Biology subjects

Wang, J.-Y.

Publications and source records attributed to Wang, J.-Y..

9 recordsLinked to original sources

bioRxiv2026

Behavioral arousal organizes visual cortical population micro-states across the sleep-wake cycle

Brain states are conventionally defined as discrete categories, such as wakefulness, NREM sleep and REM sleep. Yet, whether these labels fully capture the organization of cortical population dynamics remains unclear. Using large-field-of-view two-photon calcium imaging of layer II/III pyramidal neurons in mouse primary visual cortex (V1), we show that population activity organizes into recurring micro-states that span conventional sleep-wake boundaries. A Hidden Markov Model fitted independently of behavioral state labels identified temporally stable micro-states with structured transition pathways. Micro-state organization was more strongly aligned with a continuous behavioral arousal axis, indexed by pupil diameter and orofacial motion, than with discrete NREM-wake categories, a relationship confirmed by mediation analysis. At the circuit level, two spatially intermingled but functionally opposing neuronal ensembles tracked this arousal axis in opposite directions. These findings establish behavioral arousal, rather than discrete wake-sleep state, as the primary organizing dimension of V1 population dynamics.

neuroscience↗

bioRxiv2026

Long-range linkage maintained male-specific loci on a young Y chromosome prior to recombination shutdown

Suppression of recombination on the Y chromosome maintains linkage between male-specific loci and is commonly established by inversions. Here, we describe a young, inversion-free Y chromosome (neo-Y) in Drosophila albomicans with a unique history and paradoxical signature of exchange. Prior to recombination shutdown in males, it repeatedly recombined with the X-linked counterpart (neo-X) but at the same time preserved complete long-range linkage of the chromosome ends. By assembling multiple neo-Ys chromosomes and QTL-mapping, we show that double crossovers maintained linkage between the male-sex determining region at one end to sexually antagonistic alleles and a locus essential for spermatogenesis at the other. We argue that such long-range linkage of distal sex-specific loci disfavors inversions but instead encourages the emergence of achiasmy.

evolutionary biology↗

bioRxiv2025

A polymeric, PDMS-based large-scale skull replacement suitable for optical and mechanical access for long-term neuronal imaging, electrophysiology, and optogenetics

Many techniques to record and manipulate neuronal activity across large portions of the vertebrate brain, such as widefield and two-photon calcium imaging, electrophysiology, and optogenetics, are now available. However, few effective approaches enable both optical and mechanical access to the brain. In this work, we offer an in-depth guide for synthesizing, implanting, and using polydimethylsiloxane (PDMS) windows as skull replacements for chronic optical neuronal imaging. Furthermore, we provide instructions to perform viral injections and multi-site silicon probe implantation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/648966v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@1900a2dorg.highwire.dtl.DTLVardef@18c436corg.highwire.dtl.DTLVardef@19e6a4corg.highwire.dtl.DTLVardef@154c228_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

neuroscience↗

bioRxiv2024

CORNICHON HOMOLOG 5-dependent ER export of membrane cargoes in phosphate-starved Arabidopsis root as revealed by membrane proteomic analysis

Developing plants tolerant of low phosphate (Pi) availability is essential to reduce reliance on fertilizers and achieve agricultural sustainability. One strategy is to enhance the endoplasmic reticulum (ER) export of cargoes associated with Pi starvation and their trafficking to final destinations. However, the mechanisms underlying this process are underexplored. We recently discovered that Arabidopsis thaliana CORNICHON HOMOLOG 5 (AtCNIH5) encodes a Pi deficiency-induced ER cargo receptor that regulates Pi homeostasis. To find potential membrane cargoes of AtCNIH5, we applied the UV-cleavable 4-hexylphenylazosulfonate (Azo)-solubilized microsomal protein extraction for iTRAQ-based proteomic analysis. We identified 4,317 proteins in Pi-limited Arabidopsis roots, with 372 upregulated and 106 downregulated proteins in cnih5. Besides PHOSPHATE TRANSPORTER 1 proteins (PHT1s), downregulation of the biosynthetic or modifying enzymes for cell wall polysaccharides, very long-chain fatty acids, and their derivative extracellular aliphatic compounds is over-represented. Using the yeast split-ubiquitin and the in-planta tripartite split-GFP assays, we verified the interaction of AtCNIH5 with various downregulated transporters in cnih5, including AtPHT1s, AtOCT1, AtURGT6, AtDTX21, and AtDTX35. In addition, we demonstrated that the C-terminal acidic residue of AtCNIH5 is required for interaction with AtOCT1 but not with AtPHT1;1 or AtDTX21, indicating distinct cargo selection mechanisms. More importantly, enhancing in-situ AtCNIH5 expression/activity enhances plant growth. By analogy with transcriptional factors that govern gene expression, we propose that AtCNIH5 acts as a low Pi-responsive hub to facilitate ER export of specific membrane cargoes, providing a potential engineering strategy to improve plant fitness under suboptimal Pi supply.

