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1.
Front Oncol ; 14: 1387735, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38720807

RESUMO

Background: Rhabdomyosarcoma(RMS) is the most common soft tissue sarcoma in children and single nucleotide polymorphisms(SNPs) in certain genes influence risk of RMS. Although FOXO3 had been reported in multiple cancers including RMS, the role of FOXO3 polymorphisms in RMS remains unclear. In this case-control study, we evaluated the association of FOXO3 SNPs with RMS risk and prognosis in children. Methods: Four FOXO3 SNPs(rs17069665 A>G, rs4946936 T>C, rs4945816 C>T and rs9400241 C>A) were genotyped in 110 RMS cases and 359 controls. The associations between FOXO3 polymorphisms and RMS risk were determined by odds ratios(ORs) with 95% confidence intervals(CIs). The associations of rs17069665 and rs4946936 with overall survival in RMS children were estimated using the Kaplan-Meier method and log-rank test. Functional analysis in silico was performed to estimate the probability that rs17069665 and rs4946936 might influence the regulation of FOXO3. Results: We found that rs17069665 (GG vs. AA+AG, adjusted OR=2.96; 95%CI [1.10-3.32]; P=0.010) and rs4946936 (TC+CC vs. TT, adjusted OR=0.48; 95%CI [0.25-0.90]; P=0.023) were related to the increased and decreased RMS risk, respectively. Besides, rs17069665(P<0.001) and rs4946936(P<0.001) were associated with decreased and increased overall survival in RMS patients, respectively. Functional analysis showed that rs17069665 and rs4946936 might influence the transcription and expression of FOXO3 via altering the bindings to MYC, CTCF, and/or RELA. Conclusions: This study revealed that FOXO3 polymorphisms influence the RMS susceptibility and prognosis in children, and might altered the expression of FOXO3. FOXO3 polymorphism was suggested as a biomarker for RMS susceptibility and prognosis.

2.
STAR Protoc ; 5(2): 103006, 2024 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-38602871

RESUMO

Exploring cell-cell communication is pivotal for understanding biological processes in multicellular life forms. Here, we present a protocol that details the use of matrix decomposition to infer cell-cell communication (MDIC3) for unsupervised cell-cell communication inference. We describe steps for using the MDIC3 Python scripts to deduce cell-cell communication and identify key ligand-receptor pairs between a specific cell type pair from a single-cell gene expression dataset. This protocol has potential application in cell-cell communication inference on any species. For complete details on the use and execution of this protocol, please refer to Liu et al.1.

3.
J Ovarian Res ; 17(1): 79, 2024 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-38610028

RESUMO

OBJECTIVE: IR emerges as a feature in the pathophysiology of PCOS, precipitating ovulatory anomalies and endometrial dysfunctions that contribute to the infertility challenges characteristic of this condition. Despite its clinical significance, a consensus on the precise mechanisms by which IR exacerbates PCOS is still lacking. This study aims to harness bioinformatics tools to unearth key IR-associated genes in PCOS patients, providing a platform for future therapeutic research and potential intervention strategies. METHODS: We retrieved 4 datasets detailing PCOS from the GEO, and sourced IRGs from the MSigDB. We applied WGCNA to identify gene modules linked to insulin resistance, utilizing IR scores as a phenotypic marker. Gene refinement was executed through the LASSO, SVM, and Boruta feature selection algorithms. qPCR was carried out on selected samples to confirm findings. We predicted both miRNA and lncRNA targets using the ENCORI database, which facilitated the construction of a ceRNA network. Lastly, a drug-target network was derived from the CTD. RESULTS: Thirteen genes related to insulin resistance in PCOS were identified via WGCNA analysis. LASSO, SVM, and Boruta algorithms further isolated CAPN2 as a notably upregulated gene, corroborated by biological verification. The ceRNA network involving lncRNA XIST and hsa-miR-433-3p indicated a possible regulatory link with CAPN2, supported by ENCORI database. Drug prediction analysis uncovered seven pharmacological agents, most being significant regulators of the endocrine system, as potential candidates for addressing insulin resistance in PCOS. CONCLUSIONS: This study highlights the pivotal role of CAPN2 in insulin resistance within the context of PCOS, emphasizing its importance as both a critical biomarker and a potential therapeutic target. By identifying CAPN2, our research contributes to the expanding evidence surrounding the CAPN family, particularly CAPN10, in insulin resistance studies beyond PCOS. This work enriches our understanding of the mechanisms underlying insulin resistance, offering insights that bridge gaps in the current scientific landscape.


