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As a commonly used food additive, excessive nitrite intake seriously affects people's health in daily life. As the stomach is the main organ involved in nitrite intake, achieving fast and in situ detection of nitrite in the stomach is of great significance for avoiding the hazards caused by nitrite. However, owing to the poor stability or low sensitivity of existing fluorescent probes under acidic conditions, their application for nitrite detection within the stomach remains challenging. To solve this problem, we developed novel probes specifically designed to maintain stability and demonstrate high sensitivity to nitrite under acidic conditions. Utilizing the optimized probe (DHUROS-11), nitrite levels in environmental and real samples were successfully quantified. Notably, tracing of nitrite within the stomach of mice in real time was realized by using DHUROS-11 as the probe.
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PURPOSE: Osteosarcoma, a highly malignant primary bone tumor primarily affecting adolescents, frequently develops resistance to initial chemotherapy, leading to metastasis and limited treatment options. Our study aims to uncover novel therapeutic targets for metastatic and recurrent osteosarcoma. METHODS: In this study, we proved the potential of modulating the YAP1-regulated glutamine metabolic pathway to augment the response of OS to DFMO. We initially employed single-cell transcriptomic data to gauge the activation level of polyamine metabolism in MTAP-deleted OS patients. This was further substantiated by transcriptome sequencing data from recurrent and non-recurrent patient tissues, confirming the activation of polyamine metabolism in progressive OS. Through high-throughput drug screening, we pinpointed CIL56, a YAP1 inhibitor, as a promising candidate for a combined therapeutic strategy with DFMO. In vivo, we utilized PDX and CDX models to validate the therapeutic efficacy of this drug combination. In vitro, we conducted western blot analysis, qPCR analysis, immunofluorescence staining, and PuMA experiments to monitor alterations in molecular expression, distribution, and tumor metastasis capability. We employed CCK-8 and colony formation assays to assess the proliferative capacity of cells in the experimental group. We used flow cytometry and reactive oxygen probes to observe changes in ROS and glutamine metabolism within the cells. Finally, we applied RNA-seq in tandem with metabolomics to identify metabolic alterations in OS cells treated with a DFMO and CIL56 combination. This enabled us to intervene and validate the role of the YAP1-mediated glutamine metabolic pathway in DFMO resistance. RESULTS: Through single-cell RNA-seq data analysis, we pinpointed a subset of late-stage OS cells with significantly upregulated polyamine metabolism. This upregulation was further substantiated by transcriptomic profiling of recurrent and non-recurrent OS tissues. High-throughput drug screening revealed a promising combination strategy involving DFMO and CIL56. DFMO treatment curbs the phosphorylation of YAP1 protein in OS cells, promoting nuclear entry and initiating the YAP1-mediated glutamine metabolic pathway. This reduces intracellular ROS levels, countering DFMO's anticancer effect. The therapeutic efficacy of DFMO can be amplified both in vivo and in vitro by combining it with the YAP1 inhibitor CIL56 or the glutaminase inhibitor CB-839. This underscores the significant potential of targeting the YAP1-mediated glutamine metabolic pathway to enhance efficacy of DFMO. CONCLUSION: Our findings elucidate YAP1-mediated glutamine metabolism as a crucial bypass mechanism against DFMO, following the inhibition of polyamine metabolism. Our study provides valuable insights into the potential role of DFMO in an "One-two Punch" therapy of metastatic and recurrent osteosarcoma.
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Gene editing contributes to enhancing food security through the creation of novel foods. However, public perception of gene-edited (GE) foods is crucial to their acceptance and adoption. This study expanded the knowledge-attitude-practice model and constructed an integrated framework comprising four dimensions: demographic factors, scientific literacy and beliefs, social trust, and perceptions of gene technology, aimed at explaining the public's attitudes toward GE foods. A questionnaire survey was conducted (N = 649), revealing a positive attitude toward GE foods, with over 80% expressing a certain willingness to pay (WTP) for them. Factors such as income level, subjective knowledge, scientific beliefs, trust in scientists, trust in government, and trust in national technological capabilities and perceived benefits positively correlated with WTP. Conversely, objective knowledge, perceived risks, and perceived ethical concerns were negatively correlated with WTP. The impact of objective knowledge on attitudes toward GE foods demonstrated a significant, nonlinear relationship. Additionally, it is noteworthy that the Chinese public currently exhibits relatively low trust in national technological capabilities, necessitating vigilance against the emergence of conspiracy theories akin to those surrounding genetically modified foods. This research contributes theoretical insights into the public communication of GE foods.
