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CRISPR-Cas systems and IS200/IS605 transposon-associated TnpBs have been utilized for the development of genome editing technologies. Using bioinformatics analysis and biochemical experiments, here we present a new family of RNA-guided DNA endonucleases. Our bioinformatics analysis initially identifies the stable co-occurrence of conserved RAGATH-18-derived RNAs (reRNAs) and their upstream IS607 TnpBs with an average length of 390 amino acids. IS607 TnpBs form programmable DNases through interaction with reRNAs. We discover the robust dsDNA interference activity of IS607 TnpB systems in bacteria and human cells. Further characterization of the Firmicutes bacteria IS607 TnpB system (ISFba1 TnpB) reveals that its dsDNA cleavage activity is remarkably sensitive to single mismatches between the guide and target sequences in human cells. Our findings demonstrate that a length of 20 nt in the guide sequence of reRNA achieves the highest DNA cleavage activity for ISFba1 TnpB. A cryo-EM structure of the ISFba1 TnpB effector protein bound by its cognate RAGATH-18 motif-containing reRNA and a dsDNA target reveals the mechanisms underlying reRNA recognition by ISFba1 TnpB, reRNA-guided dsDNA targeting, and the sensitivity of the ISFba1 TnpB system to base mismatches between the guide and target DNA. Collectively, this study identifies the IS607 TnpB family of compact and specific RNA-guided DNases with great potential for application in gene editing.
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Sistemas CRISPR-Cas , Humanos , Sistemas CRISPR-Cas/genética , RNA Guia de Sistemas CRISPR-Cas/metabolismo , DNA/metabolismo , Edição de Genes , Endonucleases/metabolismo , Células HEK293 , Clivagem do DNARESUMO
The rainbow patterns of oblate spheroidal drops have been observed in experiments nearly forty years ago [Nature312, 529 (1984)10.1038/312529a0]. However, the prediction for those complex patterns has been a challenge for conventional light scattering models. The vectorial complex ray model (VCRM) allows to account for the direction, the polarization, the phase, the amplitude and the wavefront curvature of waves and provides a powerful tool for the study of the light/electromagnetic wave interaction with a homogeneous object of any shape with smooth surface. In [Opt. Lett.46, 4585 (2021)10.1364/OL.434149], the authors have reported an important breakthrough of VCRM for the three-dimensional scattering (VCRM3D) and the simulated rainbow patterns of oblate drops. The present paper is devoted to the detailed description of the numerical implementation allowing the simulation of the 3D scattering field by a nonspherical particle. Its ability to predict both the fine and coarse intensity structures of the rainbows and the near-backward scattering patterns of spheroids is demonstrated. This work opens perspectives for exploring the 3D scattering characteristics of large objects with any smooth shape and developing relevant optical techniques for particle characterization.
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The CRISPR-Cas system is a highly adaptive and RNA-guided immune system found in bacteria and archaea, which has applications as a genome editing tool and is a valuable system for studying the co-evolutionary dynamics of bacteriophage interactions. Here introduces CRISPRimmunity, a new web server designed for Acr prediction, identification of novel class 2 CRISPR-Cas loci, and dissection of key CRISPR-associated molecular events. CRISPRimmunity is built on a suite of CRISPR-oriented databases providing a comprehensive co-evolutionary perspective of the CRISPR-Cas and anti-CRISPR systems. The platform achieved a high prediction accuracy of 0.997 for Acr prediction when tested on a dataset of 99 experimentally validated Acrs and 676 non-Acrs, outperforming other existing prediction tools. Some of the newly identified class 2 CRISPR-Cas loci using CRISPRimmunity have been experimentally validated for cleavage activity in vitro. CRISPRimmunity offers the catalogues of pre-identified CRISPR systems to browse and query, the collected resources or databases to download, a well-designed graphical interface, a detailed tutorial, multi-faceted information, and exportable results in machine-readable formats, making it easy to use and facilitating future experimental design and further data mining. The platform is available at http://www.microbiome-bigdata.com/CRISPRimmunity. Moreover, the source code for batch analysis are published on Github (https://github.com/HIT-ImmunologyLab/CRISPRimmunity).
