CRISPR-free, programmable RNA pseudouridylation to suppress premature termination codons.

Nonsense mutations, accounting for >20% of disease-associated mutations, lead to premature translation termination. Replacing uridine with pseudouridine in stop codons suppresses translation termination, which could be harnessed to mediate readthrough of premature termination codons (PTCs). Here, we present RESTART, a programmable RNA base editor, to revert PTC-induced translation termination in mammalian cells. RESTART utilizes an engineered guide snoRNA (gsnoRNA) and the endogenous H/ACA box snoRNP machinery to achieve precise pseudouridylation. We also identified and optimized gsnoRNA scaffolds to increase the editing efficiency. Unexpectedly, we found that a minor isoform of pseudouridine synthase DKC1, lacking a C-terminal nuclear localization signal, greatly improved the PTC-readthrough efficiency. Although RESTART induced restricted off-target pseudouridylation, they did not change the coding information nor the expression level of off-targets. Finally, RESTART enables robust pseudouridylation in primary cells and achieves functional PTC readthrough in disease-relevant contexts. Collectively, RESTART is a promising RNA-editing tool for research and therapeutics.

MyoV: a deep learning-based tool for the automated quantification of muscle fibers.

Accurate approaches for quantifying muscle fibers are essential in biomedical research and meat production. In this study, we address the limitations of existing approaches for hematoxylin and eosin-stained muscle fibers by manually and semiautomatically labeling over 660 000 muscle fibers to create a large dataset. Subsequently, an automated image segmentation and quantification tool named MyoV is designed using mask regions with convolutional neural networks and a residual network and feature pyramid network as the backbone network. This design enables the tool to allow muscle fiber processing with different sizes and ages. MyoV, which achieves impressive detection rates of 0.93-0.96 and precision levels of 0.91-0.97, exhibits a superior performance in quantification, surpassing both manual methods and commonly employed algorithms and software, particularly for whole slide images (WSIs). Moreover, MyoV is proven as a powerful and suitable tool for various species with different muscle development, including mice, which are a crucial model for muscle disease diagnosis, and agricultural animals, which are a significant meat source for humans. Finally, we integrate this tool into visualization software with functions, such as segmentation, area determination and automatic labeling, allowing seamless processing for over 400 000 muscle fibers within a WSI, eliminating the model adjustment and providing researchers with an easy-to-use visual interface to browse functional options and realize muscle fiber quantification from WSIs.

Phage-assisted evolution of compact Cas9 variants targeting a simple NNG PAM.

Compact Cas9 nucleases hold great promise for therapeutic applications. Although several compact Cas9 nucleases have been developed, many genomic loci still could not be edited due to a lack of protospacer adjacent motifs (PAMs). We previously developed a compact SlugCas9 recognizing an NNGG PAM. Here we demonstrate that SlugCas9 displays comparable activity to SpCas9. We developed a simple phage-assisted evolution to engineer SlugCas9 for unique PAM requirements. Interestingly, we generated a SlugCas9 variant (SlugCas9-NNG) that could recognize an NNG PAM, expanding the targeting scope. We further developed a SlugCas9-NNG-based adenine base editor and demonstrated that it could be delivered by a single adeno-associated virus to disrupt PCSK9 splice donor and splice acceptor. These genome editors greatly enhance our ability for in vivo genome editing.

Engineered gut symbiont inhibits microsporidian parasite and improves honey bee survival.

Honey bees (Apis mellifera) are critical agricultural pollinators as well as model organisms for research on development, behavior, memory, and learning. The parasite Nosema ceranae, a common cause of honey bee colony collapse, has developed resistance to small-molecule therapeutics. An alternative long-term strategy to combat Nosema infection is therefore urgently needed, with synthetic biology offering a potential solution. Honey bees harbor specialized bacterial gut symbionts that are transmitted within hives. Previously, these have been engineered to inhibit ectoparasitic mites by expressing double-stranded RNA (dsRNA) targeting essential mite genes, via activation of the mite RNA interference (RNAi) pathway. In this study, we engineered a honey bee gut symbiont to express dsRNA targeting essential genes of N. ceranae via the parasite's own RNAi machinery. The engineered symbiont sharply reduced Nosema proliferation and improved bee survival following the parasite challenge. This protection was observed in both newly emerged and older forager bees. Furthermore, engineered symbionts were transmitted among cohoused bees, suggesting that introducing engineered symbionts to hives could result in colony-level protection.