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Collaborative programming is being increasingly used to overcome the difficulties of the individual programming process. In this study, we investigated the effect of collaborative perception on cognitive engagement and learning outcomes in collaborative programming. We used a quasi-experimental research to determine the differences in cognitive engagement and learning outcomes of three groups with different levels of collaborative perception. The findings highlight several important conclusions. First, there were significant differences in cognitive engagement and learning outcomes across collaborative perception groups. Students with high levels of collaborative perception demonstrate more comprehensive and diverse cognitive engagement, resulting in higher learning outcomes compared to those with lower perception. Second, students in the low collaborative perception group had more Clarification-Elaboration cognitive connections, and students in the high collaborative perception group had stronger Clarification-Positioning and Clarification-Verification cognitive connections. Third, collaborative perception positively moderated the relationship between cognitive engagement and learning outcomes. In particular, three cognitive engagement, Clarification, Elaboration, and Positioning, had a greater impact on performance when moderated by collaborative perceptions. These findings have practical implications for educators and course designers, emphasizing the importance of considering students' collaborative perception when forming groups and promoting effective collaborative programming.
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Cognição , Comportamento Cooperativo , Aprendizagem , Estudantes , Humanos , Feminino , Estudantes/psicologia , Masculino , Cognição/fisiologia , Aprendizagem/fisiologia , Adulto Jovem , Adulto , Percepção/fisiologia , AdolescenteRESUMO
Nasopharyngeal carcinoma (NPC) is a malignant tumor that occurs in the nasopharynx. Palate, lung, and nasal epithelium clone (PLUNC) has been identified as an early secreted protein that is specifically expressed in the nasopharynx. The aim of this study was to determine the role and mechanism of PLUNC in NPC. We used mRNA sequencing (seq) combined with ribosome-nascent chain complex (RNC)-seq to determine the biological role of PLUNC. The expression of epithelial-to-mesenchymal transition (EMT)-related molecules was detected by western blotting. Then, cell migration and invasion were detected by wound healing and Transwell chamber assays. NPC cells were injected into the tail vein of nude mice to explore the biological role of PLUNC in vivo. The sequencing results showed that PLUNC inhibited the progression of NPC and its expression was correlated with that of NOD-like receptors. Experiments confirmed that PLUNC inhibited the invasion and metastasis of NPC cells by promoting the ubiquitination degradation of NLRP3. PLUNC overexpression in combination with the treatment by MCC950, an inhibitor of NLRP3 inflammasome activation, was most effective in inhibiting NPC invasion and metastasis. In vivo experiments also confirmed that the combination of PLUNC overexpression and MCC950 treatment effectively inhibited the lung metastasis of NPC cells. In summary, our research suggested that PLUNC inhibited the invasion and metastasis of NPC by inhibiting NLRP3 inflammasome activation, and targeting the PLUNC-NLRP3 inflammasome axis could provide a new strategy for the diagnosis and treatment of NPC patients.