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Sistemas CRISPR-Cas , Edição de Genes , Edição de Genes/métodos , Sistemas CRISPR-Cas/genética , Bactérias/genética , Archaea/genética , ComputadoresRESUMO
The transient receptor potential (TRP) channel is a type of channel protein widely distributed in peripheral and central nervous systems. Genes encoding TRP can be regulated by natural aromatic substances and serve as a therapeutic target for many diseases. However, the role of TRP-related genes in lung adenocarcinoma (LUAD) remains unclear. In this study, we used data from TCGA to screen and identify 17 TRP-related genes that are differentially expressed between LUAD and normal lung tissues. Based on these differentially expressed genes (DEGs), we classified all patients with LUAD into two subtypes. Significant differences in prognosis, clinical features, and immune cell infiltration characteristics were observed between the two subtypes. Subsequently, a prognostic signature with 12 genes was established by applying the least absolute shrinkage and selection operator (LASSO) Cox regression method, and all patients with LUAD were classified into low- and high-risk groups. Patients with LUAD in the low-risk group had a significantly longer survival time than those in the high-risk group (p < 0.001), which was confirmed by LUAD data from the GSE72094 and GSE68571 validation datasets. Combined with clinical characteristics, the risk score was found to be an independent predictor of overall survival (OS) in patients with LUAD. Additionally, patients with high TRP scores exhibited poorer clinical characteristics and immune status while showing a sensitive response to chemotherapeutic agents. In conclusion, the TRP score is a promising biomarker for determining the prognosis, molecular subtype, tumor microenvironment, and guiding personalized treatment in patients with LUAD.
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Background: Adaptor-related protein complex 3, sigma one subunit (AP3S1) is one of the encoding subunits of the adaptor complex AP-3. However, its role in various tumor types and relationship with the tumor immune microenvironment (TIME) remains unclear. Methods: AP3S1 expression was analyzed using datasets from The Cancer Genome Atlas, Genotype-Tissue Expression, UALCAN, and HPA databases. Then, we performed a systematic analysis of the genetic alterations, clinical features, and prognostic value of AP3S1 in pan-cancer. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to identify the signaling pathways associated with AP3S1. The correlation between immune cell infiltration and AP3S1 expression was analyzed using immune cell infiltration data from the ImmuCellAI, TIMER2, and a previous study. Finally, we analyzed the association of AP3S1 with tumor mutational burden (TMB), microsatellite instability (MSI), and immune-related genes. Results: We found AP3S1 overexpression in most tumors and a significant association with low survival rates. GSEA and GSVA results show that AP3S1 is involved in tumor progression and associated with immune pathways in different tumor types. We also found that AP3S1 expression was positively correlated with the level of infiltration of immunosuppressive cells (tumor-associated macrophages, cancer-associated fibroblasts, Tregs) and negatively correlated with immune killer cells, including NK cells and CD8+ T cells, in pan-cancer. The expression of AP3S1 could affect TMB and MSI in various cancers. In addition, AP3S1 was positively correlated with most immunosuppressive genes, including PD-1, PD-L1, CTLA4, LAG3 and TIGIT in most cancer types. Conclusion: Our study reveals that AP3S1 is a potential pan-cancer oncogene and plays an essential role in tumorigenesis and cancer immunity. Elevated expression of AP3S1 indicates an immunosuppressive microenvironment and can be used as a potential prognostic biomarker and a target for immunotherapy.
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As the most abundant natural aromatic resource, lignin valorization will contribute to a feasible biobased economy. Recently, biological lignin valorization has been advocated since ligninolytic microbes possess proficient funneling pathways of lignin to valuable products. In the present study, the potential to convert an actual lignin stream into polyhydroxyalkanoates (PHAs) had been evaluated using ligninolytic genome-reduced Pseudomonas putida. The results showed that the genome-reduced P. putida can grow well on an actual lignin stream to successfully yield a high PHA content and titer. The designed fermentation strategy almost eliminated the substrate effects of lignin on PHA accumulation. Employing a fed-batch strategy produced the comparable PHA contents and titers of 0.35 g/g dried cells and 1.4 g/L, respectively. The molecular mechanism analysis unveiled that P. putida consumed more small and hydrophilic lignin molecules to stimulate cell growth and PHA accumulation. Overall, the genome-reduced P. putida exhibited a superior capacity of lignin bioconversion and promote PHA accumulation, providing a promising route for sustainable lignin valorization.
