Toxicity of fungal-derived volatile organic compounds against root-knot nematodes.

BACKGROUND: Root-knot nematodes (RKNs), including Meloidogyne species, are among the most destructive plant-parasites worldwide. Recent evidence suggests that entomopathogenic fungi (EPF) can antagonize RKNs. Such antagonistic effects are likely mediated by toxic metabolites, including volatile organic compounds (VOCs), produced by the fungi. However, how widespread these effects are across EPF species, and which VOCs mediate negative interactions between EPF and RKNs needs to be further elucidated. RESULTS: First, we evaluated the nematicidal effect of VOCs emitted by 46 EPF isolates against Meloidogyne incognita and found variable toxicity depending on the isolate. Second, we measured the nematicidal effect of highly toxic isolates, including species in the genus Talaromyces, Aspergillus, Clonostachys, and Purpureocillium and, third, we analyzed the nematicidal effect of major VOCs, including 2-methyl-1-propanol, 3-methyl-1-butanol, isopropyl alcohol and 2-methyl-3-pentanone. The mortality of M. incognita juveniles (J2s) was generally high (50%) either via airborne or in-solution contact with VOCs. Moreover, the tested VOCs significantly inhibited egg hatching, and repelled J2s away from the VOCs. CONCLUSION: This study not only provides insights into the ecological function of VOCs in the rhizosphere, but also provides new approaches for developing environmentally friendly control methods of RKNs in agroecosystems. © 2023 Society of Chemical Industry.

ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data.

SUMMARY: Recent innovations in single-cell chromatin accessibility sequencing (scCAS) have revolutionized the characterization of epigenomic heterogeneity. Estimation of the number of cell types is a crucial step for downstream analyses and biological implications. However, efforts to perform estimation specifically for scCAS data are limited. Here, we propose ASTER, an ensemble learning-based tool for accurately estimating the number of cell types in scCAS data. ASTER outperformed baseline methods in systematic evaluation on 27 datasets of various protocols, sizes, numbers of cell types, degrees of cell-type imbalance, cell states and qualities, providing valuable guidance for scCAS data analysis. AVAILABILITY AND IMPLEMENTATION: ASTER along with detailed documentation is freely accessible at https://aster.readthedocs.io/ under the MIT License. It can be seamlessly integrated into existing scCAS analysis workflows. The source code is available at https://github.com/biox-nku/aster. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Role of alternative splicing events in endometrial cancer prognosis. / é€‰æ‹©æ€§å‰ªæŽ¥äº‹ä»¶åœ¨å­å®«å† è†œç™Œé¢„åŽä¸­çš„ä½œç”¨.

OBJECTIVES: Alternative splicing (AS), as a potent and pervasive mechanism of transcriptional regulation, can expand the genome's coding capacity. Growing evidence suggests that the AS events may be associated with various types of cancer. This study aims to explore the prognostic value of AS in endometrial cancer (EC). METHODS: Differently expressed AS (DEAS) events were screened by pairing the percent spliced in (PSI) value of tumor and paracancerous tissues in The Cancer Genome Atlas (TCGA) database, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed on their parental gene analysis of organisms. Subsequently, univariate Cox analysis was used to identify the prognostic AS events and a stepwise multi-factor Cox regression analysis was performed to further construct prognostic models. Furthermore, the diagnostic value of the prognostic model was evaluated by receiver operating characteristic (ROC) curve and Kaplan-Meier analysis. Finally, the regulatory network of AS events and splicing factory in the model was also constructed. RESULTS: A total of 28 281 AS events were detected in EC. Of them, 42 DEAS were identified, and their parental genes were involved in tumor-related processes such as meiotic nuclear division, alpha-amino acid biosynthetic process, nuclear division, and so on. Univariate Cox analysis identified 2 289 prognostic-related AS events and constructed Cox prognostic models based on 7 different types and all types of AS events, in which the area under the curve of ROC of all types was as high as 0.882 and was better than that of 7 different splicing types. Finally, 12 splicing factors and AS events showed an obvious regulatory relationship. CONCLUSIONS: We use the whole genome analysis of AS events to establish a scientific prognostic prediction model for EC patients, which provides a reliable theoretical basis for the evaluation of EC clinical prognosis.

