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Yang, C.-L.

Publications and source records attributed to Yang, C.-L..

11 recordsLinked to original sources

Long-term memory performance optimization via Neural network-based curve fitting in Drosophila

Long-term memory (LTM) formation typically requires extensive training or highly salient experiences, limiting learning efficiency. Operant conditioning is generally thought to produce stronger memory than classical conditioning because of its active learning component. Unexpectedly, however, laser-based social conditioning in Drosophila melanogaster revealed that while classical paradigms yielded lower short-term memory (STM) scores but higher LTM retention, operant paradigms exhibited higher STM scores followed by rapid LTM decay. To resolve this discrepancy, we employed the AI Complex Systems Response (AI-CSR) framework, which reconstructs high-dimensional learning landscapes from sparse sampling and predicts globally optimal training conditions. Following AI-CSR optimization, operant conditioning produced a twofold increase in LTM scores, yielding the strongest 24-hour social memory performance reported in flies to date and revealing the expected superiority of active learning, which had conversely shown poorer performance under standard training protocols. In contrast, AI-CSR did not further enhance classical conditioning performance but reduced training time by 50%. Single-cell RNA sequencing revealed expanded neuronal recruitment marked by the activation and inhibition of various gene combinations. Together, these findings link circuit-level reorganization with molecular programs underlying efficient long-term memory and demonstrate how AI-guided optimization can uncover latent learning capacity in biological systems.

animal behavior and cognition↗

Cellular remodeling during photosymbiosis establishment revealed by single-cell dual proteomics

Endosymbiosis of phytoplankton in heterotrophic hosts is ecologically important and has led to key evolutionary innovations. However, the dynamic molecular processes underlying endosymbiosis establishment remain poorly understood. Here, using large-particle sorting and liquid chromatography-tandem mass spectrometry, we unravel heterogeneous changes in proteomes of the cosmopolitan ciliate Paramecium and algal endosymbiont Chlorella from engulfment to stable endosymbiosis. The initial digestion sees a sharp decline of intracellular Chlorella cells, along with host cellular reorganization involving a reduction of the cortex-localized defensive organelles, trichocysts, and proteins for intracellular transport and recycling. The remaining Chlorella cells enter a bottleneck stage characterized by energy production and cell cycle commitment before active proliferation. Comparison of Paramecium with successful and failed endosymbiosis further identifies a solute carrier transporter that potentially mediates metabolic homeostasis of the endosymbiotic system. Our study reveals inter-organismal coordination during the transition from predator-prey to host-endosymbiont relationships. The approach of time-course single-cell dual proteomics can be useful for investigating diverse interactions between microbial eukaryotes.

microbiology↗

Endosymbiotic algal photosynthesis shapes diel transcriptome architecture in its ciliate host Paramecium bursaria

How photosynthetic endosymbionts reorganize host daily regulation remains unclear. Paramecium bursaria displays pronounced day-night behaviors, but whether its algal symbionts drive host temporal programs has been unresolved. We compared host gene expressions across a 24-hour light-dark cycle in symbiotic and aposymbiotic cells. Symbiotic cells exhibit an expanded and highly temporally ordered diel transcriptome compared with aposymbiotic cells. These rhythmic programs encompass motility, signaling, metabolism, and growth regulation, consistent with observed behaviors. Symbiosis-associated rhythmic programs recruit gene families encoding post-translational regulatory domains, including kinases, ubiquitin-related factors, WD40 scaffolds, and calcium-binding proteins, despite lacking recognizable canonical clock genes. Disrupting photosynthesis with paraquat altered these temporal profiles, shifting them toward an aposymbiotic-like state. A distantly related ciliate, Tetrahymena utriculariae, with an independently evolved symbiosis, showed similar symbiosis-associated daily programs, suggesting that photosynthetic endosymbionts can act as important organizers of host daily gene regulation in endosymbiotic protists.

evolutionary biology↗

Dopaminergic Modulation of Mushroom Body Output Neurons Mediates Nociception-Induced Escape in Drosophila

