Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag.

Prime editors have a broad range of potential research and clinical applications. However, methods to delineate their genome-wide editing activities have generally relied on indirect genome-wide editing assessments or the computational prediction of near-cognate sequences. Here we describe a genome-wide approach for the identification of potential prime editor off-target sites, which we call PE-tag. This method relies on the attachment or insertion of an amplification tag at sites of prime editor activity to allow their identification. PE-tag enables genome-wide profiling of off-target sites in vitro using extracted genomic DNA, in mammalian cell lines and in the adult mouse liver. PE-tag components can be delivered in a variety of formats for off-target site detection. Our studies are consistent with the high specificity previously described for prime editor systems, but we find that off-target editing rates are influenced by prime editing guide RNA design. PE-tag represents an accessible, rapid and sensitive approach for the genome-wide identification of prime editor activity and the evaluation of prime editor safety.

Self-delivering, chemically modified CRISPR RNAs for AAV co-delivery and genome editing in vivo.

Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a 'protecting oligo'), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.

The CoFeNC@NC Catalyst with Numerous Surface Cracks Bidirectionally Catalyzes the Conversion of Polysulfides to Accelerate the Reaction Kinetics of Lithium-Sulfur Batteries.

More and more attention has been paid to lithium-sulfur (Li─S) batteries due to their high energy density and low cost. However, the intractable "shuttle effect" and the low conductivity of S and its reaction product, Li2 S, compromise battery performance. To address the inherent challenges, a hollow composite catalyst as a separator coating material is designed, in which CoFe alloy is embedded in a carbon skeleton (CoFeNC@NC). In the hybrid structure, the carbon layer can endow the batteries with high electrical conductivity, while the CoFe alloy can effectively bidirectionally catalyze the conversion between lithium polysulfides (LiPSs) and Li2 S, accelerating the reaction kinetics and reducing the dissolution of LiPSs. Furthermore, the distinctive hollow structure with a cracked surface can facilitate the exposure of a more accessible catalytically active site and enhance Li+ diffusion. Benefiting from the synergistic effects, Li─S batteries with a CoFeNC@NC catalyst achieve a high sulfur utilization (1250.8 mAh g-1 at 0.2 C), superior rate performance (756 mAh g-1 at 2 C), and excellent cycling stability (an ultralow capacity fading of 0.054% per cycle at 1 C for 1000 cycles). Even at a sulfur loading of 5.3 mg cm-2 , a high area capacity of 4.05 mAh cm-2 can still be achieved after 100 cycles, demonstrating its potential practicality.

Design and optimization of an octuple-electrode array for micro-particle chain rotation via electrorotation integrated with machine vision technology.

Microparticle rotation is an important process in biomedical engineering, such as biosensors, cell injection or cell morphology. Single particle rotation has been widely investigated, while rotation of particle chains has gained rare attention. In this paper, we utilize a noncontact manipulation method to rotate microparticle chains via electrorotation by designing an octuple-electrode array (OEA). Finite element simulations were conducted for analyzing the desired electrode field and optimizing the structure of microelectrode pairs. The direction of the electric field in the workspace is investigated with different voltage signal inputs through specially designed circuits. In the experiment, microparticles are driven to form several chains in the proposed electrode fields. With the rotation of the electric field, particle chains could be rotated synchronously. Automated rotation and detection of polystyrene microspheres and yeast cell chains are achieved using machine vision technology. Results show that the proposed method could be utilized to rotate ordered microparticles with an appropriate input signal.

The alterations of spontaneous neural activities and white matter microstructures in anti-N-methyl-D-aspartate receptor encephalitis: a resting-state fMRI and DTI study.