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Transição Epitelial-Mesenquimal , Inflamassomos , Camundongos Nus , Proteína 3 que Contém Domínio de Pirina da Família NLR , Carcinoma Nasofaríngeo , Neoplasias Nasofaríngeas , Invasividade Neoplásica , Fosfoproteínas , Proteína 3 que Contém Domínio de Pirina da Família NLR/metabolismo , Proteína 3 que Contém Domínio de Pirina da Família NLR/genética , Humanos , Carcinoma Nasofaríngeo/patologia , Carcinoma Nasofaríngeo/metabolismo , Carcinoma Nasofaríngeo/genética , Animais , Inflamassomos/metabolismo , Camundongos , Transição Epitelial-Mesenquimal/efeitos dos fármacos , Neoplasias Nasofaríngeas/patologia , Neoplasias Nasofaríngeas/metabolismo , Neoplasias Nasofaríngeas/genética , Linhagem Celular Tumoral , Fosfoproteínas/metabolismo , Fosfoproteínas/genética , Movimento Celular/efeitos dos fármacos , Sulfonas/farmacologia , Indenos/farmacologia , Sulfonamidas/farmacologia , Masculino , Furanos/farmacologia , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Ubiquitinação , Feminino , Camundongos Endogâmicos BALB C , Metástase Neoplásica , GlicoproteínasRESUMO
Rheumatoid arthritis (RA) is a chronic autoimmune disease marked by synovitis and cartilage destruction. The active compound, icariin (ICA), derived from the herb Epimedium, exhibits potent anti-inflammatory properties. However, its clinical utility is limited by its water insolubility, poor permeability, and low bioavailability. To address these challenges, we developed a multifunctional drug delivery system-adipose-derived stem cells-exosomes (ADSCs-EXO)-ICA to target active macrophages in synovial tissue and modulate macrophage polarization from M1 to M2. High-performance liquid chromatography analysis confirmed a 92.4 ± 0.008% loading efficiency for ADSCs-EXO-ICA. In vitro studies utilizing cellular immunofluorescence (IF) and flow cytometry demonstrated significant inhibition of M1 macrophage proliferation by ADSCs-EXO-ICA. Enzyme-linked immunosorbent assay, cellular transcriptomics, and real-time quantitative PCR indicated that ADSCs-EXO-ICA promotes an M1-to-M2 phenotypic transition by reducing glycolysis through the inhibition of the ERK/HIF-1α/GLUT1 pathway. In vivo, ADSCs-EXO-ICA effectively accumulated in the joints. Pharmacodynamic assessments revealed that ADSCs-EXO-ICA decreased cytokine levels and mitigated arthritis symptoms in collagen-induced arthritis (CIA) rats. Histological analysis and micro computed tomography confirmed that ADSCs-EXO-ICA markedly ameliorated synovitis and preserved cartilage. Further in vivo studies indicated that ADSCs-EXO-ICA suppresses arthritis by promoting an M1-to-M2 switch and suppressing glycolysis. Western blotting supported the therapeutic efficacy of ADSCs-EXO-ICA in RA, confirming its role in modulating macrophage function through energy metabolism regulation. Thus, this study not only introduces a drug delivery system that significantly enhances the anti-RA efficacy of ADSCs-EXO-ICA but also elucidates its mechanism of action in macrophage function inhibition.
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Tecido Adiposo , Artrite Reumatoide , Exossomos , Flavonoides , Macrófagos , Animais , Flavonoides/farmacologia , Flavonoides/química , Exossomos/metabolismo , Ratos , Macrófagos/efeitos dos fármacos , Macrófagos/metabolismo , Tecido Adiposo/citologia , Masculino , Artrite Experimental/tratamento farmacológico , Ratos Sprague-Dawley , Sistemas de Liberação de Medicamentos/métodos , Células-Tronco/metabolismo , Células-Tronco/efeitos dos fármacos , Células-Tronco Mesenquimais/metabolismo , Células-Tronco Mesenquimais/efeitos dos fármacosRESUMO
Nanomaterials excel in mimicking the structure and function of natural enzymes while being far more interesting in terms of structural stability, functional versatility, recyclability, and large-scale preparation. Herein, the story assembles hemin, histidine analogs, and G-quadruplex DNA in a catalytically competent supramolecular assembly referred to as assembly-activated hemin enzyme (AA-heminzyme). The catalytic properties of AA-heminzyme are investigated both in silico (by molecular docking and quantum chemical calculations) and in vitro (notably through a systematic comparison with its natural counterpart horseradish peroxidase, HRP). It is found that this artificial system is not only as efficient as HRP to oxidize various substrates (with a turnover number kcat of 115 s-1) but also more practically convenient (displaying better thermal stability, recoverability, and editability) and more economically viable, with a catalytic cost amounting to <10% of that of HRP. The strategic interest of AA-heminzyme is further demonstrated for both industrial wastewater remediation and biomarker detection (notably glutathione, for which the cost is decreased by 98% as compared to commercial kits).
