The specificity of the double-stranded RNA(dsRNA) used in the RNA interference(RNAi) technique is crucial for the success of sequence-specific gene silencing. Currently, RNAi-mediated insect control is a trending rese...The specificity of the double-stranded RNA(dsRNA) used in the RNA interference(RNAi) technique is crucial for the success of sequence-specific gene silencing. Currently, RNAi-mediated insect control is a trending research topic.However, the off-target effects of the dsRNA in RNAi are a major concern. In this study, the ds Hvβ’COPI(coat protein complex I, β’ subunit)-treated and untreated transcriptomes of the 28-spotted potato lady beetle(Henosepilachna vigintioctopunctata) were compared to understand its off-target gene silencing effects. The RNA-seq results revealed that 63 and 44 differentially expressed genes(DEGs) were upregulated and downregulated, respectively, in the ds Hvβ’COPI treated group as compared with the control. Validation of the differential expressions of some selected DEGs via reverse transcription-quantitative PCR(RT-qPCR) analysis confirmed the reliability of the transcriptome analysis results. Further downstream analysis revealed that there were no genes homologous with Hvβ’COPI in H. vigintioctopunctata. Additionally,no genes with a >11 bp continuous match with ds Hvβ’COPI were found in the H. vigintioctopunctata transcriptome. Six genes(Hvcitron, Hvhelicase, Hvtransposase, Hvserine, Hvdynein, and Hv E3 ubiquitin) were selected to examine the offtarget activity of ds Hvβ’COPI based on their potential involvement in various H. vigintioctopunctata metabolic pathways.The severity of silencing these six off-target genes was evaluated by employing RNAi. The RNAi results confirmed the downregulation of the expression of all six genes, although there was no significant lethality. The findings of this study will be helpful in the risk analysis of future RNAi-mediated pest control experiments.展开更多
A recent breakthrough in agricultural biotechnology is the introduction of RNAi-mediated strategies in pest control.However, the off-target effects of RNAi pest control are still not fully understood. Here, we studied...A recent breakthrough in agricultural biotechnology is the introduction of RNAi-mediated strategies in pest control.However, the off-target effects of RNAi pest control are still not fully understood. Here, we studied the off-target effects of two insecticidal siRNAs in both target and non-target insects. The results revealed that off-target effects of insecticidal siRNAs occur widely in both target and non-target insects. We classified the expression-changed genes according to their homology to the siRNA-targeted gene, related KEGG pathways with the siRNA-targeted gene and continuous matches with siRNAs. Surprisingly, the unintended significant changes in gene expression levels did not strictly match with the number of contiguous nucleotides in the siRNAs. As expected, the expression of small portions of the homologous and KEGG-related genes were significantly changed. We calculated the Shannon entropy of the transcriptome profile of the insects after injecting them with insecticidal siRNAs. Though hundreds of genes were affected in their expression levels post siRNAtreatment, the Shannon entropy of the transcriptome remained unchanged, suggesting that the transcriptome expression was balanced. Our results provide evidence that siRNAs cross-reacted with individual genes in non-target species, but did not have significant effects on the integrity of the transcriptome profiles in either target or non-target species on a genomic scale. The metric we proposed can be used to estimate the off-target effects of insecticidal siRNAs, which might be useful for evaluating the safety of RNAi in pest control.展开更多
As versatile and robust genome editing tools,clustered regularly interspaced short palindromic repeats(CRISPR)technologies have been broadly used in basic research,biotechnology,and therapeutic development.Off-target ...As versatile and robust genome editing tools,clustered regularly interspaced short palindromic repeats(CRISPR)technologies have been broadly used in basic research,biotechnology,and therapeutic development.Off-target mutagenesis by CRISPR systems has been demonstrated,and various methods have been developed to markedly increase their specificity.In this review,we highlight the efforts of producing and modifying guide RNA(gRNA)to minimize off-target activities,including sequence and structure design,tuning expression and chemical modification.The modalities of gRNA engineering can be applied across CRISPR systems.In conjunction with CRISPR protein effectors,the engineered gRNA enables efficient and precise genome editing.展开更多
CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors.Currently,poor efficiency and off-target problems have impeded the application of ...CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors.Currently,poor efficiency and off-target problems have impeded the application of CRISPR systems.The on-target efficiency has been improved in several advanced versions of CRISPR systems,whereas the off-target detection still remains a key challenge.Here,we outline the different versions of CRISPR systems and off-target detection strategies,discuss the merits and limitations of off-target detection methods,and provide potential implications for further gene editing research.展开更多
DNA is the blueprint of life,instructing the growth,development,and reproduction of an organism.Genome sequencing uncovers the codes of life,whereas genome editing could rewrite the codes,thus then leads to revolution...DNA is the blueprint of life,instructing the growth,development,and reproduction of an organism.Genome sequencing uncovers the codes of life,whereas genome editing could rewrite the codes,thus then leads to revolutionary advances in all aspects of life sciences,such as uncovering regulatory network of life,increasing the production of crops,producing new breeds of livestock,and curing genetic disorders(Liu,2017).展开更多
Site-directed RNA editing(SDRE)is invaluable to basic research and clinical applications and has emerged as a new frontier in genome editing.The past few years have witnessed a surge of interest in SDRE,with SDRE tool...Site-directed RNA editing(SDRE)is invaluable to basic research and clinical applications and has emerged as a new frontier in genome editing.The past few years have witnessed a surge of interest in SDRE,with SDRE tools emerging at a breathtaking pace.However,off-target effects of SDRE remain a tough problem,which constitutes a major hurdle to their clinical applications.Here we discuss the diverse strategies for combating off-target editing,drawing lessons from the published studies as well as our ongoing research.Overall,SDRE is still at its infancy,with significant challenges and exciting opportunities ahead.展开更多
The magnetic proximity effect enables interfacial modulation of excitonic and spin-valley properties in transition metal dichalcogenides(TMDs),offering a versatile route toward next-generation spintronic and valleytro...The magnetic proximity effect enables interfacial modulation of excitonic and spin-valley properties in transition metal dichalcogenides(TMDs),offering a versatile route toward next-generation spintronic and valleytronic devices.However,the inherently weak photoluminescence(PL)of bright excitons—suppressed by proximity-induced darkening mechanisms—hinders the optical detection of magnetic interactions.Here,we demonstrate substantial exciton emission enhancement in CrOCl/WSe_(2)(HS)and twisted 90°-CrOCl/CrOCl/WSe_(2)(THS)heterostructures by employing plasmonic Au nanopillar arrays to activate surface plasmon polariton(SPP)coupling.The neutral exciton emission intensity is enhanced by factors of 5 and 18 for HS/Au and THS/Au,respectively,with enhancements persisting under high magnetic fields and elevated temperatures(~10-fold in THS/Au).Enabled by this amplification,we observe pronounced Zeeman splitting and modified intervalley relaxation pathways,indicating significant magnetic proximity interactions.Finite-element simulations and first-principles calculations reveal that the enhancement arises from local electromagnetic field concentration and layer-dependent interfacial coupling.Our results establish SPP-assisted PL enhancement as an effective strategy for probing weak magneto-optical signatures,paving the way for detailed exploration of exciton-magnon coupling and interface-driven quantum phenomena in twodimensional(2D)magnetic heterostructures.展开更多