Cu2+ coordination-induced in situ photo-to-heat on catalytic sites to hydrolyze ß-lactam antibiotics pollutants in waters.

For degradation of ß-lactam antibiotics pollution in waters, the strained ß-lactam ring is the most toxic and resistant moiety to biodegrade and redox-chemically treat among their functional groups. Hydrolytically opening ß-lactam ring with Lewis acid catalysts has long been recognized as a shortcut, but at room temperature, such hydrolysis is too slow to be deployed. Here, we found when Cu2+ was immobilized on imine-linked COF (covalent organic framework) (Cu2+/Py-Bpy-COF, Cu2+ load is 1.43 wt%), as-prepared composite can utilize the light irradiation (wavelength range simulated sunlight) to in situ heat anchored Cu2+ Lewis acid sites through an excellent photothermal conversion to open the ß-lactam ring followed by a desired full-decarboxylation of hydrolysates. Under 1 W/cm2 simulated sunlight, Cu2+/Py-Bpy-COF powders placed in a microfiltration membrane rapidly cause a temperature rising even to ~211.7 °C in 1 min. It can effectively hydrolyze common ß-lactam antibiotics in waters and even antibiotics concentration is as high as 1 mM and it takes less than 10 min. Such photo-heating hydrolysis rate is ~24 times as high as under dark and ~2 times as high as Cu2+ homogenous catalysis. Our strategy significantly decreases the interference from generally coexisting common organics in waters and potential toxicity concerns of residual carboxyl groups in hydrolysates and opens up an accessible way for the settlement of ß-lactam antibiotics pollutants by the only energy source available, the sunlight.

Non-canonical RNA-binding protein ANXA11 regulates microRNA resorting into small extracellular vesicles to mediate cisplatin resistance.

The sensitivity of laryngeal squamous cell carcinoma (LSCC) to chemotherapy shows large heterogeneity. The role of miRNA in small extracellular vesicles (sEV) in chemotherapy resistance is under investigation. However, the regulation and sorting mechanism of sEV miRNAs remains unclear. In this study, small RNA sequencing was used to explore miRNA expression profiles in sEV of LSCC after cisplatin stimulation; RNA pull-down, mass spectrometry, and EMSA were used to clarify the binding of candidate RNA-binding protein (RBP) and candidate miRNA. Immunostaining and microRNA fluorescence in situ hybridization were performed to identify how candidate RBP affects miRNA stability and nuclear/cytoplasmic distribution. In vivo experiments were performed to verify the biological functions and response to cisplatin of candidate RBP. We found that cisplatin stimulation induced increased expression of miR-148a-3p and sEV sorting. ANXA11 binds to miR-148a-3p in a sequence-specific manner. ANXA11 inhibits tumor cell proliferation and drug resistance by binding to and retaining miR-148a-3p. Cisplatin stimulation reduced ANXA11 expression and promoted miR-148a-3p efflux through sEV pathways. ANXA11 overexpression reduced in vivo tumor proliferation and cisplatin-resistance. Taken together, ANXA11 mediates cisplatin resistance through sEV miRNA resorting. Mechanically, ANXA11 binds to miR-148a-3p in a sequence-specific manner to regulate its resorting and thus influences tumor proliferation and chemoresistance.

Directed-evolution mutations enhance DNA-binding affinity and protein stability of the adenine base editor ABE8e.

Adenine base editors (ABEs), consisting of CRISPR Cas nickase and deaminase, can chemically convert the A:T base pair to G:C. ABE8e, an evolved variant of the base editor ABE7.10, contains eight directed evolution mutations in its deaminase TadA8e that significantly increase its base editing activity. However, the functional implications of these mutations remain unclear. Here, we combined molecular dynamics (MD) simulations and experimental measurements to investigate the role of the directed-evolution mutations in the base editing catalysis. MD simulations showed that the DNA-binding affinity of TadA8e is higher than that of the original deaminase TadA7.10 in ABE7.10 and is mainly driven by electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attraction of TadA8e to DNA. We identified R111, N119 and N167 as the key mutations for the enhanced DNA binding and confirmed them by microscale thermophoresis (MST) and in vivo reversion mutation experiments. Unexpectedly, we also found that the directed mutations improved the thermal stability of TadA8e by ~ 12 °C (Tm, melting temperature) and that of ABE8e by ~ 9 °C, respectively. Our results demonstrate that the directed-evolution mutations improve the substrate-binding ability and protein stability of ABE8e, thus providing a rational basis for further editing optimisation of the system.

Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation.

Iodine-induced cleavage at phosphorothioate DNA (PT-DNA) is characterized by extremely high sensitivity (∼1 phosphorothioate link per 106 nucleotides), which has been used for detecting and sequencing PT-DNA in bacteria. Despite its foreseeable potential for wide applications, the cleavage mechanism at the PT-modified site has not been well established, and it remains unknown as to whether or not cleavage of the bridging P-O occurs at every PT-modified site. In this work, we conducted accurate ωB97X-D calculations and high-performance liquid chromatography-mass spectrometry to investigate the process of PT-DNA cleavage at the atomic and molecular levels. We have found that iodine chemoselectively binds to the sulfur atom of the phosphorothioate link via a strong halogen-chalcogen interaction (a type of halogen bond, with binding affinity as high as 14.9 kcal/mol) and thus triggers P-O bond cleavage via phosphotriester-like hydrolysis. Additionally, aside from cleavage of the bridging P-O bond, the downstream hydrolyses lead to unwanted P-S/P-O conversions and a loss of the phosphorothioate handle. The mechanism we outline helps to explain specific selectivity at the PT-modified site but also predicts the dynamic stoichiometry of P-S and P-O bond breaking. For instance, Tris is involved in the cascade derivation of S-iodo-phosphorothioate to S-amino-phosphorothioate, suppressing the S-iodo-phosphorothioate hydrolysis to a phosphate diester. However, hydrolysis of one-third of the Tris-O-grafting phosphotriester results in unwanted P-S/P-O conversions. Our study suggests that bacterial DNA phosphorothioation may more frequently occur than previous bioinformatic estimations have predicted from iodine-induced deep sequencing data.

KLHL21 suppresses gastric tumourigenesis via maintaining STAT3 signalling equilibrium in stomach homoeostasis.

OBJECTIVE: Precancerous metaplasia transition to dysplasia poses a risk for subsequent intestinal-type gastric adenocarcinoma. However, the molecular basis underlying the transformation from metaplastic to cancerous cells remains poorly understood. DESIGN: An integrated analysis of genes associated with metaplasia, dysplasia was conducted, verified and characterised in the gastric tissues of patients by single-cell RNA sequencing and immunostaining. Multiple mouse models, including homozygous conditional knockout Klhl21-floxed mice, were generated to investigate the role of Klhl21 deletion in stemness, DNA damage and tumour formation. Mass-spectrometry-based proteomics and ribosome sequencing were used to elucidate the underlying molecular mechanisms. RESULTS: Kelch-like protein 21 (KLHL21) expression progressively decreased in metaplasia, dysplasia and cancer. Genetic deletion of Klhl21 enhances the rapid proliferation of Mist1+ cells and their descendant cells. Klhl21 loss during metaplasia facilitates the recruitment of damaged cells into the cell cycle via STAT3 signalling. Increased STAT3 activity was confirmed in cancer cells lacking KLHL21, boosting self-renewal and tumourigenicity. Mechanistically, the loss of KLHL21 promotes PIK3CB mRNA translation by stabilising the PABPC1-eIF4G complex, subsequently causing STAT3 activation. Pharmacological STAT3 inhibition by TTI-101 elicited anticancer effects, effectively impeding the transition from metaplasia to dysplasia. In patients with gastric cancer, low levels of KLHL21 had a shorter survival rate and a worse response to adjuvant chemotherapy. CONCLUSIONS: Our findings highlighted that KLHL21 loss triggers STAT3 reactivation through PABPC1-mediated PIK3CB translational activation, and targeting STAT3 can reverse preneoplastic metaplasia in KLHL21-deficient stomachs.