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As the largest renewable aromatic resource, lignin is a promising feedstock for production of value-added products. However, lignin valorization has not been implemented due to the recalcitrant and heterogeneity of lignin. Herein, this work provides a systematic overview of bacterial lignin valorization for producing value-added products from the viewpoint of a cascaded conversion route. The combinatorial depolymerization strategy facilitates the yield of a lignin-derived aromatic stream suitable for the bacterial conversion. Bacterial active transports are curial to improve the uptake of lignin-derived aromatics. Intracellular metabolic pathways of bacteria assimilate heterogenous lignin-derived aromatics through "biological funnel" into central aromatic intermediates. These intermediates can be effectively metabolized in bacteria through aromatic ring cleavage pathways to enable the biosynthesis of various value-added products. The techno-economic analysis highlights that bacterial conversion improves the feasibility of co-production of value-added products from lignin. Therefore, the bacterial cascaded conversion routes hold great promise for upgrading heterogeneous lignin into value-added products and thus contribute to the profitability of lignin valorization.
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Bactérias , Lignina , Bactérias/metabolismo , Lignina/metabolismo , Redes e Vias MetabólicasRESUMO
Microbial cell factories have been widely used in the production of various chemicals. Although synthetic biology is useful in improving the cell factories, adaptation is still widely applied to enhance its complex properties. Adaptation is an important strategy for enhancing stress tolerance in microbial cell factories. Adaptation involves gradual modifications of microorganisms in a stressful environment to enhance their tolerance. During adaptation, microorganisms use different mechanisms to enhance non-preferred substrate utilization and stress tolerance, thereby improving their ability to adapt for growth and survival. In this paper, the progress on the effects of adaptation on microbial substrate utilization capacity and environmental stress tolerance are reviewed, and the mechanisms involved in enhancing microbial adaptive capacity are discussed.
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Background: Transient Receptor Potential (TRP) channel is a kind of channel protein widely distributed in peripheral and central nervous system. They can be regulated by natural aromatic substances and serve as a therapeutic target for many diseases. However, the role and function of the TRP family genes in tumours remain unclear. Methods: Gene alterations (mutation, copy number, methylation), expression, clinical features, and prognostic value of the TRP family genes were evaluated in pan-cancer using data from The Cancer Genome Atlas and Genotype-Tissue Expression databases. TRP score was calculated by the ssGSEA function of the R package "GSVA". The association of TRP score and the tumour microenvironment (TME), especially the tumour immune microenvironment (TIME), along with immunotherapy response were explored in-depth. Results: TRP family genes were involved in tumour progression and highly associated with poor prognosis in a variety of cancers. TRP score was positively associated with malignant pathways in pan-cancer, such as IL6-JAK-STAT3 signalling, interferon-gamma response, and inflammatory response. All pathways were closely associated with TIME. Elevated TRP score also correlated with multiple immune-related characteristics of the TIME in pan-cancer. Moreover, the TRP score was a predictive biomarker for immune checkpoint inhibitor (ICI) treatments in patients with tumours. Conclusions: TRP family genes play a key role in pan-cancer and are closely associated with TME. Patients with high TRP scores have excellent immune-activated TIME and immunotherapy sensitivity. Therefore, the TRP score could be a potential biomarker for patients with tumours treated with ICI.