Rechargeable Zn/Sn-air batteries have received considerable attention as promising energy storage devices.However,the electrochemical performance of these batteries is significantly constrained by the sluggish electro...Rechargeable Zn/Sn-air batteries have received considerable attention as promising energy storage devices.However,the electrochemical performance of these batteries is significantly constrained by the sluggish electrocatalytic reaction kinetics at the cathode.The integration of light energy into Zn/Sn-air batteries is a promising strategy for enhancing their performance.However,the photothermal and photoelectric effects generate heat in the battery under prolonged solar irradiation,leading to air cathode instability.This paper presents the first design and synthesis of Ni_(2)-1,5-diamino-4,8-dihydroxyanthraquinone(Ni_(2)DDA),an electronically conductiveπ-d conjugated metal-organic framework(MOF).Ni_(2)DDA exhibits both photoelectric and photothermal effects,with an optical band gap of~1.14 eV.Under illumination,Ni_(2)DDA achieves excellent oxygen evolution reaction performance(with an overpotential of 245 mV vs.reversible hydrogen electrode at 10 mA cm^(−2))and photothermal stability.These properties result from the synergy between the photoelectric and photothermal effects of Ni_(2)DDA.Upon integration into Zn/Sn-air batteries,Ni_(2)DDA ensures excellent cycling stability under light and exhibits remarkable performance in high-temperature environments up to 80℃.This study experimentally confirms the stable operation of photo-assisted Zn/Sn-air batteries under high-temperature conditions for the first time and provides novel insights into the application of electronically conductive MOFs in photoelectrocatalysis and photothermal catalysis.展开更多
Beam-tracking simulations have been extensively utilized in the study of collective beam instabilities in circular accelerators.Traditionally,many simulation codes have relied on central processing unit(CPU)-based met...Beam-tracking simulations have been extensively utilized in the study of collective beam instabilities in circular accelerators.Traditionally,many simulation codes have relied on central processing unit(CPU)-based methods,tracking on a single CPU core,or parallelizing the computation across multiple cores via the message passing interface(MPI).Although these approaches work well for single-bunch tracking,scaling them to multiple bunches significantly increases the computational load,which often necessitates the use of a dedicated multi-CPU cluster.To address this challenge,alternative methods leveraging General-Purpose computing on Graphics Processing Units(GPGPU)have been proposed,enabling tracking studies on a standalone desktop personal computer(PC).However,frequent CPU-GPU interactions,including data transfers and synchronization operations during tracking,can introduce communication overheads,potentially reducing the overall effectiveness of GPU-based computations.In this study,we propose a novel approach that eliminates this overhead by performing the entire tracking simulation process exclusively on the GPU,thereby enabling the simultaneous processing of all bunches and their macro-particles.Specifically,we introduce MBTRACK2-CUDA,a Compute Unified Device Architecture(CUDA)ported version of MBTRACK2,which facilitates efficient tracking of single-and multi-bunch collective effects by leveraging the full GPU-resident computation.展开更多
Benzalkonium chloride(BAC)is widely employed as a broad-spectrum biocide and has emerged as a significant environmental pollutant.Polymyxin B(PB)serves as the last-line defense for the treatment of Gram-negative patho...Benzalkonium chloride(BAC)is widely employed as a broad-spectrum biocide and has emerged as a significant environmental pollutant.Polymyxin B(PB)serves as the last-line defense for the treatment of Gram-negative pathogens.Previous studies reported that BAC-adapted Pseudomonas aeruginosa increased the tolerance to PB.Herein,we present the novel finding that the combination of BAC and PB exhibited synergistic antibacterial effects against P.aeruginosa.Time-killing assay demonstrated a significant reduction in bacterial cell viability.Scanning electron microscopy,zeta potential analysis,hydrophobicity measurements,and fluorescence probe analyses collectively revealed severe disruption of the cell envelope and membrane potential induced by the combination of BAC and PB.Transcriptomic analysis revealed that the BAC-PB combination notably downreg-ulated the expression of genes involved in lipid A modification and cell envelope production,including phoPQ,pmrAB,bamABCDE,lptABCDEG,lolB,yidC,and murJ.Additionally,the combination group exhibited augmented production of reactive oxygen species and diminished ATP synthesis.The expression of the genes associated with substance metabolism and energy generation was significantly impeded.This study provides significant implica-tions for the interactions of biocides and antibiotics on Gram-negative pathogens,while also addressing antibiotic resistance and developing the external treatment strategy for Pseudomonas-infected wounds and burns.展开更多
AIM:To evaluate and compare alterations in the effective lens position(ELP)and refractive outcomes among three distinct intraocular lens(IOL)types.METHODS:Patients with cataracts were enrolled and allocated to 3 group...AIM:To evaluate and compare alterations in the effective lens position(ELP)and refractive outcomes among three distinct intraocular lens(IOL)types.METHODS:Patients with cataracts were enrolled and allocated to 3 groups:Group A(implanted with the SN6CWS),Group B(implanted with the MI60),and Group C(implanted with the Aspira-aA).ELP measurements were obtained with swept-source optical coherence tomography(SS-OCT)at 1d,1wk,1mo,and 3mo postoperatively.Subjective refraction assessments were conducted at 1wk,1mo,and 3mo following surgery.RESULTS:The study included 189 eyes of 150 cataract patients(66 males).There were 77 eyes in Group A,55 eyes in Group B,and 57 eyes in Group C.The root mean square of the ELP(ELPRMS)within the initial 3mo was significantly lower for Group A than for Groups B and C.Refractive changes within Group A were not significant across the time points of 1wk,1mo,and 3mo.Conversely,both Group B and Group C demonstrated statistically significant shifts toward hyperopia from 1wk to 3mo postsurgery.CONCLUSION:Among the three IOLs examined,the SN6CWS IOL showes the greatest stability during the first 3mo postoperatively.Between 1wk and 3mo after surgery,notable hyperopic shifts are evident in eyes implanted with the MI60 and Aspira-aA IOLs,whereas refractive outcomes remain relatively constant in eyes implanted with SN6CWS IOLs.展开更多