BACKGROUND AND PURPOSE: Limited studies had jointly excavated the structural and functional changes in cognitive deficit in anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis patients. We aimed to explore these changes in anti-NMDAR patients and their effect on cognitive function. METHODS: Twenty-three patients and 25 healthy controls (HCs) underwent resting-state functional magnetic resonance imaging, diffusion tensor imaging scanning, and neuroethology tests. The significantly differentiated brain regions via the fractional amplitude of low-frequency fluctuation (fALFF) were defined as regions of interest (ROIs). Granger causal, functional connectivity, and tract-based spatial statistical analyses were applied to explore the functional changes in ROIs and assess the structural changes. RESULTS: HCs outperformed patients in Montreal Cognitive Assessment. The fALFF values of right gyrus rectus (RGR) in patients were significantly reduced. The fractional anisotropy (FA) values of WM in the genu of corpus callosum and right superior corona radiata were significantly decreased and positively associated with neuroethology testing scores. The Granger causal connectivity (GCC) from the left inferior parietal lobule to RGR was significantly decreased and positively associated with inherent vigilance. Indicated by the multiple linear regression result, decreased FA value of the right superior corona radiata might be a reliable marker that reflects the cognitive impairment. CONCLUSIONS: Significant changes in spontaneous neural activities, GCC, and WM structures in anti-NMDAR encephalitis were reported. These findings promote the understanding of underlying relationships between cerebral function, structural network alterations, and cognitive dysfunction.

Aberrant resting-state interhemispheric functional connectivity in patients with anti-N-methyl-D-aspartate receptor encephalitis.

PURPOSE: Previous studies have discovered different neuroimaging features in anti-NMDAR encephalitis associated with cognitive dysfunction. However, it is unknown whether there is a correlation between abnormal homotopic connectivity and cognitive impairment in anti-NMDAR encephalitis. We aim to explore the homotopic connectivity patterns of patients with anti-NMDAR encephalitis and their associations with clinical characteristics. METHODS: Resting-state functional magnetic resonance imaging (rs-fMRI) was performed on 29 patients with anti-NMDAR encephalitis and 26 healthy controls (HCs). Voxel-mirrored homotopic connectivity (VMHC) and multivariate pattern analysis (MVPA) were applied to analyze the imaging data. A correlation was also performed between aberrant brain regions and clinical parameters. RESULTS: Compared to HCs, the performance of alertness in the patient group was typically worse (p < 0.05). A significant decrease in VMHC was observed in many regions of the patients in comparison to HCs, including the cerebellar 6, para-hippocampal gyrus, insula, precuneus, and middle frontal gyrus (p < 0.001). The insula and middle frontal gyrus were found to show positive correlations with alertness. The MVPA method achieved a classification accuracy of 74.55% with a sensitivity of 82.76% and a specificity of 65.38% in discriminating patients from HCs. CONCLUSION: Our findings indicate that interhemispheric functional imbalance may play a significant role in the pathophysiology of cognitive dysfunction in anti-NMDAR encephalitis. The MVPA results suggest that abnormal VMHC may play a crucial role in the identification of patients with anti-NMDAR encephalitis from HCs.

Migration and transformation of main components during perishable waste bio-drying process.

Bio-drying can significantly reduce the moisture content of waste. The factors, functional microorganisms, and the transformation of main components were investigated during bio-drying of perishable waste. This study provides a scientific basis for the improvement of the bio-drying process and the necessity for secondary pollutant control. Reaction temperature and microbial biomass were main factors during the bio-drying process. The ideal bio-drying conditions included an initial temperature above 20 °C, intermittent ventilation, and appropriate microbial inoculation. The main microorganisms included Alcaligenes, Aquamicrobium, and Brevundimonas. From each gram of the carbonaceous, nitrogenous, sulfur-containing compounds, and phosphorus-containing substances in the perishable waste, approximately 0.74 g, 0.66 g, 0.40 g, and 0.94 g, respectively, were transferred as gas-phase products; consisting mainly of ammonia and volatile organic compounds: 2-heptanone, dimethyl heptanone, and benzene. In the leachate, the respective amounts of the carbonaceous, nitrogenous, sulfur-containing compounds, and phosphorus-containing substances were 3.20 × 10-3 g, 4.08 × 10-3 g, 0.33 g, and 9.52 × 10-3 g, while those of the residual substances remaining in solid were 0.26 g, 0.33 g, 0.28 g, and 0.05 g.

