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1.
Molecules ; 29(7)2024 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-38611743

RESUMO

Benzene is the typical volatile organic compound (VOC) of indoor and outdoor air pollution, which harms human health and the environment. Due to the stability of their aromatic structure, the catalytic oxidation of benzene rings in an environment without an external energy input is difficult. In this study, the efficient degradation of benzene at room temperature was achieved by constructing Ag and Ni bimetallic active site catalysts (AgNi/BCN) supported on boron-carbon-nitrogen aerogel. The atomic-scale Ag and Ni are uniformly dispersed on the catalyst surface and form Ag/Ni-C/N bonds with C and N, which were conducive to the catalytic oxidation of benzene at room temperature. Further catalytic reaction mechanisms indicate that benzene reacted with ·OH to produce R·, which reacted with O2 to regenerate ·OH. Under the strong oxidation of ·OH, benzene was oxidized to form alcohols, carboxylic acids, and eventually CO2 and H2O. This study not only significantly reduces the energy consumption of VOC catalytic oxidation, but also improves the safety of VOC treatment, providing new ideas for the low energy consumption and green development of VOC treatment.

2.
Cell Prolif ; : e13646, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38623945

RESUMO

Transglutaminase 2 (Tgm2) plays an essential role in hepatic repair following prolonged toxic injury. During cholestatic liver injury, the intrahepatic cholangiocytes undergo dynamic tissue expansion and remodelling, referred to as ductular reaction (DR), which is crucial for liver regeneration. However, the molecular mechanisms governing the dynamics of active cells in DR are still largely unclear. Here, we generated Tgm2-knockout mice (Tgm2-/-) and Tgm2-CreERT2-Rosa26-mTmG flox/flox (Tgm2CreERT2-R26T/Gf/f) mice and performed a three-dimensional (3D) collagen gel culture of mouse hepatocytes to demonstrate how Tgm2 signalling is involved in DR to remodel intrahepatic cholangiocytes. Our results showed that the deletion of Tgm2 adversely affected the functionality and maturity of the proliferative cholangiocytes in DR, thus leading to more severe cholestasis during DDC-induced liver injury. Additionally, Tgm2 hepatocytes played a crucial role in the regulation of DR through metaplasia. We unveiled that Tgm2 regulated H3K4me3Q5ser via serotonin to promote BMP signalling activation to participate in DR. Besides, we revealed that the activation or inhibition of BMP signalling could promote or suppress the development and maturation of cholangiocytes in DDC-induced DR. Furthermore, our 3D collagen gel culture assay indicated that Tgm2 was vital for the development of cholangiocytes in vitro. Our results uncovered a considerable role of BMP signalling in controlling metaplasia of Tgm2 hepatocytes in DR and revealed the phenotypic plasticity of mature hepatocytes.

3.
Opt Express ; 32(6): 9105-9115, 2024 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-38571151

RESUMO

The strong interaction between light and matter is one of the current research hotspots in the field of nanophotonics, and provides a suitable platform for fundamental physics research such as on nanolasers, high-precision sensing in biology, quantum communication and quantum computing. In this study, double Rabi splitting was achieved in a composite structure monolayer MoS2 and a single Ag@Au hollow nanocube (HNC) in room temperature mainly due to the two excitons in monolayer MoS2. Moreover, the tuning of the plasmon resonance peak was realized in the scattering spectrum by adjusting the thickness of the shell to ensure it matches the energy of the two excitons. Two distinct anticrossings are observed at both excitons resonances, and large double Rabi splittings (90 meV and 120 meV) are obtained successfully. The finite-difference time domain (FDTD) method was also used to simulate the scattering spectra of the nanostructures, and the simulation results were in good agreement with the experimental results. Additionally, the local electromagnetic field ability of the Ag@Au hollow HNC was proved to be stronger by calculating and comparing the mode volume of different nanoparticles. Our findings provides a good platform for the realization of strong multi-mode coupling and open up a new way to construct nanoscale photonic devices.