Electrical and electronic devices face significant challenges in heatmanagement due to their compact size and high heat flux,which negatively impact performance and reliability.Conventional coolingmethods,such as forc...Electrical and electronic devices face significant challenges in heatmanagement due to their compact size and high heat flux,which negatively impact performance and reliability.Conventional coolingmethods,such as forced air cooling,often struggle to transfer heat efficiently.In contrast,thermoelectric coolers(TECs)provide an innovative active cooling solution to meet growing thermal management demands.In this research,a refrigerant based on mono ethylene glycol and distilled water was used instead of using gases,in addition to using thermoelectric cooling units instead of using a compressor in traditional refrigeration systems.This study evaluates the performance of a Peltierbased thermalmanagement systemby analyzing the effects of using two,three,and four Peltiermodules on cooling rates,power consumption,temperature reduction,and system efficiency.Experimental results indicate that increasing the number of Peltier modules significantly enhances cooling performance.The four-module system achieved an optimal balance between cooling speed and energy efficiency,reducing the temperature of a liquidmixture(30% mono ethylene glycol+70% distilled water plus laser dyes)to 8℃ in just 17 min.It demonstrated a cooling rate of 0.794℃/min and a high coefficient of performance(COP)of 1.2 while consuming less energy than the two-and three-module systems.Furthermore,the study revealed that increasing the number of modules led to faster air cooling and improved temperature reduction.These findings highlight the importance of selecting the optimal number of Peltier modules to enhance efficiency and cooling speed whileminimizing energy consumption.This makes TEC technology a sustainable and effective solution for applications requiring rapid and reliable thermal management.展开更多
The magnetic properties and Kondo effect in Ce3TiBi5 with a quasi-one-dimensional structure were investigated using in situ high-pressure resistivity measurements up to 48 GPa.At ambient pressure,Ce_(3)TiBi_(5) underg...The magnetic properties and Kondo effect in Ce3TiBi5 with a quasi-one-dimensional structure were investigated using in situ high-pressure resistivity measurements up to 48 GPa.At ambient pressure,Ce_(3)TiBi_(5) undergoes an antiferromagnetic(AFM)transition at T_(N)∼5 K.Under high pressures within 8.9 GPa,we find that Kondo scattering contributes differently to the high-temperature resistance,R(T),depending on the applied current direction,demonstrating a significantly anisotropic Kondo effect.The complete P–T phase diagram has been constructed,in which the pressure dependence of T_(N) exhibits a dome-like shape.The AFM order remains robust under pressure,even when the coherence temperature T^(*) far exceeds 300 K.We attribute the observed anisotropic Kondo effect and the robust AFM to the underlying anisotropy in electronic hybridization under high pressure.展开更多
In winter 2018,an aerosol physicochemical experiment was conducted in the Western Pacific Ocean(WPO)aboard the Research Vessel KEXUE of Chinese Academy of Sciences.This study systematically investigated both natural a...In winter 2018,an aerosol physicochemical experiment was conducted in the Western Pacific Ocean(WPO)aboard the Research Vessel KEXUE of Chinese Academy of Sciences.This study systematically investigated both natural and anthropogenic effects on marine aerosols optical properties,as well as the applicability of multi-satellite products and IMPROVE equation.The averaged aerosol optical depth(AOD500 nm)was 0.31±0.16 andÅngström exponent440–675 nm was 0.29±0.30.In offshore China,significant anthropogenic emissions affected the marine environment.In remote WPO,dust aerosols transported from northern China,Siberia,Central Asia,and those settling from the upper troposphere originating from north Africa,Arabian peninsula,and western India,were dominant.The spatial trends of AOD were opposite in the mid-latitude and southern seas of WPO.The highest AOD,0.32±0.23,appeared along the coast of South Asia at mid-latitude,decreasing from offshore seas to remote oceans.In low-latitude and equatorial seas,AOD significantly increased from coast to remote oceans.Ångström exponent dropped significantly from the coast to remote oceans as anthropogenic influence diminished across the entire WPO.Correlation analysis showed that both MODIS-C6 and Himawari AOD prod-ucts showed similar applicability in coastal urban areas,while Himawari AOD is highly recommended for coastal background and marine environment due to its finer resolution.The extinction coefficient derived from PM_(2.5) chemical compositions using IMPROVE algorithm exhibited a significant correlation(R^(2)=0.58)with the con-currently measured AOD in the absence of long-distance transport,suggesting that the IMPROVE is a reasonable proxy of the columnar average of marine aerosol extinctions free from transport influences.展开更多
This paper prepared a novel as-cast W-Zr-Ti metallic ESM using high-frequency vacuum induction melting technique.The above ESM performs a typical elastic-brittle material feature and strain rate strengthening behavior...This paper prepared a novel as-cast W-Zr-Ti metallic ESM using high-frequency vacuum induction melting technique.The above ESM performs a typical elastic-brittle material feature and strain rate strengthening behavior.The specimens exhibit violent chemical reaction during the fracture process under the impact loading,and the size distribution of their residual debris follows Rosin-Rammler model.The dynamic fracture toughness is obtained by the fitting of debris length scale,approximately 1.87 MPa·m~(1/2).Microstructure observation on residual debris indicates that the failure process is determined by primary crack propagation under quasi-static compression,while it is affected by multiple cracks propagation in both particle and matrix in the case of dynamic impact.Impact test demonstrates that the novel energetic fragment performs brilliant penetration and combustion effect behind the front target,leading to the effective ignition of fuel tank.For the brittleness of as-cast W-ZrTi ESM,further study conducted bond-based peridynamic(BB-PD)C++computational code to simulate its fracture behavior during penetration.The BB-PD method successfully captured the fracture process and debris cloud formation of the energetic fragment.This paper explores a novel as-cast metallic ESM,and provides an available numerical avenue to the simulation of brittle energetic fragment.展开更多
Background:While the treatment of metastatic renal cell carcinoma(mRCC)is evolving due to immune checkpoint inhibitors(ICIs),optimal strategies for later lines of therapy have yet to be defined.The combination of lenv...Background:While the treatment of metastatic renal cell carcinoma(mRCC)is evolving due to immune checkpoint inhibitors(ICIs),optimal strategies for later lines of therapy have yet to be defined.The combination of lenvatinib and everolimus represents a viable option,and the present review aimed to summarize its activity,effectiveness,and safety.Methods:A systematic review of the literature was conducted using PubMed,targeting studies published between 2018 and 2025.Eligible studies included English-language prospective and retrospective trials reporting survival outcomes in mRCC patients treated with lenvatinib and everolimus after at least one ICI-containing regimen.Results:Nine studies met the inclusion criteria,encompassing a total of 441 patients.The lenvatinib and everolimus combination was primarily used in the third and subsequent lines of therapy.Median overall survival ranged from 7.5 to 24.5 months,while median progression-free survival was more consistent,between 6.1 and 6.7 months,except for one study reporting 12.9 months.Objective response rates varied widely(14.0%–55.7%).Adverse events of grade≥3 did not exceed the expected rate,with diarrhoea and proteinuria as the most reported events.Dose reductions and treatment discontinuations due to toxicity occurred but were generally lower than in prior pivotal trials.Conclusions:Real-world evidence suggests that lenvatinib and everolimus represent an effective and safe option after ICI failure in mRCC patients.Nevertheless,the lack of randomized phase III trials and the heterogeneity of existing studies highlight the need for more robust prospective research to guide post-ICI therapeutic strategies.展开更多