In Drosophila, noxious heat is detected by peripheral nociceptors expressing transient receptor potential (TRP) channels, including Painless and TrpA1, and rapidly triggers escape behavior. Although peripheral transduction has been defined in detail, the central circuits and neuromodulatory mechanisms that translate nociceptor activity into escape decisions remain poorly understood. Here, we combine targeted behavioral perturbations with anatomical tracing to delineate a nociception-to-escape pathway that engages dopaminergic modulation of mushroom body (MB) output. Kir2.1-mediated silencing across candidate neurotransmitter systems revealed a specific requirement for MB-innervating dopaminergic neurons (DANs)--particularly subsets within the protocerebral posterior lateral 1 (PPL1) and protocerebral anterior medial (PAM) clusters--for robust nociception-induced escape. Anterograde trans-Tango tracing from painless- and trpA1-expressing nociceptors labeled these MB dopaminergic neurons as direct postsynaptic partners, consistent with convergence of distinct nociceptor inputs onto a shared dopaminergic pathway. Finally, silencing a subset of mushroom body output neurons (MBONs) delayed escape without overtly disrupting baseline locomotion, supporting a model in which dopaminergic signaling recruits MB output to shape defensive action selection. Together, our results define a multi-layer circuit motif linking peripheral nociception to MB-dependent escape and provide a framework for dissecting how neuromodulation gates rapid defensive behaviors.

neuroscience↗

Kidney kallikrein-1 contributes to cleavage of gamma-ENaC in vivo

The epithelial sodium channel (ENaC) is essential for sodium reabsorption and potassium homeostasis in the distal nephron, where its activity is controlled by mineralocorticoid signaling and downstream proteolytic processing of channel subunits. While cleavage of the {gamma}-ENaC subunit has been implicated in aldosterone-mediated sodium transport, the identity of mineralocorticoid receptor (MR)-regulated proteases responsible for this process remains uncertain. Here, we investigated the role of kallikrein-1 (encoded by Klk1), a serine protease expressed in the connecting tubule and cortical collecting duct (CNT/CCD), as a mediator of ENaC activation. Using CRISPR/Cas9, we generated a conditional Klk1-floxed allele and established mice with CNT/CCD-specific deletion of Klk1 by crossing with Calb1-Cre (CNT-Klk1-/-). On a low sodium, high potassium diet, CNT-Klk1-/- mice exhibited [~]85% less renal kallikrein-1 expression, yet maintained normal serum electrolytes, urinary potassium excretion, and aldosterone responses. Western blot analysis revealed significantly less cleavage of {gamma}-ENaC and -ENaC in CNT-Klk1-/- kidneys, accompanied by more total NCC abundance. Despite impaired ENaC proteolysis, amiloride-sensitive sodium excretion was preserved, indicating intact ENaC function. These findings identify renal kallikrein-1 as a protease that contributes to ENaC subunit processing in vivo. However, the absence of overt sodium or potassium handling defects in CNT-Klk1-/- mice suggests that kallikrein-1 deficiency is not sufficient to disrupt overall ENaC function, likely due to compensatory mechanisms from redundant proteolytic or non-proteolytic pathways. Together, our results refine the role of kallikrein-1 as a modulator, rather than a sole determinant, of ENaC activation and highlight the complexity of aldosterone-dependent sodium transport in the distal nephron. New & NoteworthyUsing a novel connecting tubule / cortical collecting duct specific kallikrein-1 knockout model, we show that {gamma}- and -ENaC cleavage is impaired by loss of renal kallikrein-1 without major disturbances in sodium or potassium handling. These findings highlight redundancy among ENaC regulatory pathways and suggest that proteolytic cleavage, while biochemically evident, may not be an accurate marker of ENaC-mediated sodium transport under physiological stress.

physiology↗

Fine-tuning RIPENING INHIBITOR (RIN) expression by introducing allelic mutations in its promoter using CRISPR/Cas9 multiplex editing

