Biology subjects

zhang, m.

Publications and source records attributed to zhang, m..

8 recordsLinked to original sources

bioRxiv2024

Suaeda Salsa Hyperspectral Index (SSHI) for mapping S. salsa in coastal wetlands using hyperspectral satellite imagery

Suaeda Salsa (S. salsa), a pioneer species with short and red-purplish plants in the intertidal zones, has significant ecological, economic, recreational and tourism values. Timely monitoring of S. salsa is crucial for understanding its dynamics and sustainable management of coastal wetlands. Hyperspectral satellite offers valuable opportunities due to its detailed spectral information. This study proposed a Suaeda Salsa Hyperspectral Index (SSHI) for S. salsa mapping based on hyperspectral satellite imagery. The SSHI was developed by considering the large within-class spectral variations of cover types at coastal wetlands, accounting for the spectral correlations in hyperspectral data, and employing dynamic band selection on a per-pixel basis to optimize the separation of S. salsa from other land covers. [Formula] (1+ L), where i[isin][499nm, 611nm], j[isin][628nm, 851nm], L= 0.5. We applied SSHI on ZY1-02D/E AHSI images over Yellow River Delta (YRD) and Liao River Delta (LRD), China during 2021 to 2023. Based on SSHI, a simple thresholding method and a random forest (RF) model were used to map S. salsa. Our results showed that the overall accuracies of S. salsa maps achieved 87.96%[~]89.43% (YRD) and 92.03%[~]93.36% (LRD) using thresholds, and 92.62%[~]94.05% (YRD) and 94.74%[~]94.79% (LRD) using RF. For RF, incorporating SSHI improves S. salsa producers accuracies (users accuracies) by 1.02%[~]6.85% (2.26%[~]6.25%) compared to those without SSHI, proving the effectiveness of SSHI. The S. salsa maps reveal notable temporal variations, reflecting the impacts of climate change and human activities. SSHI is also applicable to other hyperspectral imagery, such as GF-5B and PRISMA.

ecology↗

bioRxiv2024

Modelling cell type-specific lncRNA regulatory network in autism with Cycle

Autism spectrum disorder (ASD) is a class of complex neurodevelopment disorders with high genetic heterogeneity. Long non-coding RNAs (lncRNAs) are vital regulators that perform specific functions within diverse cell types and play pivotal roles in neurological diseases including ASD. Therefore, studying the specific regulation of lncRNAs in various cell types is crucial for deciphering ASD molecular mechanisms. Existing computational methods utilize bulk transcriptomics data across all of cells or samples, which could reveal the commonalities of lncRNA regulation in the pathogenesis of ASD, but ignore the specificity of lncRNA regulation across various cell types. Here, we present Cycle (Cell type-specific lncRNA regulatory network) to construct the landscape of cell type-specific lncRNA regulation in ASD. We have found that each ASD cell type is unique in lncRNA regulation, and more than one-third and all of cell type-specific lncRNA regulatory networks are characterized as scale-free and small-world, respectively. Across 17 ASD cell types, we have discovered 19 rewired and 11 conserved modules, and eight rewired and three conserved hubs underlying within the discovered cell type-specific lncRNA regulatory networks. Moreover, the discovered rewired and conserved modules and hubs are significantly enriched in ASD-related terms. Furthermore, more similar ASD cell types tend to be connected with higher strength in the constructed cell similarity network. Finally, the comparison results demonstrate that Cycle is a potential method for uncovering cell type-specific lncRNA regulation.

bioinformatics↗

bioRxiv2022

Genetic Diversity of Candidatus Liberibacter asiaticus Based on Four Hypervariable Genomic Regions in China