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Hemina , Hemina/química , Hemina/metabolismo , Quadruplex G , Análise Custo-Benefício/métodos , Simulação de Acoplamento Molecular/métodos , Catálise , Nanoestruturas/química , Águas Residuárias/químicaRESUMO
Ru-based electrochemiluminescence (ECL) coordination polymers are widely employed for bioanalysis and medical diagnosis. However, commonly used Ru-based coordination polymers face the limitation of low efficiency due to the long distance between the ECL reagent and the coreactant dispersed in detecting solution. Herein, we report a dual-ligand self-enhanced ECL coordination polymer, composed of tris(4,4'-dicarboxylic acid-2,2'-bipyridyl) ruthenium(II) dichloride (Ru(dcbpy)32+) as ECL reactant ligand and ethylenediamine (EDA) as corresponding coreactant ligand into Zn2+ metal node, termed Zn-Ru-EDA. Zn-Ru-EDA shows excellent ECL performance which is attributed to the effective intramolecular electron transport between the two ligands. Furthermore, the dual-ligand polymer allows an anodic low excitation potential (+1.09 V) luminescence. The shift in the energy level of the highest occupied molecular orbital (HOMO) upward after the synthesis of the Zn-Ru-EDA has resulted in a reduced excitation potential. The low excitation potential reduced biomolecular damage and the destruction of the modified electrodes. The ECL biosensor has been constructed using Zn-Ru-EDA with high ECL efficiency for the ultrasensitive detection of a bacterial infection and sepsis biomarker, procalcitonin (PCT), in the range from 1.00 × 10-6 to 1.00 × 10 ng·mL-1 with outstanding selectivity, and the detection limit was as low as 0.47 fg·mL-1. Collectively, the dual-ligand-based self-enhanced polymer may provide an ideal strategy for high ECL efficiency improvement as well as designing new self-enhanced multiple-ligand-based coordination in sensitive biomolecular detection for early disease diagnostics.
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Técnicas Eletroquímicas , Medições Luminescentes , Polímeros , Pró-Calcitonina , Rutênio , Ligantes , Polímeros/química , Pró-Calcitonina/sangue , Pró-Calcitonina/análise , Humanos , Rutênio/química , Complexos de Coordenação/química , Limite de Detecção , Técnicas Biossensoriais , Etilenodiaminas/químicaRESUMO
BACKGROUND: APLNR is a G protein-coupled receptor and our previous study had revealed that APLNR could inhibit nasopharyngeal carcinoma (NPC) growth and metastasis. However, the role of APLNR in regulating PD-L1 expression and immune escape in NPC is unknown. METHODS: We analyzed the expression and correlation of APLNR and PD-L1 in NPC tissues and cells. We investigated the effect of APLNR on PD-L1 expression and the underlying mechanism in vitro and in vivo. We also evaluated the therapeutic potential of targeting APLNR in combination with PD-L1 antibody in a nude mouse xenograft model. RESULTS: We found that APLNR was negatively correlated with PD-L1 in NPC tissues and cells. APLNR could inhibit PD-L1 expression by binding to the FERM domain of JAK1 and blocking the interaction between JAK1 and IFNGR1, thus suppressing IFN-γ-mediated activation of the JAK1/STAT1 pathway. APLNR could also inhibit NPC immune escape by enhancing IFN-γ secretion and CD8+ T-cell infiltration and reducing CD8+ T-cell apoptosis and dysfunction. Moreover, the best effect was achieved in inhibiting NPC growth in nude mice when APLNR combined with PD-L1 antibody. CONCLUSIONS: Our study revealed a novel mechanism of APLNR regulating PD-L1 expression and immune escape in NPC and suggested that APLNR maybe a potential therapeutic target for NPC immunotherapy.