Particle focusing mechanisms in λ-DNA solution flowing in a straight microchannel.

Most biological fluids (such as blood, saliva, and lymph) in nature have certain viscoelasticity and are beginning to be used as the carrying fluids for viscoelastic microfluidics. However, the particle-focusing mechanisms in these new biological viscoelastic fluids are still unclear. In this work, the particle-focusing mechanisms in λ-DNA solutions were systematically explored. We first explored the particle focusing dynamics in a square cross-section under varied flow rates to uncover the effects of flow rate on particle focusing. Three focusing stages, from the classic five-position viscoelastic focusing to single-stream focusing and finally to multiplex-stream focusing, were clearly demonstrated. In addition, the particle focusing process along the channel length was demonstrated, and a first-fast-and-then-slow focusing process was clearly observed. Then, the effects of λ-DNA concentrations on particle focusing were explored and compared using the solutions with 0-25 ppm λ-DNA. Finally, we discussed the inferences of blockage ratio on particle focusing by changing the particle diameter and cross-sectional dimensions. Our work may provide a deeper understanding on the particle focusing mechanisms in biological viscoelastic fluids and lays a foundation for the subsequent particle counting and analysis and the development of low-cost portable flow cytometers.

Elasto-inertial particle focusing in sinusoidal microfluidic channels.

Dean flow existing in sinusoidal channels could enhance the throughput and efficiency for elasto-inertial particle focusing. However, the fundamental mechanisms of elasto-inertial focusing in sinusoidal channels are still unclear. This work employs four microfluidic devices with symmetric and asymmetric sinusoidal channels to explore the elasto-inertial focusing mechanisms over a wide range of flow rates. The effects of rheological property, flow rate, sinusoidal channel curvature, particle size, and asymmetric geometry on particle focusing performance are investigated. It is intriguing to find that the Dean flow makes a substantial contribution to the particle elasto-inertial focusing. The results illustrate that a better particle focusing performance and a faster focusing process are obtained in the sinusoidal channel with a small curvature radius due to stronger Dean flow. In addition, the particle focusing performance is also related to particle diameter and rheological properties, the larger particles show a better focusing performance than smaller particles, and the smaller flow rate is required for particles to achieve stable focusing at the outlet in the higher concentration of polyvinylpyrrolidone solutions. Our work offers an increased knowledge of the mechanisms of elasto-inertial focusing in sinusoidal channels. Ultimately, these results provide supportive guidelines into the design and development of sinusoidal elasto-inertial microfluidic devices for high-performance focusing.

Tailoring Magnetism of Graphene Nanoflakes via Tip-Controlled Dehydrogenation.

Atomically precise graphene nanoflakes called nanographenes have emerged as a promising platform to realize carbon magnetism. Their ground state spin configuration can be anticipated by Ovchinnikov-Lieb rules based on the mismatch of π electrons from two sublattices. While rational geometrical design achieves specific spin configurations, further direct control over the π electrons offers a desirable extension for efficient spin manipulations and potential quantum device operations. To this end, we apply a site-specific dehydrogenation using a scanning tunneling microscope tip to nanographenes deposited on a Au(111) substrate, which shows the capability of precisely tailoring the underlying π-electron system and therefore efficiently manipulating their magnetism. Through first-principles calculations and tight-binding mean-field-Hubbard modeling, we demonstrate that the dehydrogenation-induced Au-C bond formation along with the resulting hybridization between frontier π orbitals and Au substrate states effectively eliminate the unpaired π electron. Our results establish an efficient technique for controlling the magnetism of nanographenes.

Visible Light-sensitized CO2 Methanation along a Relaxed Heat Available Route.