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Neoplasias , Microambiente Tumoral , Humanos , Fatores Imunológicos/uso terapêutico , Imunoterapia , Neoplasias/tratamento farmacológico , Neoplasias/terapia , Prognóstico , Microambiente Tumoral/genéticaRESUMO
Background: Lung squamous cell carcinoma (LUSC) is a malignant tumour of the lung epithelium. A hypoxic environment can promote tumour cell proliferation and invasion. Therefore, this study aims to explore hypoxia-related genes and construct reliable models to predict the prognosis, cellular processes, immune microenvironment and target compounds of lung squamous carcinoma. Methods: The transcriptome data and matched clinical information of LUSC were retrieved from The Cancer Genome Atlas (TCGA) database. The GSVA algorithm calculated each LUSC patient's hypoxia score, and all LUSC patients were divided into the high hypoxia score group and low hypoxia score group. Weighted gene co-expression network analysis (WGCNA) and differential expression analysis were performed to screen out differentially expressed hypoxia-related genes (DE-HRGs) in LUSC microenvironment, and the underlying regulatory mechanism of DE-HRGs in LUSC was explored through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Hereafter, we established a prognosis-related genetic signature for DE-HRGs using univariate and multivariate Cox regression analyses. The relationship between gene signature and immune cells was further evaluated. Finally, the Comparative Toxicogenomics Database (CTD) was utilized to predict the targeted drugs for the prognostic genes. Results: We obtained 376 DE-HRGs. Functional enrichment analysis indicated that the DE-HRGs were involved in the cell cycle-related regulatory processes. Next, we developed and validated 3 HRGs-based prognostic signature for LUSC, including HELLS, GPRIN1, and FAM83A. Risk score is an independent prognostic factor for LUSC. Functional enrichment analysis and immune landscape analysis suggested that the risk scoring system might be involved in altering the immune microenvironment of LUSC patients to influence patient outcomes. Ultimately, a total of 92 potential compounds were predicted for the three prognostic genes. Conclusion: In summary, we developed and validated a hypoxia-related model for LUSC, reflecting the cellular processes and immune microenvironment characteristics and predicting the prognostic outcomes and targeted compounds.
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Background: Inducible co-stimulator (ICOS) is a cell-enhanced co-stimulatory receptor that has shown great potential in the regulation of innate and adaptive immunity. However, the role of ICOS in lung adenocarcinoma (LUAD) remains unclear. Methods: We used data from the Cancer Genome Atlas(TCGA) database to identify the expression and prognostic role of ICOS in LUAD. The results were validated using Gene Expression Omnibus(GEO) and Kaplan-Meier plotter databases. A model with predictive performance for overall survival of LUAD patients was constructed using fitted ICOS expression and other clinical parameters. We explored the biological function of ICOS. Subsequently, we further analysed and validated the effect of ICOS expression on tumour immune microenvironment (TIME) and survival. Finally, the CellMiner database was used to determine the relationship between ICOS expression and drug sensitivity. Results: ICOS expression is significantly associated with poor prognosis in multiple cancers, especially LUAD, and is a good predictor of overall survival in LUAD patients. The biological function is to promote autoimmunity and inhibit cell proliferation. ICOS-related survival prediction model developed to more accurately predict 1-, 3- and 5-year survival probabilities for LUAD patients. In addition, we can use the expression of ICOS to effectively assess patient malignancy, prognosis, TIME status and clinical combination of drugs. Conclusion: Our results suggest that ICOS is correlated with prognosis and immune infiltrating levels in LUAD. Higher ICOS expression predicts better TIME. This study provides a novel strategy for the development of immunotherapeutic and prognostic markers in LUAD.
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Airy published his theory in the 1830s to remedy the problem of infinite intensity in the rainbow angles of a spherical droplet predicted by geometrical optics. This theory has been studied by mathematicians and physicists since then from different points of view. In what concerns the scattering diagram around the rainbow angles, Airy theory has been improved by researchers in order to predict correctly the intensity of the supernumerary bows. However, it is known that the positions and the intensities of the supernumerary bows predicted by Airy theory differ from those of rigorous Debye theory with increasing order p and the scattering angles from the rainbow angle. In the present Letter, we will show that this discrepancy is caused by the approximations in Airy theory and can be revised by combining the vectorial complex ray model and physical optics (PO). The former permits us to calculate rigorously the amplitudes and phases of all rays and predicts precisely the scattering pattern except for the main bows. The combination with PO predicts very precisely all the supernumerary bows for both perpendicular and parallel polarization. This method can be applied directly to the light scattering of non-spherical particles with smooth surfaces.