4.
iScience ; 27(3): 109278, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38482502

RESUMO

Epigenetic modifications have emerged as key regulators of metabolism-related complex diseases including the alcoholic fatty liver disease (AFLD) prevalent chronic liver disorder with significant economic implications. Building upon previous research that emphasizes ten-eleven translocation (TET) proteins' involvement in adipocyte insulin sensitization and fatty acid oxidation, we explored the role of TET2 protein in AFLD pathogenesis which catalyzes 5-methylcytosine into 5-hydroxymethylcytosine in DNA/RNA. Our findings revealed that TET2 deficiency exacerbates AFLD progression. And TET2 influenced the expression and activity of sterol regulatory element binding protein 1 (SREBP1), a key regulator of hepatic lipid synthesis, by modulating Srebp1 mRNA retention. Employing RIP-qPCR and bisulfite sequencing techniques, we provided evidence of TET2-mediated epigenetic modifications on Srebp1 mRNA, thereby affecting lipid metabolism. Through elucidating the role of methylation in RNA nuclear retention via paraspeckles, our study enhances understanding of AFLD pathogenesis from an epigenetic perspective, paving the way for identifying potential therapeutic targets.

5.
RNA ; 30(5): 548-559, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38531647

RESUMO

N 1-methyl adenosine (m1A) is a widespread RNA modification present in tRNA, rRNA, and mRNA. m1A modification sites in tRNAs are evolutionarily conserved and its formation on tRNA is catalyzed by methyltransferase TRMT61A and TRMT6 complex. m1A promotes translation initiation and elongation. Due to its positive charge under physiological conditions, m1A can notably modulate RNA structure. It also blocks Watson-Crick-Franklin base-pairing and causes mutation and truncation during reverse transcription. Several misincorporation-based high-throughput sequencing methods have been developed to sequence m1A. In this study, we introduce a reduction-based m1A sequencing (red-m1A-seq). We report that NaBH4 reduction of m1A can improve the mutation and readthrough rates using commercially available RT enzymes to give a better positive signature, while alkaline-catalyzed Dimroth rearrangement can efficiently convert m1A to m6A to provide good controls, allowing the detection of m1A with higher sensitivity and accuracy. We applied red-m1A-seq to sequence human small RNA, and we not only detected all the previously reported tRNA m1A sites, but also new m1A sites in mt-tRNAAsn-GTT and 5.8S rRNA.


Assuntos
RNA de Transferência , RNA , Humanos , Metilação , RNA de Transferência/química , RNA/genética , tRNA Metiltransferases/genética , tRNA Metiltransferases/metabolismo , Metiltransferases/metabolismo , RNA Mensageiro/genética
6.
Pest Manag Sci ; 2024 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-38459943

RESUMO

BACKGROUND: The ladybeetle, Coccinella septempunctata, an important predator, is widely used to control aphids, whiteflies, mites, thrips, and lepidopteran pests. Diapause control technology is key to extending C. septempunctata shelf-life and commercialization. Lipid accumulation is a major feature of reproductive diapause, but the function of AKH signaling as a regulator of lipid mobilization in reproductive diapause remains unclear. This study aimed to identify and characterize AKH and AKHR genes, and clarify their functions in reproductive diapause. RESULTS: The relative expression levels of CsAKH and CsAKHR were the highest in the head and fat body, respectively, and were significantly decreased under diapause conditions, both in developmental stages and tissues (head, midgut, fat body, and ovary). Furthermore, CsAKH and CsAKHR expression was increased significantly after juvenile hormone (JH) injection, but CsMet silencing significantly inhibited CsAKH and CsAKHR expression, whereas CsMet knockdown blocked the induction effect of JH. CsAKH and CsAKHR knockdown significantly reduced water content, increased lipid storage, and promoted the expression of genes related to lipid synthesis, but significantly blocked ovarian development, and induced forkhead box O (FOXO) gene expression in C. septempunctata under reproduction conditions. By contrast, injection of AKH peptide significantly inhibited FOXO expression, reduced lipid storage, and increased water content in C. septempunctata under diapause conditions. CONCLUSION: These results indicate that CsAKH and CsAKHR are involved in the regulation of lipid accumulation and ovarian development during diapause in C. septempunctata, and provide a promising target for manipulating C. septempunctata diapause. © 2024 Society of Chemical Industry.

