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Biology subjects

Chen, W.-J.

Publications and source records attributed to Chen, W.-J..

9 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↗

SSNA1 organizes the distal luminal centriolar network and promotes ciliogenesis without microtubule association

The distal lumen of the centriole plays a critical role in ciliogenesis, yet the molecular composition, spatial organization, and targeting hierarchy of distal luminal proteins remain poorly understood. In this study, we identify Sjogrens syndrome nuclear autoantigen 1 (SSNA1) as a bona fide centriolar protein and a key regulator of ciliogenesis in mammalian cells. Using our newly developed knockout (KO)-validated antibody, we show that, contrary to previous reports, SSNA1 does not reside in the nucleus, midbody, or ciliary axoneme. Instead, super-resolution imaging combined with expansion microscopy (ExM) reveals that SSNA1 localizes to the distal lumen of centrioles and the basal bodies of both primary and motile cilia, where it is arranged in a ring-like configuration with 9-fold symmetry and apart from centriolar microtubules. Molecular dissection using tag-free SSNA1, its oligomerization-deficient mutants, and microtubule co-pelleting assays further demonstrates that SSNA1, previously described as a microtubule nucleator, stabilizer, and branching factor, does not bind microtubules in vitro. Interactor screening and KO analysis unveil a hierarchical targeting network involving a C2CD3-SSNA1-LRRCC1 axis in the distal lumen. Functional characterization indicates that although dispensable for cell division, overall centriole organization and duplication, SSNA1 promotes cilia assembly by facilitating CP110 removal. Our findings redefine the physiological role of SSNA1 as part of the distal luminal module contributing to ciliogenesis and provide new insights into the molecular architecture and functional relevance of the distal centriolar lumen. SignificanceCentrioles template the assembly of cilia and flagella, whose dysfunction causes human diseases known as ciliopathies. Key centriolar structures - the cartwheel in the proximal lumen, the inner scaffold in the central lumen, and the distal and subdistal appendages outside the distal lumen - have been extensively characterized. However, the molecular organization and functional relevance of the distal lumen remain largely unexplored. Here, we identify SSNA1 as a novel centriolar component at the distal lumen and an essential regulator of ciliogenesis. Our work challenges the long-held view of SSNA1 as a microtubule-associated protein and provides new insights into the architecture, interaction network, targeting hierarchy, and function of the distal centriolar lumen, exemplifying how it modulates centriolar organization and drives ciliogenesis.

cell biology↗

MdLRR-RLK1-MdATG3 module enhances the resistance of apples to abiotic stress via autophagy

LRR-RLKs play a key role in plant responses to stress, although their physiological functions under abiotic stress are not yet fully understood. MdLRR-RLK1 was found to regulate plant growth and development and to increase tolerance to salt and drought stress. MdLRR-RLK1 interacts with MdATG3, which ubiquitinates and degrades MdLRR-RLK1. MdATG3 enhances salt and drought tolerance through autophagy, interacting with MdATG8F/I-like in apple. These findings reveal the interaction between MdLRR-RLK1 and MdATG3, suggesting mechanisms that regulate apple growth and resistance to abiotic stress.

molecular biology↗

A new story of four Hexapoda classes: Protura as the sister to all other hexapods

Insects represent the most diverse animal group, yet previous phylogenetic analyses based on the morphological and molecular data have failed to agree on the evolutionary relationships of early insects and their six-legged relatives (together constituting the clade Hexapoda). In particular, the phylogenetic positions of the three early-diverging hexapod groups, the coneheads (Protura), springtails (Collembola), and two-pronged bristletails (Diplura), have been debated for over a century, with alternative topologies implying drastically different scenarios of the evolution of the insect body plan and hexapod terrestrialisation. We addressed this issue by sampling of all hexapod orders, and experimented with a broad range of across-site compositional heterogeneous models designed to tackle ancient divergences. Our analyses support Protura as the earliest-diverging hexapod lineage (Protura-sister) and Collembola as a sister group to the Diplura, a clade we refer to as Antennomusculata characterised by the shared possession of internal muscles in the antennal flagellum. The universally recognized Ellipura hypothesis is recovered under the site-homogenous LG model. Our cross-validation analysis shows that the CAT-GTR model that recovers Protura-sister fits significantly better than homogenous model. Furthermore, as a very unusual group, Protura as the first diverging lineage of hexapods is also supported by other lines of evidence, such as mitogenomics, comparative embryology, and sperm morphology. The backbone phylogeny of hexapods recovered in this study will facilitate the exploration of the underpinnings of hexapod terrestrialisation and mega-diversity.