Assuntos
Resistência à Insulina , MicroRNAs , Síndrome do Ovário Policístico , RNA Longo não Codificante , Humanos , Feminino , Resistência à Insulina/genética , Síndrome do Ovário Policístico/genética , RNA Longo não Codificante/genética , Algoritmos , Biologia Computacional , Calpaína/genética
4.
Turk Neurosurg ; 34(3): 407-414, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38650553

RESUMO

AIM: To evaluate and compare clinical outcomes between the posterior short-segment pedicle fixation with injured vertebra fixation (PSPFI) and fixation without injured vertebra fixation (PSPF) for thoracolumbar burst fracture (TLBF). MATERIAL AND METHODS: In this retrospective study, a total of 78 patients with TLBF were included and assigned to PSPFI (n=46) and PSPF (n=32) groups. The operative time, blood loss, perioperative complications, Oswestry disability index (ODI), and visual analog pain score (VAS) were examined immediately after surgery, 1 month, 3 months, and 1 year after surgery. Moreover, the postoperative vertebral height correction rate and postoperative Cobb angle correction rate were examined immediately and 1 year after surgery, as well as the corrected vertebral height loss rate and Cobb angle correction loss rate. RESULTS: No significant difference was identified in terms of operative time, blood loss, perioperative complications, ODI, and VAS after surgery (p > 0.05) between the PSPFI and PSPF groups. Moreover, the postoperative vertebral height correction rate and postoperative Cobb angle correction rate showed no difference between the groups as well. However, the PSPFI group had a significantly lower loss rate in terms of corrected vertebral height loss rate and Cobb angle correction loss rate than the PSPF group 1 year after surgery (p < 0.05). CONCLUSION: PSPFI and PSPF achieve similar clinical outcomes. However, posterior short-segment pedicle fixation with injured vertebra significantly maintains vertebral height correction rate and Cobb angle correction rate, which serve as a better choice for the treatment of TLBF.


Assuntos
Fixação Interna de Fraturas , Vértebras Lombares , Fraturas da Coluna Vertebral , Vértebras Torácicas , Humanos , Estudos Retrospectivos , Masculino , Fraturas da Coluna Vertebral/cirurgia , Feminino , Vértebras Torácicas/cirurgia , Vértebras Torácicas/lesões , Vértebras Lombares/cirurgia , Vértebras Lombares/lesões , Adulto , Resultado do Tratamento , Pessoa de Meia-Idade , Fixação Interna de Fraturas/métodos , Duração da Cirurgia , Complicações Pós-Operatórias/etiologia , Adulto Jovem , Fusão Vertebral/métodos
5.
Bioorg Chem ; 147: 107358, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38626490

RESUMO

VEGFR-2 is an attractive target for the development of anti-tumor drugs and plays a crucial role in tumor angiogenesis. This study reports a series of novel thiophene-3-carboxamide derivatives based on PAN-90806 as VEGFR-2 inhibitors, among which compound 14d exhibits excellent anti-proliferative activity against HCT116, MCF7, PC3, and A549 cell lines, and has effective VEGFR-2 inhibitory activity with an IC50 value of 191.1 nM. Additionally, CETSA results indicated that VEGFR-2 was a relevant target of compound 14d in the cell lines, and compound 14d could also inhibit VEGFR-2 protein phosphorylation in A549 cell line. Furthermore, compound 14d inhibited colony formation, cell migration, and HUVECs tube formation in a dose-dependent manner. The mechanism by which 14d induced cancer cell death involves blocking the cell cycle, increasing ROS production, inducing apoptosis, and dose-dependently reducing the levels of phosphorylated ERK and MEK. Molecular docking and molecular dynamics simulations had shown that compound 14d could stably bind to the active site of VEGFR-2. These results confirmed that compound 14d might be a promising lead compound for anti-angiogenesis.


