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Abstract DNA base editors enable direct editing of adenine (A), cytosine (C), or guanine (G), but there is no base editor for direct thymine (T) editing currently. Here we develop two deaminase-free glycosylase-based base editors for direct T editing (gTBE) and C editing (gCBE) by fusing Cas9 nickase (nCas9) with engineered human uracil DNA glycosylase (UNG) variants. By several rounds of structure-informed rational mutagenesis on UNG in cultured human cells, we obtain gTBE and gCBE with high activity of T-to-S (i.e., T-to-C or T-to-G) and C-to-G conversions, respectively. Furthermore, we conduct parallel comparison of gTBE/gCBE with those recently developed using other protein engineering strategies, and find gTBE/gCBE show the outperformance. Thus, we provide several base editors, gTBEs and gCBEs, with corresponding engineered UNG variants, broadening the targeting scope of base editors.

Abstract Hepatitis B virus is a globally distributed pathogen and the history of HBV infection in humans predates 10000 years. However, long-term evolutionary history of HBV in Eastern Eurasia remains elusive. We present 34 ancient HBV genomes dating between approximately 5000 to 400 years ago sourced from 17 sites across Eastern Eurasia. Ten sequences have full coverage, and only two sequences have less than 50% coverage. Our results suggest a potential origin of genotypes B and D in Eastern Asia. We observed a higher level of HBV diversity within Eastern Eurasia compared to Western Eurasia between 5000 and 3000 years ago, characterized by the presence of five different genotypes (A, B, C, D, WENBA), underscoring the significance of human migrations and interactions in the spread of HBV. Our results suggest the possibility of a transition from non-recombinant subgenotypes (B1, B5) to recombinant subgenotypes (B2 - B4). This suggests a shift in epidemiological dynamics within Eastern Eurasia over time. Here, our study elucidates the regional origins of prevalent genotypes and shifts in viral subgenotypes over centuries.

Abstract Developing in situ/operando spectroscopic techniques with high sensitivity and reproducibility is of great importance for mechanistic investigations of surface-mediated electrochemical reactions. Herein, we report the fabrication of highly ordered rhombic gold nanocube superlattices (GNSs) as substrates for surface-enhanced infrared absorption spectroscopy (SEIRAS) with significantly enhanced SEIRA effect, which can be controlled by manipulating the randomness of GNSs. Finite difference time domain simulations reveal that the electromagnetic effect accounts for the significantly improved spectroscopic vibrations on the GNSs. In situ SEIRAS results show that the vibrations of CO on the Cu2O surfaces have been enhanced by 2.4 ± 0.5 and 18.0 ± 1.3 times using GNSs as substrates compared to those on traditional chemically deposited gold films in acidic and neutral electrolytes, respectively. Combined with isotopic labeling experiments, the reaction mechanisms for C-C coupling of CO electroreduction on Cu-based catalysts are revealed using the GNSs substrates.

Abstract Understanding the structure-stability relationship of catalysts is imperative for the development of high-performance electrocatalytic devices. Herein, we utilize operando attenuated total reflectance surface-enhanced infrared absorption spectroscopy (ATR-SEIRAS) to quantitatively monitor the evolution of Cu single-atom catalysts (SACs) during the electrochemical reduction of CO2 (CO2RR). Cu SACs are converted into 2-nm Cu nanoparticles through a reconstruction process during CO2RR. The evolution rate of Cu SACs is highly dependent on the substrates of the catalysts due to the coordination difference. Density functional theory calculations demonstrate that the stability of Cu SACs is highly dependent on their formation energy, which can be manipulated by controlling the affinity between Cu sites and substrates. This work highlights the use of operando ATR-SEIRAS to achieve mechanistic understanding of structure-stability relationship for long-term applications.

