Biology subjects

Ling, M.

Publications and source records attributed to Ling, M..

5 recordsLinked to original sources

bioRxiv2026

Single-Cell Metagenomics Links Plasmid-Derived Antimicrobial Resistance to Hosts in the Pig Gut Microbiome

Antimicrobial exposure can alter gut resistance reservoirs, but bulk metagenomics alone often cannot distinguish whether observed changes reflect expansion of bacterial hosts, altered abundance of plasmid-derived sequences, or redistribution of mobile elements across host backgrounds. Here, we combined longitudinal bulk short-read metagenomics with selected bulk long-read and single-cell shotgun metagenomic sequencing to analyse faecal samples from six Danish pigs over 11 weeks, including an unplanned tiamulin exposure affecting the three pigs housed on the right side of the stable. We constructed a catalogue of 885 plasmid-derived sequences collapsed into 195 bins. Twenty-eight bins and 212 contigs carried resistance annotations, including ribosomal-target markers relevant to pleuromutilin exposure. Single-cell evidence linked subsets of plasmid-derived bins and contigs to bacterial host taxa, enabling host-resolved inspection of resistance-associated plasmid-derived features in longitudinal bulk metagenomes. The microbiome-wide plasmid-derived-sequence prevalence screen identified two bins with post-event associations, whereas resistance-gene abundance and host-attributed plasmid-derived-sequence abundance screens identified no significant host-resolved associations. Because exposure was unplanned and confounded with pen side and disease signs, treatment-response results are exploratory. The main contribution is a single-cell-informed microbial ecology workflow for linking plasmid-derived resistance features to host backgrounds and longitudinal abundance patterns in complex gut

microbiology↗

bioRxiv2022

KAT5 activity regulates G0-like states in human gliomas

In solid tumors, G0-like states are likely critical for maintaining developmental hierarchies and cellular heterogeneity and promoting tumor growth/recurrence, yet little is known about tumor G0 states or regulation of their ingress/egress. To discover G0-like states and their regulators for glioblastoma (GBM), we analyzed G0 populations in an orthotopic model of GBM using single cell RNA-seq and performed a genome-wide CRISPR-Cas9 screen in patient-derived GBM stem-like cells (GSCs) for genes that trap cells in G0 when inhibited. We identify the protein acetyltransferase KAT5 as a key regulator of transcriptional, epigenetic, and proliferative heterogeneity impacting transitions into G0-like states. KAT5 activity suppresses the emergence of non-dividing subpopulations with oligodendrocyte progenitor and radial glial cell characteristics both in vitro and in a human GSC brain tumor model. In primary gliomas, KAT5 activity is dynamic with KAT5low tumor cells displaying quiescent properties, while KAT5 activity overall increases from low to high grade tumors and is associated with worse patient outcomes.

cancer biology↗

bioRxiv2022

Structure and Protein-Protein Interactions of Ice Nucleation Proteins Drive Their Activity

ABSTRACTMicrobially-produced ice nucleating proteins (INpro) are unique molecular structures with the highest known catalytic efficiency for ice formation. Their critical role in rain formation and frost damage of crops together with their diverse commercial applications warrant an in-depth under-standing of their inherent ice nucleation mechanism. We used the machine-learning based software Al-phaFold to develop the first ab initio structural model of a bacterial INpro which is a novel beta-helix structure consisting of repeated stacks of two beta strands connected by two sharp turns. Using the synchrotron radiation circular dichroism, we validated the {beta}-strand content of the model. Combining functional studies of purified recombinant INpro, electron microscopy and modeling, we further demonstrate that the formation of dimers and higher-order oligomers is key to INpro activity. This work presents a major advance in understanding the molecular foundation for bacterial ice-nucleation activity and the basis for investigating the mechanistic role of INpro-induced ice formation in the atmosphere, and for commercial design and production of ice-nucleating particles for industrial applications.

microbiology↗

bioRxiv2020

Comparison of High-Throughput Single-Cell RNA Sequencing Data Processing Pipelines

With the development of single-cell RNA sequencing (scRNA-seq) technology, it has become possible to perform large-scale transcript profiling for tens of thousands of cells in a single experiment. Many analysis pipelines have been developed for data generated from different high-throughput scRNA-seq platforms, bringing a new challenge to users to choose a proper workflow that is efficient, robust and reliable for a specific sequencing platform. Moreover, as the amount of public scRNA-seq data has increased rapidly, integrated analysis of scRNA-seq data from different sources has become increasingly popular. How-ever, it remains unclear whether such integrated analysis would be biased if the data were processed by different upstream pipelines. In this study, we encapsulated seven existing high-throughput scRNA-seq data processing pipelines with Nextflow, a general integrative workflow management framework, and evaluated their performances in terms of running time, computational resource consumption, and data processing consistency using nine public datasets generated from five different high-throughput scRNA-seq platforms. Our work provides a useful guideline for the selection of scRNA-seq data processing pipelines based on their performances on different real datasets. In addition, these guidelines can serve as a performance evaluation framework for future developments in high-throughput scRNA-seq data processing.

bioinformatics↗

bioRxiv2019

Signaling Diversity Enabled by Rap1-Regulated Plasma Membrane ERK with Distinct Temporal Dynamics

A variety of different signals induce specific responses through a common, ERK-dependent kinase cascade. It has been suggested that signaling specificity can be achieved through precise temporal regulation of ERK activity. Given the wide distrubtion of ERK susbtrates across different subcellular compartments, it is important to understand how ERK activity is temporally regulated at specific subcellular locations. To address this question, we have expanded the toolbox of FRET-based ERK biosensors by creating a series of improved biosensors targeted to various subcellular regions via sequence specific motifs to measure spatiotemporal changes in ERK enzymatic activity. Using these sensors, we showed that EGF induces sustained ERK activity near the plasma membrane in sharp contrast to the transient activity observed in the cytopolasm and nucleus. Furthermore, EGF-induced plasma membrane ERK activity involves Rap1, a noncanonical activator, and controls cell morphology and EGF-induced membrane protrusion dynamics. Our work strongly supports that spatial and temporal regulation of ERK activity is integrated to control signaling specificity from a single extracellular signal to multiple cellular processes.

cell biology↗