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The measurement of hotspot electron temperature is a paramount technique of implosion physics research in inertial confinement fusion. This study proposes a novel quasi-coaxis dual-energy flat spectral response high-resolution X-ray imaging instrument comprising a dual-channel total-reflection Kirkpatrick-Baez microscope and two flat non-periodic multilayer mirrors, which can image at 6.4 ± 0.5 and 9.67 ± 0.5 keV simultaneously. Various theoretical simulations were performed to verify the performance and feasibility of the imaging instrument, which was assembled and characterized in a laboratory. Experimental results show that the imaging instrument could achieve a high spatial resolution of 5 µm in a ± 150 µm field of view (FOV), the root mean square(RMS) deviation values of the measured reflection efficiency are 1.71% and 1.82% for the 6.4 keV and 9.67 keV imaging channels, respectively, in the ± 150 µm FOV.
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A new method for measuring the time-dependent drive flux at the hohlraum center is proposed as a better alternative to conventional wall-based techniques. The drive flux here is obtained by simultaneous measurement of the reemitted flux and shock velocity from a three-layered "cakelike" sample. With these two independent observables, the influence induced by the uncertainty of the material parameters of the sample can be effectively decreased. The influence from the closure of the laser entrance hole, which was the main challenge in conventional wall-based techniques, was avoided through localized reemitted flux measurement, facilitating drive flux measurement throughout the entire time history. These studies pave a new way for probing the time-dependent drive flux, for both cylindrical hohlraums and novel hohlraums with six laser entrance holes.
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BACKGROUND: Sorting nexin-20 (SNX20) is a member of the sorting nexin family of proteins. It plays a crucial role in the regulation of innate immunity. However, the prognostic risk, potential mechanisms, immunotherapy, and other functions of SNX20 in lung adenocarcinoma (LUAD) remain unclear. METHODS: We analyzed and validated the expression and prognostic role of SNX20 in LUAD through a combination of The Cancer Genome Atlas, Gene Expression Omnibus, Oncomine, TIMER, and Human Protein Atlas databases. Further, we analyzed the correlation between SNX20 expression and clinical characteristics of LUAD, and the prognostic value of SNX20 in LUAD was evaluated. Using fitted SNX20 expression and other clinical parameters, a predictive model with predictive performance for the overall survival of patients with LUAD was constructed. The potential biological function of SNX20 in LUAD was explored using gene set enrichment analysis. In addition, we analyzed the correlation between SNX20 expression and the immune microenvironment and survival. RESULTS: SNX20 was downregulated in most cancer types, was associated with poor prognosis in LUAD and could be an independent prognostic factor for patients with LUAD. The predictive model developed by us had good predictive power for determining the overall survival of patients with LUAD. Biofunctional analysis revealed that genes co-expressed with SNX20 mainly promoted the immune process and inhibited the cell proliferation process in LUAD. We observed that high expression of SNX20 was accompanied by a better immune microenvironment and survival in patients with LUAD. Furthermore, the LUAD immune response was elevated with an increase in SNX20 expression. Finally, we found that SNX20 expression was significantly associated with various tumor-infiltrating immune cells, and it was widely involved in regulating various immune molecules in LUAD and affecting immune infiltration in the tumor microenvironment. CONCLUSION: Our results suggested that SNX20 is a potential immune-related biomarker and therapeutic target associated with the prognosis of patients with LUAD. This provided a new strategy for the development of immunotherapeutic and prognostic markers in LUAD.