Abstract Elucidating the synergistic catalytic mechanism between multiple active centers is of great significance for heterogeneous catalysis; however, finding the corresponding experimental evidence remains challenging owing to the complexity of catalyst structures and interface environment. Here we construct an asymmetric TeN2–CuN3 double-atomic site catalyst, which is analyzed via full-range synchrotron pair distribution function. In electrochemical CO2 reduction, the catalyst features a synergistic mechanism with the double-atomic site activating two key molecules: operando spectroscopy confirms that the Te center activates CO2, and the Cu center helps to dissociate H2O. The experimental and theoretical results reveal that the TeN2–CuN3 could cooperatively lower the energy barriers for the rate-determining step, promoting proton transfer kinetics. Therefore, the TeN2–CuN3 displays a broad potential range with high CO selectivity, improved kinetics and good stability. This work presents synthesis and characterization strategies for double-atomic site catalysts, and experimentally unveils the underpinning mechanism of synergistic catalysis.

Abstract The enolimine-ketoenamine tautomerism has been utilised to construct 2D covalent organic frameworks (COFs) with a higher level of chemical robustness and superior photoelectronic activity. However, it remains challenging to fully control the tautomeric states and correlate their tautomeric structure-photoelectronic properties due to the mobile equilibrium of proton transfer between two other atoms. We show that symmetry-asymmetry tautomerisation from diiminol to iminol/cis-ketoenamine can be stabilised and switched in a crystalline, porous, and dynamic 3D COF (dynaCOF-301) through concerted structural transformation and host-guest interactions upon removal and adaptive inclusion of various guest molecules. Specifically, the tautomeric dynaCOF-301 is constructed by linking the hydroquinone with a tetrahedral building block through imine linkages to form 7-fold interwoven diamondoid networks with 1D channels. Reversible framework deformation and ordering-disordering transition are determined from solvated to activated and hydrated phases, accompanied by solvatochromic and hydrochromic effects useful for rapid, steady, and visual naked-eye chemosensing.

Abstract Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions of ATE1 arise from its unique enzymatic activity to covalently attach an arginine onto its protein substrates in a tRNA-dependent manner. However, how ATE1 (and other aminoacyl-tRNA transferases) hijacks tRNA from the highly efficient ribosomal protein synthesis pathways and catalyzes the arginylation reaction remains a mystery. Here, we describe the three-dimensional structures of Saccharomyces cerevisiae ATE1 with and without its tRNA cofactor. Importantly, the putative substrate binding domain of ATE1 adopts a previously uncharacterized fold that contains an atypical zinc-binding site critical for ATE1 stability and function. The unique recognition of tRNAArg by ATE1 is coordinated through interactions with the major groove of the acceptor arm of tRNA. Binding of tRNA induces conformational changes in ATE1 that helps explain the mechanism of substrate arginylation.

Here the authors show that the RRM of RbFox accomplishes extraordinary sequence specificity by employing functionally and structurally distinct binding modes - one for its cognate RNA and one for all non-cognate RNAs.

Droplet generators convert mechanical movements of droplets into small-scale electricity. Here, Tang et al. report a humidity-driven power generator by utilizing daily humidity fluctuation in atmosphere enabling continuous generation of electricity upon moisture absorption and desorption cycles.

In vivo decorporation of U(VI) from bones is an unsolved challenge because of the formation of stable uranium phosphate complexes. Here, the authors develop a hydroxypyridonone-based ligand with strong uranium complexation and low cytotoxicity. They find this ligand effectively removes uranium from kidney and bones in mice, and is suitable for oral administration.

Pentamidine and melarsoprol are primary drugs used to treat the lethal human sleeping sickness caused by the parasite Trypanosoma brucei. Cross-resistance to these two drugs has recently been linked to aquaglyceroporin 2 of the trypanosome (TbAQP2). TbAQP2 is the first member of the aquaporin family described as capable of drug transport; however, the underlying mechanism remains unclear. Here, we present cryo-electron microscopy structures of TbAQP2 bound to pentamidine or melarsoprol. Our structural studies, together with the molecular dynamic simulations, reveal the mechanisms shaping substrate specificity and drug permeation. Multiple amino acids in TbAQP2, near the extracellular entrance and inside the pore, create an expanded conducting tunnel, sterically and energetically allowing the permeation of pentamidine and melarsoprol. Our study elucidates the mechanism of drug transport by TbAQP2, providing valuable insights to inform the design of drugs against trypanosomiasis., (© 2024. The Author(s).)