7.
Sci Total Environ ; 924: 171329, 2024 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-38462006

RESUMO

Phenolic compounds, abundant secondary metabolites in plants, profoundly influence soil ecosystems, plant growth, and interactions with herbivores. In this study, we explore the intricate relationships between phenolics, soil microbes, and gall formation in Ageratina adenophora (A. adenophora), an invasive plant species in China known for its allelopathic traits. Using metabolomic and microbial profiling, significant differences in soil microbial composition and metabolite profiles were observed between bulk and rhizosphere soil samples. Phenolics influenced bacterial communities, with distinct microbial populations enriched in each soil type. Additionally, phenolics impacted soil metabolic processes, with variations observed in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis between different soil treatments. Analysis of phenolic content in plant and soil samples revealed considerable variations, with higher concentrations observed in certain plant tissues and soil types. Bioactive phenols extracted from plant and soil samples were identified using gas chromatography/mass spectrometry (GC-MS), providing insights into the diverse chemical composition of these compounds. Furthermore, the effects of phenolics on plant growth and gall formation were investigated. Phenols exhibited both stimulatory and inhibitory effects on plant growth, with optimal concentrations promoting emergence but higher concentrations hindering growth. Gall formation was influenced by phenolic concentrations, leading to structural alterations in stem tissue and gall morphology. Histochemical analysis revealed starch and lipid accumulation in gall tissues, indicating metabolic changes induced by phenolics. The presence of phenolics disrupted tissue structures and influenced vascular bundle orientation in gall tissues. Overall, our study highlights the multifaceted roles of phenolic compounds in soil ecosystems, plant development, and gall formation, facilitating the utilization of secondary metabolites in agriculture.


Assuntos
Ecossistema , Solo , Solo/química , Desenvolvimento Vegetal , Plantas/metabolismo , Fenóis/metabolismo , Dispersão Vegetal , Microbiologia do Solo , Raízes de Plantas/metabolismo
8.
Mol Cell ; 84(3): 596-610.e6, 2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-38215754

RESUMO

Although DNA N6-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present Direct-Read 6mA sequencing (DR-6mA-seq), an antibody-independent method, to measure 6mA at base resolution. DR-6mA-seq employs a unique mutation-based strategy to reveal 6mA sites as misincorporation signatures without any chemical or enzymatic modulation of 6mA. We validated DR-6mA-seq through the successful mapping of the well-characterized G(6mA)TC motif in the E. coli DNA. As expected, when applying DR-6mA-seq to mammalian systems, we found that genomic DNA (gDNA) 6mA abundance is generally low in most mammalian tissues and cells; however, we did observe distinct gDNA 6mA sites in mouse testis and glioblastoma cells. DR-6mA-seq provides an enabling tool to detect 6mA at single-base resolution for a comprehensive understanding of DNA 6mA in eukaryotes.


Assuntos
Metilação de DNA , Escherichia coli , Animais , Camundongos , Escherichia coli/genética , Genoma/genética , DNA/metabolismo , Eucariotos/genética , Desoxiadenosinas/genética , Mamíferos/metabolismo
9.
Int J Biol Macromol ; 258(Pt 1): 128104, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37977460

