Biology subjects

Geng, M.

Publications and source records attributed to Geng, M..

8 recordsLinked to original sources

bioRxiv2025

Rapid ecosystem collapse and biofilter formation following seabed methane leakage

Globally, vast amounts of methane are trapped within subseafloor gas hydrates. Recent evidence suggests that climate- and human-induced perturbations can destabilize gas hydrates and trigger methane release, yet the response of deep-sea ecosystems to these changes remains poorly understood. Here we show multi-year in situ monitoring of seabed ecosystem following methane leakage induced by hydrate exploration activities. Within just two years, benthic microbial and eukaryotic diversity in the affected areas declined significantly, while microbial and macrofaunal abundance increased. Integrated geochemical and omics analyses reveal the rapid successional shift of seabed ecosystem to a novel chemosynthetic system. Aerobic methanotrophs (Methyloprofundus) co-established with unexpectedly fast growing anaerobic methanotrophic archaea (ANME-3), accompanied by a rapid recruitment of opportunistic polychaetes that bioirrigated the seabed to >50 cm depths. The active animal-microbe interactions sustained exceptionally high rates of methane oxidation that utilized diverse electron acceptors. We demonstrate that methane hydrate destabilization can trigger rapid collapse of native seabed ecosystem while driving the formation of an effective methane biofilter consuming this potent greenhouse gas much faster than previously estimated. Understanding seabed ecosystem response and feedback is critical for predicting benthic methane cycling under ongoing global change and for developing sustainable strategies for methane hydrate resource management.

ecology↗

bioRxiv2025

A simplified MiMe for producing clonal gametes to enable synthetic apomixis in allotetraploid Brassica napus

Synthetic apomixis has been established in Arabidopsis and rice by combining MiMe that produces clonal unreduced gametes with the factors inducing parthenogenesis or haploids. The MiMe requires the simultaneous inactivation of three genes, which imposes challenges for its application in polyploids harbouring multiple copies for each gene. Here, we demonstrate that mutating two genes in the allotetraploid oil crop Brassica napus effectively converts meiosis into mitosis-like division, producing over 95% viable clonal gametes and thus establishing a simplified MiMe system in polyploids.

plant biology↗

bioRxiv2025

The HORMA-domain protein ASY1 recruits the plant-specific cyclin SDS to promote DMC1-mediated meiotic recombination

The chromosome axis is a proteinaceous scaffold essential for crossover formation in meiosis. While the axis associated HORMA-domain protein ASY1 is known to be necessary for the localization of the recombinase DMC1 to the axis, the molecular mechanism linking ASY1 to DMC1 loading remains unclear. Here, we demonstrate that ASY1 directly recruits the plant-specific cyclin SDS to chromosomes, which ensures efficient DMC1 localization and interhomolog recombination. Live-cell imaging and immunodetection revealed that SDS localizes to chromosomes from leptotene to zygotene and dissociates from chromosomes after pachytene resembling DMC1 dynamics. Biochemical assays demonstrated a direct interaction between ASY1 and SDS. Further analyses revealed that ASY1s closure motif, a conformational regulatory element, is required for SDS recruitment despite being dispensable for ASY1s own chromosome association. Moreover, unlike in sds mutants, depletion of the DMC1 inhibitor FIGL1-FLIP complex failed to restore DMC1 foci in asy1 mutants, positioning ASY1 upstream of both positive (SDS) and negative (FIGL1-FLIP) regulators of DMC1. These findings establish ASY1 as a key coordinator of meiotic recombination, bridging chromosome axis architecture with recombinase dynamics to control crossover formation and genome stability.

plant biology↗

bioRxiv2024

Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes

Characterizing shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and novel biological functions. However, it is unclear if such coordination extends to translation. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of translation efficiency covariation (TEC), identifying coordinated translation patterns across cell types. We nominate candidate mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and uncovers gene functions that are not evident from RNA or protein co-expression. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish TEC as a conserved organizing principle of mammalian transcriptomes.

bioinformatics↗

bioRxiv2024

ASY3 has dosage-dependent diverse effects on meiotic crossover formation

Crossovers create genetic diversity and are required for equal chromosome segregation during meiosis. Their number and distribution are highly regulated by different, yet not fully understood mechanisms including crossover interference. Crucial for crossover formation is the chromosome axis. Here, we explore the function of the axis protein ASY3. To this end, we use the allotetraploid species Brassica napus and due to its polyploid nature, this system allows a fine-grained dissection of the dosage of meiotic regulators. The simultaneous mutation of all four ASY3 alleles results in defective synapsis and drastic reduction of crossovers, which is largely rescued by the presence of only one functional ASY3 allele. Crucially, while the number of class I crossovers in mutants with two functional ASY3 alleles is comparable to that in wildtype, this number is significantly increased in mutants with only one functional ASY3 allele, indicating that reducing the dosage of ASY3 increases crossover formation. Moreover, the class I crossovers on each bivalent in mutants with one functional ASY3 allele follow a random distribution, indicating compromised crossover interference. These results reveal the dosage-dependent distinct effects of ASY3 on crossover formation, and provide insights into the role of chromosome axis in patterning recombination.