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Antígeno B7-H1 , Camundongos Nus , Carcinoma Nasofaríngeo , Neoplasias Nasofaríngeas , Evasão Tumoral , Animais , Feminino , Humanos , Masculino , Camundongos , Antígeno B7-H1/metabolismo , Antígeno B7-H1/imunologia , Linfócitos T CD8-Positivos/imunologia , Linhagem Celular Tumoral , Regulação para Baixo , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Interferon gama/metabolismo , Janus Quinase 1/metabolismo , Camundongos Endogâmicos BALB C , Carcinoma Nasofaríngeo/imunologia , Carcinoma Nasofaríngeo/patologia , Neoplasias Nasofaríngeas/imunologia , Neoplasias Nasofaríngeas/patologia , Receptores Acoplados a Proteínas G/metabolismo , Receptores Acoplados a Proteínas G/genética , Receptores Acoplados a Proteínas G/imunologia , Receptores de Interferon/genética , Receptores de Interferon/metabolismo , Fator de Transcrição STAT1/metabolismo , Evasão Tumoral/efeitos dos fármacos , Ensaios Antitumorais Modelo de XenoenxertoRESUMO
LncRNAs play various effects, mostly by sponging with miRNAs. Based on public databases integrating bioinformatics analyses and further validation in breast cancer (BC) tissue and cell lines, the effect of lncRNA AFAP1-AS1 on breast cancer cell proliferation and migration was verified. It might work via the miR-21/PTEN axis. The expression of AFAP1-AS1, which was significantly upregulated in BC tissues and cell lines, was correlated with old age and lymph node metastasis of patients with BC. Knockdown of AFAP1-AS1 inhibited the proliferation and migration of BC cells in vitro and in vivo. And downregulated miR-21 expression and upregulated PTEN expression additionally. Mechanistically, the knockdown of lncRNA AFAP1-AS1 upregulated PTEN expression and consequently attenuated miR-21-mediated enhanced BC cell proliferation and migration. LncRNA AFAP1-AS1 is a potential prognostic biomarker for BC patients.
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Self-assembling peptides represent a captivating area of study in nanotechnology and biomaterials. This interest is largely driven by their unique properties and the vast application potential across various fields such as catalytic functions. However, design complexities, including high-dimensional sequence space and structural diversity, pose significant challenges in the study of such systems. In this work, we explored the possibility of self-assembled peptides to catalyze the hydrolysis of hydrosilane for hydrogen production using ab initio calculations and carried out wet-lab experiments to confirm the feasibility of these catalytic reactions under ambient conditions. Further, we delved into the nuanced interplay between sequence, structural conformation, and catalytic activity by combining modeling with experimental techniques such as transmission electron microscopy and nuclear magnetic resonance and proposed a dual mode of the microstructure of the catalytic center. Our results reveal that although research in this area is still at an early stage, the development of self-assembled peptide catalysts for hydrogen production has the potential to provide a more sustainable and efficient alternative to conventional hydrogen production methods. In addition, this work also demonstrates that a computation-driven rational design supplemented by experimental validation is an effective protocol for conducting research on functional self-assembled peptides.