Halide perovskites exhibit exceptional optoelectronic properties for photoelectrochemical production of solar fuels and chemicals but their instability in aqueous electrolytes hampers their application. Here we present ultrastable perovskite CsPbBr 3 -based photoanodes achieved with both multifunctional glassy carbon and boron-doped diamond sheets coated with Ni nanopyramids and NiFeOOH. These perovskite photoanodes achieve record operational stability in aqueous electrolytes, preserving 95% of their initial photocurrent density for 168 h of continuous operation with the glassy carbon sheets and 97% for 210 h with the boron-doped diamond sheets, due to the excellent mechanical and chemical stability of glassy carbon, boron-doped diamond, and nickel metal. Moreover, these photoanodes reach a low water-oxidation onset potential close to +0.4 V RHE and photocurrent densities close to 8 mA cm -2 at 1.23 V RHE , owing to the high conductivity of glassy carbon and boron-doped diamond and the catalytic activity of NiFeOOH. The applied catalytic, protective sheets employ only earth-abundant elements and straightforward fabrication methods, engineering a solution for the success of halide perovskites in stable photoelectrochemical cells., (© 2024. The Author(s).)

Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture., (© 2023. The Author(s).)

Converting low-grade heat from environment into electricity shows great sustainability for mitigating the energy crisis and adjusting energy configurations. However, thermally rechargeable devices typically suffer from poor conversion efficiency when a semiconductor is employed. Breaking the convention of thermoelectric systems, we propose and demonstrate a new zinc ion thermal charging cell to generate electricity from low-grade heat via the thermo-extraction/insertion and thermodiffusion processes of insertion-type cathode (VO 2 -PC) and stripping/plating behaviour of Zn anode. Based on this strategy, an impressively high thermopower of ~12.5 mV K -1 and an excellent output power of 1.2 mW can be obtained. In addition, a high heat-to-current conversion efficiency of 0.95% (7.25% of Carnot efficiency) is achieved with a temperature difference of 45 K. This work, which demonstrates extraordinary energy conversion efficiency and adequate energy storage, will pave the way towards the construction of thermoelectric setups with attractive properties for high value-added utilization of low-grade heat., (© 2022. The Author(s).)

Proprioceptive neurons (PNs) are essential for the proper execution of all our movements by providing muscle sensory feedback to the central motor network. Here, using deep single cell RNAseq of adult PNs coupled with virus and genetic tracings, we molecularly identify three main types of PNs (Ia, Ib and II) and find that they segregate into eight distinct subgroups. Our data unveil a highly sophisticated organization of PNs into discrete sensory input channels with distinct spatial distribution, innervation patterns and molecular profiles. Altogether, these features contribute to finely regulate proprioception during complex motor behavior. Moreover, while Ib- and II-PN subtypes are specified around birth, Ia-PN subtypes diversify later in life along with increased motor activity. We also show Ia-PNs plasticity following exercise training, suggesting Ia-PNs are important players in adaptive proprioceptive function in adult mice.

Cancer has no borders: Generation and analysis of molecular data across multiple centers worldwide is necessary to gain statistically significant clinical insights for the benefit of patients. Here we conceived and standardized a proteotype data generation and analysis workflow enabling distributed data generation and evaluated the quantitative data generated across laboratories of the international Cancer Moonshot consortium. Using harmonized mass spectrometry (MS) instrument platforms and standardized data acquisition procedures, we demonstrate robust, sensitive, and reproducible data generation across eleven international sites on seven consecutive days in a 24/7 operation mode. The data presented from the high-resolution MS1-based quantitative data-independent acquisition (HRMS1-DIA) workflow shows that coordinated proteotype data acquisition is feasible from clinical specimens using such standardized strategies. This work paves the way for the distributed multi-omic digitization of large clinical specimen cohorts across multiple sites as a prerequisite for turning molecular precision medicine into reality.

Microresonator frequency combs harness the nonlinear Kerr effect in an integrated optical cavity to generate a multitude of phase-locked frequency lines. The line spacing can reach values in the order of 100 GHz, making it an attractive multi-wavelength light source for applications in fiber-optic communications. Depending on the dispersion of the microresonator, different physical dynamics have been observed. A recently discovered comb state corresponds to the formation of mode-locked dark pulses in a normal-dispersion microcavity. Such dark-pulse combs are particularly compelling for advanced coherent communications since they display unusually high power-conversion efficiency. Here, we report the first coherent-transmission experiments using 64-quadrature amplitude modulation encoded onto the frequency lines of a dark-pulse comb. The high conversion efficiency of the comb enables transmitted optical signal-to-noise ratios above 33 dB, while maintaining a laser pump power level compatible with state-of-the-art hybrid silicon lasers.

