Biology subjects

Huang, R.

Publications and source records attributed to Huang, R..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Dopaminergic processes predict temporal distortions in event memory

Our memories do not simply keep time -- they warp it, bending the past to fit the structure of our experiences. For example, people tend to remember items as occurring farther apart in time if they spanned a change in context, or event boundary, compared to the same context. While these distortions could sacrifice precise timing, they might also serve to divide and organize information into distinct memories. In the current study, we combined functional magnetic resonance imaging (fMRI; n = 32) with eye-tracking (n = 28) to test whether activation of the dopaminergic system, known to influence encoding and time perception, predicts time dilation between adjacent events in memory. Participants encoded item sequences while listening to tones that mostly repeated over time, forming a stable auditory context, but occasionally switched, creating an event boundary. We found that boundaries predicted greater retrospective estimates of time between item pairs. Critically, tone switches significantly activated the ventral tegmental area (VTA), a key midbrain dopaminergic region, and these responses predicted greater time dilation between item pairs that spanned those switches. Boundaries furthermore predicted a momentary increase in blinks. Activation of the VTA predicted blinking in general, consistent with the idea that blink behavior is a potential marker of dopaminergic activity. On a larger timescale, higher blink counts predicted greater time dilation in memory, but only for boundary-spanning item pairs. Together, these findings suggest that dopaminergic processes are sensitive to event structure and may drive temporal distortions that help to separate memories of distinct events.

neuroscience↗

bioRxiv2025

Self-contrastive learning enables interference-resilient and generalizable fluorescence microscopy signal detection without interference modeling

Every weak signal in fluorescence microscopy may contain critical biological information. However, the inter-ference resilience required to detect such signals has traditionally relied on task-specific interference modeling, which limits generalizability. Here, we present a self-contrastive learning-based signal detection solution that achieves interference resilience without the need for interference modeling, thereby offering high generalizability. The method, DEep PAttern Fitting (DEPAF), is a module that contrasts asynchronously generated data views from asymmetric model paths to extract signals from interference, while incorporating highly parallel signal recognition and localization in the process. Benchmarking shows that DEPAF substantially improves signal detection performance across diverse imaging modalities and dimensions, especially under challenging conditions such as low SNRs and ultra-high signal densities. It is also compatible with, and consistently enhances the performance of various imaging techniques, such as super-resolution imaging, spatial transcriptomic imaging, and two-photon calcium imaging. Notably, DEPAF relies only on image patches with signal patterns and one tunable hyperparameter to adapt to new tasks, making it accessible to users without domain-specific expertise and lowering the barrier to broader adoption. DEPAF is expected to advance the signal-centric fluorescence microscopy techniques and inspire further advancements, especially in the era of image-based multi-omics.

bioinformatics↗

bioRxiv2025

Hemodynamic traveling waves transport musical codes faster than language codes via shared bilateral streams

What takes precedence in our brain: music or language? Here we used rapid phase-encoded fMRI to explore spatiotemporal brain dynamics during naturalistic music and language tasks, seeking to track down the entire perception-to-production process and compare the speed of information transfer between the two domains. We found largely shared streams of traveling waves bilaterally, along which musical codes were transported faster than language codes for identical visual input.

neuroscience↗

bioRxiv2025

Emergence of isochorismate-based salicylic acid biosynthesis within Brassicales

Salicylic acid (SA) is a major defense phytohormone. In Arabidopsis thaliana, the isochorismate (IC) pathway is the primary route for pathogen-induced SA biosynthesis. First, the IC synthase (ICS) catalyzes the isomerization of chorismate to IC in chloroplasts. Second, the chloroplast-localized MATE transporter EDS5 appears to transport IC from chloroplasts to the cytosol. Cytosolic IC is then further converted to SA via the GH3 amino acid-conjugating enzyme PBS3. While this pathway is genetically well-characterized in A. thaliana, its evolutionary origin and conservation remain controversial. In this study, through comprehensive phylogenetic, structural, and functional analyses, we demonstrate that the IC pathway emerged within the Brassicales order in a time span between the divergence of Carica papaya and Capparis spinosa. The evolution of the IC pathway was driven by three key adaptations during the time span: (1) enhancement of ICS activity, (2) neofunctionalization of EDS5 after duplication of its ancestral gene, and (3) evolution of a PBS3, whose activity is specialized for glutamate-conjugation to IC. Structural modeling and functional assays reveal that an enhanced salt bridge network in ICS enhanced its activity. One of the duplicated genes, EDS5, acquired key amino acid substitutions in the C-lobe, which likely contributed to the EDS5 neofunctionalization. In addition, the functional PBS3 clade, including A. thaliana PBS3, is restricted to a Brassicales clade. Taken together, this study addresses the evolutionary trajectory of IC-based SA biosynthesis.

plant biology↗

bioRxiv2025

Chronic replication stress-mediated genomic instability disrupts placenta development in mice

Abnormal placentation drives many pregnancy-related pathologies and poor fetal outcomes, but the underlying molecular causes are understudied. Here, we show that persistent replication stress due to mutations in the MCM2-7 replicative helicase disrupts placentation and reduces embryo viability in mice. MCM-deficient embryos exhibited normal morphology but their placentae had a drastically diminished junctional zone (JZ). Whereas cell proliferation in the labyrinth zone (LZ) remained unaffected, JZ cell proliferation was reduced during development. MCM2-7 deficient trophoblast stem cells (TSCs) failed to maintain stemness, suggesting that replication stress affects the initial trophoblast progenitor pool in a manner that preferentially impacts the developing JZ. In contrast, pluripotency of mouse embryonic stem cells with MCM2-7 deficiency were not affected. Developing female mice deficient for FANCM, a protein involved in replication-associated DNA repair, also had placentae with a diminished JZ. These findings indicate that replication stress-induced genomic instability compromises embryo outcomes by impairing placentation.