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The scattering patterns near the primary rainbow of oblate drops are simulated by extending the vectorial complex ray model (VCRM) [Opt. Lett.36, 370 (2011)OPLEDP0146-959210.1364/OL.36.000370] to three-dimensional (3D) calculations. With the curvature of a wavefront as an intrinsic property of a ray, this advanced ray model permits, in principle, to predict the amplitudes and phases of all emergent rays with a rigorous algebraic formalism. This Letter reports a breakthrough of VCRM for 3D scattering with a line-by-line triangulation interpolation algorithm allowing to calculate the total complex amplitude of a scattered field. This makes possible to simulate not only the skeleton (geometrical rainbow angles, hyperbolic-umbilic caustics), but also the coarse (Airy bows, lattice) and fine (ripple fringes) structures of the generalized rainbow patterns (GRPs) of oblate drops. The simulated results are found qualitatively and quantitatively in good agreement with experimental scattering patterns for drops of different aspect ratios. The physical interpretation of the GRPs is also given. This work opens up prominent perspectives for simulating and understanding the 3D scattering of large particles of any shape with a smooth surface by VCRM.
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In inertial confinement fusion, quantitative and high-spatial resolution ([Formula: see text]m) measurements of the X-rays self-emitted by the hotspot are critical for studying the physical processes of the implosion stagnation stage. Herein, the 8 ± 0.39-keV monochromatic X-ray distribution from the entire hotspot is quantitatively observed in 5-[Formula: see text]m spatial resolution using a Kirkpatrick-Baez microscope, with impacts from the responses of the diagnosis system removed, for the first time, in implosion experiments at the 100 kJ laser facility in China. Two-dimensional calculations along with 2.5% P2 drive asymmetry and 0.3 ablator self-emission are congruent with the experimental results, especially for the photon number distribution, hotspot profile, and neutron yield. Theoretical calculations enabled a better understanding of the experimental results. Furthermore, the origins of the 17.81% contour profile of the deuterium-deuterium hotspot and the accurate Gaussian source approximation of the core emission area in the implosion capsule are clarified in detail. This work is significant for quantitatively exploring the physical conditions of the hotspot and updating the theoretical model of capsule implosion.
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Chitinases play an important role in many industrial processes, including the preparation of oligosaccharides with potential applications. In the present study, a 1,713 bp gene of Chi1602, derived from a marine bacterium Microbulbifer sp. BN3, encoding a GH18 family chitinase, was expressed at high levels in Pichia pastoris. Distinct from most of the marine chitinases, the recombinant chitinase 1602 exhibited maximal activity at 60 °C and over a broad pH range between 5.0 and 9.0, and was stable at 50 °C and over the pH range 4.0-9.0. The hydrolytic products derived from colloidal chitins comprised mainly (GlcNAc)2 and GlcNAc, indicating that rChi1602 is a GH18 processive chitinase in conformity with its hypothetical structure. However, rChi1602 showed traces of ß-N-acetylglucosaminidase activity on substrates such as powder chitin, chitosan, and ethylene glycol chitin. The thermophilic rChi1602, which manifests adaptation to a wide pH range and can be expressed at a high level in P. pastoris, is advantageous for applications in industrial processes.
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Alteromonadaceae/enzimologia , Quitinases/genética , Regulação Enzimológica da Expressão Gênica/genética , Pichia/genética , Temperatura , Quitinases/metabolismo , Concentração de Íons de HidrogênioRESUMO
Chitinases play an important role in the process of chitin bioavailability. In this study, we cloned a new chitinase gene and characterized its recombinant protein. The new 1251 bp gene of chitinase (ChiT-7) was cloned from the metagenome of the mangrove tidal flat soil in the city of Zhangzhou in Fujian Province (China) by genome walking. The gene encoded a mature protein with 381 amino acids, which manifested certain sequence similarity (59% identity) to characterized GH18 chitinases. The mature protein of ChiT-7 was successfully expressed in E. coli BL21 (DE3). After purification, the specific activity of the recombinant enzyme was 0.63 U/mg at the optimal pH of 6.0 and the optimal temperature of 45 °C. The rChiT-7 was active over a wide pH range, and the residual enzyme activity reached 80% or higher at 30 °C-50 °C. rChiT-7 hydrolyzed colloidal chitin with (GlcNAc)2 and GlcNAc as the main final products. Structural analysis of ChiT-7 indicated that ChiT-7 could be a processive chitinase. rChiT-7 manifested characteristics analogous to those of fungi and actinomycetes and exhibited sequence homology.