RESUMO

In biological control programs, knowledge about diapause regulation in natural enemy insects provides important insight for improving long-term storage, transportation, and field adoption of these biological control agents. As a natural predator of agricultural pests, the lady beetle Coccinella septempunctata has been commercially mass-cultured and widely employed in pest management. In some insects, insulin signaling, in conjunction with the downstream transcription factor Forkhead box O (FoxO), are master regulators of multiple physiological processes involved in diapause, but it is unclear whether insulin signaling and FoxO affect the diapause of C. septempunctata. In this study, we use a combination of approaches to demonstrate that insulin signaling and FoxO mediate the diapause response in C. septempunctata. In diapausing beetles, application of exogenous insulin and knocking down expression of CsFoxo with RNA interference (RNAi) both rescued beetles from developmental arrest. In non-diapausing beetles, knocking down expression of the insulin receptor (CsInR) with RNA interference (RNAi) arrested ovarian development and decreased juvenile hormone (JH) content to levels comparable to the diapause state. Taken together, these results suggest that a shutdown of insulin signaling prompts the activation of the downstream FoxO gene, leading to the diapause phenotype.


Assuntos
Besouros , Diapausa , Humanos , Animais , Besouros/genética , Insulina/metabolismo , Fatores de Transcrição Forkhead/metabolismo , Transdução de Sinais
10.
Acc Chem Res ; 57(1): 47-58, 2024 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-38079380

RESUMO

ConspectusRNA molecules are not merely a combination of four bases of A, C, G, and U. Chemical modifications occur in almost all RNA species and play diverse roles in gene expression regulation. The abundant cellular RNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA), are known to have the highest density of RNA modifications, which exert critical functions in rRNA and tRNA biogenesis, stability, and subsequent translation. In recent years, modifications on low-abundance RNA species in mammalian cells, such as messenger RNA (mRNA), regulatory noncoding RNA (ncRNA), and chromatin-associated RNA (caRNA), have been shown to contain multiple different chemical modifications with functional significance.As the most abundant mRNA modification in mammals, N6-methyladenosine (m6A) affects nearly every stage of mRNA processing and metabolism, with the antibody-based m6A-MeRIP-seq (methylated RNA immunoprecipitation sequencing) followed by high-throughput sequencing widely employed in mapping m6A distribution transcriptome-wide in diverse biological systems. In addition to m6A, other chemical modifications such as pseudouridine (Ψ), 2'-O-methylation (Nm), 5-methylcytidine (m5C), internal N7-methylguanosine (m7G), N1-methyladenosine (m1A), N4-acetylcytidine (ac4C), etc. also exist in polyA-tailed RNA in mammalian cells, requiring effective mapping approaches for whole-transcriptome profiling of these non-m6A mRNA modifications. Like m6A, the antibody-based enrichment followed by sequencing has been the primary method to study distributions of these modifications. Methods to more quantitatively map these modifications would dramatically improve our understanding of distributions and modification density of these chemical marks on RNA, thereby bettering informing functional implications. In this Account, aimed at both single-base resolution and modification fraction quantification, we summarize our recent advances in developing a series of chemistry- or biochemistry-based methods to quantitatively map RNA modifications, including m6A, Ψ, m5C, m1A, 2'-O-methylation (Nm), and internal m7G, in mammalian mRNA at base resolution. These new methods, including m6A-SAC-seq, eTAM-seq, BID-seq, UBS-seq, DAMM-seq, m1A-quant-seq, Nm-Mut-seq, and m7G-quant-seq, promise to conduct base-resolution mapping of most major mRNA modifications with low RNA input and uncover dynamic changes in modification stoichiometry during biological and physiological processes, facilitating future investigations on these RNA modifications in regulating cellular gene expression and as potential biomarkers for clinical diagnosis and prognosis. These quantitative sequencing methods allow the mapping of most mRNA modifications with limited input sample requirements. The same modifications on diverse RNA species, such as caRNA, ncRNA, nuclear nascent RNA, mitochondrial RNA, cell-free RNA (cfRNA), etc., could be sequenced using the same methods.