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Hidrogênio , Peptídeos , Hidrogênio/química , Catálise , Peptídeos/química , Modelos Moleculares , HidróliseRESUMO
Peptides that self-assemble exhibit distinct three-dimensional structures and attributes, positioning them as promising candidates for biocatalysts. Exploring their catalytic processes enhances our comprehension of the catalytic actions inherent to self-assembling peptides, laying a theoretical foundation for creating novel biocatalysts. The investigation into the intricate reaction mechanisms of these entities is rendered challenging due to the vast variability in peptide sequences, their aggregated formations, supportive elements, structures of active sites, types of catalytic reactions, and the interplay between these variables. This complexity hampers the elucidation of the linkage between sequence, structure, and catalytic efficiency in self-assembling peptide catalysts. This chapter delves into the latest progress in understanding the mechanisms behind peptide self-assembly, serving as a catalyst in hydrolysis and oxidation reactions, and employing computational analyses. It discusses the establishment of models, selection of computational strategies, and analysis of computational procedures, emphasizing the application of modeling techniques in probing the catalytic mechanisms of peptide self-assemblies. It also looks ahead to the potential future trajectories within this research domain. Despite facing numerous obstacles, a thorough investigation into the structural and catalytic mechanisms of peptide self-assemblies, combined with the ongoing advancement in computational simulations and experimental methodologies, is set to offer valuable theoretical insights for the development of new biocatalysts, thereby significantly advancing the biocatalysis field.
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Biocatálise , Peptídeos , Peptídeos/química , Hidrólise , Oxirredução , Domínio Catalítico , Simulação de Dinâmica Molecular , Catálise , Modelos MolecularesRESUMO
Although fullerene derivatives such as [6,6]-phenyl-C61/C71-butyric acid methyl ester (PC61BM/PC71BM) have dominated the the photoactive acceptor materials in bulk heterojunction organic solar cells (OSCs) for decades, they have several drawbacks such as weak absorption, limited structural tunability, prone to aggregation, and high costs of production. Constructing non-fullerene small molecules with three-dimensional (3D) molecular geometry is one of the strategies to replace fullerenes in OSCs. In this study, a 3D molecule, contorted hexa-cata-hexabenzocoronene tetra perylenediimide (HBC-4-PDI), was designed and synthesized. HBC-4-PDI shows a wide and strong light absorption in the whole UV-vis region as well as suitable energy levels as an acceptor for OSCs. More importantly, the 3D construction effectively reduced the self-aggregation of c-HBC, leading to an appropriate scale phase separation of the blend film morphology in OSCs. A preliminary power conversion efficiency of 2.70 % with a champion open-circuit voltage of 1.06â V was obtained in OSCs with HBC-4-PDI as the acceptor, which was the highest among the previously reported OSCs based on c-HBC derivatives. The results indicated that HBC-4-PDI may serve as a good non-fullerene acceptor for OSCs.
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Circular mRNA (cmRNA) is particular useful due to its high resistance to degradation by exonucleases, resulting in greater stability and protein expression compared to linear mRNA. T cell receptor (TCR)-engineered T cells (TCR-T) represent a promising means of treating viral infections and cancer. This study aimed to evaluate the feasibility and efficacy of cmRNA in antigen-specific-TCR discovery and TCR-T therapy. Using human cytomegalovirus (CMV) pp65 antigen as a model, we found that the expansion of pp65-responsive T cells was induced more effectively by monocyte-derived dendritic cells transfected with pp65-encoding cmRNA compared with linear mRNA. Subsequently, we developed cmRNA-transduced pp65-TCR-T (cm-pp65-TCR-T) that specifically targets the CMV-pp65 epitope. Our results showed that pp65-TCR could be expressed on primary T cells for more than 7 days. Moreover, both in vitro killing and in vivo CDX models demonstrated that cm-pp65-TCR-T cells specifically and persistently kill pp65-and HLA-expressing tumor cells, significantly prolonging the survival of mice. Collectively, our results demonstrated that cmRNA can be used as a more effective technical approach for antigen-specific TCR isolation and identification, and cm-pp65-TCR-T may provide a safe, non-viral, non-integrated therapeutic approach for controlling CMV infection, particularly in patients who have undergone allogeneic hematopoietic stem cell transplantation.