Lithium metal batteries(LMBs)have been regarded as one of the most promising alternatives in the post-lithium battery era due to their high energy density,which meets the needs of light-weight electronic devices and l...Lithium metal batteries(LMBs)have been regarded as one of the most promising alternatives in the post-lithium battery era due to their high energy density,which meets the needs of light-weight electronic devices and long-range electric vehicles.However,technical barriers such as dendrite growth and poor Li plating/stripping reversibility severely hinder the practical application of LMBs.However,lithium nitrate(LiNO_(3))is found to be able to stabilize the Li/electrolyte interface and has been used to address the above challenges.To date,considerable research efforts have been devoted toward understanding the roles of LiNO_(3) in regulating the surface properties of Li anodes and toward the development of many effective strategies.These research efforts are partially mentioned in some articles on LMBs and yet have not been reviewed systematically.To fill this gap,we discuss the recent advances in fundamental and technological research on LiNO_(3) and its derivatives for improving the performances of LMBs,particularly for Li-sulfur(S),Li-oxygen(O),and Li-Li-containing transition-metal oxide(LTMO)batteries,as well as LiNO_(3)-containing recipes for precursors in battery materials and interphase fabrication.This review pays attention to the effects of LiNO_(3) in lithium-based batteries,aiming to provide scientific guidance for the optimization of electrode/electrolyte interfaces and enrich the design of advanced LMBs.展开更多
Bacille Calmette-Guérin(BCG)vaccine is designed to provide protection against tuberculosis(TB).However,numerous epidemiological,clinical,and immunological studies have shown that BCG vaccination affects neonatal ...Bacille Calmette-Guérin(BCG)vaccine is designed to provide protection against tuberculosis(TB).However,numerous epidemiological,clinical,and immunological studies have shown that BCG vaccination affects neonatal and infant mortality,which may be related to the reduction of TB-unrelated infections and diseases by BCG vaccine.We aimed to discuss the off-target effects of BCG vaccine on un-TB infections and diseases,as well as the potential mechanism and influencing factors.Literature was retrieved mainly from PubMed using medical subject headings"BCG,variations,and non-specific,heterologous or off-target".Studies have showed that BCG vaccination can prevent various heterologous infections,including respiratory tract infections,leprosy,and malaria,treat viral infections including human papillomavirus and herpes simplex virus infection as immunotherapy,and improve the immune responses as vaccine adjuvant.Besides,BCG vaccine can reduce the recurrence rate of non-muscle-invasive bladder cancer,and may provide protection against autoimmune diseases.These off-target effects of BCG vaccine are thought to be achieved by modulating heterologous lymphocyte responses or inducing trained immunity,which were found to be sex-differentiated and affected by the BCG vaccine strains,sequence or time of vaccination.展开更多
Small interfering RNA(siRNA)is often used for function study and expression regulation of specific genes,as well as the development of small molecule drugs.Selecting siRNAs with high inhibition and low off-target effe...Small interfering RNA(siRNA)is often used for function study and expression regulation of specific genes,as well as the development of small molecule drugs.Selecting siRNAs with high inhibition and low off-target effects from massive can-didates is always a great challenge.Increasing experimentally-validated samples can prompt the development of machine-learning-based algorithms,including Support Vector Machine(SVM),Convolutional Neural Network(CNN),and Graph Neural Network(GNN).However,these methods still suffer from limited accuracy and poor generalization in designing potent and specific siRNAs.In this study,we propose a novel approach for siRNA inhibition and off-target effect prediction,named AttSiOff.It combines a self-attention-based siRNA inhibition predictor with an mRNA searching package and an off-target filter.The predictor gives the inhibition score via analyzing the embedding of siRNA and local mRNA sequences,generated from the pre-trained RNA-FM model,as well as other meaningful prior-knowledge-based features.Self-attention mechanism can detect potentially decisive features,which may determine the inhibition of siRNA.It captures global and local dependencies more efficiently than normal convolutions.The tenfold cross-validation results indicate that our model outperforms all existing methods,achieving PCC of 0.81,SPCC of 0.84,and AUC of 0.886.It also reaches better performance of generalization and robustness on cross-dataset validation.In addition,the mRNA searching package could find all mature mRNAs for a given gene name from the GENOMES database,and the off-target filter can calculate the amount of unwanted off-target binding sites,which affects the specificity of siRNA.Experiments on five mature siRNA drugs,as well as a new target gene(AGT),show that AttSioff has excellent convenience and operability in practical applications.展开更多
Targeted genome modifications with the Cas9/gRNA system derived from the clustered regularly interspaced short palin- dromic repeat/CRISPR-associated （CRISPR/Cas） system have been successfully used in cultured human...Targeted genome modifications with the Cas9/gRNA system derived from the clustered regularly interspaced short palin- dromic repeat/CRISPR-associated （CRISPR/Cas） system have been successfully used in cultured human cells as well as in most model organisms, including zebrafish （Danio rerio）, mouse, and fruit fly （Chang et al., 2013; Cong et al., 2013; Gratz et al., 2013; Hwang et al., 2013; Jao et al., 2013; Shen et al., 2013; Wei et al., 2013）. Its application in zebrafish is particu- larly attractive due to the ease of handling this organism and the simple application of this method by direct injection of Cas9/ gRNA. However, the information about its specificity in this organism is very limited and needs further evaluation. In addition, it is conceivable that a Cas9 mRNA optimized for zebrafish codon preference could enhance its activity.展开更多
基金supported by the National Natural Science Foundation of China(31972269 and 32172500)the National Key R&D Program of China(2017YFD0200900)。
文摘The specificity of the double-stranded RNA(dsRNA) used in the RNA interference(RNAi) technique is crucial for the success of sequence-specific gene silencing. Currently, RNAi-mediated insect control is a trending research topic.However, the off-target effects of the dsRNA in RNAi are a major concern. In this study, the ds Hvβ’COPI(coat protein complex I, β’ subunit)-treated and untreated transcriptomes of the 28-spotted potato lady beetle(Henosepilachna vigintioctopunctata) were compared to understand its off-target gene silencing effects. The RNA-seq results revealed that 63 and 44 differentially expressed genes(DEGs) were upregulated and downregulated, respectively, in the ds Hvβ’COPI treated group as compared with the control. Validation of the differential expressions of some selected DEGs via reverse transcription-quantitative PCR(RT-qPCR) analysis confirmed the reliability of the transcriptome analysis results. Further downstream analysis revealed that there were no genes homologous with Hvβ’COPI in H. vigintioctopunctata. Additionally,no genes with a >11 bp continuous match with ds Hvβ’COPI were found in the H. vigintioctopunctata transcriptome. Six genes(Hvcitron, Hvhelicase, Hvtransposase, Hvserine, Hvdynein, and Hv E3 ubiquitin) were selected to examine the offtarget activity of ds Hvβ’COPI based on their potential involvement in various H. vigintioctopunctata metabolic pathways.The severity of silencing these six off-target genes was evaluated by employing RNAi. The RNAi results confirmed the downregulation of the expression of all six genes, although there was no significant lethality. The findings of this study will be helpful in the risk analysis of future RNAi-mediated pest control experiments.
