlo simulation. This study examines the accuracy and convergence of the stochastic material point method. The stochastic material point method offers a new option when solving stochastic dynamics problems of metals involving large deformation and strong nonlinearity, since the method is convenient and efficient.