Assuntos
Inibidores da Angiogênese , Antineoplásicos , Proliferação de Células , Relação Dose-Resposta a Droga , Ensaios de Seleção de Medicamentos Antitumorais , Inibidores de Proteínas Quinases , Tiofenos , Receptor 2 de Fatores de Crescimento do Endotélio Vascular , Humanos , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/antagonistas & inibidores , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/metabolismo , Tiofenos/farmacologia , Tiofenos/química , Tiofenos/síntese química , Inibidores da Angiogênese/farmacologia , Inibidores da Angiogênese/química , Inibidores da Angiogênese/síntese química , Proliferação de Células/efeitos dos fármacos , Relação Estrutura-Atividade , Inibidores de Proteínas Quinases/farmacologia , Inibidores de Proteínas Quinases/química , Inibidores de Proteínas Quinases/síntese química , Antineoplásicos/farmacologia , Antineoplásicos/química , Antineoplásicos/síntese química , Estrutura Molecular , Descoberta de Drogas , Movimento Celular/efeitos dos fármacos , Apoptose/efeitos dos fármacos , Simulação de Acoplamento Molecular , Linhagem Celular Tumoral
6.
Front Oncol ; 14: 1335009, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38651156

RESUMO

Background: Based on pharmacoeconomics, drug availability and actual treatment, optimal treatment regimens for Chinese non-small-cell lung carcinoma (NSCLC) patients over 70 years old are needed. Methods: This multicenter, single-arm pilot trial enrolled patients with advanced non-squamous NSCLC who refused systemic chemotherapy. Eligible patients received anlotinib (12 mg/day, d1-14, Q3W) until disease progression, intolerant toxicities, or withdrawal from the study. The primary endpoint was progression-free survival (PFS). Results: Forty-nine patients were screened between January 2019 and September 2021, of whom 40 patients were eligible. The median age was 76 years. With a median follow-up period of 16.20 (95% CI: 8.77, 25.10) months, the median PFS was 5.45 months (95% CI: 3.52-9.23) and the median overall survival was 10.32 months (95% CI: 6.44-12.78). Three patients achieved a partial response and 34 had stable disease, with an objective response rate of 7.5% and a disease control rate of 92.5%. Thirty-three (82.5%; 33/40) patients reported treatment-related adverse events (TRAEs) of any grade, and the incidence rate of grade ≥3 TRAEs was 35% (14/40). The most common grade ≥3 TRAEs were hypertension (4/40; 10.0%), hand-foot syndrome (3/40; 7.5%), and proteinuria (2/40; 5.0%). Conclusion: Anlotinib treatment was feasible and safe in Chinese elderly patients with advanced non-squamous NSCLC who did not receive any systemic chemotherapy.

7.
Am J Otolaryngol ; 45(4): 104301, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38688091

RESUMO

OBJECTIVE: This study aimed to compare the efficacy of balloon Eustachian tuboplasty (BET) plus tympanostomy tube insertion (TTI) and simple TTI for postirradiation otitis media with effusion (OME) in patients with nasopharyngeal carcinoma. METHOD: This study included 36 patients (51 ears) with OME after the first radiotherapy course for nasopharyngeal carcinoma and categorized them into the BET + TTI and simple TTI groups. Effective rates, pure tone hearing threshold, Eustachian tube function score, and complication incidences were compared. RESULTS: The effective rates of the BET+TTI and TTI groups were 93.75 % and 75 %, respectively, with no statistically significant difference (P = 0.29). The pure tone hearing threshold examination at 9 months postoperatively revealed significantly lower mean air-pure tone and air-bone gap in both the BET + TTI and TTI groups than preoperatively. Eustachian Tube Dysfunction Questionnaire-7 (ETDQ-7) scores at every postoperative visit were significantly higher than preoperative scores in the two groups (all P < 0.05); ETDQ-7 score reduction in the BET + TTI group at 3, 9, and 12 months postoperatively was significantly higher than that in the TTI group. Otorrhea and recurrence both occurred in the BET+TTI and TTI groups, but the BET+TTI group demonstrated a lower incidence. CONCLUSION: BET + TTI is an effective treatment method for postirradiation OME.