Improvement of NOx uptake/release over Pd/Beta by propylene: shielding effect of intermediates on adsorbed NOx species.

Passive NOx adsorbers (PNAs) are capable of trapping NOx at low temperature and releasing the trapped NOx into the gas circuit at higher temperatures, where downstream NOx reduction catalysts are activated. Hydrocarbons have a significant effect on the performance of PNAs, nonetheless research in this area has been overlooked. Here the chemistry of NOx adsorption and desorption in the presence of C3H6 was studied. For different pore-size zeolites (BEA, MFI and CHA), the addition of C3H6 always increased the NOx adsorption capacity at a low temperature and raised the NOx desorption temperature. Spectroscopic and computational investigations were performed using the model Pd/Beta to unravel the relevant mechanism. Fourier transform infrared (FTIR) spectra indicated that more Pd+ was formed in the presence of C3H6, which contributed to higher NOx storage capacity. An intermediate Pd-NC3H6O was probed and its evolution procedure was modeled by density functional theory (DFT) calculations. The results showed that a shielding effect of Pd-NC3H6O on Pd+-NO improved the NOx desorption temperature. This investigation has important implications for how short-chain olefins and even more complex gas mixtures affect the NOx adsorption and desorption performance of Pd/zeolite.

Study on the efficient removal of azo dyes by heterogeneous photo-Fenton process with 3D flower-like layered double hydroxide.

As organic dyes are the main pollutants in water pollution, seeking effective removal solutions is urgent for humans and the environment. A novel environmentally friendly three-dimensional CoFe-LDHs (3D CoFe-LDHs) catalyst was synthesized by one-step hydrothermal method. Scanning electron microscopy, energy dispersive spectroscopy, Fourier transform infrared spectra, X-ray diffraction, X-ray photoelectron spectroscopy, Brunauer-Emmett-Teller technique as well as UV-Vis diffuse reflectance spectra were used to characterize the prepared samples. The experimental results revealed that 3D CoFe-LDHs exhibited a rapid decolorization of methyl orange and Rhodamine B by heterogeneous photo-Fenton process after reaching the adsorption equilibrium, and the final decolorization efficiency reached 91.18% and 93.56%, respectively. On the contrary, the decolorizing effect of 3D CoFe-LDHs on neutral blue was relatively weak. The initial concentrations of azo dyes, pH and H2O2 concentration affected the decolorization of dyes and the catalyst maintained excellent reusability and stability after reuse over five cycles. The quenching experiments found that •OH, •O2 - and h+ were the main active substances and reaction mechanisms were further proposed. The study suggests that the synergistic effect of photocatalysis and Fenton oxidation process significantly improved the removal of azo dyes and the synthesized catalyst had potentially promising applications for difficult-to-biodegrade organic pollutants in wastewater.

Fe3O4 and Au nanoparticles dispersed on the graphene support as a highly active catalyst toward the reduction of 4-nitrophenol.

We report a highly efficient and reusable bifunctional nanostructured composite catalyst synthesized by a scalable facile hydrothermal method which enables the precise control of size and morphology of nanoparticles, wherein Au nanoparticles (NPs) and Fe3O4 particles exhibit excellent dispersing ability on the rGO (reduced graphene oxide) sheet surface (designated as rGO/Fe3O4/Au) to avoid adverse agglomeration between the nano particles and overlapping of the rGO sheets concurrently. The resultant bifunctional composite shows a high performance in the catalytic reduction of 4-nitrophenol (4-NP) with a conversion of 97% in 5 min and presents good reusability through highly efficient recovery by using external magnetic fields. In particular, there was no significant loss in catalytic activity of the reused catalysts even after being recycled for 8 cycles, displaying attractive potential in industrial applications where separation and recycling are imperative. The rational design provides an approach to synthesize a graphene-based composite with an interesting structure and multi-functional properties as well.

Abnormal global and local connectivity in patients with anti-N-methyl-D-aspartate receptor encephalitis: A resting-state functional MRI study.