High-intensity focused ultrasound in the management of adenomyosis: long-term results from a single center.

OBJECTIVE: To investigate the long-term clinical outcomes of patients with adenomyosis treated by high-intensity focused ultrasound (HIFU). MATERIALS AND METHODS: From June 2012 to January 2020, 2311 patients with adenomyosis were treated with HIFU at our center, 1982 patients who have complete clinical data were retrospectively reviewed. Among the patients who completed the follow-up, 485 were treated with HIFU alone, 289 were treated with HIFU followed by GnRH-a, 255 were treated with HIFU combined with Mirena and 594 were treated with HIFU combined with GnRH-a and Mirena. The dysmenorrhea severity pain score and average menorrhagia severity score before and at 3 months, 6 months, 1 year, 2 years, 3 years and 5 years after HIFU were compared. The adverse effects were recorded. In addition, the efficacy between patients treated with GnRH-a and/or Mirena were compared. RESULTS: After HIFU ablation, the dysmenorrhea severity pain score and the menorrhagia severity score were significantly decreased at each follow-up time point. However, it was observed that as the follow-up time increased, the effective rate of HIFU treatment in improving dysmenorrhea and menorrhagia decreased. The 6 months and 3 years follow-up results showed that the efficacy of HIFU combined with Mirena and HIFU combined with GnRH-a and Mirena were significantly higher than HIFU alone and HIFU combined with GnRH-a (p < 0.05). The major complications were rare. CONCLUSION: HIFU is a safe and effective treatment for patients with adenomyosis. HIFU combined with Mirena or HIFU combined with GnRH-a and Mirena can significantly enhance the long-term treatment results.

A potential regulatory network among WDR86-AS1, miR-10b-3p, and LITAF is possibly involved in preeclampsia pathogenesis.

Preeclampsia (PE), a pregnancy-specific disorder, is a leading cause of perinatal maternal and fetal mortality and morbidity. Impaired migration and invasion of trophoblastic cells and an imbalanced systemic maternal inflammatory response have been proposed as possible causes of pathogenesis of PE. Comparative analysis of PE-affected placentas and healthy placentas has uncovered differentially expressed long noncoding RNAs, microRNAs, and mRNAs. This study was conducted to investigate the effect of a regulatory network among these RNAs on PE pathogenesis. Long noncoding RNA WDR86-AS1, microRNA miR-10b-3p, and mRNA of protein LITAF were identified by screening of genes in existing databases with aberrant expression in PE-affected placentas and potential mutual interactions as revealed by TargetScan, miRanda, and PicTar analyses. This study identified their expression in PE-affected and healthy placentas by RT-PCR. An in vitro experiment was performed on human trophoblast HTR-8/SVneo cells cultured under normoxic or hypoxic conditions. MiR-10b-3p targets were identified in luciferase reporter assays and RNA pull-down assays. The mouse model of PE was set up using a soluble form of FLT-1 for in vivo testing. Lower levels of miR-10b-3p but higher expression of WDR86-AS1 and LITAF were observed in PE-affected placentas and trophoblast cells under hypoxia. WDR86-AS1 and LITAF mRNA were confirmed as targets of miR-10b-3p. WDR86-AS1 downregulated miR-10b-3p but promoted LITAF expression. Microarray analyses revealed that LITAF controlled the inflammatory responses and migration and proliferation of HTR-8/SVneo cells under hypoxia. Indeed, knockdown of WDR86-AS1 and LITAF or overexpression of miR-10b-3p attenuated the hypoxia-induced inhibition of cellular viability, migration, and invasion. Moreover, miR-10b-3p overexpression attenuated the pathological symptoms caused by soluble FLT-1 in vivo. In summary, the WDR86-AS1/miR-10b-3p/LITAF network is probably involved in PE pathogenesis.