Biology subjects

Lee, H.-W.

Publications and source records attributed to Lee, H.-W..

13 recordsLinked to original sources

bioRxiv2026

Chronic Disease Emergence in Coevolving Social Networks via Behavioral Feedback and Demographic Turnover

Chronic diseases emerge within social systems where individuals reorganize their ties, adapt their behaviors, and turn over through demographic processes; yet, how these coupled dynamics shape long-run disease trajectories remains poorly understood. We developed an agent-based model of how the network structure, behavioral adaptation, and population renewal jointly generate cardiovascular disease incidence in an evolving population. The model integrated age-dependent intrinsic risk from the Framingham Risk Score framework, behavioral transmission through social ties, homophily-driven network formation, and demographic turnover across simulated populations of up to 420 agents and horizons of 18-240 months. Highly connected agents showed lower simulated incidence than weakly connected agents (adjusted hazard ratio 0.43; 95% confidence interval 0.33, 0.57; top-tertile degree indicator) after adjustment for age, sex, smoking, blood pressure, body-mass index, physical activity, and diet. Individual disease probability rose with ego-network disease prevalence (Pearsons r = 0.703, p < 0.001). Global sensitivity analysis identified baseline incidence, activity level, and behavioral transmission as dominant drivers (78% of variance). Bayesian calibration concentrated within the empirical acceptance region, with posterior standard deviation of 12% of prior. These results point toward a systems-level understanding of non-communicable disease emergence.

evolutionary biology↗

bioRxiv2026

Spatial and temporal representations are organized along a stable coding gradient in the medial entorhinal cortex

The medial entorhinal cortex (MEC) has classically been viewed as a spatial coding region, but growing evidence indicates that it also contains temporal representations. However, how spatial and temporal codes are organized within the MEC remains unclear. Here we recorded MEC neurons with high-density silicon probes while mice performed a MEC-dependent timing task and a virtual reality spatial navigation task in a similar head-fixed setup. We found that spatial and temporal representations were partially overlapping but systematically biased across the MEC population. Grid cells and non-grid cells with strong spatial tuning were less likely to show reliable time-locked activity during the timing task. In contrast, neurons with weaker spatial tuning more flexibly shifted their coding scheme to temporal coding during timing task. Moreover, spatial tuning strength and its negative relationship with temporal tuning were preserved in a distinct open field environment, indicating that the coding preferences of individual neurons are constrained by a stable network-level organization. Together, these findings suggest MEC is organized along a coding gradient, ranging from dedicated stable spatial coding neurons to more flexible spatial or temporal coding neurons which represent information according to cognitive demands.

neuroscience↗

bioRxiv2026

Small Molecule Regulation of CLOCK:BMAL1 DNA Binding Activity

CLOCK:BMAL1 is a bHLH-PAS transcription factor complex that utilizes its bHLH (basic helix-loop-helix) domains to bind E-box motifs in DNA and tandem PAS (PER-ARNT-SIM) domains to heterodimerize and interact with regulatory proteins to generate circadian rhythms. PAS domains are evolutionarily conserved modules that frequently bind small molecule ligands within buried cavities to perform sensory and signal transduction functions. CLOCK and BMAL1 PAS domains have cavities that could be leveraged to regulate the transcription factor, and consequently, the circadian clock. Using NMR spectroscopy, we identified small molecules that bind within a cavity inside the PAS-A domain of CLOCK and its paralog NPAS2, which sits at an important flexible junction in the structured core of the heterodimer. We identified a gatekeeping mutant in the core of CLOCK PAS-A that significantly decreased ligand binding affinity. High-pressure NMR studies showed that ligand binding or the gatekeeping mutant significantly stabilized the domain. Finally, we showed that ligands induced dose-dependent displacement of CLOCK:BMAL1 from DNA in vitro. Together, these data demonstrate that small molecules can regulate DNA binding by the circadian transcription factor CLOCK:BMAL1 through occupancy of a PAS domain cavity.

biochemistry↗

bioRxiv2025

Tandem association of CLOCK:BMAL1 complexes on DNA enables recruitment of CBP/p300 through multivalent interactions

The basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) transcription factor CLOCK:BMAL1 interacts with E-box motifs in the context of nucleosomes to elicit a circadian pattern of gene expression that oscillates with approximately 24 hour periodicity. Core clock genes and other highly rhythmic targets of CLOCK:BMAL1 typically possess a tandem arrangement of E-boxes that is required for robust oscillations. Here, we show that the presence of tandem E-boxes enables CLOCK:BMAL1 to bind more internal sites on the nucleosome, leading to release of DNA from the histone core and the presentation of multiple coactivator binding motifs in close proximity to facilitate multivalent interactions with the coactivator CBP/p300. We show that the transactivation domain (TAD) of BMAL1, essential for CLOCK:BMAL1 activity, interacts with several modular domains of CBP. Deletion of these CBP domains or chemical inhibition of protein-protein interactions with CBP significantly reduces or eliminates CLOCK:BMAL1-driven activity. Altogether, this suggests that multivalent interactions with CBP may play a role in the ability of tandem CLOCK:BMAL1 heterodimers to recruit this limiting cofactor in cells.

biophysics↗

bioRxiv2025

Structured experience shapes strategy learning and neural dynamics in the medial entorhinal cortex

Animals can solve new, complex tasks by reusing and adapting what theyve learned before. This kind of flexibility depends not just on having prior experience, but on how that experience was structured in the first place. The design of early training curriculum is especially important: poorly structured experiences can hinder abstraction and limit generalization, while carefully structured training promotes more flexible and adaptive behavior. Yet, the neural mechanisms supporting this process remain unclear. To investigate how early training shapes learning we first trained recurrent neural networks (RNNs) on variants of an odor-timing task previously used to study complex timing behavior in mice. We then tested the RNN predictions on how previous experience affects generalization using behavioral and electrophysiological recordings in mice trained on the same task using staged training sequences. RNNs and mice trained without well-structured early experience developed rigid strategies and made repeated errors. In contrast, those given more balanced early training were better able to generalize and showed similar neural activity patterns that reflected the tasks underlying temporal structure. Using dynamical systems approaches, we reveal a mechanism for this effect: networks trained with appropriately structured curricula developed distinct dynamical motifs that support the correct abstractions when complexity was increased. Networks that lacked early training or received remedial curricula developed single fixed-point solutions that failed to generalize beyond the training stimuli. Together, these findings demonstrate that it is not just the presence of prior experience, but its structure, that governs how flexible and generalizable knowledge emerges in both biological systems and computational models.

neuroscience↗

bioRxiv2024

SLC35A2 modulates paramyxovirus fusion events during infection

Paramyxoviruses are significant human and animal pathogens that include mumps virus (MuV), Newcastle disease virus (NDV) and the murine parainfluenza virus Sendai (SeV). Despite their importance, few host factors implicated in paramyxovirus infection are known. Using a recombinant SeV expressing destabilized GFP (rSeVCdseGFP) in a loss-of-function CRISPR screen, we identified the CMP-sialic acid transporter (CST) gene SLC35A1 and the UDP-galactose transporter (UGT) gene SLC35A2 as essential for paramyxovirus infection. SLC35A1 knockout (KO) cells showed significantly reduced binding and infection of SeV, NDV and MuV due to the lack of cell surface sialic acids, which act as their receptors. However, SLC35A2 KO cells revealed unknown critical roles for this factor in virus-cell and cell-to-cell fusion events during infection with different paramyxoviruses. While the UGT was essential for virus-cell fusion during SeV entry to the cell, it was not required for NDV or MuV entry. Importantly, the UGT promoted the formation of larger syncytia during MuV infection, suggesting a role in cell-to-cell virus spread. Our findings demonstrate that paramyxoviruses can bind to or enter A549 cells in the absence of canonical galactose-bound sialic-acid decorations and show that the UGT facilitates paramyxovirus fusion processes involved in entry and spread.

microbiology↗

bioRxiv2023

Isoform-specific C-terminal phosphorylation drives autoinhibition of Casein Kinase 1

