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Deaminases have important uses in modification detection and genome editing. However, the range of applications is limited by the small number of characterized enzymes. To expand the toolkit of deaminases, we developed an in vitro approach that bypasses a major hurdle with their toxicity in cells. We assayed 175 putative cytosine deaminases on a variety of substrates and found a broad range of activity on double- and single-stranded DNA in various sequence contexts, including CpG-specific deaminases and enzymes without sequence preference. We also characterized enzyme selectivity across six DNA modifications and reported enzymes that do not deaminate modified cytosines. The detailed analysis of diverse deaminases opens new avenues for biotechnological and medical applications. As a demonstration, we developed SEM-seq, a non-destructive single-enzyme methylation sequencing method using a modification-sensitive double-stranded DNA deaminase. The streamlined protocol enables accurate, base-resolution methylome mapping of scarce biological material, including cell-free DNA and 10 pg input DNA.
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Citosina Desaminase , Epigenoma , DNA/genética , Citosina , DNA de Cadeia Simples/genética , Citidina Desaminase/genéticaRESUMO
Circular RNA (circRNA) has recently gained attention for its emerging biological activities, relevance to disease, potential as biomarkers, and promising an alternative modality for RNA vaccines. Nevertheless, sequencing circRNAs has presented challenges. In this context, we introduce a novel circRNA sequencing method called Induro-RT mediated circRNA-sequencing (IMCR-seq), which relies on a group II intron reverse transcriptase with robust rolling circle reverse transcription activity. The IMCR-seq protocol eliminates the need for conventional circRNA enrichment methods such as rRNA depletion and RNaseR digestion yet achieved the highest circRNA enrichment and detected 6-1000 times more circRNAs for the benchmarked human samples compared to other methods. IMCR-seq is applicable to any organism, capable of detecting circRNAs of longer than 7000 nucleotides, and is effective on samples as small as 10 ng of total RNA. These enhancements render IMCR-seq suitable for clinical samples, including disease tissues and liquid biopsies. We demonstrated the clinical relevance of IMCR-seq by detecting cancer-specific circRNAs as potential biomarkers from IMCR-seq results on lung tumor tissues together with blood plasma samples from both a healthy individual and a lung cancer patient. In summary, IMCR-seq presents an efficient and versatile circRNA sequencing method with high potential for research and clinical applications.
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Neoplasias Pulmonares , RNA Circular , Análise de Sequência de RNA , RNA Circular/genética , Humanos , Análise de Sequência de RNA/métodos , Neoplasias Pulmonares/genética , Biomarcadores Tumorais/genética , Transcrição Reversa , Sequenciamento de Nucleotídeos em Larga Escala/métodosRESUMO
Rationally modulating the binding strength of reaction intermediates on surface sites of copper-based catalysts could facilitate C-C coupling to generate multicarbon products in an electrochemical CO2 reduction reaction. Herein, theoretical calculations reveal that cascade Ag-Cu dual sites could synergistically increase local CO coverage and lower the kinetic barrier for CO protonation, leading to enhanced asymmetric C-C coupling to generate C2H4. As a proof of concept, the Cu3N-Ag nanocubes (NCs) with Ag located in partial Cu sites and a Cu3N unit center are successfully synthesized. The Faraday efficiency and partial current density of C2H4 over Cu3N-Ag NCs are 7.8 and 9.0 times those of Cu3N NCs, respectively. In situ spectroscopies combined with theoretical calculations confirm that Ag sites produce CO and Cu sites promote asymmetric C-C coupling to *COCHO, significantly enhancing the generation of C2H4. Our work provides new insights into the cascade catalysis strategy at the atomic scale for boosting CO2 to multicarbon products.
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With more flexible active sites and intermetal interaction, dual-atom catalysts (DACs) have emerged as a new frontier in various electrocatalytic reactions. Constructing a typical p-d orbital hybridization between p-block and d-block metal atoms may bring new avenues for manipulating the electronic properties and thus boosting the electrocatalytic activities. Herein, we report a distinctive heteronuclear dual-metal atom catalyst with asymmetrical FeSn dual atom sites embedded on a two-dimensional C2N nanosheet (FeSn-C2N), which displays excellent oxygen reduction reaction (ORR) performance with a half-wave potential of 0.914 V in an alkaline electrolyte. Theoretical calculations further unveil the powerful p-d orbital hybridization between p-block stannum and d-block ferrum in FeSn dual atom sites, which triggers electron delocalization and lowers the energy barrier of *OH protonation, consequently enhancing the ORR activity. In addition, the FeSn-C2N-based Zn-air battery provides a high maximum power density (265.5 mW cm-2) and a high specific capacity (754.6 mA h g-1). Consequently, this work validates the immense potential of p-d orbital hybridization along dual-metal atom catalysts and provides new perception into the logical design of heteronuclear DACs.
