Biology subjects

Chou, S.-J.

Publications and source records attributed to Chou, S.-J..

6 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↗

bioRxiv2025

A 3D Amphioxus Brain Atlas Illuminates the Blueprint of the Ancestral Chordate Brain

Comparative studies on highly complex vertebrate brains have provided insights into the evolutionary history of morphological diversity. However, a long-standing question in vertebrate brain evolution is how the fundamental blueprint emerged. To probe the cellular and molecular origins of brain architecture in the chordate lineage, we performed single-nucleus RNA-seq combined with spatial transcriptomics and generated a three-dimensional cell atlas of the basal chordate amphioxus central nervous system (CNS). This atlas reveals a tripartite organization along the anterior-posterior axis of the adult amphioxus brain, with a rostral retinal/hypothalamic region followed by a di-mesencephalon and caudally, the hindbrain and spinal cord. Notably, we show that the amphioxus brain contains cell clusters resembling the zona limitans intrathalamica and midbrain-hindbrain boundary, both of which demarcate the major brain compartments. Furthermore, expression profiling and gene ontology enrichment analyses support that the cell clusters located in the rostral part of the amphioxus forebrain correspond to vertebrate retinal primordium and hypothalamic cells. However, the absence of key telencephalic marker expression in the amphioxus anterior forebrain suggests that the telencephalon likely represents a vertebrate innovation. Together, our findings establish a spatial transcriptomic framework for the amphioxus CNS and provide a critical link for understanding the evolution of the complex vertebrate brain.

evolutionary biology↗

bioRxiv2023

Transcriptome and translatome comparison of tissues from Arabidopsis thaliana

Translation is one of the multiple complementary steps that orchestrates gene activity. In contrast to the straightforwardness of transcriptional surveys, genome-wide profiles of the translational landscape of plant cells remain technically challenging and are less well explored. Protein-coding genes are expressed at a variable degree of efficiency, resulting in pronounced discordance among the regulatory levels that govern gene activity. Ribo-Seq provides an extremely useful tool for estimating translation efficiency, but limited data sets are available for plants. Here, we provide comparative inventories of expressed and translated RNA populations, generated by mRNA sequencing (RNA-Seq) and ribosome footprinting (Ribo-Seq) of shoots and roots of Arabidopsis thaliana seedlings. Our data set provides information on the translational fitness of protein-coding mRNAs and lncRNAs that may aid in obtaining a comprehensive picture of the regulatory levels governing genes activity across the genome.

plant biology↗

bioRxiv2022

The antibacterial T6SS of Agrobacterium tumefacien promotes disease occurrence and influences crown gall microbiota composition

The type VI secretion system (T6SS) is deployed by many proteobacteria to secrete effector proteins into bacterial competitors for competition or eukaryotic cells for pathogenesis. Agrobacteria, a group of soil-borne phytopathogens causing crown gall disease on various plant species, deploys the T6SS to attack closely- and distantly-related bacterial species in vitro and in planta. Current evidence suggests that the T6SS is not essential for pathogenesis under direct inoculation but it remains unknown whether the T6SS influences natural disease incidence or the microbial community within crown galls (i.e., gallobiome). To address these two key questions, we established a soil inoculation method on wounded tomato seedlings that mimics natural infections and developed a bacterial 16S rRNA gene amplicon enrichment sequencing platform. By comparing the Agrobacterium wild-type strain C58 with two T6SS mutants, we demonstrate that the T6SS influences both disease occurrence and gallobiome composition. Based on multiple inoculation trials across seasons, all three strains could induce tumors but the mutants had significantly lower disease incidences. The season of inoculation played a more important role than the T6SS in shaping the gallobiome. The influence of T6SS was evident in summer, in which two Sphingomonas species and the family Burkhoderiaceae were enriched in the gallobiome induced by the mutants. Further in vitro competition and colonization assay demonstrated the T6SS-mediated antagonism to a Sphingomonas sp. R1 strain isolated from tomato rhizosphere in this study. In conclusion, this work demonstrates that the Agrobacterium T6SS promotes tumorigenesis in infection process and provides competitive advantages in gall-associated microbiota. IMPORTANCEThe T6SS is widespread among Proteobacteria and used for interbacterial competition by agrobacteria, which are soil inhabitants and opportunistic bacterial pathogens causing crown gall disease in a wide range of plants. Current evidence indicates that the T6SS is not required for gall formation when agrobacteria are inoculated directly on plant wounding sites. However, in natural settings, agrobacteria may need to compete with other bacteria in bulk soil to gain access to plant wounds and influence microbial community inside crown galls. The role of the T6SS in these critical aspects of disease ecology have remained largely unknown. In this study, we successfully developed a Soil Inoculation method coupled with Blocker-mediated enrichment of Bacterial 16S rRNA gene Amplicon Sequencing, named as SI-BBacSeq, to address these two important questions. We provided evidence that the T6SS promotes disease occurrence and influences crown gall microbiota composition by interbacterial competition.

