Biology subjects

Chou, M.-Y.

Publications and source records attributed to Chou, M.-Y..

7 recordsLinked to original sources

bioRxiv2026

A Distinct Layer 1 Astrocyte Program Shapes Perisynaptic Structure and Calcium Signaling in Mouse Motor Cortex

Although layer-specific molecular and morphological diversity among cortical astrocytes is increasingly well established, how these distinct states are linked to specialized calcium signaling and maintained in the adult cortex remains unclear. Here, combining super-resolution structural imaging, two-photon calcium imaging, and analysis of public single-cell and spatial transcriptomic resources, we identify Layer 1 (L1) astrocytes in mouse primary motor cortex as a distinct superficial astrocyte program. These cells occupy compact territories yet contain dense synapse-associated loop-like structures and display frequent, fast, broadly spreading calcium events that engage a large fraction of the territory. Transcriptomic analyses identify Id1 and Id3 as enriched components of this superficial program. CRISPR-Cas9 deletion of Id1 and Id3 in adult astrocytes selectively disrupts L1 and superficial Layer 2/3 (L2/3) astrocytes, expanding territory size, reducing fine-process complexity, and suppressing calcium activity. Thus, adult layer-specific transcriptional programs maintain specialized astrocyte structure and signaling. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/712002v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@89c916org.highwire.dtl.DTLVardef@1f0d71eorg.highwire.dtl.DTLVardef@bb02f3org.highwire.dtl.DTLVardef@1bedf7e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LILayer 1 astrocytes in mouse motor cortex have compact, loop-rich nanoarchitecture C_LIO_LILayer 1 astrocytes show fast, frequent, widespread calcium events C_LIO_LISingle-cell data define a superficial astrocyte state enriched for Id1 and Id3 C_LIO_LIAdult Id1/Id3 loss selectively disrupts Layer 1 astrocyte structure and calcium C_LI In BriefBhattacharjee et al., identify a specialized Layer 1 astrocyte state in mouse motor cortex, defined by compact, loop-rich nanoarchitecture and unusually high calcium signaling. Id1/Id3 deletion selectively disrupts this superficial program, linking layer-specific astrocyte form and function to adult transcriptional control.

neuroscience↗

bioRxiv2024

Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (Panicum virgatum L.) significantly impacts plant microbiomes

Switchgrass (Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remains unclear. To address this, wildtype and QsuB engineered switchgrass were grown in switchgrass field soils and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiSeq amplicon sequencing of ITS and 16S rDNA. Compared to wildtype, QsuB engineered switchgrass hosted different microbial communities in roots, rhizosphere, and leaves. Specifically, QsuB engineered plants had a lower abundance of arbuscular mycorrhizal fungi (AMF). Additionally, QsuB engineered plants had fewer Actinobacteriota in root and rhizosphere samples. These findings may indicate that changes in the plant metabolism impact both organismal groups similarly, or potential interactions between AMF and the bacterial community. This study enhances understanding of plant-microbiome interactions by providing baseline microbial data for developing beneficial bioengineering strategies and by assessing non-target impacts of engineered plant traits on the plant microbiome.

microbiology↗

bioRxiv2023

hnRNP A1 induces aberrant CFTR exon 9 splicing via a newly discovered Exonic Splicing Silencer element.

RNA-protein interactions play a key role in the aberrant splicing of CFTR exon 9. Exon 9 skipping leads to the production of a non-functional chloride channel associated with severe forms of cystic fibrosis. The missplicing depends primarily on variations in the polymorphic (TG)mTn locus upstream of exon 9. At the pre-mRNA level, it generates an extended UG-rich binding site for TDP-43, associated with hnRNP A1 recruitment, and prevention of exon 9 3 splicing site (3ss) recognition. While TDP-43 is the dominant inhibitor of exon 9 inclusion, the role of hnRNP A1, a protein with two RNA recognition motifs (RRM1 and RRM2) and a glycine-rich domain, remained unclear. In this work, we have studied the interaction between hnRNP A1 and the CFTR pre-mRNA using NMR spectroscopy and Isothermal Thermal Calorimetry (ITC). The affinities are submicromolar and ITC data suggest that the separate RRMs as well as tandem RRMs form 1:1 complexes. NMR titrations reveal that hnRNP A1 interacts with model CTFR 3ss sequences in a fast exchange regime at the NMR timescale. Splicing assays finally show that this hnRNP A1 binding site represents a previously unknown exonic splicing silencer element. Together, our results shed light on the mechanism of aberrant CFTR exon 9 splicing.

biochemistry↗

bioRxiv2023

Identification of anti-fungal bioactive terpenoids from the bioenergy crop switchgrass (Panicum virgatum)