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Efficient and sustainable energy development is a powerful tool for addressing the energy and environmental crises. Single-atom catalysts (SACs) have received high attention for their extremely high atom utilization efficiency and excellent catalytic activity, and have broad application prospects in energy development and chemical production. M-N4 is an active center model with clear catalytic activity, but its catalytic properties such as catalytic activity, selectivity, and durability need to be further improved. Adjustment of the coordination environment of the central metal by incorporating heteroatoms (e.g., sulfur) is an effective and feasible modification method. This paper describes the precise synthetic methods for introducing sulfur atoms into M-N4 and controlling whether they are directly coordinated with the central metal to form a specific coordination configuration, the application of sulfur-doped carbon-based single-atom catalysts in electrocatalytic reactions such as ORR, CO2RR, HER, OER, and other electrocatalytic reaction are systematically reviewed. Meanwhile, the effect of the tuning of the electronic structure and ligand configuration parameters of the active center due to doped sulfur atoms with the improvement of catalytic performance is introduced by combining different characterization and testing methods. Finally, several opinions on development of sulfur-doped carbon-based SACs are put forward.
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Accurately detecting distant evolutionary relationships between proteins remains an ongoing challenge in bioinformatics. Search methods based on primary sequence struggle to accurately detect homology between sequences with less than 20% amino acid identity. Profile- and structure-based strategies extend sensitive search capabilities into this twilight zone of sequence similarity but require slow pre-processing steps. Recently, whole-protein and positional embeddings from deep neural networks have shown promise for providing sensitive sequence comparison and annotation at long evolutionary distances. Embeddings are generally faster to compute than profiles and predicted structures but still suffer several drawbacks related to the ability of whole-protein embeddings to discriminate domain-level homology, and the database size and search speed of methods using positional embeddings. In this work, we show that low-dimensionality positional embeddings can be used directly in speed-optimized local search algorithms. As a proof of concept, we use the ESM2 3B model to convert primary sequences directly into the 3D interaction (3Di) alphabet or amino acid profiles and use these embeddings as input to the highly optimized Foldseek, HMMER3, and HH-suite search algorithms. Our results suggest that positional embeddings as small as a single byte can provide sufficient information for dramatically improved sensitivity over amino acid sequence searches without sacrificing search speed.
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Algoritmos , Proteínas , Alinhamento de Sequência , Proteínas/genética , Proteínas/química , Sequência de Aminoácidos , Biologia Computacional/métodos , AminoácidosRESUMO
In order to evaluate the influence of global warming on the ecosystem processes in marine environments, the changes in colonization dynamics of periphytic microbiota were studied using the periphytic ciliate communities as the test organism fauna under a continuous warming gradient of 22â (control), 25â, 28â, 31â, and 34 â. The results demonstrated that (1) the test ciliate communities generally showed a similar temporal pattern in within the colonization process under the water temperatures from 22 up to 28â; however, (2) the colonization dynamics were significantly changed, and the fitness of colonization curves to the MacArthur-Wilson model equation was failed under the temperature increased by 6 â, and (3) the loading or assimilative capacity of the test aquatic ecosystem was decreased with the increase of water temperature. Therefore, this study suggests that continuous warming may significantly drive the colonization dynamics of periphytic ciliates in marine ecosystems.
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Cilióforos , Ecossistema , Aquecimento Global , Cilióforos/fisiologia , TemperaturaRESUMO
To investigate effects of salinity variability on colonization dynamics of periphytic protozoan fauna, a 21-day study was conducted in temperature-controlled circulation systems (TCCSs). Periphytic protozoan communities were incubated using glass slides as artificial substrata in five TCCS aquaria with a large-scale salinity gradient of 9, 19, 29 (control), 39, and 49 PSU, respectively. The colonization dynamics were observed on days 3, 5, 7, 10, 14, and 21. The colonization dynamics were well fitted to the MacArthur-Wilson and logistic model equations in colonization and growth curves in all five treatments, respectively. However, the maximum species richness and abundance were reduced, and the colonization patterns were significantly shifted in four treatments with salinity changed by 20 PSU compared to the control (29 PSU). Thus, it is suggested that the large-scale salinity variability may reduce the species richness significantly and affect colonization dynamics of periphytic protozoan fauna in marine environments.