Casein kinase 1 {delta} (CK1{delta}) controls essential biological processes including circadian rhythms and Wnt signaling, but how its activity is regulated is not well understood. CK1{delta} is inhibited by autophosphorylation of its intrinsically disordered C-terminal tail. Two CK1 splice variants, {delta}1 and {delta}2, are known to have very different effects on circadian rhythms. These variants differ only in the last 16 residues of the tail, referred to as the extreme C-termini (XCT), but with marked changes in potential phosphorylation sites. Here we test if the XCT of these variants have different effects in autoinhibition of the kinase. Using NMR and HDX-MS, we show that the {delta}1 XCT is preferentially phosphorylated by the kinase and the {delta}1 tail makes more extensive interactions across the kinase domain. Mutation of {delta}1-specific XCT phosphorylation sites increases kinase activity both in vitro and in cells and leads to changes in circadian period, similar to what is reported in vivo. Mechanistically, loss of the phosphorylation sites in XCT disrupts tail interaction with the kinase domain. {delta}1 autoinhibition relies on conserved anion binding sites around the CK1 active site, demonstrating a common mode of product inhibition of CK1{delta}. These findings demonstrate how a phosphorylation cycle controls the activity of this essential kinase. SignificanceSubtle control of kinase activity is critical to physiologic modulation of multiple physiological processes including circadian rhythms. CK1{delta} and the closely related CK1{varepsilon} regulate circadian rhythms by phosphorylation of PER2, but how kinase activity itself is controlled is not clear. Building on the prior observation that two splice isoforms of CK1{delta} regulate the clock differently, we show that the difference maps to three phosphorylation sites in the variably spliced region (XCT) that cause feedback inhibition of the kinase domain. More broadly, the data suggest a general model where CK1 activity on diverse substrates can be controlled by signaling pathways that alter tail phosphorylation. These inhibitory phosphorylation sites could also be targets for new therapeutic interventions.

biochemistry↗

bioRxiv2023

Medial entorhinal cortex plays a specialized role in learning of flexible, context-dependent interval timing behavior

Episodic memory requires encoding the temporal structure of experience and relies on brain circuits in the medial temporal lobe, including the medial entorhinal cortex (MEC). Recent studies have identified MEC time cells, which fire at specific moments during interval timing tasks, collectively tiling the entire timing period. It has been hypothesized that MEC time cells could provide temporal information necessary for episodic memories, yet it remains unknown whether MEC time cells display learning dynamics required for encoding different temporal contexts. To explore this, we developed a novel behavioral paradigm that requires distinguishing temporal contexts. Combined with methods for cellular resolution calcium imaging, we find that MEC time cells display context-dependent neural activity that emerges with task learning. Through chemogenetic inactivation we find that MEC activity is necessary for learning of context-dependent interval timing behavior. Finally, we find evidence of a common circuit mechanism that could drive sequential activity of both time cells and spatially selective neurons in MEC. Our work suggests that the clock-like firing of MEC time cells can be modulated by learning, allowing the tracking of various temporal structures that emerge through experience.

neuroscience↗

bioRxiv2022

B-Myb association with DNA is mediated by its negative regulatory domain and Cdk phosphorylation

B-Myb is a highly conserved member of the vertebrate Myb family of transcription factors that plays a critical role in cell-cycle progression and proliferation. Myb proteins activate Myb-dependent promoters by interacting specifically with Myb binding site (MBS) sequences using their DNA binding domain (DBD). Transactivation of MBS promoters by B-Myb is repressed by its negative regulatory domain (NRD), and phosphorylation of the NRD by Cdk2-CyclinA relieves the repression to activate B-Myb dependent promoters. The structural mechanisms underlying autoinhibition and activation have been poorly characterized. We determined that a region in the B-Myb NRD (residues 510-600) directly associates with the DBD and inhibits DBD binding to the MBS DNA sequence. We demonstrate that phosphorylation of the NRD at T515, T518, and T520 is sufficient to disrupt the interaction between the NRD and the DBD, which results in increased affinity for MBS DNA and increased B-Myb-dependent promoter activation. Our biochemical characterization of B-Myb autoregulation and the activating effects of phosphorylation provides insight into how B-Myb functions as a site-specific transcription factor.