8.
BMC Urol ; 24(1): 87, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38627797

RESUMO

JC polyomavirus (JCPyV) is a human polyomavirus that can establish lifelong persistent infection in the majority of adults. It is typically asymptomatic in immunocompetent individuals. However, there is a risk of developing progressive multifocal leukoencephalopathy (PML) in immunocompromised or immunosuppressed patients. Though JCPyV commonly resides in the kidney-urinary tract, its involvement in urinary system diseases is extremely rare. Here, we reported a case of a 60-year-old male patient with coronavirus disease 2019 (COVID-19) infection who developed hemorrhagic cystitis after receiving treatment with nirmatrelvir 300 mg/ritonavir 100 mg quaque die (QD). Subsequent metagenomic next-generation sequencing (mNGS) confirmed the infection to be caused by JCPyV type 2. Then, human immunoglobulin (PH4) for intravenous injection at a dose of 25 g QD was administered to the patient. Three days later, the hematuria resolved. This case illustrates that in the setting of compromised host immune function, JCPyV is not limited to causing central nervous system diseases but can also exhibit pathogenicity in the urinary system. Moreover, mNGS technology facilitates rapid diagnosis of infectious etiology by clinical practitioners, contributing to precise treatment for patients.


Assuntos
COVID-19 , Cistite Hemorrágica , Vírus JC , Leucoencefalopatia Multifocal Progressiva , Infecções por Polyomavirus , Humanos , Masculino , Pessoa de Meia-Idade , COVID-19/complicações , Vírus JC/fisiologia , Infecções por Polyomavirus/complicações , Infecções por Polyomavirus/diagnóstico
9.
Virol J ; 21(1): 56, 2024 03 06.
Artigo em Inglês | MEDLINE | ID: mdl-38448926

RESUMO

BACKGROUND: Southwest China is one of the largest karst regions in the world. Karst environment is relatively fragile and vulnerable to human activities. Due to the discharge of sewage and domestic garbage, the karst system may be polluted by pathogenic bacteria. The detection of bacterial distribution and identification of phage capable of infecting them is an important approach for environmental assessment and resource acquisition. METHODS: Bacteria and phages were isolated from karst water in southwest China using the plate scribing and double plate method, respectively. Isolated phage was defined by transmission electron microscopy, one-step growth curve and optimal multiplicity of infection (MOI). Genomic sequencing, phylogenetic analysis, comparative genomic and proteomic analysis were performed. RESULTS: A Klebsiella quasipneumoniae phage was isolated from 32 isolates and named KL01. KL01 is morphologically identified as Caudoviricetes with an optimal MOI of 0.1, an incubation period of 10 min, and a lysis period of 60 min. The genome length of KL01 is about 45 kb, the GC content is 42.5%, and it contains 59 open reading frames. The highest average nucleotide similarity between KL01 and a known Klebsiella phage 6939 was 83.04%. CONCLUSIONS: KL01 is a novel phage, belonging to the Autophagoviridae, which has strong lytic ability. This study indicates that there were not only some potential potentially pathogenic bacteria in the karst environment, but also phage resources for exploration and application.


Assuntos
Bacteriófagos , Humanos , Bacteriófagos/genética , Filogenia , Proteômica , Klebsiella/genética , Bactérias , China
10.
J Environ Manage ; 356: 120615, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38518499

RESUMO

Anaerobic digestion (AD) is a prevalent waste activated sludge (WAS) treatment, and optimizing methane production is a core focus of AD. Two DESs were developed in this study and significantly increased methane production, including choline chloride-urea (ChCl-Urea) 390% and chloride-ethylene glycol (ChCl-EG) 540%. Results showed that ChCl-Urea mainly disrupted extracellular polymeric substances (EPS) structures, aiding in initial sludge solubilization during pretreatment. ChCl-EG, instead, induced sludge self-driven organic solubilization and enhanced hydrolysis and acidification processes during AD process. Based on the extent to which the two DESs promoted AD for methane production, the AD process can be divided into stage Ⅰ and stage Ⅱ. In stage Ⅰ, ChCl-EG promoted methanogenesis more significantly, microbiological analysis showed both DESs enriched aceticlastic methanogens-Methanosarcina. Notably, ChCl-Urea particularly influenced polysaccharide-related metabolism, whereas ChCl-EG targeted protein-related metabolism. In stage Ⅱ, ChCl-Urea was more dominant than ChCl-EG, ChCl-Urea bolstered metabolism and ChCl-EG promoted genetic information processing in this stage. In essence, this study investigated the microbial mechanism of DES-enhanced sludge methanogenesis and provided a reference for future research.