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Biodiversidade , Cilióforos , Monitoramento Ambiental , Salinidade , Modelos Logísticos , EcossistemaRESUMO
Low-dose computer tomography (LDCT) has been widely used in medical diagnosis. Various denoising methods have been presented to remove noise in LDCT scans. However, existing methods cannot achieve satisfactory results due to the difficulties in (1) distinguishing the characteristics of structures, textures, and noise confused in the image domain, and (2) representing local details and global semantics in the hierarchical features. In this paper, we propose a novel denoising method consisting of (1) a 2D dual-domain restoration framework to reconstruct noise-free structure and texture signals separately, and (2) a 3D multi-depth reinforcement U-Net model to further recover image details with enhanced hierarchical features. In the 2D dual-domain restoration framework, the convolutional neural networks are adopted in both the image domain where the image structures are well preserved through the spatial continuity, and the sinogram domain where the textures and noise are separately represented by different wavelet coefficients and processed adaptively. In the 3D multi-depth reinforcement U-Net model, the hierarchical features from the 3D U-Net are enhanced by the cross-resolution attention module (CRAM) and dual-branch graph convolution module (DBGCM). The CRAM preserves local details by integrating adjacent low-level features with different resolutions, while the DBGCM enhances global semantics by building graphs for high-level features in intra-feature and inter-feature dimensions. Experimental results on the LUNA16 dataset and 2016 NIH-AAPM-Mayo Clinic LDCT Grand Challenge dataset illustrate the proposed method outperforms the state-of-the-art methods on removing noise from LDCT images with clear structures and textures, proving its potential in clinical practice.
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Pulmão , Redes Neurais de Computação , Razão Sinal-Ruído , Tomografia Computadorizada por Raios X , Humanos , Tomografia Computadorizada por Raios X/métodos , Pulmão/diagnóstico por imagem , Algoritmos , Processamento de Imagem Assistida por Computador/métodos , Doses de RadiaçãoRESUMO
Low-dose computed tomography (LDCT) has been widely used in medical diagnosis. In practice, doctors often zoom in on LDCT slices for clearer lesions and issues, while, a simple zooming operation fails to suppress low-dose artifacts, leading to distorted details. Therefore, numerous LDCT super-resolution (SR) methods have been proposed to promote the quality of zooming without the increase of the dose in CT scanning. However, there are still some drawbacks that need to be addressed in existing methods. First, the region of interest (ROI) is not emphasized due to the lack of guidance in the reconstruction process. Second, the convolutional blocks extracting fix-resolution features fail to concentrate on the essential multi-scale features. Third, a single SR head cannot suppress the residual artifacts. To address these issues, we propose an LDCT CT joint SR and denoising reconstruction network. Our proposed network consists of global dual-guidance attention fusion modules (GDAFMs) and multi-scale anastomosis blocks (MABs). The GDAFM directs the network to focus on ROI by fusing the extra mask guidance and average CT image guidance, while the MAB introduces hierarchical features through anastomosis connections to leverage multi-scale features and promote the feature representation ability. To suppress radial residual artifacts, we optimize our network using the feedback feature distillation mechanism (FFDM) which shares the backbone to learn features corresponding to the denoising task. We apply the proposed method to the 3D-IRCADB and PANCREAS datasets to evaluate its ability on LDCT image SR reconstruction. The experimental results compared with state-of-the-art methods illustrate the superiority of our approach with respect to peak signal-to-noise (PSNR), structural similarity (SSIM), and qualitative observations. Our proposed LDCT joint SR and denoising reconstruction network has been extensively evaluated through ablation, quantitative, and qualitative experiments. The results demonstrate that our method can recover noise-free and detail-sharp images, resulting in better reconstruction results. Code is available at https://github.com/neu-szy/ldct_sr_dn_w_ffdm .