plant biology↗

bioRxiv2024

Phosphate Starvation-Induced CORNICHON HOMOLOG 5 as Endoplasmic Reticulum Cargo Receptor for PHT1 Transporters in Arabidopsis

Inorganic phosphate (Pi) is essential for plant growth and is acquired and distributed by the plasma membrane PHOSPHATE TRANSPORTER 1 proteins (PHT1s). Enhancing the abundance of PHT1s at the cell surface thus ensures plant productivity and sustainable agriculture. CORNICHON HOMOLOG proteins (CNIHs) are conserved eukaryotic cargo receptors that mediate the selective endoplasmic reticulum (ER) export of membrane proteins. In this study, we identified the Arabidopsis thaliana CNIH5 (AtCNIH5) as a Pi starvation-inducible gene, preferentially expressed in vascular tissues and outer root cell layers above the meristem. AtCNIH5 co-localizes to the AtSAR1A/AtSEC16A/AtSEC24A-labeled ER exit sites and interacts with AtPHT1;1. Loss of AtCNIH5 confers reduced shoot Pi levels under Pi sufficiency due to the reduced translocation of Pi from roots to shoots, as well as decreased Pi uptake under Pi deficiency. The cnih5 mutant exhibits decreased abundance of AtPHT1s but increased PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 (AtPHF1), which enables the ER exit of PHT1s. The cnih5 mutant also shows a lower plasma membrane targeting efficiency of split-GFP tagged-AtPHT1;1 in the root hair and the epidermis within the root transition/elongation zone. Consistently, dysfunctional AtCNIH5 exerts a suppressive effect on the growth of phf1 and alleviates Pi toxicity in the Pi overaccumulator pho2. However, the in vivo protein-protein interaction and degradation assays indicated that AtCNIH5 is not a direct target of AtPHO2. Our findings unveil that AtCNIH5 is a low Pi-responsive ER cargo receptor that interplays with AtPHF1 to promote the plasma membrane targeting of AtPHT1s in a cell-type-dependent manner.

plant biology↗

bioRxiv2023

Conflict between short- and long-term experiences affects visual perception by modulating sensory or motor response system: evidence from Bayesian inference models

Huge studies have explored the effects of short-and long-term experiences on visual perception, respectively. However, no study investigated whether and how the conflict between the two types of experiences affected our visual perception. To address this question, we adopted a task of estimating simulated self-motion directions (i.e., headings) from optic flow, in which a long-term experience - straight-forward motion is more often than lateral motion - plays an important role. The long-term experience is learned daily or encoded in our brains from birth. The heading directions in the experiment were selected from three different distributions, generating different conflicts between short-and long-term experiences. The results showed that both estimation errors and sizes of serial dependence of previously seen headings on current heading estimates varied when the experience conflict changed. Finally, we developed two Bayesian inference models, assuming that the experience conflict affected visual perception by influencing the sensory representations likelihood distribution or motor decision process. We found that both models captured participants estimation errors and serial dependences well in three distributions. In conclusion, the current study revealed the effects of the conflict between short-and long-term experiences on visual perception and preliminarily uncovered that Bayesian inference theory could explain the effects. Moreover, the study implied that the experience conflict affected visual perception by modulating our sensory or motor response systems.