evolutionary biology↗

Empagliflozin reduces neointimal formation and vascular smooth muscle cell proliferation via the suppression of PDGF-related signaling

ObjectiveEmerging evidence has documented the beneficial effects of sodium glucose cotransporter 2 (SGLT2) inhibitors on reducing cardiovascular events. Beyond glucose regulation, the mechanisms behind their cardioprotective effects still remained unresolved. This study aims to investigate whether these benefits are mediated by their effects on vascular smooth muscle cell (VSMC) functions. Approach and ResultsTreatment of non-diabetic rats with empagliflozin (a SGLT2 inhibitor) attenuated balloon injury-induced neointimal formation in carotid arteries. In vitro, treatment of rat VSMCs with empagliflozin reduced platelet-derived growth factor (PDGF)-BB-induced proliferation and migration. Moreover, empagliflozin-treated VSMCs did not undergo apoptosis and cytosis. Notably, treating VSMCs with empagliflozinsuppressed the activation of PDGF-related signaling, such as that related to the phosphorylation of PDGF receptor b (PDGF-Rb), Akt, and STAT3. Furthermore, overactivation of PDGF-related signaling attenuated the inhibitory effects of empagliflozin on VSMC proliferation and migration. The relevant in vitro findings were corroborated in the neointima of empagliflozin-treated rats. The fact that minimal SGLT2 was discovered in rat VSMCs and SGLT2 silencing did not alter the effect of empagliflozin supported the SGLT2-independent effect of empagliflozin on VSMC functions. ConclusionsThis study highlights the crucial role of PDGF-related signaling in mediating the beneficial effects of empagliflozin on VSMC functions and/or neointimal formation, which are independent of its effects on SGLT2 and glucose metabolism.

molecular biology↗

MdMYB44-like positively regulates salt and drought tolerance via the MdPYL8-MdPP2CA module in apple

Abscisic acid (ABA) is involved in salt and drought stress responses, but the underlying molecular mechanism remains unclear. Here, we demonstrated that the overexpression of MdMYB44-like, an R2R3-MYB transcription factor (TF), significantly increases the salt and drought tolerance of transgenic apple and Arabidopsis. MdMYB44-like inhibits the transcription of MdPP2CA, which encodes a type 2C protein phosphatase that acts as a negative regulator in ABA response, thereby enhancing ABA signaling-mediated salt and drought tolerance. Furthermore, we found that MdMYB44-like and MdPYL8, an ABA receptor, form a protein complex that further enhances the transcriptional inhibition of the MdPP2CA promoter by MdMYB44-like. Significantly, we discovered that MdPP2CA can interfere with the physical association between MdMYB44-like and MdPYL8 in the presence of ABA, partially blocking the inhibitory effect of the MdMYB44-like-MdPYL8 complex on the MdPP2CA promoter. Thus, MdMYB44-like, MdPYL8, and MdPP2CA form a regulatory loop that tightly controls ABA signaling homeostasis under salt and drought stress. Our data revealed a previously unidentified mechanism by which MdMYB44-like precisely modulates ABA-mediated salt and drought tolerance in apple through the MdPYL8-MdPP2CA module.

plant biology↗

Cilium proteomics reveals Numb as a positive regulator of the Hedgehog signaling pathway