microbiology↗

bioRxiv2021

Identification of a developmental switch in information transfer between whisker S1 and S2 cortex in mice

The whiskers of rodents are a key sensory organ that provides critical tactile information for animal navigation and object exploration throughout life. Previous work has explored the developmental sensory-driven activation of the primary sensory cortex processing whisker information (wS1), also called barrel cortex. This body of work has shown that the barrel cortex is already activated by sensory stimuli during the first post-natal week. However, it is currently unknown when over the course of development these stimuli begin being processed by higher order cortical areas, such as secondary whisker somatosensory area (wS2). Here we investigate for the first time the developmental engagement of wS2 by sensory stimuli and the emergence of cortico-cortical communication from wS1 to wS2. Using in vivo wide-field imaging and electrophysiological recordings in control and conditional knock-out mice we find that wS1 and wS2 are able to process bottom-up information coming from the thalamus already right after birth. We identify that it is only at the end of the first post-natal week that wS1 begins to provide excitation into wS2, a connection which begins to acquire feed-forward inhibition characteristics after the second post-natal week. Therefore, we have uncovered a developmental window during which excitatory versus inhibitory functional connectivity between wS1 and wS2 takes place.

neuroscience↗

bioRxiv2021

Complete genome sequence of Xylella taiwanensis and comparative analysis of virulence gene content with Xylella fastidiosa

The bacterial genus Xylella contains plant pathogens that are major threats to agriculture in America and Europe. Although extensive research was conducted to characterize different subspecies of Xylella fastidiosa (Xf), comparative analysis at above-species levels were lacking due to the unavailability of appropriate data sets. Recently, a bacterium that causes pear leaf scorch (PLS) in Taiwan was described as the second Xylella species (i.e., Xylella taiwanensis; Xt). In this work, we report the complete genome sequence of Xt type strain PLS229T. The genome-scale phylogeny provided strong support that Xf subspecies pauca (Xfp) is the basal lineage of this species and Xylella was derived from the paraphyletic genus Xanthomonas. Quantification of genomic divergence indicated that different Xf subspecies share [~]87-95% of their chromosomal segments, while the two Xylella species share only [~]66-70%. Analysis of overall gene content suggested that Xt is most similar to Xf subspecies sandyi (Xfs). Based on the existing knowledge of Xf virulence genes, the homolog distribution among 28 Xylella representatives was examined. Among the 11 functional categories, those involved in secretion and metabolism are the most conserved ones with no copy number variation. In contrast, several genes related to adhesins, hydrolytic enzymes, and toxin-antitoxin systems are highly variable in their copy numbers. Those virulence genes with high levels of conservation or variation may be promising candidates for future studies. In summary, the new genome sequence and analysis reported in this work contributed to the study of several important pathogens in the family Xanthomonadaceae. Contribution to the FieldXylella fastidiosa is a plant-pathogenic bacterium with multiple subspecies that are major threats to agriculture in America and Europe. Although extensive research has been conducted, comparative analysis of this species with other bacteria is lacking due to the unavailability of known close relatives. In this work, we report the complete genome sequence of Xylella taiwanensis, a newly described species within the same genus. This new data set and our focused analysis helped to better understand the evolutionary relationships among different Xylella lineages and their genomic diversity. Moreover, detailed examination of their virulence genes identified those that are either highly conserved or variable, providing promising candidates for future studies to further investigate the molecular mechanisms of Xylella virulence.

genomics↗