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Infecções por Citomegalovirus , Transplante de Células-Tronco Hematopoéticas , Humanos , Animais , Camundongos , Infecções por Citomegalovirus/genética , Infecções por Citomegalovirus/terapia , Citomegalovirus/genética , Linfócitos T , Receptores de Antígenos de Linfócitos T/genética , Proteínas da Matriz Viral/genéticaRESUMO
Developing low-cost and self-supported bifunctional catalysts for highly efficient water splitting devices is of great significance. Herein, different from previously reported NiFe2O4-based electrocatalysts, we have grown nano-NiFe2O4 directly onto the iron foil (IF) surface and in situ introduced Sn4+ into NiFe2O4. The resulting experimental phenomena confirmed that the as-synthesized Sn-NiFe2O4/IF can deliver large-current densities (>1000 mA cm-2) during oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) processes at a low overpotential. The needed overpotentials at the current density of 10 and 1000 mA cm-2 are 231 and 368 mV for OER and 57 and 439 mV for HER, respectively. Additionally, when applied for the two-electrode water splitting, the corresponding needed voltage for Sn-NiFe2O4/IF at the current density of 10 mA cm-2 was only 1.56 V, which was comparable to the commercial Pt/C-RuO2/IF electrode. Thus, the introduced Sn4+ greatly enhanced the electrocatalytic property of Sn-NiFe2O4/IF, resulting in a superior bifunctional catalyst that can be applied for large-scale hydrogen production.
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Genomic abnormalities are strongly associated with cancer and infertility. In this study, we develop a simple and efficient method - multiple genetic abnormality sequencing (MGA-Seq) - to simultaneously detect structural variation, copy number variation, single-nucleotide polymorphism, homogeneously staining regions, and extrachromosomal DNA (ecDNA) from a single tube. MGA-Seq directly sequences proximity-ligated genomic fragments, yielding a dataset with concurrent genome three-dimensional and whole-genome sequencing information, enabling approximate localization of genomic structural variations and facilitating breakpoint identification. Additionally, by utilizing MGA-Seq, we map focal amplification and oncogene coamplification, thus facilitating the exploration of ecDNA's transcriptional regulatory function.
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Variações do Número de Cópias de DNA , Oncogenes , Genômica/métodos , Regulação da Expressão Gênica , DNARESUMO
Tea leaf spot caused by Didymella bellidis can seriously reduce the productivity and quality of tea (Camellia sinensis var. sinensis) leaves in Guizhou Province, southwest China. Analysis of the relationship between messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) of tea could provide insights into the plant-pathogen interaction. In this study, high-throughput sequencing of mRNAs and lncRNAs from tea leaves during infection by D. bellidis was conducted using the Illumina Novaseq 6000 platform. Infection by D. bellidis hyphae resulted in up- or downregulation of 553 and 191 of the differentially expressed mRNAs (DEmRNAs), respectively. As the S gene number (total number of genes with significantly differential expression annotated in the specified Gene Ontology [GO] database), three were enriched with respect to the defense response to the fungus at the biological process level. Expression of the DEmRNAs peroxidase 21 (TEA000222.1) and mcht-2 (TEA013240.1) originating from tea leaves were upregulated during challenge by D. bellidis hyphae, whereas expression of the LRR receptor-like serine/threonine-protein kinase ERECTA (TEA016781.1) gene was downregulated. The infection of D. bellidis hyphae resulted in up- or downregulation of 227 and 958 of the differentially expressed lncRNAs (DElncRNAs). The DEmRNAs associated with uncharacterized LOC101499401 (TEA015626.1), uncharacterized protein (TEA014125.1), structural maintenance of chromosomes protein 1 (TEA001660.1), and uncharacterized protein (TEA017727.1) occurred as a result of cis regulation by DElncRNAs MSTRG.20036, MSTRG.3843, MSTRG.26132, and MSTRG.56701, respectively. The expression profiling and lncRNA/mRNA association prediction in the tea leaves infected by D. bellidis will provide a valuable resource for further research into disease resistance.