OBJECTIVE: We decided to investigate the changes of global and local connectivity in anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis patients based on eigenvector centrality (EC) and regional homogeneity (ReHo). We sought new biomarkers to identify the patients based on multivariate pattern analysis (MVPA). METHODS: Functional MRI (fMRI) was performed on all participants. EC, ReHo and MVPA were used to analyze the fMRI images. The correlation between the global or local connectivity and neuropsychology tests was detected. RESULTS: The MoCA scores of the patients were lower than those of the healthy controls (HCs), while the HAMD24 and HAMA scores of the patients were higher than those of the HCs. Increased EC values in the right calcarine (CAL.R) and decreased EC values in the right putamen (PUT.R) distinguished these subjects with anti-NMDAR encephalitis from HCs. The higher ReHo values in the left postcentral gyrus (PoCG.L) were detected in the patients. The correlation analysis showed that the EC values in the PUT.R were negatively correlated with HAMD24 and HAMA scores, while the ReHo values in the PoCG.L were negatively correlated with MoCA scores. Better classification performance was reached in the EC-based classifier (AUC = 0.80), while weaker classification performance was achieved in the ReHo-based classifier (AUC = 0.74) or the classifier based on EC and ReHo (AUC = 0.74). The brain areas with large weights were located in the frontal lobe, parietal lobe, cerebellum and basal ganglia. CONCLUSION: Our findings suggest that abnormal global and local connectivity may play an important part in the pathophysiological mechanism of neuropsychiatric symptoms in the anti-NMDAR encephalitis patients. The EC-based classifier may be better than the ReHo-based classifier in identifying anti-NMDAR encephalitis patients.

Increasing intracellular dNTP levels improves prime editing efficiency.

In primary cell types, intracellular deoxynucleotide triphosphate (dNTP) levels are tightly regulated in a cell cycle-dependent manner. We report that prime editing efficiency is increased by mutations that improve the enzymatic properties of Moloney murine leukemia virus reverse transcriptase and treatments that increase intracellular dNTP levels. In combination, these modifications produce substantial increases in precise editing rates.

Effect of sodium ions on RNA duplex stability.

The standard sodium concentration for RNA optical melting experiments is 1.021 M. Algorithms that predict Tm, ΔG°37, and secondary structure from sequence generally rely on parameters derived from optical melting experiments performed in 1.021 M sodium. Physiological monovalent cation concentrations are much lower than 1.021 M. In fact, many molecular biology techniques require buffers containing monovalent cation concentrations other than 1.021 M. Predictions based on the 1.021 M Na(+) parameters may not be accurate when the monovalent cation concentration is not 1.021 M. Here, we report thermodynamic data from optical melting experiments for a set of 18 RNA duplexes, each melted over a wide range of sodium ion concentrations (71, 121, 221, and 621 mM). Using these data and previously published data for the same sequences melted in 1.021 M Na(+), we report Tm and ΔG°37 correction factors to scale the standard 1.021 M Na(+) RNA parameters to other sodium ion concentrations. The recommended Tm correction factor predicts the melting temperature within 0.7 °C, and the recommended ΔG°37 correction factor predicts the free energy within 0.14 kcal/mol. These correction factors can be incorporated into prediction algorithms that predict RNA secondary structure from sequence and provide Tm and ΔG°37 values for RNA duplexes.

Abnormalities in modular connectivity of functional brain networks and cognitive changes in patients with anti -N-methyl-D-aspartate receptor encephalitis.

OBJECTIVE: To explore potential mechanisms of cognitive changes in patients with anti-NMDAR encephalitis (ANMDARE) from intramodule and intermodule effects of brain functional networks. METHODS: Resting-state functional MRI(rs-fMRI) imaging data was collected from 30 ANMDARE and 30 healthy controls (HCs). A brain functional matrix was constructed, and sparsity was established by module similarity. For both groups, changes in functional connectivity (FC) within and between modules was calculated, and whole-brain functional topology was analyzed. Finally, the association of brain functional with cognitive function in ANMDARE was further analyzed. RESULTS: Compared to HCs, ANMDARE had enhanced connectivity within the modules that included the occipito-parietal-temporal and parahippocampal gyri. ANMDARE had significantly higher participation coefficients (PC) in the right inferior frontal gyrus than HCs and significantly lower PC in the left superior parietal lobule, left caudate nucleus, and right putamen. No statistically significant differences in global topological properties were found between the two groups. No correlations were found between functional and structural brain indicators and the Cognitive Assessment Scale and the Emotional Deficit Scale. CONCLUSIONS: Patients with ANMDARE are manifested by enhanced intramodular FC and intermodular connectivity changes in the brain. This may help to understand the pathophysiological mechanisms of the disease from a global perspective.