Assuntos
RNA de Transferência , Transcriptoma , Animais , Metilação , Sequência de Bases , RNA Mensageiro/metabolismo , RNA de Transferência/genética , RNA de Transferência/metabolismo , RNA/metabolismo , Mamíferos/genética , Mamíferos/metabolismo
11.
Environ Res ; 245: 117901, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38092235

RESUMO

Polycyclic aromatic hydrocarbons (PAHs) are significant petroleum pollutants that have long-term impacts on human health and ecosystems. However, assessing their toxicity presents challenges due to factors such as cost, time, and the need for comprehensive multi-component analysis methods. In this study, we utilized network toxicity models, enrichment analysis, and molecular docking to analyze the toxicity mechanisms of PAHs at different levels: compounds, target genes, pathways, and species. Additionally, we used the maximum acceptable concentration (MAC) value and risk quotient (RQ) as an indicator for the potential ecological risk assessment of PAHs. The results showed that higher molecular weight PAHs had increased lipophilicity and higher toxicity. Benzo[a]pyrene and Fluoranthene were identified as core compounds, which increased the risk of cancer by affecting core target genes such as CCND1 in the human body, thereby influencing signal transduction and the immune system. In terms of biological species, PAHs had a greater toxic impact on aquatic organisms compared to terrestrial organisms. High molecular weight PAHs had lower effective concentrations on biological species, and the ecological risk was higher in the Yellow River Delta region. This research highlights the potential application of network toxicity models in understanding the toxicity mechanisms and species toxicity of PAHs and provides valuable insights for monitoring, prevention, and ecological risk assessment of these pollutants.


Assuntos
Poluentes Ambientais , Petróleo , Hidrocarbonetos Policíclicos Aromáticos , Poluentes Químicos da Água , Humanos , Hidrocarbonetos Policíclicos Aromáticos/toxicidade , Hidrocarbonetos Policíclicos Aromáticos/análise , Ecossistema , Poluentes Ambientais/toxicidade , Poluentes Ambientais/análise , Petróleo/toxicidade , Petróleo/análise , Simulação de Acoplamento Molecular , Poluentes Químicos da Água/toxicidade , Poluentes Químicos da Água/análise , Monitoramento Ambiental , Medição de Risco , China , Sedimentos Geológicos/análise
12.
Insect Mol Biol ; 33(1): 17-28, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37707297

RESUMO

In insects, vitellogenin (Vg) is generally viewed as a female-specific protein. Its primary function is to supply nutrition to developing embryos. Here, we reported Vg from the male adults of a natural predator, Chrysopa pallens. The male Vg was depleted by RNAi. Mating with Vg-deficient male downregulated female Vg expression, suppressed ovarian development and decreased reproductive output. Whole-organism transcriptome analysis after male Vg knockdown showed no differential expression of the known spermatogenesis-related regulators and seminal fluid protein genes, but a sharp downregulation of an unknown gene, which encodes a testis-enriched big protein (Vcsoo). Separate knockdown of male Vg and Vcsoo disturbed the assembly of spermatid cytoplasmic organelles in males and suppressed the expansion of ovary germarium in mated females. These results demonstrated that C. pallens male Vg signals through the downstream Vcsoo and regulates male and female reproduction.


Assuntos
Testículo , Vitelogeninas , Feminino , Masculino , Animais , Vitelogeninas/genética , Vitelogeninas/metabolismo , Insetos/genética , Reprodução , Gametogênese
13.
Nat Protoc ; 19(2): 517-538, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37968414

RESUMO

Pseudouridine (Ψ) is an abundant RNA modification that is present in and affects the functions of diverse non-coding RNA species, including rRNA, tRNA and small nuclear RNA. Ψ also exists in mammalian mRNA and probably exhibits functional roles; however, functional investigations of mRNA Ψ modifications in mammals have been hampered by the lack of a quantitative method that detects Ψ at base precision. We have recently developed bisulfite-induced deletion sequencing (BID-seq), which provides the community with a quantitative method to map RNA Ψ distribution transcriptome-wide at single-base resolution. Here, we describe an optimized BID-seq protocol for mapping Ψ distribution across cellular mRNAs, which includes fast steps in both library preparation and data analysis. This protocol generates highly reproducible results by inducing high deletion ratios at Ψ modification within diverse sequence contexts, and meanwhile displayed almost zero background deletions at unmodified uridines. When used for transcriptome-wide Ψ profiling in mouse embryonic stem cells, the current protocol uncovered 8,407 Ψ sites from as little as 10 ng of polyA+ RNA input. This optimized BID-seq workflow takes 5 days to complete and includes four main sections: RNA preparation, library construction, next-generation sequencing (NGS) and data analysis. Library construction can be completed by researchers who have basic knowledge and skills in molecular biology and genetics. In addition to the experimental protocol, we provide BID-pipe ( https://github.com/y9c/pseudoU-BIDseq ), a user-friendly data analysis pipeline for Ψ site detection and modification stoichiometry quantification, requiring only basic bioinformatic and computational skills to uncover Ψ signatures from BID-seq data.