Huanglongbing (HLB; greening disease), caused by Candidatus Liberibacter asiaticus (CLas), is the most damaging citrus disease worldwide. The disease has spread throughout the citrus-producing regions of Guangxi, Guangdong, Fujian, and others in China. A total of 1,789 HLB-like symptomatic or asymptomatic samples were collected from the Guangxi and Fujian provinces of China to decipher the genetic diversity of CLas and its correlation with pathogenicity and host range. The disease was the most severe in orange and the least in pomelo. CLas bacteria associated with the specific geographical and citrus variety infected more than 50% of the HLB-like symptomatic samples. We identified a total of 6,286 minor variations by comparing 35 published CLas genomes and observed a highly heterogeneous variation distribution across the genome. Highly diverse regions, including two prophages, were generally more unstable and prone to lose. In the collected CLas strains, four highly diverse non-prophage segments and three prophage segments in the prophage region were chosen for PCR amplification and genotyping. Four hypervariable regions were used to decipher CLas diversity. A total of 100 strains were divided into four groups, of which 90 strains were clustered into two clades with 15 reported reference genomes, while 10 were grouped in two clades separately from the reported genomes. This study provides insight into the molecular characteristics and genetic variations of different CLas strains in China and might help develop HLB prevention and control strategies. ImportanceThe objective of the present study is to characterize the hypervariable genomic region sequence, decipher the genetic diversity of CLas strains from China, understand how various strains differ, and lay the foundation for developing HLB prevention and control strategies.

microbiology↗

bioRxiv2020

CPEB2 m6A Methylation Regulates BTB Permeability via Affecting Splicing Factor SRSF5 Stability

The existence of the blood tumor barrier (BTB) severely hinders the delivery of anti-tumor drugs to gliomas, affecting the targeted therapeutic effects of drugs. Therefore, BTB selective opening has become a hot spot for glioma treatment. This study found that the up-regulated METTL3 and IGF2BP3 in GECs increase the stability of CPEB2 mRNA through m6A methylation of CPEB2 mRNA; CPEB2 binds and increases the stability of splicing factor SRSF5 mRNA; SRSF5 promotes the ETS1 exon inclusion; P51-ETS1 promotes the transcriptional expression of tight junction related proteins ZO-1, occludin and claudin-5, regulating BTB permeability. CPEB2, SRSF5 and P51-ETS1 alone or in combination can effectively enhance the role of Dox in promoting glioma cell apoptosis through BTB. The results of this study provide a new theoretical and experimental basis for the molecular regulation of BTB from the perspective of epigenetics, as well as new ideas for the comprehensive treatment of glioma.

cancer biology↗

bioRxiv2020

Introduction of a precocious metamorphosis BmNPV infection in the latter half of the fifth instar silkworm larvae

The silkworm, Bombyx mori, is a complete metamorphosis insect, the model to study insect physiology and biochemistry. Bombyx mori nucleopolyhedrovirus (BmNPV) is a principal pathogen of the silkworm and its host range is restricted to silkworm larvae, requiring interaction with larvae to accomplish virus replication. Prothoracic glands (PGs) are a model for synthetic ecdysone with regulating insect growth and development. This study performed a transcriptome analysis of silkworm PGs after BmNPV infection. Transcriptome data were annotated with KEGG, GO, and shown to be of high quality by RT-qPCR. The spatial expression profiles of BmJing and BmAryl indicate that they may be specifically expressed in silkworm PGs. The RT-qPCR results of the DEGs in the PGs of BmNPV-infected larvae at 24, 48, and 72 h and at the developmental stages of days-6 and 7, comparing to day-3, reveal that the DEGs may be related to the BmNPV infection via promoting early maturation in the latter half of the silkworm fifth instar. This study is the first report on the identification of possible genes in PGs correlating with the precocious molting and metamorphosis of silkworm larvae under BmNPV infection in the latter half of the fifth instar. Our findings will help to address the interactions between BmNPV infection and host developmental response. This work provides a new perspective on BmNPV infection and host developmental response, as well as suggesting candidate genes for further research.

molecular biology↗

bioRxiv2020

A single-cell transcriptome atlas of the aging human and macaque retina

The human retina is a complex neural tissue that detects light and sends visual information to the brain. However, the molecular and cellular processes that underlie aging primate retina remain unclear. Here, we provide a comprehensive transcriptomic atlas based on 119,520 single cells of the foveal and peripheral retina of humans and macaques covering different ages. The molecular features of retinal cells differed between the two species, suggesting the distinct regional and species specializations of the human and macaque retinae. In addition, human retinal aging occurred in a region- and cell-type- specific manner. Aging of human retina exhibited a foveal to peripheral gradient. MYO9A- rods and a horizontal cell subtype were greatly reduced in aging retina, indicating their vulnerability to aging. Moreover, we generated a dataset showing the cell-type- and region- specific gene expression associated with 55 types of human retinal disease, which provides a foundation to understand the molecular and cellular mechanisms underlying human retinal diseases. Together, these datasets are valuable for understanding the molecular characteristics of primate retina, as well as the molecular regulation of aging progression and related diseases.