Tomato is one of the most produced and consumed vegetables globally due to its nutritional benefits, sensory characteristics, and cultural importance. However, tomato fruit has a short shelf-life, which can be extended by postharvest techniques, but often at the expense of fruit quality, leading to consumer dissatisfaction. To address this challenge, we modified the upstream regulatory regions of Ripening inhibitor (RIN), a master regulator of tomato fruit ripening, utilizing a CRISPR/Cas9 multiplex system. This approach enabled the creation of a population of tomato fruit with mutations of varying severity, which could have far-reaching effects on the RIN-induced gene regulatory network in tomato fruit, leading to downstream changes in fruit traits. We have generated 264 first-generation (T0) transgenic lines of RIN promoter mutants with diverse genetic lesions and RIN transcriptional levels. Our study revealed a non-linear relationship between promoter mutations and gene expression, highlighting the potential roles of certain types of mutations in regulating RIN transcription. Future work will focus on evaluating fruit traits from mutants with pronounced changes in RIN expression, as well as performing transcriptomic analysis to explore the mechanisms underlying fruit quality modifications due to genome editing.

plant biology↗

Distinct cell types along thick ascending limb express pathways for monovalent and divalent cation transport

Kidney thick ascending limb cells reabsorb sodium, potassium, calcium, and magnesium and contribute to urinary concentration. These cells are typically viewed as of a single type that recycles potassium across the apical membrane and generates a lumen-positive transepithelial voltage driving calcium and magnesium reabsorption, although variability in potassium channel expression has been reported. Additionally, recent transcriptomic analyses suggest that different cell types exist along this segment, but classifications have varied and have not led to a new consensus model. We used immunolocalization, electrophysiology and enriched single nucleus RNA-Seq to identify thick ascending limb cell types in rat, mouse and human. We identified three major TAL cell types defined by expression of potassium channels and claudins. One has apical potassium channels, low basolateral potassium conductance, and is bordered by a sodium-permeable claudin. A second lacks apical potassium channels, has high basolateral potassium conductance and is bordered by calcium- and magnesium-permeable claudins. A third type also lacks apical potassium channels and has a high basolateral potassium conductance, but these cells are ringed by sodium-permeable claudins. The recognition of diverse cell types resolves longstanding questions about how solute transport can be modulated selectively and how disruption of these cells leads to human disease.

physiology↗

Haplotype-aware multiomics unveils the regulatory basis of haplodiplontic life-cycle differentiation in a cosmopolitan marine alga

Gephyrocapsa huxleyi (formerly Emiliania huxleyi), a key coccolithophore alga influencing the global carbon cycle through photosynthesis and calcification, undergoes a haplodiplontic sexual life cycle with a calcifying non-flagellate diploid and a non-calcifying biflagellate haploid stage. To reveal the molecular basis of their morpho-physiological distinctions, we generated chromosome-level genome assemblies and compared the transcriptomes, proteomes, and methylomes for a pair of isogenic haploid and diploid model strains and conducted haplotype-aware analyses of their multiomic features. In addition to calcification and flagella, transcriptomes and proteomes of haploid and diploid cells modulate their differentiation in photosynthesis, sulfatases, DMSP degradation, DNA replication, and endomembrane system and transport. Haploid-diploid differential gene expression can be partially attributable to allelic imbalance (allele-specific expression) in diploid cells. Gene transcript abundance is positively associated with both CG and CHG gene-body DNA methylation, which can be inheritable, allele-specific, and differentiated between life-cycle phases. This multiomic study unravels the regulatory basis of unicellular algal life-cycle differentiation and provides valuable resources for investigating the ecologically important coccolithophore algae.

genomics↗

Enriched Single-Nucleus RNA-Sequencing reveals unique attributes of distal convoluted tubule cells