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RNA Longo não Codificante , RNA Longo não Codificante/genética , Perfilação da Expressão Gênica/métodos , RNA Mensageiro/genética , CháRESUMO
Precise regulation of the peptide self-assembly into ordered nanostructures with intriguing properties has attracted intense attention. However, predicting peptide assembly at atomic resolution is a challenge due to both the structural flexibility of peptides and the associated huge computational costs. A machine learning-guided adaptive parametrization method was proposed for developing a mixed atomic and coarse-grained (CG) model through a multiobjective optimization strategy. Our model incorporates the united-atom (UA) model for diphenylalanine (P) and the polarizable electrostatic-variable coarse-grained (VaCG) model for aqueous ionic liquid [BMIM]+[BF4]- solution. In this mixed model, the coupling van der Waals (vdW) interaction is addressed by introducing virtual sites (VS) in the UA model to interact with solvent CG beads. The coupling parameters, including the electrostatic parameter and vdW parameters, are automatically optimized through ML-guided adaptive parametrization. The performance of this model was tested by some microstructural properties, e.g., the average number of P-P intermolecular hydrogen bonds (HBs) and radius distribution functions (RDFs) between P and different fragments of IL, in comparison with all-atom (AA) simulations. The computational cost is significantly reduced using such a parametrization scheme, which could search tens of thousands of force-field parameter sets, while needing only a small fraction of them to be assessed with molecular dynamics (MD) simulations. We used such a mixed resolution model to investigate the self-assembly in IL-water mixtures with variants of IL concentration (X). The long-range-ordered fibril structure is formed in a pure water system (X = 0). With an increase of IL concentrations, the formation of an ordered self-assembly nanostructure is prohibited, instead forming branched fibril at X = 2 mol % or amorphous aggregates when X > 10 mol %, resulting from the interplay between π-stacking and HB interactions between P and IL. The qualitative agreement between the simulated structures and the observed morphologies in experiments indicates the applicability of ML-guided parametrization strategy in the study of complex systems, such as polymers, lipid bilayers, and polysaccharides.
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The proton-activated chloride (PAC) channel plays critical roles in ischemic neuron death, but its activation mechanisms remain elusive. Here, we investigated the gating of PAC channels using its novel bifunctional modulator C77304. C77304 acted as a weak activator of the PAC channel, causing moderate activation by acting on its proton gating. However, at higher concentrations, C77304 acted as a weak inhibitor, suppressing channel activity. This dual function was achieved by interacting with 2 modulatory sites of the channel, each with different affinities and dependencies on the channel's state. Moreover, we discovered a protonation-independent voltage activation of the PAC channel that appears to operate through an ion-flux gating mechanism. Through scanning-mutagenesis and molecular dynamics simulation, we confirmed that E181, E257, and E261 in the human PAC channel serve as primary proton sensors, as their alanine mutations eliminated the channel's proton gating while sparing the voltage-dependent gating. This proton-sensing mechanism was conserved among orthologous PAC channels from different species. Collectively, our data unveils the polymodal gating and proton-sensing mechanisms in the PAC channel that may inspire potential drug development.
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Seeking and constructing superior photoactive materials have the potential to improve the performance of photoelectrochemical (PEC) biosensors. In this work, we proposed a novel mimosa-like ternary inorganic composite with a significantly enhanced light-harvesting ability and photogenerated carrier separation rate. This ternary photoactive material was obtained via electrodeposition of gold nanoparticles (Au) on the surface of transition metal sulfide composite of CdS and NiS (CdS-NiS/Au). The experimental results showed that the high initial photocurrent was acquired on CdS-NiS/Au (68-fold higher than that of individual CdS) with the synergistic effect of p-n heterojunction, Schottky junction, and the eminent optical properties of gold nanoparticles. Meanwhile, using silver nanoclusters prepared by link DNA protection as an effective quencher, integrating the duplex-specific nuclease-assisted rolling circle amplification strategy, a "Signal ON" PEC biosensor was fabricated for the detection of microRNA 21 (miRNA 21). With the release of the quencher, the recovered photocurrent is able to achieve determination of miRNA 21 within the range from 10 aM to 1 pM with a detection limit down to 4.6 aM (3σ). Importantly, this work not only provides a superb idea for designing ternary inorganic heteromaterials with exceptional photoactive ability but also allows the detection of other biomarkers by selecting appropriate recognition units.