plant biology↗

bioRxiv2022

Engineering bacterial blight-resistant plants through CRISPR/Cas9-targeted editing of the MeSWEET10a promoter in cassava

Cassava starch is a widely used raw materials for industrial production. However, cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) results in severe yield losses and is the most destructive bacterial disease in all worldwide cassava planting regions. This study showed that editing of the promoter in the disease-susceptibility gene MeSWEET10a of SC8 cassava confers resistance to CBB. All mutated cassava lines had normal morphological and yield-related traits as the wild type. The results lay a research foundation for breeding cassava resistant to bacterial blight. HighlightsMeSWEET10a gene in SC8 cultivar is hijacked by TALE20 from Xam11 strain. Editing of the MeSWEET10a promoter in SC8 cultivar confers resistance to CBB. All the mutated cassava lines had similar yield-related traits compared to wild-type.

plant biology↗

bioRxiv2019

RiboFlow, RiboR and RiboPy: An ecosystem for analyzing ribosome profiling data at read length resolution

SummaryRibosome occupancy measurements enable protein abundance estimation and infer mechanisms of translation. Recent studies have revealed that sequence read lengths in ribosome profiling data are highly variable and carry critical information. Consequently, data analyses require the computation and storage of multiple metrics for a wide range of ribosome footprint lengths. We developed a software ecosystem including a new efficient binary file format named ribo. Ribo files store all essential data grouped by ribosome footprint lengths. Users can assemble ribo files using our RiboFlow pipeline that processes raw ribosomal profiling sequencing data. RiboFlow is highly portable and customizable across a large number of computational environments with built-in capabilities for parallelization. We also developed interfaces for writing and reading ribo files in the R (RiboR) and Python (RiboPy) environments. Using RiboR and RiboPy, users can efficiently access ribosome profiling quality control metrics, generate essential plots, and carry out analyses. Altogether, these components create a complete software ecosystem for researchers to study translation through ribosome profiling. Availability and ImplementationFor a quickstart, please see https://ribosomeprofiling.github.io. Source code, installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling

bioinformatics↗

bioRxiv2018

Occidiofungin, an actin binding antifungal with in vivo efficacy in a vulvovaginal candidiasis infection

Current antifungal treatment options are plagued with rapidly increasing occurrence of resistance, high degree of toxicity and a limited spectrum of activity. The need to develop a novel antifungal with a unique target, wider spectrum of activity, and reduced toxicity to the host, is urgent. We have identified and characterized one such compound named occidiofungin that is produced by the soil bacterium Burkholderia contaminans MS14. This study identifies the primary cellular target of the antifungal, which was determined to be actin. Actin binding metabolites are generally characterized by their ability to inhibit polymerization or depolymerization of actin filaments, which presumably accounts for their severe toxicity. Occidiofungin, instead, has a subtler effect on actin dynamics that triggers apoptotic cell death. We were able to demonstrate the effectiveness of the antifungal in treating a vulvovaginal yeast infection in a murine model. This discovery puts occidiofungin in a unique class of actin-binding antifungal compounds with minimal reported toxicity to the host. The results of this study are important for the development of a novel class of antifungals that could fill the existing gap in treatment options for fungal infections.\n\nAuthor summaryWidespread resistance to antifungal compounds currently in use has been alarming. Identification and development of a new class of antifungals with a novel cellular target is desperately needed. This study describes the assays carried out to determine the molecular target and evaluate efficacy of one such novel antifungal compound called occidiofungin. Occidiofungin modified with a functional alkyne group enabled affinity purification assays and localization studies in yeast. These studies led to the identification of the actin binding property of occidiofungin. Actin-binding by secondary metabolites often exhibit severe host toxicity, but this does not appear to be the case for occidiofungin. We have previously been able to administer occidiofungin to mice at concentrations in the range of 5 mg/kg without any serious complications. We were able to demonstrate the effectiveness of the antifungal in treating a vaginal fungal infection in a murine model. The results outlined in this manuscript establish that occidiofungin is an efficacious compound with a novel molecular target, putting it in a completely new class of antifungals.

microbiology↗