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Artefatos , Tomografia Computadorizada por Raios X , Tomografia Computadorizada por Raios X/métodos , Humanos , Processamento de Imagem Assistida por Computador/métodos , Doses de Radiação , Razão Sinal-Ruído , Algoritmos , Retroalimentação , Redes Neurais de ComputaçãoRESUMO
Objective: Ulcerative colitis (UC) and metabolic dysfunction-associated steatotic liver disease (MASLD) are closely intertwined; however, the precise molecular mechanisms governing their coexistence remain unclear. Methods: We obtained UC (GSE75214) and MASLD (GSE151158) datasets from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were acquired by the 'edgeR' and 'limma' packages of R. We then performed functional enrichment analysis of common DEGs. Hub genes were selected using the cytoHubba plugin and validated using GSE87466 for UC and GSE33814 for MASLD. Immunohistochemistry was employed to validate the hub genes' expression in clinical samples. Immune infiltration and gene set enrichment analyses of the hub genes were performed. Finally, we estimated the Spearman's correlation coefficients for the clinical correlation of the core genes. Results: Within a cohort of 26 differentially regulated genes in both UC and MASLD, pathways involving cytokine-mediated signaling, cell chemotaxis, and leukocyte migration were enriched. After further validation, CXCR4, THY1, CCL20, and CD2 were identified as the hub genes. Analysis of immune infiltration patterns highlighted an association between elevated pivotal gene expression and M1 macrophage activation. Immunohistochemical staining revealed widespread expression of pivotal genes in UC- and MASLD-affected tissues. Furthermore, significant correlations were observed between the increased expression of hub genes and biochemical markers, such as albumin and prothrombin time. Conclusion: This bioinformatics analysis highlights CXCR4, THY1, CCL20, and CD2 as crucial genes involved in the co-occurrence of UC and MASLD, providing insights into the underlying mechanisms of these two conditions.
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Colite Ulcerativa , Fígado Gorduroso , Doenças Metabólicas , Humanos , Colite Ulcerativa/genética , Albuminas , Movimento CelularRESUMO
The pollution of microplastics (MPs) to the marine environment has become a widespread focus of attention. To assess MP-induced ecotoxicity on marine ecosystems, periphytic protozoan communities were used as test organisms and exposed to five concentrations of MPs: 0, 1, 5, 25, and 125 mg l-1. Protozoan samples were collected using microscope slides from coastal waters of the Yellow Sea, northern China. A total of 13 protozoan species were identified and represented different tolerance to MP-induced ecotoxicity. Inhibition effects of MPs on the test protozoan communities were clearly shown in terms of both the species richness and individual abundance and followed linear relationships to MP concentrations. The community patterns were driven by MPs and significantly shifted at concentrations over 5 mg l-1. Our findings demonstrated that MPs may induce the community-level ecotoxic response of periphytic protozoan fauna and followed significant community dynamics. Thus, it is suggested that periphytic protozoan fauna may be used as useful community-based test model organisms for evaluating MP-induced ecotoxicity in marine environments.
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Cilióforos , Poluentes Químicos da Água , Ecossistema , Biodiversidade , Monitoramento Ambiental , Microplásticos , Plásticos , Cilióforos/fisiologia , Poluentes Químicos da Água/toxicidadeRESUMO
The ideal interface design between the metal and substrate is crucial in determining the overall performance of the alkyne semihydrogenation reaction. Single-atom alloys (SAAs) with isolated dispersed active centers are ideal media for the study of reaction effects. Herein, a charge-asymmetry "armor" SAA (named Pd1Fe SAA@PC), which consists of a Pd1Fe alloy core and a semiconducting P-doped C (PC) shell, is rationally designed as an ideal catalyst for the selective hydrogenation of alkynes with high efficiency. Multiple spectroscopic analyses and density functional theory calculations have demonstrated that Pd1Fe SAA@PC is dual-regulated by lattice tensile and Schottky effects, which govern the selectivity and activity of hydrogenation, respectively. (1) The PC shell layer applied an external traction force causing a 1.2% tensile strain inside the Pd1Fe alloy to increase the reaction selectivity. (2) P doping into the C-shell layer realized a transition from a p-type semiconductor to an n-type semiconductor, thereby forming a unique Schottky junction for advancing alkyne semihydrogenation activity. The dual regulation of lattice strain and the Schottky effect ensures the excellent performance of Pd1Fe SAA@PC in the semihydrogenation reaction of phenylethylene, achieving a conversion rate of 99.9% and a selectivity of 98.9% at 4 min. These well-defined interface modulation strategies offer a practical approach for the rational design and performance optimization of semihydrogenation catalysts.
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Double-atom catalysts (DACs) with asymmetric coordination are crucial for enhancing the benefits of electrochemical carbon dioxide reduction and advancing sustainable development, however, the rational design of DACs is still challenging. Herein, this work synthesizes atomically dispersed catalysts with novel sulfur-bridged Cu-S-Ni sites (named Cu-S-Ni/SNC), utilizing biomass wool keratin as precursor. The plentiful disulfide bonds in wool keratin overcome the limitations of traditional gas-phase S ligand etching process and enable the one-step formation of S-bridged sites. X-ray absorption spectroscopy (XAS) confirms the existence of bimetallic sites with N2Cu-S-NiN2 moiety. In H-cell, Cu-S-Ni/SNC shows high CO Faraday efficiency of 98.1% at -0.65 V versus RHE. Benefiting from the charge tuning effect between the metal site and bridged sulfur atoms, a large current density of 550 mA cm-2 can be achieved at -1.00 V in flow cell. Additionally, in situ XAS, attenuated total reflection surface-enhanced infrared absorption spectroscopy (ATR-SEIRAS), and density functional theory (DFT) calculations show Cu as the main adsorption site is dual-regulated by Ni and S atoms, which enhances CO2 activation and accelerates the formation of *COOH intermediates. This kind of asymmetric bimetallic atom catalysts may open new pathways for precision preparation and performance regulation of atomic materials toward energy applications.