Longitudinal alterations of cortical structural-functional coupling in temporal lobe epilepsy.

BACKGROUND AND PURPOSE: To investigate the longitudinal alterations of cortical structural-functional coupling (SF coupling) in patients with temporal lobe epilepsy (TLE) over a 2-year follow-up, thereby exploring the neuropathophysiological mechanisms of TLE. METHODS: Twenty-eight TLE patients and 42 age- and gender-matched healthy controls (HCs) were recruited. We used resting-state functional MRI and diffusion-weighted imaging to estimate and compare SF coupling at the multiscale network level (whole-brain, modular, and regional levels). Then, we analyzed the relationships between the spatial patterns of SF coupling, the principal functional connectivity (FC) gradient, and the functional participation coefficient (PC). Finally, we related regional SF coupling changes between baseline and follow-up to the expression of regional TLE-specific genes. RESULTS: Compared with HCs, TLE patients showed higher baseline SF couplings within the whole-brain, limbic, and default-mode modules. SF couplings within visual and dorsal attention modules were increased at follow-up compared to baseline. In all three groups, the spatial patterns of SF coupling aligned with the principal FC gradient and the functional PC. The longitudinal change in regional SF coupling in TLE patients was significantly positively correlated with the expression of the CUX2 gene. CONCLUSIONS: Aberrant SF coupling was revealed in TLE and related to macroscale cortical hierarchies, functional segregation, and TLE-specific gene expression; these data help increase our understanding of the neuropathophysiological mechanisms underlying TLE.

Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates.

Reverse transcriptases, used in prime editing systems, exhibit lower fidelity, processivity and dNTP affinity than many DNA-dependent DNA polymerases. We report that a DNA-dependent DNA polymerase (phi29), untethered from Cas9, enables editing from a synthetic, end-stabilized DNA-containing template at up to 60% efficiency in human cells. Compared to prime editing, DNA polymerase editing avoids autoinhibitory intramolecular base pairing of the template, facilitates template synthesis and supports larger insertions (>100 nucleotides).

Self-delivering CRISPR RNAs for AAV Co-delivery and Genome Editing in vivo.

Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a "protecting oligo"), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.

Addressing the dNTP bottleneck restricting prime editing activity.

Prime editing efficiency is modest in cells that are quiescent or slowly proliferating where intracellular dNTP levels are tightly regulated. MMLV-reverse transcriptase - the prime editor polymerase subunit - requires high intracellular dNTPs levels for efficient polymerization. We report that prime editing efficiency in primary cells and in vivo is increased by mutations that enhance the enzymatic properties of MMLV-reverse transcriptase and can be further complemented by targeting SAMHD1 for degradation.

A Fluorescent Reporter Mouse for In Vivo Assessment of Genome Editing with Diverse Cas Nucleases and Prime Editors.

CRISPR-based genome-editing technologies, including nuclease editing, base editing, and prime editing, have recently revolutionized the development of therapeutics targeting disease-causing mutations. To advance the assessment and development of genome editing tools, a robust mouse model is valuable, particularly for evaluating in vivo activity and delivery strategies. In this study, we successfully generated a knock-in mouse line carrying the Traffic Light Reporter design known as TLR-multi-Cas variant 1 (TLR-MCV1). We comprehensively validated the functionality of this mouse model for both in vitro and in vivo nuclease and prime editing. The TLR-MCV1 reporter mouse represents a versatile and powerful tool for expediting the development of editing technologies and their therapeutic applications.