neuroscience↗

bioRxiv2020

The COMPASS-like complex modulates fungal development and pathogenesis by regulating H3K4me3-mediated targeted gene expression in Magnaporthe oryzae

Histone H3K4 methylation is catalysed by the multi-protein complex known as the Set1/COMPASS or MLL/COMPASS-like complex, an element that is highly evolutionarily conserved from yeast to humans. However, the components and mechanisms by which the COMPASS-like complex targets the H3K4 methylation of plant pathogenic genes in fungi remain elusive. Here we present a comprehensive analysis combining biochemical, molecular, and genome-wide approaches to characterize the roles of the COMPASS-like family in Magnaporthe oryzae, a model plant fungal pathogen. We purified and identified six conserved subunits of COMPASS from the rice blast fungus M. oryzae, i.e., MoBre2 (Cps60/ASH2L), MoSpp1 (Cps40/Cfp1), MoSwd2 (Cps35), MoSdc1 (Cps25/DPY30), MoSet1 (MLL/ALL) and MoRbBP5 (Cps50), using an affinity tag on MoBre2. We determined the SPRY domain of MoBre2 can recognize directly with DPY30 domain of MoSdc1 in vitro. Furthermore, we found that deletion of the genes encoding COMPASS subunits of MoBre2, MoSpp1 and MoSwd2 caused similar defects regarding invasive hyphal development and pathogenicity. Genome-wide profiling of H3K4me3 revealed that the it has remarkable co-occupancy at the TSS regions of target genes. Significantly, these target genes are often involved in spore germination and pathogenesis. Decreased gene expression caused by the deletion of MoBre2, MoSwd2 or MoSpp1 gene was highly correlated with decrease in H3K4me3. Taken together, these results suggest that MoBre2, MoSpp1, and MoSwd2 function as a whole COMPASS complex, contributing to fungal development and pathogenesis by regulating H3K4me3-targeted genes in M. oryzae.

microbiology↗

bioRxiv2019

Comparative investigation into formycin A and pyrazofurin A biosynthesis reveals branch pathways for the construction of C-nucleoside scaffolds

Formycin A (FOR-A) and pyrazofurin A (PRF-A) are purine-related C-nucleoside antibiotics, in which ribose and a pyrazole-derived base are linked by a C-glycosidic bond, however, the logic underlying the biosynthesis of these molecules has remained largely unexplored. Here, we report the discovery of the pathways for FOR-A and PRF-A biosynthesis from diverse actinobacteria, and demonstrate that their biosynthesis is initiated by a lysine N6-monooxygenase. Moreover, we show that the forT and prfE (individually related to FOR-A and PRF-A biosynthesis) mutants are correspondingly capable of accumulating the unexpected pyrazole-related intermediates, compound 11 and 9a. We also decipher the enzymatic basis of ForT/PrfE for the C-glycosidic bond formation in FOR-A/PRF-A biosynthesis. To our knowledge, ForT/PrfE represents the first example of {beta}-RFA-P ({beta}-ribofuranosyl-aminobenzene 5-phosphate) synthase-like enzymes governing C-nucleoside scaffold construction in natural product biosynthesis. These data establish a foundation for combinatorial biosynthesis of related purine nucleoside antibiotics, and also open the way for target-directed genome mining of PRF-A/FOR-A related antibiotics.\n\nIMPORTANCEFormycin A (FOR-A) and pyrazofurin A (PRF-A) are well known for their unusual chemical structures and remarkable biological activities. Actually, deciphering FOR-A/PRF-A biosynthesis will not only expand biochemical repertoire for novel enzymatic reactions, but also permit the target-oriented genome mining of FOR-A/PRF-A related C-nucleoside antibiotics.

biochemistry↗