Assuntos
Solventes Eutéticos Profundos , Esgotos , Esgotos/química , Anaerobiose , Eliminação de Resíduos Líquidos/métodos , Colina/química , Metano , Ureia/química , Reatores Biológicos
11.
J Med Virol ; 96(3): e29498, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38436148

RESUMO

The outbreak of coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health. In parallel with vaccines, efficacious antivirals are urgently needed. SARS-CoV-2 main protease (Mpro) is an attractive drug target for antiviral development owing to its key roles in virus replication and host immune evasion. Due to the limitations of currently available methods, the development of novel high-throughput screening assays is of the highest importance for the discovery of Mpro inhibitors. In this study, we first developed an improved fluorescence-based assay for rapid screening of Mpro inhibitors from an anti-infection compound library using a versatile dimerization-dependent red fluorescent protein (ddRFP) biosensor. Utilizing this assay, we identified MG-101 as a competitive Mpro inhibitor in vitro. Moreover, our results revealed that ensitrelvir is a potent Mpro inhibitor, but baicalein, chloroquine, ebselen, echinatin, and silibinin are not. Therefore, this robust ddRFP assay provides a faithful avenue for rapid screening and evaluation of Mpro inhibitors to fight against COVID-19.


Assuntos
COVID-19 , Proteases 3C de Coronavírus , Humanos , SARS-CoV-2 , Inibidores de Proteases/farmacologia , Antivirais/farmacologia
13.
Comput Struct Biotechnol J ; 23: 1051-1064, 2024 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38455068

RESUMO

Gastric cancer (GC) poses a significant health challenge worldwide, necessitating the identification of predictive biomarkers to improve prognosis. Dysregulated lipid metabolism is a well-recognized hallmark of tumorigenesis, prompting investigation into apolipoproteins (APOs). In this study, we focused on apolipoprotein D (APOD) following comprehensive analyses of APOs in pan-cancer. Utilizing data from the TCGA-STAD and GSE62254 cohorts, we elucidated associations between APOD expression and multiple facets of GC, including prognosis, tumor microenvironment (TME), cancer biomarkers, mutations, and immunotherapy response, and identified potential anti-GC drugs. Single-cell analyses and immunohistochemical staining confirmed APOD expression in fibroblasts within the GC microenvironment. Additionally, we independently validated the prognostic significance of APOD in the ZN-GC cohort. Our comprehensive analyses revealed that high APOD expression in GC patients was notably associated with unfavorable clinical outcomes, reduced microsatellite instability and tumor mutation burden, alterations in the TME, and diminished response to immunotherapy. These findings provide valuable insights into the potential prognostic and therapeutic implications of APOD in GC.

14.
Heliyon ; 10(3): e24589, 2024 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-38314288

RESUMO

Based on the observed biological activity of 1,2,4-triazin-5-one derivatives and their cyclic analogues, a novel series of 7H-thiazolo[3,2-b]-1,2,4-triazin-7-one derivatives that contain ester moiety compounds 3a-3g, carboxylic acid moiety compounds 4a-4g and piperazine amide moiety compounds 5a-5k at position-3 of the thiazolotriazinone scaffold were synthesized. The intermolecular cyclization occurred regioselectively at N2-position of 1,2,4-triazine ring was characterized by X-ray single-crystal diffraction analysis. The in vitro biological activities of the target compounds were assayed against some bacterial strains. Compared with ciprofloxacin, compounds 3g and 4g exhibited more excellent antibacterial activity, especially the activity against Staphylococcus aureus and Escherichia coli, showing that the fluorine at the para position of the benzyl group would be the best choice. In addition, compounds 4e-4g with carboxylic acid moiety can enhance the antibacterial activity. Compounds 5g-5k containing bulky 1-(substituted phenyl)piperazine moiety were found with slightly less biological activity. Similar to ciprofloxacin, the docking result of target compounds with DNA topoisomerase II indicates the carboxyl group of the target compounds with carboxylic acid moiety has a crucial salt bridge interaction with Mg2+ in the protein.