Assuntos
Pseudouridina , Transcriptoma , Animais , Camundongos , Pseudouridina/análise , Pseudouridina/genética , RNA Mensageiro/genética , Perfilação da Expressão Gênica/métodos , RNA Ribossômico/genética , Mamíferos/genética
14.
J Environ Manage ; 351: 119837, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38154225

RESUMO

Phosphate concentrations in eutrophic surface waters are usually low, and efficient removal of low concentration phosphate remains a challenge. In this study, Ca-doped LaMnO3 synthesized at doping ratios, designated as CaxLa1-xMnO3 (x = 0, 0.2, 0.4, 0.7), were compared. It was found that, the adsorption capacity of Ca0.4La0.6MnO3 material reached 63.01 mg/g at pH = 5, increased by 63.6% over the undoped LaMnO3 perovskite. For long-term adsorption, Ca0.4La0.6MnO3 could constantly adsorb phosphate to avoid phosphate accumulation (<0.05 mg/L). This proves that Ca0.4La0.6MnO3 has the ability to control dynamic water eutrophication. Characterization and density functional theory results confirmed that CaxLa1-xMnO3 can increase the content of mesopores and oxygen vacancies, providing additional active sites. This reduces the adsorption energy of the La site, promotes electron transfer, and increases its affinity. It provides a new method for removing low-concentration phosphates.


Assuntos
Fosfatos , Poluentes Químicos da Água , Adsorção , Fosfatos/química , Água , Concentração de Íons de Hidrogênio , Cinética
15.
J Vis Exp ; (201)2023 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-38078604

RESUMO

The egg parasitoids, Trichogramma spp, are recognized as efficient biological control agents against various lepidopteran pests in agriculture and forests. The immature stages of Trichogramma offspring develop within the host egg, exhibiting remarkable diminutiveness (approximately 0.5 mm in adult length). RNA-interference (RNAi) methodology has emerged as a crucial tool for elucidating gene functions in numerous organisms. However, manipulating RNAi in certain small parasitoid species, such as Trichogramma, has generally posed significant challenges. In this study, we present an efficient RNAi method in Trichogramma denrolimi. The outlined procedure encompasses the acquisition and isolation of individual T. dendrolimi specimens from host eggs, the design and synthesis of double-stranded RNA (dsRNA), the in vitro transplantation and cultivation of T. dendrolimi pupae, the micro-injection of dsRNA, and the subsequent assessment of target gene knockdown through RT-qPCR analysis. This study furnishes a comprehensive, visually detailed procedure for conducting RNAi experiments in T. dendrolimi, thereby enabling researchers to investigate the gene regulation in this species. Furthermore, this methodology is adaptable for RNAi studies or micro-injections in other Trichogramma species with minor adjustments, rendering it a valuable reference for conducting RNAi experiments in other endoparasitic species.