Plant derived bioactive small molecules have attracted attention of scientists across fundamental and applied scientific disciplines. We seek to understand the influence of these phytochemicals on functional phytobiomes. Increased knowledge of specialized metabolite bioactivities could inform strategies for sustainable crop production. Our recent investigations of metabolomes of the upland and lowland ecotypes of the bioenergy crop switchgrass (Panicum virgatum) revealed large differences in types and abundances of terpenoid specialized metabolites. We hypothesized that - consistent with accumulating evidence that switchgrass genotype impacts microbiome assembly - differential terpenoid accumulation contributes to switchgrass ecotype-specific microbiome composition. An initial in vitro plate-based disc diffusion screen of 18 switchgrass root derived fungal isolates revealed differential responses to upland- and lowland-isolated metabolites. To identify specific fungal growth-modulating metabolites, we tested fractions from root extracts on three ecologically important fungal isolates - Linnemania elongata, Trichoderma sp. and Fusarium sp. Saponins and diterpenoids were identified as the most prominent antifungal metabolites. Finally, analysis of liquid chromatography-purified terpenoids revealed fungal inhibition structure - activity relationships (SAR). Saponin antifungal activity was primarily determined by the number of sugar moieties - saponins glycosylated at a single core position were inhibitory whereas saponins glycosylated at two core positions were inactive. Saponin core hydroxylation and acetylation were also associated with reduced activity. Diterpenoid activity required the presence of an intact furan ring for strong fungal growth inhibition. This study demonstrates that switchgrass genotype-specific metabolites differentially inhibit fungal isolates from the root and rhizosphere, supporting the hypothesis that these small molecules contribute to microbiome assembly and function.

plant biology↗

bioRxiv2022

Structural analyses of the plant PRT6-UBR box in the Cys-Arg/N-degron pathway and insights into the plant submergence response

The submergence response in higher plants is highly dependent on the protein stability of group VII ethylene response factors, which are primarily degraded through the oxygen-dependent Cys-Arg branch of the N-degron pathway of targeted proteolysis. Knockout of PRT6, an E3 ligase and a vital component of the N-degron pathway, improves submergence tolerance in Arabidopsis and barley but is associated with side effects such as germination deficiency. In this study, we determined structures of rice and Arabidopsis PRT6-UBR box in complex with various Arg/N-degron related peptides. We identified two highly conserved motifs in the plant PRT6-UBR box, which is responsible for Cys-Arg/N-degron recognition. Structural and mutagenesis studies revealed the importance of two conserved motifs for Cys-Arg/N-degron recognition. The phenotype of Arabidopsis seedlings with PRT6-UBR mutants in these newly identified conserved motifs showed superior submergence survival suggesting that rational manipulation of the PRT6-UBR box can improve flood tolerance. Our results provide an engineering platform for generating crops with improved submergence tolerance.

biochemistry↗

bioRxiv2020

Hyperlocal variation in soil iron and rhizosphere microbiome determines disease development in amenity turfgrass

Dollar spot, caused by the fungal pathogen Clarireedia spp., is an economically important disease of amenity turfgrass in temperate climates worldwide. This disease often occurs in a highly variable manner, even on a local scale with relatively uniform environmental conditions. The objective of this study was to investigate mechanisms behind this local variation, focusing on contributions of the soil and rhizosphere microbiome. Turfgrass, rhizosphere, and bulk soil samples were taken from within a 256 m2 area of healthy turfgrass, transported to a controlled environment chamber, and inoculated with C. jacksonii. Bacterial communities were profiled targeting the 16s rRNA gene, and 16 different soil chemical properties were assessed. Despite their initial uniform appearance, the samples differentiated into highly susceptible and moderately susceptible groups following inoculation in the controlled environment chamber. The highly susceptible samples harbored a unique rhizosphere microbiome with lower relative abundance of antibiotic-producing bacterial taxa and higher predicted abundance of genes associated with xenobiotic biodegradation pathways. In addition, stepwise regression revealed that bulk soil iron content was the only significant soil characteristic that positively regressed with decreased dollar spot susceptibility during the peak disease development stage. These findings suggest that localized variation in soil iron induces the plant to select for a particular rhizosphere microbiome that alters the disease outcome. More broadly, further research in this area may indicate how plot-scale variability in soil properties can drive variable plant disease development through alterations in the rhizosphere microbiome. IMPORTANCEDollar spot is the most economically important disease of amenity turfgrass, and more fungicides are applied targeting dollar spot than any other turfgrass disease. Dollar spot symptoms are small (3-5 cm), circular patches that develop in a highly variable manner within plot-scale even under seemingly uniform conditions. The mechanism behind this variable development is unknown. This study observed that differences in dollar spot development over a 256 m2 area were associated with differences in bulk soil iron concentration and correlated with a particular rhizosphere microbiome. These findings provide important clues for understanding the mechanisms behind the highly variable development of dollar spot, which may offer important clues for innovative control strategies. Additionally, these results also suggest that small changes in soil properties can alter plant activity and hence the plant-associated microbial community which has important implications for a broad array of important agricultural and horticultural plant pathosystems.

microbiology↗

bioRxiv2020

G protein-Coupled Receptor Distribution Impacts the Effectiveness of Signal Transmission.

Numbers of activated receptor dictate efficacy of neurotransmitter stimulation. Many PLC coupled receptors activated by ligands elicit canonical downstream Gq/11 pathway to induce endogenous Ca2+ gated chloride channels. The coupling from receptors to effectors was analyzed in Xenopus oocytes expressing genetically modified angiotensin receptor type 1 receptor (AT1R). The latency between ATII binding and Ca2+-induced Cl- current surge was inversely correlated. AT1R activation triggered a chain of chemical reactions, of which the products were playing messengers for subsequent events. Messenger accumulation must rate-limit the agonism. For accurate quantification the speed of ATII triggered the i Cl-. The T-form AT1R-IRK1 fusion exhibits faster induction compared to the M-form. The latency of the recorded none vanished i Cl-, marking the lowest genuine calcium activation, took place at earlier time point by the timer time. The evoked i Cl- however reached similar maximal amplitudes. This kinetic effect raises the possibility to use temporal coding to complement amplitude coding (analogous to FM versus AM radio transmission) for receptor-agonist pairs.

neuroscience↗