基金funded by grants from the National Science and Technology Major Project of China(2016ZX08011002)。
文摘A recent breakthrough in agricultural biotechnology is the introduction of RNAi-mediated strategies in pest control.However, the off-target effects of RNAi pest control are still not fully understood. Here, we studied the off-target effects of two insecticidal siRNAs in both target and non-target insects. The results revealed that off-target effects of insecticidal siRNAs occur widely in both target and non-target insects. We classified the expression-changed genes according to their homology to the siRNA-targeted gene, related KEGG pathways with the siRNA-targeted gene and continuous matches with siRNAs. Surprisingly, the unintended significant changes in gene expression levels did not strictly match with the number of contiguous nucleotides in the siRNAs. As expected, the expression of small portions of the homologous and KEGG-related genes were significantly changed. We calculated the Shannon entropy of the transcriptome profile of the insects after injecting them with insecticidal siRNAs. Though hundreds of genes were affected in their expression levels post siRNAtreatment, the Shannon entropy of the transcriptome remained unchanged, suggesting that the transcriptome expression was balanced. Our results provide evidence that siRNAs cross-reacted with individual genes in non-target species, but did not have significant effects on the integrity of the transcriptome profiles in either target or non-target species on a genomic scale. The metric we proposed can be used to estimate the off-target effects of insecticidal siRNAs, which might be useful for evaluating the safety of RNAi in pest control.
基金supported by the National Key Research and Development Program of China(2018YFA0801401 and 2019YFA0802801)the National Natural Science Foundation of China 31871345+1 种基金the Young Thousand Talented Program from Wuhan Universitythe startup funding from Wuhan University to H.Y.
文摘As versatile and robust genome editing tools,clustered regularly interspaced short palindromic repeats(CRISPR)technologies have been broadly used in basic research,biotechnology,and therapeutic development.Off-target mutagenesis by CRISPR systems has been demonstrated,and various methods have been developed to markedly increase their specificity.In this review,we highlight the efforts of producing and modifying guide RNA(gRNA)to minimize off-target activities,including sequence and structure design,tuning expression and chemical modification.The modalities of gRNA engineering can be applied across CRISPR systems.In conjunction with CRISPR protein effectors,the engineered gRNA enables efficient and precise genome editing.
基金supported by the grants 81771230(W.C.),31922048(E.Z.)and 31522037(H.Y.)from the National Natural Science Foundation of China.
文摘CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors.Currently,poor efficiency and off-target problems have impeded the application of CRISPR systems.The on-target efficiency has been improved in several advanced versions of CRISPR systems,whereas the off-target detection still remains a key challenge.Here,we outline the different versions of CRISPR systems and off-target detection strategies,discuss the merits and limitations of off-target detection methods,and provide potential implications for further gene editing research.
基金supported by the National Key R&D Program of China(2017YFC1001901)the National Natural Science Foundation(31971365 and 31601196)the Guangzhou Science and Technology Project(201803010020 and 201707010085).
文摘DNA is the blueprint of life,instructing the growth,development,and reproduction of an organism.Genome sequencing uncovers the codes of life,whereas genome editing could rewrite the codes,thus then leads to revolutionary advances in all aspects of life sciences,such as uncovering regulatory network of life,increasing the production of crops,producing new breeds of livestock,and curing genetic disorders(Liu,2017).
基金supported by the start-up package of the ShanghaiTech University.
文摘Site-directed RNA editing(SDRE)is invaluable to basic research and clinical applications and has emerged as a new frontier in genome editing.The past few years have witnessed a surge of interest in SDRE,with SDRE tools emerging at a breathtaking pace.However,off-target effects of SDRE remain a tough problem,which constitutes a major hurdle to their clinical applications.Here we discuss the diverse strategies for combating off-target editing,drawing lessons from the published studies as well as our ongoing research.Overall,SDRE is still at its infancy,with significant challenges and exciting opportunities ahead.
基金the National Natural Science Foundation of China(No.52373311)the Innovation Program for Quantum Science and Technology(No.2021ZD0301605)+3 种基金provided by the National Natural Science Foundation of China(Nos.92263202 and 12374020)the National Key Research and Development Program of China(No.2020YFA0711502)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB33000000)support from the Australian Research Council(ARC Discovery Project,No.DP180102976).
文摘The magnetic proximity effect enables interfacial modulation of excitonic and spin-valley properties in transition metal dichalcogenides(TMDs),offering a versatile route toward next-generation spintronic and valleytronic devices.However,the inherently weak photoluminescence(PL)of bright excitons—suppressed by proximity-induced darkening mechanisms—hinders the optical detection of magnetic interactions.Here,we demonstrate substantial exciton emission enhancement in CrOCl/WSe_(2)(HS)and twisted 90°-CrOCl/CrOCl/WSe_(2)(THS)heterostructures by employing plasmonic Au nanopillar arrays to activate surface plasmon polariton(SPP)coupling.The neutral exciton emission intensity is enhanced by factors of 5 and 18 for HS/Au and THS/Au,respectively,with enhancements persisting under high magnetic fields and elevated temperatures(~10-fold in THS/Au).Enabled by this amplification,we observe pronounced Zeeman splitting and modified intervalley relaxation pathways,indicating significant magnetic proximity interactions.Finite-element simulations and first-principles calculations reveal that the enhancement arises from local electromagnetic field concentration and layer-dependent interfacial coupling.Our results establish SPP-assisted PL enhancement as an effective strategy for probing weak magneto-optical signatures,paving the way for detailed exploration of exciton-magnon coupling and interface-driven quantum phenomena in twodimensional(2D)magnetic heterostructures.