Assuntos
Himenópteros , Mariposas , Parasitos , Vespas , Animais , Interferência de RNA , Himenópteros/fisiologia , Agricultura , Vespas/genética
16.
Methods Enzymol ; 692: 23-38, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37925181

RESUMO

Posttranscriptional RNA modifications occur in almost all types of RNA in all life forms. As an abundant RNA modification in mammals, pseudouridine (Ψ) regulates diverse biological functions of different RNA species such as ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), etc. However, the functional investigation of mRNA pseudouridine (Ψ) has been hampered by the lack of a quantitative method that can efficiently map Ψ transcriptome-wide. We developed bisulfite-induced deletion sequencing (BID-seq), with the optimized bisulfite-based chemical reaction to convert pseudouridine selectively and completely into Ψ-BS adduct without cytosine deamination. The Ψ-BS adduct can be further read out as deletion signatures during reverse transcription. The deletion ratios induced by Ψ sites were used for estimating the modification stoichiometry at each modified site. BID-seq starts with 10-20 ng polyA+ RNA and detects thousands of mRNA Ψ sites with stoichiometry information in cell lines and tissues. We uncovered consensus motifs for Ψ in mammalian mRNA and assigned specific 'writer' proteins to individual Ψ deposition. BID-seq also confirmed the presence of Ψ within stop codons of mammalian mRNA. BID-seq set the stage for future investigations of Ψ functions in diverse biological processes.


Assuntos
Pseudouridina , RNA , Animais , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Pseudouridina/metabolismo , RNA/metabolismo , Sulfitos/metabolismo , RNA Ribossômico/metabolismo , RNA de Transferência/metabolismo , Processamento Pós-Transcricional do RNA , Mamíferos/genética , Mamíferos/metabolismo
17.
Methods Enzymol ; 692: 39-54, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37925186

RESUMO

The human AlkB family proteins, such as FTO and ALKBH5, are known to mediate RNA m6A demethylation. However, although ALKBH7 localizes in mitochondria and affects metabolism, the detailed biological function and mechanism have remained unknown for years. We developed Demethylation-Assisted Multiple Methylation sequencing (DAMM-seq) to simultaneously detect N1-methyladenosine (m1A), N3-methylcytidine (m3C), N1-methylguanosine (m1G) and N2,N2-dimethylguanosine (m22G) methylations in both steady-state RNA and nascent RNA, and discovered that human ALKBH7 demethylates m22G and m1A within mt-Ile and mt-Leu1 pre-tRNA regions, respectively, in mitochondrial polycistronic RNA. DAMM-seq quantitatively and sensitively monitors the methylation stoichiometry change at pre-tRNA junctions within nascent mt-RNA, revealing the target region where ALKBH7 regulates RNA processing and local structural switch of polycistronic mt-RNAs. A new RNA demethylase in human cells was characterized through the base-resolution quantification of multiple RNA methylations in nascent mt-RNA, resolving the long-standing question about the functional substrate of ALKBH7.


Assuntos
Precursores de RNA , RNA de Transferência , Humanos , Metilação , RNA Mitocondrial/genética , RNA Mitocondrial/metabolismo , RNA de Transferência/metabolismo , RNA/química , Homólogo AlkB 5 da RNA Desmetilase/química , Homólogo AlkB 5 da RNA Desmetilase/metabolismo , Dioxigenase FTO Dependente de alfa-Cetoglutarato/química , Dioxigenase FTO Dependente de alfa-Cetoglutarato/metabolismo
18.
Front Immunol ; 14: 1286820, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37915585

RESUMO

The post-transcriptional RNA modifications impact the dynamic regulation of gene expression in diverse biological and physiological processes. Host RNA modifications play an indispensable role in regulating innate immune responses against virus infection in mammals. Meanwhile, the viral RNAs can be deposited with RNA modifications to interfere with the host immune responses. The N6-methyladenosine (m6A) has boosted the recent emergence of RNA epigenetics, due to its high abundance and a transcriptome-wide widespread distribution in mammalian cells, proven to impact antiviral innate immunity. However, the other types of RNA modifications are also involved in regulating antiviral responses, and the functional roles of these non-m6A RNA modifications have not been comprehensively summarized. In this Review, we conclude the regulatory roles of 2'-O-methylation (Nm), 5-methylcytidine (m5C), adenosine-inosine editing (A-to-I editing), pseudouridine (Ψ), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), and N4-acetylcytidine (ac4C) in antiviral innate immunity. We provide a systematic introduction to the biogenesis and functions of these non-m6A RNA modifications in viral RNA, host RNA, and during virus-host interactions, emphasizing the biological functions of RNA modification regulators in antiviral responses. Furthermore, we discussed the recent research progress in the development of antiviral drugs through non-m6A RNA modifications. Collectively, this Review conveys knowledge and inspiration to researchers in multiple disciplines, highlighting the challenges and future directions in RNA epitranscriptome, immunology, and virology.