BackgroundThe distal convoluted tubule (DCT) comprises two subsegments, DCT1 and DCT2, with different functional and molecular characteristics. The functional and molecular distinction between these segments, however, has been controversial. MethodsTo understand the heterogeneity within the DCT population with better clarity, we enriched for DCT nuclei by using a mouse line combining "Isolation of Nuclei TAgged in specific Cell Types" and NCC (sodium chloride cotransporter)-driven inducible Cre recombinase. We sorted the fluorescently labeled DCT nuclei using Fluorescence-Activated Nucleus Sorting, and performed single nucleus transcriptomics. ResultsAmong 25,183 DCT cells, 70% were from DCT1 and 30% from DCT2. Additionally, there was a small population (<1%) enriched in proliferation-related genes, such asTop2a, Cenpp, and Mki67. Both DCT1 and DCT2 express NCC, magnesium transport genes are more abundant along DCT1; whereas calcium, electrogenic sodium and potassium transport genes are more abundant along DCT2. The transition between these two segments are gradual with a transitional zone where DCT1 and DCT2 cells are interspersed. The expression of the homeobox genes is not consistent between all DCT cells, suggesting that they develop along different trajectories. ConclusionTranscriptomics analysis of an enriched rare cell population using genetically targeted approach offers better clarification of the function and classification. The DCT segment is short, yet, can be separated into two sub-types that serve distinct functions, and are speculated to derive from different origins during development. Significance StatementHigh-resolution snRNAseq data indicate a clear separation between primary sites of calcium and magnesium handling within DCT. Both DCT1 and DCT2 express Slc12a3, but these subsegments serve distinctive functions, with more abundant magnesium handling genes along DCT1 and more calcium handling genes along DCT2. The data also provides insight into the plasticity of the distal nephron-collecting duct junction, formed from cells of separate embryonic origins. By focusing/changing gradients of gene expression, the DCT can morph into different physiological cell states on demand.

physiology↗

Single-cell transcriptomics unveils xylem cell development and evolution

As the most abundant tissue on Earth1, xylem is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells2. In most angiosperms, fusiform cells are a combination of vessel elements for water transportation and libriform fibers for mechanical support, while both functions are performed together by tracheids in other vascular plants2. However, little is known about the developmental programs and evolutionary relationships of these xylem cell types. Through both single-cell and laser-capture microdissection transcriptomic profiling, here we demonstrate the developmental lineages of ray and fusiform cells in stem-differentiating xylem across four divergent woody angiosperms. Cross-species analyses of single-cell trajectories reveal highly conserved ray, yet variable fusiform, lineages across angiosperms. Core eudicots Populus trichocarpa and Eucalyptus grandis share nearly identical fusiform lineages. The tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed character3, 4, exhibit strong transcriptomic similarity to vessel elements but not libriform fibers, suggesting that water transportation, instead of mechanical support, is the major feature. We also found that the more basal angiosperm Liriodendron chinense has a fusiform lineage distinct from that in core eudicots. This evo-developmental framework provides a comprehensive understanding of the formation of xylem cell lineages across multiple plant species spanning over a hundred million years of evolutionary history5.

plant biology↗

ezGeno: An Automatic Model Selection Package for Genomic Data Analysis

To facilitate the process of tailor-making a deep neural network for exploring the dynamics of genomic DNA, we have developed a hands-on package called ezGeno that automates the search process of various parameters and network structure. ezGeno considers three different sets of search spaces, namely, the number of filters, dilation factors, and the connectivity between different layers. ezGeno can be applied to any kind of 1D genomic input such as genomic sequences, histone modifications, DNase feature data and so on. Combinations of multiple abovementioned 1D features are also applicable. Specifically, for the task of predicting TF binding using genomic sequences as the input, ezGeno can consistently return the best performing set of parameters and network structure, as well as highlight the important segments within the original sequences. For the task of predicting tissue-specific enhancer activity using both sequence and DNase feature data as the input, ezGeno also regularly outperforms the hand-designed models. In this study, we demonstrate that ezGeno is superior in efficiency and accuracy when compared to AutoKeras, a general open-source AutoML package. The average AUC of ezGeno is also consistently higher than the result of using a one-layer DeepBind model. With the flexibility of ezGeno, we expect that this package can provide future researchers not only support of model design in their analysis of genomic studies but also more insights into the regulatory landscape. AvailabilityThe ezGeno package can be freely accessed at https://github.com/ailabstw/ezGeno. ContactDr. Chien-Yu Chen, chienyuchen@ntu.edu.tw

bioinformatics↗