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Developing high-performance Pt-based catalysts with low Pt loading is crucial but challenging for CO oxidation at temperatures below 100 °C. Herein, we report a Pt-based catalyst with only a 0.15 wt% Pt loading, which consists of Pt-Ti intermetallic single-atom alloy (ISAA) and Pt nanoparticles (NP) co-supported on a defective TiO2 support, achieving a record high turnover frequency of 11.59 s-1 at 80 °C and complete conversion of CO at 120 °C. This is because the coexistence of Pt-Ti ISAA and Pt NP significantly alleviates the competitive adsorption of CO and O2, enhancing the activation of O2. Furthermore, Pt single atom sites are stabilized by Pt-Ti ISAA, resulting in distortion of the TiO2 lattice within Pt-Ti ISAA. This distortion activates the neighboring surface lattice oxygen, allowing for the simultaneous occurrence of the Mars-van Krevelen and Langmuir-Hinshelwood reaction paths at low temperatures.
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BACKGROUND: The understanding of the heterogeneous cellular microenvironment of colonic polyps in paediatric patients with solitary juvenile polyps (SJPs), polyposis syndrome (PJS) and Peutz-Jeghers syndrome (PJS) remains limited. METHODS: We conducted single-cell RNA sequencing and multiplexed immunohistochemistry (mIHC) analyses on both normal colonic tissue and different types of colonic polyps obtained from paediatric patients. RESULTS: We identified both shared and disease-specific cell subsets and expression patterns that played important roles in shaping the unique cellular microenvironments observed in each polyp subtype. As such, increased myeloid, endothelial and epithelial cells were the most prominent features of SJP, JPS and PJS polyps, respectively. Noticeably, memory B cells were increased, and a cluster of epithelial-mesenchymal transition (EMT)-like colonocytes existed across all polyp subtypes. Abundant neutrophil infiltration was observed in SJP polyps, while CX3CR1hi CD8+ T cells and regulatory T cells (Tregs) were predominant in SJP and JPS polyps, while GZMAhi natural killer T cells were predominant in PJS polyps. Compared with normal colonic tissues, myeloid cells exhibited specific induction of genes involved in chemotaxis and interferon-related pathways in SJP polyps, whereas fibroblasts in JPS polyps had upregulation of myofiber-associated genes and epithelial cells in PJS polyps exhibited induction of a series of nutrient absorption-related genes. In addition, the TNF-α response was uniformly upregulated in most cell subsets across all polyp subtypes, while endothelial cells and fibroblasts separately showed upregulated cell adhesion and EMT signalling in SJP and JPS polyps. Cell-cell interaction network analysis showed markedly enhanced intercellular communication, such as TNF, VEGF, CXCL and collagen signalling networks, among most cell subsets in polyps, especially SJP and JPS polyps. CONCLUSION: These findings strengthen our understanding of the heterogeneous cellular microenvironment of polyp subtypes and identify potential therapeutic approaches to reduce the recurrence of polyps in children.
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Pólipos do Colo , Humanos , Criança , Linfócitos T CD8-Positivos , Células Endoteliais , Microambiente Celular , Comunicação CelularRESUMO
Monitoring the dynamic changes of cellular tRNA pools is challenging, due to the extensive post-transcriptional modifications of individual species. The most critical component in tRNAseq is a processive reverse transcriptase (RT) that can read through each modification with high efficiency. Here we show that the recently developed group-II intron RT Induro has the processivity and efficiency necessary to profile tRNA dynamics. Using our Induro-tRNAseq, simpler and more comprehensive than the best methods to date, we show that Induro progressively increases readthrough of tRNA over time and that the mechanism of increase is selective removal of RT stops, without altering the misincorporation frequency. We provide a parallel dataset of the misincorporation profile of Induro relative to the related TGIRT RT to facilitate the prediction of non-annotated modifications. We report an unexpected modification profile among human proline isoacceptors, absent from mouse and lower eukaryotes, that indicates new biology of decoding proline codons.