Assuntos
Processamento Pós-Transcricional do RNA , RNA Viral , Animais , Metilação , RNA Viral/genética , Imunidade Inata , Antivirais , Mamíferos/genética
19.
Life (Basel) ; 13(10)2023 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-37895461

RESUMO

Flower-rich habitats are crucial for promoting biodiversity and ecosystem services within agricultural ecosystems, such as pollination and pest control. The present study investigates the efficacy of employing floral structures as a criterion for the selection of plant species in order to enhance the attraction of natural enemies within cucumber greenhouses, consequently augmenting floral resources. The results of our study provide evidence that flower strips have a beneficial effect on the fitness of critical natural predators, while not facilitating the proliferation of detrimental insect species. These findings exhibit potential for enhancing pest-management services in the agricultural sector. The findings of our study demonstrate that pest levels within greenhouse environments closely resemble those observed in real-world commercial cropping systems. As a result, the introduction of Coccinella septempunctata and Menochilus sexmaculatus biocontrol agents is confirmed to be a reliable and efficient method for pest management. The phenomenon of predator-prey density dependency is recognized as a crucial element in the implementation of biological control strategies. Furthermore, we investigate the impact of floral resources on the reproductive capacity of indigenous predators. The impact of Coriandrum sativum on fertility is substantial, indicating that the presence of a varied plant assortment with overlapping flowering periods can prolong the availability of floral resources. This study highlights the significance of flower-rich habitats and deliberate plant selection in augmenting biodiversity, ecosystem services, and pest management within agricultural settings. The implementation of conservation biological control technologies presents supplementary ecological advantages, thus offering practical implications for the promotion of sustainable agricultural practices.

20.
Front Physiol ; 14: 1243753, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37693004

RESUMO

Introduction: Trichogramma wasps are egg parasitoids of agricultural lepidopteran pests. The sex of Trichogramma is determined by its ploidy as well as certain sex ratio distorters, such as the endosymbiotic bacteria Wolbachia spp. and the paternal sex ratio (PSR) chromosome. The sex determination systems of hymenopterans, such as Trichogramma spp., involve cascades of the genes transformer (tra), transformer-2 (tra2), and doublesex (dsx) and are associated with sex-specific tra and dsx splicing. First, these genes and their sex-specific variants must be identified to elucidate the interactions between the sex ratio disorders and the sex determination mechanism of Trichogramma. Methods: Here, we characterized the sex determination genes tra, tra2, and dsx in Trichogramma dendrolimi. Sex-specific tra and dsx variants were detected in cDNA samples obtained from both male and female Trichogramma wasps. They were observed in the early embryos (1-10 h), late embryos (12-20 h), larvae (32 h and 48 h), pre-pupae (96 h), and pupae (144 h, 168 h, 192 h, and 216 h) of both male and female T. dendrolimi offspring. Results: We detected female-specific tra variants throughout the entire early female offspring stage. The male-specific variant began to express at 9-10 h as the egg was not fertilized. However, we did not find any maternally derived, female-specific tra variant in the early male embryo. This observation suggests that the female-specific tra variant expressed in the female embryo at 1-9 h may not have originated from the maternal female wasp. Discussion: The present study might be the first to identify the sex determination genes and sex-specific gene splicing in Trichogramma wasps. The findings of this study lay the foundation for investigating the sex determination mechanisms of Trichogramma and other wasps. They also facilitate sex identification in immature T. dendrolimi and the application of this important egg parasitoid in biological insect pest control programs.

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