基金supported by the National Natural Science Foundation of China(No.62464010)Spring City Plan-Special Program for Young Talents(K202005007)+2 种基金Yunnan Talents Support Plan for Young Talents(XDYC-QNRC-2022-0482)Yunnan Local Colleges Applied Basic Research Projects(202101BA070001-138)Frontier Research Team of Kunming University 2023.
文摘Rechargeable Zn/Sn-air batteries have received considerable attention as promising energy storage devices.However,the electrochemical performance of these batteries is significantly constrained by the sluggish electrocatalytic reaction kinetics at the cathode.The integration of light energy into Zn/Sn-air batteries is a promising strategy for enhancing their performance.However,the photothermal and photoelectric effects generate heat in the battery under prolonged solar irradiation,leading to air cathode instability.This paper presents the first design and synthesis of Ni_(2)-1,5-diamino-4,8-dihydroxyanthraquinone(Ni_(2)DDA),an electronically conductiveπ-d conjugated metal-organic framework(MOF).Ni_(2)DDA exhibits both photoelectric and photothermal effects,with an optical band gap of~1.14 eV.Under illumination,Ni_(2)DDA achieves excellent oxygen evolution reaction performance(with an overpotential of 245 mV vs.reversible hydrogen electrode at 10 mA cm^(−2))and photothermal stability.These properties result from the synergy between the photoelectric and photothermal effects of Ni_(2)DDA.Upon integration into Zn/Sn-air batteries,Ni_(2)DDA ensures excellent cycling stability under light and exhibits remarkable performance in high-temperature environments up to 80℃.This study experimentally confirms the stable operation of photo-assisted Zn/Sn-air batteries under high-temperature conditions for the first time and provides novel insights into the application of electronically conductive MOFs in photoelectrocatalysis and photothermal catalysis.
基金supported by the National Research Foundation of Korea(NRF)funded by the Ministry of Science and ICT(MSIT)(No.RS-2022-00143178)the Ministry of Education(MOE)(Nos.2022R1A6A3A13053896 and 2022R1F1A1074616),Republic of Korea.
文摘Beam-tracking simulations have been extensively utilized in the study of collective beam instabilities in circular accelerators.Traditionally,many simulation codes have relied on central processing unit(CPU)-based methods,tracking on a single CPU core,or parallelizing the computation across multiple cores via the message passing interface(MPI).Although these approaches work well for single-bunch tracking,scaling them to multiple bunches significantly increases the computational load,which often necessitates the use of a dedicated multi-CPU cluster.To address this challenge,alternative methods leveraging General-Purpose computing on Graphics Processing Units(GPGPU)have been proposed,enabling tracking studies on a standalone desktop personal computer(PC).However,frequent CPU-GPU interactions,including data transfers and synchronization operations during tracking,can introduce communication overheads,potentially reducing the overall effectiveness of GPU-based computations.In this study,we propose a novel approach that eliminates this overhead by performing the entire tracking simulation process exclusively on the GPU,thereby enabling the simultaneous processing of all bunches and their macro-particles.Specifically,we introduce MBTRACK2-CUDA,a Compute Unified Device Architecture(CUDA)ported version of MBTRACK2,which facilitates efficient tracking of single-and multi-bunch collective effects by leveraging the full GPU-resident computation.
基金supported by the National Natural Science Foundation of China(No.32170121).
文摘Benzalkonium chloride(BAC)is widely employed as a broad-spectrum biocide and has emerged as a significant environmental pollutant.Polymyxin B(PB)serves as the last-line defense for the treatment of Gram-negative pathogens.Previous studies reported that BAC-adapted Pseudomonas aeruginosa increased the tolerance to PB.Herein,we present the novel finding that the combination of BAC and PB exhibited synergistic antibacterial effects against P.aeruginosa.Time-killing assay demonstrated a significant reduction in bacterial cell viability.Scanning electron microscopy,zeta potential analysis,hydrophobicity measurements,and fluorescence probe analyses collectively revealed severe disruption of the cell envelope and membrane potential induced by the combination of BAC and PB.Transcriptomic analysis revealed that the BAC-PB combination notably downreg-ulated the expression of genes involved in lipid A modification and cell envelope production,including phoPQ,pmrAB,bamABCDE,lptABCDEG,lolB,yidC,and murJ.Additionally,the combination group exhibited augmented production of reactive oxygen species and diminished ATP synthesis.The expression of the genes associated with substance metabolism and energy generation was significantly impeded.This study provides significant implica-tions for the interactions of biocides and antibiotics on Gram-negative pathogens,while also addressing antibiotic resistance and developing the external treatment strategy for Pseudomonas-infected wounds and burns.
基金Supported by the Zhejiang Medical Health Science and Technology Project(No.2021KY217)the Basic Public Welfare Research Project of Wenzhou Municipal Science and Technology Bureau(No.2024Y1221).
文摘AIM:To evaluate and compare alterations in the effective lens position(ELP)and refractive outcomes among three distinct intraocular lens(IOL)types.METHODS:Patients with cataracts were enrolled and allocated to 3 groups:Group A(implanted with the SN6CWS),Group B(implanted with the MI60),and Group C(implanted with the Aspira-aA).ELP measurements were obtained with swept-source optical coherence tomography(SS-OCT)at 1d,1wk,1mo,and 3mo postoperatively.Subjective refraction assessments were conducted at 1wk,1mo,and 3mo following surgery.RESULTS:The study included 189 eyes of 150 cataract patients(66 males).There were 77 eyes in Group A,55 eyes in Group B,and 57 eyes in Group C.The root mean square of the ELP(ELPRMS)within the initial 3mo was significantly lower for Group A than for Groups B and C.Refractive changes within Group A were not significant across the time points of 1wk,1mo,and 3mo.Conversely,both Group B and Group C demonstrated statistically significant shifts toward hyperopia from 1wk to 3mo postsurgery.CONCLUSION:Among the three IOLs examined,the SN6CWS IOL showes the greatest stability during the first 3mo postoperatively.Between 1wk and 3mo after surgery,notable hyperopic shifts are evident in eyes implanted with the MI60 and Aspira-aA IOLs,whereas refractive outcomes remain relatively constant in eyes implanted with SN6CWS IOLs.