15.
Brief Bioinform ; 25(2)2024 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-38324623

RESUMO

Recent advances in spatially resolved transcriptomics (SRT) have brought ever-increasing opportunities to characterize expression landscape in the context of tissue spatiality. Nevertheless, there still exist multiple challenges to accurately detect spatial functional regions in tissue. Here, we present a novel contrastive learning framework, SPAtially Contrastive variational AutoEncoder (SpaCAE), which contrasts transcriptomic signals of each spot and its spatial neighbors to achieve fine-grained tissue structures detection. By employing a graph embedding variational autoencoder and incorporating a deep contrastive strategy, SpaCAE achieves a balance between spatial local information and global information of expression, enabling effective learning of representations with spatial constraints. Particularly, SpaCAE provides a graph deconvolutional decoder to address the smoothing effect of local spatial structure on expression's self-supervised learning, an aspect often overlooked by current graph neural networks. We demonstrated that SpaCAE could achieve effective performance on SRT data generated from multiple technologies for spatial domains identification and data denoising, making it a remarkable tool to obtain novel insights from SRT studies.


Assuntos
Perfilação da Expressão Gênica , Transcriptoma , Redes Neurais de Computação
16.
Sheng Wu Gong Cheng Xue Bao ; 40(2): 496-506, 2024 Feb 25.
Artigo em Chinês | MEDLINE | ID: mdl-38369836

RESUMO

The conventional peptide substrates of SARS-CoV-2 main protease (Mpro) are frequently associated with high cost, unstable kinetics, and multistep synthesis. Hence, there is an urgent need to design affordable and stable Mpro substrates for pharmacological research. Herein, we designed a functional Mpro substrate based on a dimerization-dependent red fluorescent protein (ddRFP) for the evaluation of Mpro inhibitors in vitro. The codon-optimized DNA fragment encoding RFP-A1 domain, a polypeptide linker containing Mpro cleavage sequence (AVLQS), and the RFP-B1 domain was subcloned into the pET-28a vector. After transformation into Escherichia coli Rosetta(DE3) cells, the kanamycin resistant transformants were selected. Using a low temperature induction strategy, most of the target proteins (ddRFP-M) presented in the supernatant fractions were collected and purified by a HisTrapTM chelating column. Subsequently, the inhibition of Mpro by ensitrelvir and baicalein was assessed using ddRFP-M assay, and the biochemical properties of ddRFP-M substrate were analyzed. Our results showed that the fluorogenic substrate ddRFP-M was successfully prepared from E. coli cells, and this biosensor exhibited the expected specificity, sensitivity, and reliability. In conclusion, the production of the fluorogenic substrate ddRFP-M provides an expedient avenue for the assessment of Mpro inhibitors in vitro.


Assuntos
Técnicas Biossensoriais , COVID-19 , Proteases 3C de Coronavírus , Humanos , Dimerização , Proteína Vermelha Fluorescente , SARS-CoV-2/genética , Escherichia coli/genética , Corantes Fluorescentes , Reprodutibilidade dos Testes , Peptídeos , Inibidores de Proteases , Simulação de Acoplamento Molecular
17.
Patterns (N Y) ; 5(2): 100911, 2024 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-38370122

RESUMO

Crosstalk among cells is vital for maintaining the biological function and intactness of systems. Most existing methods for investigating cell-cell communications are based on ligand-receptor (L-R) expression, and they focus on the study between two cells. Thus, the final communication inference results are particularly sensitive to the completeness and accuracy of the prior biological knowledge. Because existing L-R research focuses mainly on humans, most existing methods can only examine cell-cell communication for humans. As far as we know, there is currently no effective method to overcome this species limitation. Here, we propose MDIC3 (matrix decomposition to infer cell-cell communication), an unsupervised tool to investigate cell-cell communication in any species, and the results are not limited by specific L-R pairs or signaling pathways. By comparing it with existing methods for the inference of cell-cell communication, MDIC3 obtained better performance in both humans and mice.