Understanding nanoscale thermal transport is of substantial importance for designing contemporary semiconductor technologies. Heat removal from small sources is well established to be severely impeded compared to diffusive predictions due to the ballistic nature of the dominant heat carriers. Experimental observations are commonly interpreted through a reduction of effective thermal conductivity, even though most measurements only probe a single aggregate thermal metric. Here, we employ thermoreflectance thermal imaging to directly visualise the 2D temperature field produced by localised heat sources on InGaAs with characteristic widths down to 100 nm. Besides displaying effective thermal performance reductions up to 50% at the active junctions in agreement with prior studies, our steady-state thermal images reveal that, remarkably, 1-3 μm adjacent to submicron devices the crosstalk is actually reduced by up to fourfold. Submicrosecond transient imaging additionally shows responses to be faster than conventionally predicted. A possible explanation based on hydrodynamic heat transport, and some open questions, are discussed.

Kerr nonlinearity-based frequency combs and solitons have been generated from on-chip microresonators. The initiation of the combs requires global or local anomalous dispersion which leads to many limitations, such as material choice, film thickness, and spectral ranges where combs can be generated, as well as fabrication challenges. Using a concentric racetrack-shaped resonator, we show that such constraints can be lifted and resonator dispersion can be engineered to be anomalous over moderately broad bandwidth. We demonstrate anomalous dispersion in a 300 nm thick silicon nitride film, suitable for semiconductor manufacturing but previously thought to result in waveguides with high normal dispersion. Together with a mode-selective, tapered coupling scheme, we generate coherent mode-locked frequency combs. Our method can realize anomalous dispersion for resonators at almost any wavelength and simultaneously achieve material and process compatibility with semiconductor manufacturing.Kerr frequency comb generation from microresonators requires anomalous dispersion, imposing restrictions on materials and resonator design. Here, Kim et al. propose a concentric racetrack-resonator design where the dispersion can be engineered to be anomalous via resonant mode coupling.

Centrosome amplification is frequent in cancer, but the underlying mechanisms remain unclear. Here we report that disruption of the Kruppel-like factor 14 (KLF14) gene in mice causes centrosome amplification, aneuploidy and spontaneous tumorigenesis. Molecularly, KLF14 functions as a transcriptional repressor of Plk4, a polo-like kinase whose overexpression induces centrosome overduplication. Transient knockdown of KLF14 is sufficient to induce Plk4-directed centrosome amplification. Clinically, KLF14 transcription is significantly downregulated, whereas Plk4 transcription is upregulated in multiple types of cancers, and there exists an inverse correlation between KLF14 and Plk4 protein expression in human breast and colon cancers. Moreover, KLF14 depletion promotes AOM/DSS-induced colon tumorigenesis. Our findings reveal that KLF14 reduction serves as a mechanism leading to centrosome amplification and tumorigenesis. On the other hand, forced expression of KLF14 leads to mitotic catastrophe. Collectively, our findings identify KLF14 as a tumour suppressor and highlight its potential as biomarker and therapeutic target for cancer.

Photonic methods of radio-frequency waveform generation and processing can provide performance advantages and flexibility over electronic methods due to the ultrawide bandwidth offered by the optical carriers. However, bulk optics implementations suffer from the lack of integration and slow reconfiguration speed. Here we propose an architecture of integrated photonic radio-frequency generation and processing and implement it on a silicon chip fabricated in a semiconductor manufacturing foundry. Our device can generate programmable radio-frequency bursts or continuous waveforms with only the light source, electrical drives/controls and detectors being off-chip. It modulates an individual pulse in a radio-frequency burst within 4 ns, achieving a reconfiguration speed three orders of magnitude faster than thermal tuning. The on-chip optical delay elements offer an integrated approach to accurately manipulating individual radio-frequency waveform features without constraints set by the speed and timing jitter of electronics, and should find applications ranging from high-speed wireless to defence electronics.