In photocatalysis, the resulted heat by the relaxation of most of incident light no longer acts as the industrially favorite driving force back to the target photo-reaction due to more or less the negative relation between photocatalytic efficiency and temperature. Here, we reported a visible light-sensitized protocol that completely reversed the negatively temperature-dependent efficiency in photo-driven CO2 methanation with saturated water vapor. Uniform Pt/N-TiO2/PDI self-assembly material decisively injects the excited electron of PDI sensitizer into N-TiO2 forming Ti-H hydride which is crucially temperature-dependent nucleophilic species to dominate CO2 methanation, rather than conventionally separated and trapped electrons on the conductor band. Meanwhile, the ternary composite lifts itself temperature from room temperature to 305.2 °C within 400s only by the failure excitation upon simulated sunlight of 2.5 W/cm2, and smoothly achieves CO2 methanation with a record number of 4.98 mmol g-1 h-1 rate, compared to less than 0.02 mmol g-1 h-1 at classic Pt/N-TiO2/UV photocatalysis without PDI sensitization. This approach can reuse ~53.9% of the relaxed heat energy from the incident light thereby allow high-intensity incident light as strong as possible within a flowing photo-reactor, opening the most likely gateways to industrialization.

TEMPO/PhI(OAc)2 promotes the α-aminophosphinoylation of alcohols with amines and H-phosphine oxides in aqueous medium.

A novel method for synthesizing α-aminoalkyl phosphine oxides in aqueous medium, using Ar2P(O)-H reagents, alcohols and amines, is described. This method: (i) allows for the smooth aminophosphinoylation of alcohols with amines and H-phosphine oxides under mild conditions; (ii) provides an efficient and alternative approach to access various α-aminoalkylphosphine oxides. Although various amines exhibited remarkable versatility and tolerance for functional groups in this reaction, alcohols and H-phosphine oxides demonstrated limited applicability as reactants. Hence, further investigation using a wider range of substrates is crucial. The postulated mechanism indicated that the three-component reaction followed the imine pathway due to the in situ oxidation of alcohol to aldehyde.

NaIO4/air-initiated phosphorylation of alcohols with H-phosphine oxides for the construction of P(O)-O bonds in water.

A facile and efficient protocol for P(O)-O bond formation was discovered through NaIO4/air-initiated phosphorylation of alcohols with H-phosphine oxides in water. This reaction showed good functional group tolerance and a broad substrate scope, providing an alternative method for constructing P(O)-O bonds. Mechanistic studies suggested that a phosphoryl radical-involving process from H-phosphine oxides facilitated the phosphorylation of alcohols under air.

Iodomethane in C1 chemistry: application in palladium-catalyzed [2 + 2 + 1] annulation.

An efficient palladium-catalyzed [2 + 2 + 1] annulation of 3-iodochromones, bridged olefins, and iodomethane is described, affording a range of chromone-containing polycyclic compounds. Additionally, the corresponding deuterated products were smoothly obtained with iodomethane-d3 instead of iodomethane. Moreover, the synthetic utility of this method is further substantiated by gram scale preparation and application to late-stage modification of estrone.

Impact of chemotherapy delay on long-term prognosis of laparoscopic radical surgery for locally advanced gastric cancer: a pooled analysis of four randomized controlled trials.

BACKGROUND: Adjuvant chemotherapy following curative surgery for locally advanced gastric cancer (AGC) significantly improves long-term patient prognosis. However, delayed chemotherapy (DC), in which patients are unable to receive timely treatment, is a common phenomenon in clinical practice for various reasons. This study aimed to investigate the impact of DC on the prognosis of patients with stage II-III locally AGC and explore the associated risk factors. METHODS: Data from four prospective studies were included in the pooled analysis. The planned chemotherapy (PC) group was defined as the time interval between surgery and the first chemotherapy ≤ 49 d, while the DC group was defined as the time interval between surgery and chemotherapy > 49 d. The prognosis, recurrence, and risk factors were compared, and a nomogram for predicting DC was established. RESULTS: In total, 596 patients were included, of whom 531 (89.1%) had PC and 65 (10.9%) had DC. Survival analysis revealed that the 5-year overall survival (OS) and disease-free survival (DFS) were significantly lower in the DC group than those in the PC group (log-rank P < 0.001). Cox univariable and multivariable analyses showed that DC was an independent risk factor for OS and DFS in stage II-III patients (P < 0.05). Based on the significant factors for DC, a prediction model was established that had a good fit, high accuracy (AUC = 0.780), and clinical applicability in both the training and validation sets. CONCLUSION: Delayed chemotherapy after gastrectomy is associated with poor long-term prognosis in patients with locally advanced stage II-III GC disease. But standardized, full-cycle adjuvant chemotherapy after surgery may play a remedial role, and can to a certain extent compensate the poor effects caused by delayed chemotherapy.