The transduction of Hedgehog (Hh) signaling relies on the primary cilium, a cell surface organelle serving as a signaling hub for the cell. Using proximity labeling and quantitative proteomics, we identified Numb as a new ciliary protein that positively regulates Hh signaling. Numb localizes to the ciliary pocket and acts as an endocytic adaptor to incorporate Ptch1 into clathrin-coated vesicles, thereby promoting Ptch1 exit from the cilium, a key step in Hh signaling activation. Numb loss hampers Sonic Hedgehog (Shh)-induced Ptch1 departure from the cilium, resulting in reduced activation of Hh signaling. Numb loss in spinal neural progenitors reduces Shh-induced differentiation into Nkx2.2-positive progenitors, a process reliant on high Hh signaling activity. Genetic ablation of Numb in the developing cerebellum impaired the proliferation of granule cell precursors, a Hh-dependent process, resulting in reduced cerebellar size. This study highlights Numb as a critical regulator of Ptch1 levels in the cilium during Hh signal activation and demonstrates the key role of ciliary pocket-mediated endocytosis in modulating the transduction of cell signaling.

cell biology↗

Genome structures resolve the early diversification of teleost fishes

Accurate species phylogenies are a prerequisite for evolutionary research. Teleosts are by far the largest and the most diversified group of extant vertebrates, but relationships among the three oldest lineages of extant teleosts remain unresolved. Based on seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (bony-tongues) in a monophyletic group sister to all other teleosts, i.e., the Clupeocephala lineage. This finding resolves over 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies. One-Sentence SummaryWhole-genome analyses place Elopomorpha (tarpons, eels) and Osteoglossomorpha (bony-tongues) as sister groups at the deepest branching of crown teleosts.

evolutionary biology↗

Molecular Survey for Selected Viral Pathogens in Wild Leopard Cats (Prionailurus bengalensis) in Taiwan with an Emphasis on the Spatial and Temporal Dynamics of Carnivore Protoparvovirus 1

The leopard cat (Prionailurus bengalensis) has been listed as an endangered species under the Wildlife Conservation Act in Taiwan since 2009. In this study, we targeted viral pathogens, included carnivore protoparvovirus 1 (CPPV-1), feline leukemia virus (FeLV), feline immunodeficiency virus (FIV), coronavirus (CoV), and canine morbillivirus (CMV), using molecular screening. The spatial and temporal dynamics of the target pathogens were evaluated. Through sequencing and phylogenetic analysis, we aimed to clarify the phylogenetic relationship of isolated viral pathogens between leopard cats and domestic carnivores. Samples from 23 and 29 leopard cats that were live-trapped and found dead, respectively, were collected from Miaoli County from 2015 to 2019 in northwestern Taiwan. CPPV-1 and coronavirus were detected in leopard cats. The prevalence (95% confidence interval) of CPPV-1, and CoV was 63.5% (50.4%-76.6%) and 8.8% (0%-18.4%), respectively. The majority of sequences of each CPPV-1 strain amplified from Taiwanese leopard cats and domestic carnivores were identical. All the amplified CoV sequences from leopard cats were identified as feline coronavirus. The spatial and temporal aggregation of CPPV-1 infection in leopard cats was not determined in the sampling area, which indicated a wide distribution of CPPV-1 in the leopard cat habitat. We consider sympatric domestic carnivores to be the probable primary reservoir for the pathogens identified. We strongly recommend establishing efforts to manage CPPV-1 and FCoV in the leopard cat habitat, with an emphasis on vaccination programs and population control measures for free-roaming dogs and cats. IMPORTANCEThe leopard cat (Prionailurus bengalensis) is an endangered species in Taiwan. The effects of infectious diseases on the wildlife population have increasingly been recognized. In this study, we targeted highly pathogenic viral pathogens in wild cat species, included carnivore protoparvovirus 1 (CPPV-1), feline leukemia virus (FeLV), feline immunodeficiency virus (FIV), coronavirus (CoV), and canine morbillivirus (CMV), using molecular screening. Furthermore, we collected the epidemiological and phylogenetic data to understand the spatial and temporal dynamics of the target pathogens in the wild leopard cat population and identified the possible origin of target pathogens. Based on our study, we consider sympatric domestic carnivores to be the probable primary reservoir for the pathogens identified. Our study provides a deeper understanding related to the distribution of target viral pathogens in the wild leopard cats. The information is essential for leopard cat conservation and pathogen management.

ecology↗