the-plant-infection-test-spray-wound-mediated-inoculation-with-plant

The Plant Infection Test: Spray and Wound-Mediated Inoculation with the Plant Pathogen <em>Magnaporthe Grisea</em>

Plants possess a powerful system to defend themselves against potential threats by pathogenic fungi. For agriculturally important plants, however, current ...

optimized-intravenous-injection-in-adult-zebrafish

Optimized Intravenous Injection in Adult Zebrafish

Intravenous (IV) injection is widely recognized as the most effective and commonly utilized method for achieving systemic delivery of substances in ...

Beijing University of Agriculture

The University of Hong Kong

Hong Kong Science Park

Ash1 is a known H3K36-specific histone demethylase that is required for normal Hox gene expression and fertility in  and mammals. However, little is known about the expression and function of the fungal ortholog of Ash1 in phytopathogenic fungus . Here we report that MoKMT2H, an Ash1-like protein, is required for conidium germination and virulence in rice. We obtained  null mutant (Δ) using a target gene replacement strategy. In the Δ null mutants, global histone methyltransferase modifications (H3K4me3, H3K9me3, H3K27me3, and H3K36me2/3) of the genome were unaffected. The Δ mutants showed no defect in vegetative hyphal growth, conidium morphology, conidiation, or disease lesion formation on rice leaves. However, the  deletion mutants were delayed for conidium germination and consequently had decreased virulence. Taken together, our results indicated that MoKMT2H plays an important role in conidium germination during appressorium formation in the rice blast fungus and perhaps other pathogenic plant fungi.

An Ash1-Like Protein MoKMT2H Null Mutant Is Delayed for Conidium Germination and Pathogenesis in .

Isocitrate dehydrogenase 2 (IDH2) mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia (CN-AML) but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2 and IDH2 AML and reported their pathologic, functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co-expressing FLT3 and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to adulthood, full-blown leukemia ensued with multi-lineage dysplasia, increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. Tg(Runx1:FLT3IDH2) but not Tg(Runx1:FLT3IDH2) zebrafish showed an increase in T-cell development at embryonic and adult stages. Single-cell transcriptomic analysis revealed increased myeloid skewing, differentiation blockade and enrichment of leukemia-associated gene signatures in both zebrafish models. Tg(Runx1:FLT3IDH2) but not Tg(Runx1:FLT3IDH2) zebrafish showed an increase in interferon signals at the adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion, the zebrafish models of IDH2 mutated AML recapitulated the morphologic, clinical, functional and transcriptomic characteristics of human diseases, and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening.

Transgenic IDH2 and IDH2 zebrafish models recapitulated features of human acute myeloid leukemia.

Correction: Transgenic IDH2 and IDH2 zebrafish models recapitulated features of human acute myeloid leukemia.

Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4% vs 70%-80%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites. This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders.

Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing.

Third-generation sequencing techniques have become increasingly popular due to their capacity to produce long, high-quality reads. Effective comparative analysis across various samples and sequencing platforms is essential for understanding biological mechanisms and establishing benchmark baselines. However, existing tools for long-read sequencing predominantly focus on quality control (QC) and processing for individual samples, complicating the comparison of multiple datasets. The lack of comprehensive tools for data comparison and visualization presents challenges for researchers with limited bioinformatics experience. To address this gap, we present Giraffe (https://github.com/lrslab/Giraffe_View), a Python3-based command-line tool designed for comparative analysis and visualization across diverse samples and platforms. Giraffe facilitates the assessment of read quality, sequencing bias, and genomic regional methylation proportions for both DNA and direct RNA sequencing reads. Its effectiveness has been demonstrated in various scenarios, including comparisons of sequencing methods (whole genome amplification vs. shotgun), sequencing platforms (Oxford Nanopore Technology, ONT vs. Pacific Biosciences, PacBio), tissues (kidney marrow with and without blood), and biological replicates (kidney marrows).

ArticleTotal : 2	Year
Publication title Cited by 9	2018
Publication title Cited by 5	2024

Article	Year
An Ash1-Like Protein MoKMT2H Null Mutant Is Delayed for Conidium Germination and Pathogenesis in . BioMed research international\| PubMed ID: 27747223	2016
Transgenic IDH2 and IDH2 zebrafish models recapitulated features of human acute myeloid leukemia. Oncogene\| PubMed ID: 36739363	2023
Correction: Transgenic IDH2 and IDH2 zebrafish models recapitulated features of human acute myeloid leukemia. Oncogene\| PubMed ID: 36922683	2023
Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing. Scientific data\| PubMed ID: 37563176	2023
Giraffe: A tool for comprehensive processing and visualization of multiple long-read sequencing data. Computational and structural biotechnology journal\| PubMed ID: 39279873	2024

Xuan Sun

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