文摘Electrical and electronic devices face significant challenges in heatmanagement due to their compact size and high heat flux,which negatively impact performance and reliability.Conventional coolingmethods,such as forced air cooling,often struggle to transfer heat efficiently.In contrast,thermoelectric coolers(TECs)provide an innovative active cooling solution to meet growing thermal management demands.In this research,a refrigerant based on mono ethylene glycol and distilled water was used instead of using gases,in addition to using thermoelectric cooling units instead of using a compressor in traditional refrigeration systems.This study evaluates the performance of a Peltierbased thermalmanagement systemby analyzing the effects of using two,three,and four Peltiermodules on cooling rates,power consumption,temperature reduction,and system efficiency.Experimental results indicate that increasing the number of Peltier modules significantly enhances cooling performance.The four-module system achieved an optimal balance between cooling speed and energy efficiency,reducing the temperature of a liquidmixture(30% mono ethylene glycol+70% distilled water plus laser dyes)to 8℃ in just 17 min.It demonstrated a cooling rate of 0.794℃/min and a high coefficient of performance(COP)of 1.2 while consuming less energy than the two-and three-module systems.Furthermore,the study revealed that increasing the number of modules led to faster air cooling and improved temperature reduction.These findings highlight the importance of selecting the optimal number of Peltier modules to enhance efficiency and cooling speed whileminimizing energy consumption.This makes TEC technology a sustainable and effective solution for applications requiring rapid and reliable thermal management.
基金supported by the National Key Research and Development Program of Chinathe National Natural Science Foundation of China (Grant Nos.2024YFA1408000,12474097,and2023YFA1406001)+2 种基金the Guangdong Provincial Quantum Science Strategic Initiative (Grant No.GDZX2201001)the Center for Computational Science and Engineering at Southern University of Science and Technology,the Major Science and Technology Infrastructure Project of Material Genome Big-science Facilities Platform supported by Municipal Development and Reform Commission of Shenzhen(for J.L.Z.and Y.L.)the Chinese funding sources applied via HPSTAR。
文摘The magnetic properties and Kondo effect in Ce3TiBi5 with a quasi-one-dimensional structure were investigated using in situ high-pressure resistivity measurements up to 48 GPa.At ambient pressure,Ce_(3)TiBi_(5) undergoes an antiferromagnetic(AFM)transition at T_(N)∼5 K.Under high pressures within 8.9 GPa,we find that Kondo scattering contributes differently to the high-temperature resistance,R(T),depending on the applied current direction,demonstrating a significantly anisotropic Kondo effect.The complete P–T phase diagram has been constructed,in which the pressure dependence of T_(N) exhibits a dome-like shape.The AFM order remains robust under pressure,even when the coherence temperature T^(*) far exceeds 300 K.We attribute the observed anisotropic Kondo effect and the robust AFM to the underlying anisotropy in electronic hybridization under high pressure.
基金supported by the CAS Strategic Priority Research Program(No.XDB0760102),the Ministry of Science and Technology of China(No.2022YFF0802501)the Major Science and Technology Infrastructure Maintenance and Transformation Project of the Chinese Academy of Sciences,Shanghai Science and Technology Innovation Action Plan-Phospherus Project(No.23YF1426200)the National Key Research and Development Program of China(No.2024YFE0212200).
文摘In winter 2018,an aerosol physicochemical experiment was conducted in the Western Pacific Ocean(WPO)aboard the Research Vessel KEXUE of Chinese Academy of Sciences.This study systematically investigated both natural and anthropogenic effects on marine aerosols optical properties,as well as the applicability of multi-satellite products and IMPROVE equation.The averaged aerosol optical depth(AOD500 nm)was 0.31±0.16 andÅngström exponent440–675 nm was 0.29±0.30.In offshore China,significant anthropogenic emissions affected the marine environment.In remote WPO,dust aerosols transported from northern China,Siberia,Central Asia,and those settling from the upper troposphere originating from north Africa,Arabian peninsula,and western India,were dominant.The spatial trends of AOD were opposite in the mid-latitude and southern seas of WPO.The highest AOD,0.32±0.23,appeared along the coast of South Asia at mid-latitude,decreasing from offshore seas to remote oceans.In low-latitude and equatorial seas,AOD significantly increased from coast to remote oceans.Ångström exponent dropped significantly from the coast to remote oceans as anthropogenic influence diminished across the entire WPO.Correlation analysis showed that both MODIS-C6 and Himawari AOD prod-ucts showed similar applicability in coastal urban areas,while Himawari AOD is highly recommended for coastal background and marine environment due to its finer resolution.The extinction coefficient derived from PM_(2.5) chemical compositions using IMPROVE algorithm exhibited a significant correlation(R^(2)=0.58)with the con-currently measured AOD in the absence of long-distance transport,suggesting that the IMPROVE is a reasonable proxy of the columnar average of marine aerosol extinctions free from transport influences.
文摘This paper prepared a novel as-cast W-Zr-Ti metallic ESM using high-frequency vacuum induction melting technique.The above ESM performs a typical elastic-brittle material feature and strain rate strengthening behavior.The specimens exhibit violent chemical reaction during the fracture process under the impact loading,and the size distribution of their residual debris follows Rosin-Rammler model.The dynamic fracture toughness is obtained by the fitting of debris length scale,approximately 1.87 MPa·m~(1/2).Microstructure observation on residual debris indicates that the failure process is determined by primary crack propagation under quasi-static compression,while it is affected by multiple cracks propagation in both particle and matrix in the case of dynamic impact.Impact test demonstrates that the novel energetic fragment performs brilliant penetration and combustion effect behind the front target,leading to the effective ignition of fuel tank.For the brittleness of as-cast W-ZrTi ESM,further study conducted bond-based peridynamic(BB-PD)C++computational code to simulate its fracture behavior during penetration.The BB-PD method successfully captured the fracture process and debris cloud formation of the energetic fragment.This paper explores a novel as-cast metallic ESM,and provides an available numerical avenue to the simulation of brittle energetic fragment.