animal behavior and cognition↗

bioRxiv2022

SERM: a self-consistent deep learning solution forrapid and accurate gene expression recovery

Single cell RNA sequencing (scRNA-seq) is a promising technique to determine the states of individual cells and classify novel cell subtypes. Computationally, the processing of scRNA-seq data presents a daunting challenge because of the noisy nature and humongous size and dimensionality of the data. Compromised solution by omitting the genes with low expression is commonly taken in current scRNA-seq analysis, which leads to inaccurate gene counts. In this paper, we introduce a broadly applicable data-driven gene expression recovery framework, referred to as the self-consistent expression recovery machine (SERM), to impute the missing gene expression. Using deep learning, SERM first learns from a subset of the noisy gene expression data to estimate the underlying data distribution. SERM then recovers the overall gene expression data by imposing a self-consistency on the gene expression matrix, thus ensuring that the expression levels are similarly distributed in different parts of the matrix. We show that SERM significantly improves the accuracy of gene imputation with at least 100-fold increase in computational efficiency in comparison to the state-of-the-art techniques. Thus SERM promises to provide an urgently needed computational solution for rapid and accurate recovery of big genomic expression data. SERM is available as a web-based computational tool (https://www.analyxus.com/compute/serm) and its source codes can be found in https://github.com/xinglab-ai/self-consistent-expression-recovery-machine.

bioinformatics↗

bioRxiv2021

The plastid genome characteristics of a moth orchid (Phalaenopsis wilsoniii, Orchidaceae)

Phalaenopsis wilsonii is a typical deciduous species in the horticulturally well-known genus, Phalaenopsis. Tshi species is belonging to the section Aphyllae in moth orchid, and is endemic to South China. Although the Aphyllae section display the deciduous feature that is unique in this genus, their genetic information is still insufficient and limited them as breeding parent in moth orchid. Here, we reported and characterized the complete chloroplast genome for Phalaenopsis wilsonii. We found the total size of the chloroplast genome was 145,373 bp, constituting of a large single copy (LSC) region (84,996 bp), a small single-copy region (10,668 bp) and two inverted repeats (IRs) regions (24,855 bp). Based on homologous searching on database, we annotated 76 protein-coding genes, 38 tRNA, and 8 rRNA. The phylogenetic reconstruction revealed that P. wilsonii show the closest relationship with P. lowii within subgenus Parishianae.

genomics↗

bioRxiv2020

Human Surfactant Protein D Binds S1 and Receptor Binding Domain of Spike protein and acts as an entry inhibitor of SARS-CoV-2 Pseudotyped viral particles in vitro

Human SP-D is a potent innate immune molecule whose presence at pulmonary mucosal surfaces allows immune surveillance role against pulmonary pathogens. Higher levels of serum SP-D have been reported in patients with severe acute respiratory syndrome coronavirus-1 (SARS-CoV). Studies have suggested the ability of human SP-D to recognise spike glycoprotein of SARS-CoV; its interaction with HCoV-229E strain leads to viral inhibition in human bronchial epithelial (16HBE) cells. Previous studies have reported that a recombinant fragment of human SP-D (rfhSP-D) composed of 8 Gly-X-Y repeats, neck and CRD region, can act against a range of viral pathogens including influenza A Virus and Respiratory Syncytial Virus in vitro, in vivo and ex vivo models. In this context, this study was aimed at examining the likely protective role of rfhSP-D against SARS-CoV-2 infection. rfhSP-D showed a dose-responsive binding to S1 spike protein of SARS-CoV-2 and its receptor binding domain. Importantly, rfhSP-D inhibited interaction of S1 protein with the HEK293T cells overexpressing Angiotensin Converting Enzyme 2. The protective role of rfhSP-D against SARS-CoV-2 infection as an entry inhibitor was further validated by the use of pseudotyped lentiviral particles expressing SARS-CoV-2 S1 protein; ~0.5 RLU fold reduction in viral entry was seen following rfhSP-D treatment (10 g/ml). The results highlight the therapeutic potential of rfhSP-D in SARS-CoV-2 infection and merits pre-clinical studies in murine models.

microbiology↗