18.
J Cancer ; 15(6): 1762-1769, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38370381

RESUMO

Background: The potential relation of methyltransferase-like gene polymorphisms and epithelial ovarian cancer (EOC) remains unclear. Methods: Five SNPs (METTL5 rs3769767 A>G, METTL16 rs1056321 T>C, METTL5 rs10190853 G>A, METTL5 rs3769768 G>A and METTL16 rs11869256 A>G) of methyltransferase-like genes was selected trough NCBI dbSNP database. Two hundred and eighty-eight cases and 361 controls were enrolled from three hospitals in South China to conduct the case-control study. Genomic DNA was abstracted from peripheral blood and genotyped through a TapMan assay. Stratified analysis was conducted to explore the association of rs10190853, rs3769768, rs11869256 genotype and EOC susceptibility. The combination analysis was adopted to evaluate the relation between inferred haplotypes of the METTL5, METTL16 genes and EOC risk. Multifactor dimensionality reduction (MDR) analysis was performed to verify the interaction of SNPs. Results: Among the five analyzed SNPs, METTL5 rs3769768 AA exhibited a significant association with increased EOC risk, while METTL5 rs10190853 GA, METTL16 rs11869256 GA was certified to decrease the susceptibility of EOC. The stratified analysis further revealed the harmful effect of METTL5 rs3769768 AA in EOC patients. On the contrary, METTL16 rs11869256 AG/GG and METTL5 rs10190853 AA showed the reduced risk of EOC in patients of specific subgroups. Combination analysis identified that haplotypes AAA highly connected with reduced risk of EOC. MDR analysis revealed that these SNPs existed no specific interactions. Conclusion: METTL5 rs3769768 was related to increased risk of EOC. METTL5 rs10190853 and METTL16 rs11869256 decreased the susceptibility in EOC. METTL5 and METTL16 could be potential target of molecular therapy and prognosis markers.

19.
Bioresour Technol ; 397: 130491, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38408502

RESUMO

This study introduced two deep eutectic solvents, ChCl/oxalic acid (CO) and ChCl/ethylene glycol (CE), into a 34-day co-composting process of distillery sludge and distiller's grains waste to address challenges related to NH3 emissions. The addition of DES increased dissolved organic carbon by 68% to 92%, offering more utilizable carbon for microorganisms. SYTO9/PI staining and enzyme activity tests showed the CE group had higher bacterial activity and metabolic levels during the thermophilic phase than the control. Bacterial community analysis revealed that early dominance of Lactobacillus and Lysinibacillus in CE accelerated the onset of the thermophilic phase, reduced pile pH, and significantly decreased urease production by reducing Ureibacillus. Consequently, CE treatment substantially dropped NH3 emissions by 73% and nitrogen loss by 54%. Besides, CE fostered a more abundant functional microbial community during the cooling and maturation phases, enhancing deep degradation and humification of organic matter.


Assuntos
Compostagem , Esgotos , Esgotos/química , Amônia/metabolismo , Solventes Eutéticos Profundos , Solventes , Carbono , Bactérias/metabolismo , Nitrogênio/metabolismo , Solo
20.
Hortic Res ; 11(2): uhad295, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38404593

RESUMO

Powdery mildew (PM) is one of the most destructive diseases that threaten cucumber production globally. Efficient breeding of novel PM-resistant cultivars will require a robust understanding of the molecular mechanisms of cucumber resistance against PM. Using a genome-wide association study, we detected a locus significantly correlated with PM resistance in cucumber stem, pm-s5.1. A 1449-bp insertion in the CsMLO8 coding region at the pm-s5.1 locus resulted in enhanced stem PM resistance. Knockout mutants of CsMLO8 and CsMLO11 generated by CRISPR/Cas9 both showed improved PM resistance in the stem, hypocotyl, and leaves, and the double mutant mlo8mlo11 displayed even stronger resistance. We found that reactive oxygen species (ROS) accumulation was higher in the stem of these mutants. Protein interaction assays suggested that CsMLO8 and CsMLO11 could physically interact with CsRbohD and CsCRK2, respectively. Further, we showed that CsMLO8 and CsCRK2 competitively interact with the C-terminus of CsRbohD to affect CsCRK2-CsRbohD module-mediated ROS production during PM defense. These findings provide new insights into the understanding of CsMLO proteins during PM defense responses.

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