文摘Background:While the treatment of metastatic renal cell carcinoma(mRCC)is evolving due to immune checkpoint inhibitors(ICIs),optimal strategies for later lines of therapy have yet to be defined.The combination of lenvatinib and everolimus represents a viable option,and the present review aimed to summarize its activity,effectiveness,and safety.Methods:A systematic review of the literature was conducted using PubMed,targeting studies published between 2018 and 2025.Eligible studies included English-language prospective and retrospective trials reporting survival outcomes in mRCC patients treated with lenvatinib and everolimus after at least one ICI-containing regimen.Results:Nine studies met the inclusion criteria,encompassing a total of 441 patients.The lenvatinib and everolimus combination was primarily used in the third and subsequent lines of therapy.Median overall survival ranged from 7.5 to 24.5 months,while median progression-free survival was more consistent,between 6.1 and 6.7 months,except for one study reporting 12.9 months.Objective response rates varied widely(14.0%–55.7%).Adverse events of grade≥3 did not exceed the expected rate,with diarrhoea and proteinuria as the most reported events.Dose reductions and treatment discontinuations due to toxicity occurred but were generally lower than in prior pivotal trials.Conclusions:Real-world evidence suggests that lenvatinib and everolimus represent an effective and safe option after ICI failure in mRCC patients.Nevertheless,the lack of randomized phase III trials and the heterogeneity of existing studies highlight the need for more robust prospective research to guide post-ICI therapeutic strategies.
基金supported by the Yunnan Fundamental Research Projects(Grant Nos.202401AU070163 and 202501AT070298)the Yunnan Engineering Research Center Innovation Ability Construction and Enhancement Projects(Grant No.2023-XMDJ-00617107)+5 种基金the University Service Key Industry Project of Yunnan Province(Grant No.FWCY-ZD2024005)the Expert Workstation Support Project of Yunnan Province(Grant No.202405AF140069)the Scientific Research Foundation of Kunming University of Science and Technology(Grant No.20220122)the Analysis and Test Foundation of Kunming University of Science and Technology(Grant No.2023T20220122)the Natural Science Foundation of Inner Mongolia Autonomous Region of China(Grant No.2025QN02057)the Ordos City Strategic Pioneering Science and Technology Special Program for New Energy(Grant No.DC2400003365).
文摘Lithium metal batteries(LMBs)have been regarded as one of the most promising alternatives in the post-lithium battery era due to their high energy density,which meets the needs of light-weight electronic devices and long-range electric vehicles.However,technical barriers such as dendrite growth and poor Li plating/stripping reversibility severely hinder the practical application of LMBs.However,lithium nitrate(LiNO_(3))is found to be able to stabilize the Li/electrolyte interface and has been used to address the above challenges.To date,considerable research efforts have been devoted toward understanding the roles of LiNO_(3) in regulating the surface properties of Li anodes and toward the development of many effective strategies.These research efforts are partially mentioned in some articles on LMBs and yet have not been reviewed systematically.To fill this gap,we discuss the recent advances in fundamental and technological research on LiNO_(3) and its derivatives for improving the performances of LMBs,particularly for Li-sulfur(S),Li-oxygen(O),and Li-Li-containing transition-metal oxide(LTMO)batteries,as well as LiNO_(3)-containing recipes for precursors in battery materials and interphase fabrication.This review pays attention to the effects of LiNO_(3) in lithium-based batteries,aiming to provide scientific guidance for the optimization of electrode/electrolyte interfaces and enrich the design of advanced LMBs.
文摘Bacille Calmette-Guérin(BCG)vaccine is designed to provide protection against tuberculosis(TB).However,numerous epidemiological,clinical,and immunological studies have shown that BCG vaccination affects neonatal and infant mortality,which may be related to the reduction of TB-unrelated infections and diseases by BCG vaccine.We aimed to discuss the off-target effects of BCG vaccine on un-TB infections and diseases,as well as the potential mechanism and influencing factors.Literature was retrieved mainly from PubMed using medical subject headings"BCG,variations,and non-specific,heterologous or off-target".Studies have showed that BCG vaccination can prevent various heterologous infections,including respiratory tract infections,leprosy,and malaria,treat viral infections including human papillomavirus and herpes simplex virus infection as immunotherapy,and improve the immune responses as vaccine adjuvant.Besides,BCG vaccine can reduce the recurrence rate of non-muscle-invasive bladder cancer,and may provide protection against autoimmune diseases.These off-target effects of BCG vaccine are thought to be achieved by modulating heterologous lymphocyte responses or inducing trained immunity,which were found to be sex-differentiated and affected by the BCG vaccine strains,sequence or time of vaccination.
基金supported by grants from the National Natural Science Foundation of China(No.62103262)the Shanghai Pujiang Programme(No.21PJ1407700)。
文摘Small interfering RNA(siRNA)is often used for function study and expression regulation of specific genes,as well as the development of small molecule drugs.Selecting siRNAs with high inhibition and low off-target effects from massive can-didates is always a great challenge.Increasing experimentally-validated samples can prompt the development of machine-learning-based algorithms,including Support Vector Machine(SVM),Convolutional Neural Network(CNN),and Graph Neural Network(GNN).However,these methods still suffer from limited accuracy and poor generalization in designing potent and specific siRNAs.In this study,we propose a novel approach for siRNA inhibition and off-target effect prediction,named AttSiOff.It combines a self-attention-based siRNA inhibition predictor with an mRNA searching package and an off-target filter.The predictor gives the inhibition score via analyzing the embedding of siRNA and local mRNA sequences,generated from the pre-trained RNA-FM model,as well as other meaningful prior-knowledge-based features.Self-attention mechanism can detect potentially decisive features,which may determine the inhibition of siRNA.It captures global and local dependencies more efficiently than normal convolutions.The tenfold cross-validation results indicate that our model outperforms all existing methods,achieving PCC of 0.81,SPCC of 0.84,and AUC of 0.886.It also reaches better performance of generalization and robustness on cross-dataset validation.In addition,the mRNA searching package could find all mature mRNAs for a given gene name from the GENOMES database,and the off-target filter can calculate the amount of unwanted off-target binding sites,which affects the specificity of siRNA.Experiments on five mature siRNA drugs,as well as a new target gene(AGT),show that AttSioff has excellent convenience and operability in practical applications.
基金partially supported by the National Natural Science Foundation of China (No. 31110103904)the National Program on Key Basic Research Project (973 Program) of the Ministry of Science and Technology of China (Nos. 2011CBA01000 and 2012CB945101)
文摘Targeted genome modifications with the Cas9/gRNA system derived from the clustered regularly interspaced short palin- dromic repeat/CRISPR-associated （CRISPR/Cas） system have been successfully used in cultured human cells as well as in most model organisms, including zebrafish （Danio rerio）, mouse, and fruit fly （Chang et al., 2013; Cong et al., 2013; Gratz et al., 2013; Hwang et al., 2013; Jao et al., 2013; Shen et al., 2013; Wei et al., 2013）. Its application in zebrafish is particu- larly attractive due to the ease of handling this organism and the simple application of this method by direct injection of Cas9/ gRNA. However, the information about its specificity in this organism is very limited and needs further evaluation. In addition, it is conceivable that a Cas9 mRNA optimized for zebrafish codon preference could enhance its activity.