Controlling flat-foot limit cycle walkers with compliant joints based on local stability variation.

This study investigates local stability of a four-link limit cycle walking biped with flat feet and compliant ankle joints. Local stability represents the behavior along the solution trajectory between Poincare sections, which can provide detailed information about the evolution of disturbances. The effects of ankle stiffness and foot structure on local stability are studied. In addition, we apply a control strategy based on local stability analysis to the limit cycle walker. Control is applied only in the phases with poor local stability. Simulation results show that the energy consumption is reduced without sacrificing disturbance rejection ability. This study may be helpful in motion control of limit cycle bipedal walking robots with flat feet and ankle stiffness and understanding of human walking principles.

Appraisal of surgical outcomes and oncological efficiency of intraoperative adverse events in robotic radical gastrectomy for gastric cancer.

BACKGROUND: Surgical quality control is a crucial determinant of evaluating the tumor efficacy. OBJECTIVE: To assess the ClassIntra grade for quality control and oncological outcomes of robotic radical surgery for gastric cancer (GC). METHODS: Data of patients undergoing robotic radical surgery for GC at a high-volume center were retrospectively analyzed. Patients were categorized into two groups, the intraoperative adverse event (iAE) group and the non-iAE group, based on the occurrence of intraoperative adverse events. The iAEs were further classified into five sublevels (ranging from I to V according to severity) based on the ClassIntra grade. Surgical performance was assessed using the Objective Structured Assessment of Technical Skill (OSATS) and the General Error Reporting Tool. RESULTS: This study included 366 patients (iAE group: n = 72 [19.7%] and non-iAE group: n = 294 [80.3%]). The proportion of ClassIntra grade II patients was the highest in the iAE group (54.2%). In total and distal gastrectomies, iAEs occurred most frequently in the suprapancreatic area (50.0% and 54.8%, respectively). In total gastrectomy, grade IV iAEs were most common during lymph node dissection in the splenic hilum area (once for bleeding [grade IV] and once for injury [grade IV]). The overall survival (OS) and disease-free survival of the non-iAE group were significantly better than those of the iAE group (Log rank P < 0.001). Uni- and multi-variate analyses showed that iAEs were key prognostic indicators, independent of tumor stage and adjuvant chemotherapy (P < 0.001). CONCLUSION: iAEs in patients who underwent robotic radical gastrectomy significantly correlated with the occurrence of postoperative complications and a poor long-term prognosis. Therefore, utilization and inclusion of ClassIntra grading as a crucial surgical quality control and prognostic indicator in the routine surgical quality evaluation system are recommended.

Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2.

Multivalent drugs targeting homo-oligomeric viral surface proteins, such as the SARS-CoV-2 trimeric spike (S) protein, have the potential to elicit more potent and broad-spectrum therapeutic responses than monovalent drugs by synergistically engaging multiple binding sites on viral targets. However, rational design and engineering of nanoscale multivalent protein drugs are still lacking. Here, we developed a computational approach to engineer self-assembling trivalent microproteins that simultaneously bind to the three receptor binding domains (RBDs) of the S protein. This approach involves four steps: structure-guided linker design, molecular simulation evaluation of self-assembly, experimental validation of self-assembly state, and functional testing. Using this approach, we first designed trivalent constructs of the microprotein miniACE2 (MP) with different trimerization scaffolds and linkers, and found that one of the constructs (MP-5ff) showed high trimerization efficiency, good conformational homogeneity, and strong antiviral neutralizing activity. With its trimerization unit (5ff), we then engineered a trivalent nanobody (Tr67) that exhibited potent and broad neutralizing activity against the dominant Omicron variants, including XBB.1 and XBB.1.5. Cryo-EM complex structure confirmed that Tr67 stably binds to all three RBDs of the Omicron S protein in a synergistic form, locking them in the "3-RBD-up" conformation that could block human receptor (ACE2) binding and potentially facilitate immune clearance. Therefore, our approach provides an effective strategy for engineering potent protein drugs against SARS-CoV-2 and other deadly coronaviruses.