biochemistry↗

bioRxiv2022

Ultramicrobacteria in various fermented cabbages

Little is known about the ultramicrobial communities of foods. Several bacteria, including pathogenic species, can form ultramicrobial communities when exposed to harsh conditions, making their detection via conventional culture techniques difficult. This study aimed to explore ultramicrobial communities within the microbial communities of fermented cabbage products, such as kimchi, sauerkraut, and suancai, which are produced through specific manufacturing methods based on the laws and culture of respective regions. We used single-molecule real-time sequencing with tangential flow filtration for fermented cabbages after pre-filtration and transmission electron microscopy to confirm the identity of ultramicrobacteria (UMB).To the best of our knowledge, this is the first study to identify the differences between ultramicrobial communities and microbial communities of fermented cabbages. Although the size of the ultramicrobial communities was smaller than that of the latter, their diversity was not lower. In addition, some UMB underwent cell shrinkage due to unfavorable environments, while others maintained their small size regardless. Major pathogens were not detected in the ultramicrobial communities of fermented cabbages. Nevertheless, several suspicious strains were detected. Our method can be used to screen food materials for the presence of UMB undetectable via conventional methods. Ultramicrobial and microbial communities were efficiently separated using tangential flow filtration and analyzed via single-molecule real-time sequencing. The ultramicrobial communities of fermented vegetables were different from conventional microbial communities. This study provides new insights into the ecology of UMB in foods.

microbiology↗

bioRxiv2020

Inverse oculomotor responses of achiasmatic mice expressing a transfer-defective Vax1 mutant

In binocular animals that exhibit stereoscopic visual responses, the axons of retinal ganglion cells (RGCs) connect to brain areas bilaterally by forming a commissure called the optic chiasm (OC). Ventral anterior homeobox 1 (Vax1) contributes to formation of the OC, acting endogenously in optic pathway cells and exogenously in growing RGC axons. Here, we generated Vax1AA/AA mice expressing the Vax1AA mutant, which is incapable of intercellular transfer. We found that RGC axons cannot take up Vax1AA protein from Vax1AA/AA mouse optic stalk (OS) cells, of which maturation is delayed, and fail to access the midline. Consequently, RGC axons of Vax1AA/AA mice connect exclusively to ipsilateral brain areas, resulting in the reduced visual acuity and the abnormal oculomotor responses. Together, our study provides physiological evidences for the necessity of intercellular transfer of Vax1 and the importance of the bilateral RGC axon projection in visuomotor responses.

developmental biology↗

bioRxiv2019

The CRY1 tail controls circadian timing by regulating its association with CLOCK:BMAL1

Circadian rhythms are generated by a transcription-translation feedback loop that establishes cell-autonomous biological timing of ~24-hours. A prevalent human variation in the core clock gene cryptochrome 1, Cry1{Delta}11, lengthens circadian period to cause Delayed Sleep Phase Disorder (DSPD). CRY1 has a 55 kDa photolyase homology region (PHR) followed by a ~100 residue tail that is intrinsically disordered; the {Delta}11 variant lacks a short segment encoded by Exon 11 within its tail. We show here that the disordered tail of CRY1 interacts directly with its PHR, and that Exon 11 is necessary and sufficient to disrupt the interaction between CRY1 and CLOCK, a subunit of the primary circadian transcription factor. Competition between PER2 and the tail for the CRY1 PHR suggests a regulatory role for the tail in the early morning, when CRY1 binds to CLOCK:BMAL1 on DNA independently of PER2. Discovery of this autoregulatory role for mammalian CRY1 highlights functional conservation with plant and insect cryptochromes, which also utilize PHR-tail interactions to reversibly control their activity.\n\nOne Sentence SummaryThe disordered tail of the CRY1 protein regulates interactions between CRY1 and other core circadian rhythm proteins.

biochemistry↗

bioRxiv2018

Gradual repression of selenoprotein W ensures physiological bone remodelling

Selenoproteins containing selenium in the form of selenocysteine are critical for bone remodelling. However, their mechanism of action is not well understood. Here, we report the identification of selenoprotein W (SELENOW) through large-scale mRNA profiling of receptor activator of nuclear factor (NF)-{kappa}B ligand (RANKL)-induced osteoclast differentiation, as a protein that is downregulated via RANKL/RANK/tumour necrosis factor receptor-associated factor 6/p38 signalling. RNA sequencing analysis revealed that SELENOW regulates osteoclastogenic genes. SELENOW overexpression enhanced osteoclastogenesis in vitro via nuclear translocation of NF-{kappa}B and nuclear factor of activated T-cells cytoplasmic 1, whereas its loss suppressed osteoclast formation. SELENOW-deficient and SELENOW-overexpressing mice exhibited osteopetrosis and osteoporosis, respectively. Ectopic SELENOW expression stimulated cell-cell fusion critical for osteoclast maturation as well as bone resorption. Thus, RANKL-dependent repression of SELENOW maintains proper osteoclast differentiation and blocks osteoporosis caused by overactive osteoclasts. These findings demonstrate a biological link between selenium and bone metabolism.

physiology↗