developmental biology↗

bioRxiv2025

Characterization of conformational dynamics and allostery of the catalytic domain of human mitochondrial YME1L protease

Mitochondrial proteostasis is essential to maintain cellular function and survival. YME1L protease is an important contributor to proteostasis which belongs to the AAA+ (ATPases Associated with diverse cellular Activities) protease family and is anchored to the inner mitochondrial membrane. YME1L plays a pivotal role in mitochondrial protein quality control by selectively degrading misfolded and native proteins. The precise mechanisms by which nucleotide binding and hydrolysis influence YME1Ls conformational dynamics, proteolytic activity, and stability remain unclear. Here we characterize the conformational dynamics and allosteric regulation of the YME1L catalytic domain. Using a hexameric soluble YME1L construct, we employ hydrogen/deuterium exchange mass spectrometry (HDX-MS) and nuclear magnetic resonance (NMR) spectroscopy to demonstrate that nucleotide binding reduces the backbone flexibility and modulates the side-chain dynamics of the AAA+ domain, while Zn{superscript 2} binding stabilizes the protease domain. We also reveal novel long-range allostery between the AAA+ and protease domains of YME1L, mediated by a critical salt bridge on the inter-domain interface. We show the importance of the salt bridge in facilitating ATP-dependent substrate degradation by YME1L. Additionally, we show that ATP binding stabilizes the structure of the catalytic domain of YME1L and protects it from chemical modification- and heat-induced aggregation. These findings explain the nucleotide-driven regulation of YME1L and provide novel insights into understanding its proteolytic activity and structural stability under physiological and stress conditions.

biophysics↗

bioRxiv2025

Building an atlas of mechanobiology: high-throughput contractility screen of 2418 kinase inhibitors in five primary human cell types reveals selective divergent responses among related cell types

Cellular mechanical forces play crucial roles in both normal physiology and disease, yet drug discovery efforts targeting mechanobiology have been limited in part by assumptions about the conservation of contractile pathways across cell types. Here, we present the first high-throughput contractility screen of an annotated kinase inhibitor library, evaluating 2,418 compounds across five primary human cell types using the FLECS (Fluorescent Elastomer Contractility Sensors) platform. Quantification of contractile responses revealed selective divergent responses among related cell types. Clustering analysis identified distinct mechanobiological profiles and novel pathway associations that challenge the assumption that contractile pathways are too highly conserved for selective targeting. This systematic approach supports wider adoption of mechanical phenotypic screening as a viable strategy for discovering cell-type specific contractile pathway modulators for a broad range of mechanically-driven disease indications.

bioengineering↗

bioRxiv2024

Sexual Failure Decreases Sweet Taste Perception in Male Drosophila via Dopaminergic Signaling

Sweet taste perception, a critical aspect of the initiation of feeding behavior, is primarily regulated by an animals internal metabolic state. However, non-metabolic factors, such as motivational and emotional states, can also influence peripheral sensory processing and hence feeding behavior. While mating experience is known to induce motivational and emotional changes, its broader impact on other innate behaviors, such as feeding, remains largely uncharacterized. In this study, we demonstrated that mating failure of male fruit flies suppressed sweet taste perception via dopamine signaling in specific neural circuitry. Upon repetitive failure in courtship, male flies exhibited a sustained yet reversible decline of sweet taste perception, as measured by the proboscis extension reflex (PER) towards sweet tastants as well as the neuronal activity of sweet-sensing Gr5a+ neurons in the proboscis. Mechanistically, we identified a small group of dopaminergic neurons projecting to the subesophageal zone (SEZ) and innervating with Gr5a+ neurons as the key modulator. Repetitive sexual failure decreased the activity of these dopaminergic neurons and in turn suppressed Gr5a+ neurons via Dop1R1 and Dop2R receptors. Our findings revealed a critical role for dopaminergic signaling in integrating reproductive experience with appetitive sensory processing, providing new insights into the complex interactions between different innate behaviors and the role of brains reward systems in regulating internal motivational and emotional states.

neuroscience↗

bioRxiv2024

BEVA2.0: Modular Assembly of Golden Gate-Compatible Vectors with Expanded Utility for Genetic Engineering

This expansion for the modular vector assembly platform BEVA (Bacterial Expression Vector Archive) introduces 11 new BEVA parts including two new cloning site variants, two new antibiotic resistance modules, three new origins of replication, and four new accessary modules. As a result, the modular system is now doubled in size and expanded in its capacity to produce diverse replicating plasmids. Furthermore, it is now amenable to genetic engineering methods involving genome-manipulation of target strains through deletions or integrations. In addition to introducing the new modules, we provide several BEVA-derived Golden Gate cloning plasmids that are used to validate parts and that may be useful for genetic engineering of proteobacteria and other bacteria. We also introduce new parts to allow compatibility with the CIDAR MoClo parts libraries.

synthetic biology↗

bioRxiv2024

Harnessing Protein Language Model for Structure-Based Discovery of Highly Efficient and Robust PET Hydrolases

Plastic waste, particularly polyethylene terephthalate (PET), presents significant environmental challenges, prompting extensive research into enzymatic biodegradation. Existing PET hydrolases are limited to a narrow sequence space and demonstrate insufficient performance for biodegradation. This study introduces a novel discovery pipeline that combines protein language models (PLMs) with a structural representation tree to identify enzymes based on structural similarity. Using the crystal structure of IsPETase as a template, we employed PLMs and a representation tree to efficiently search and cluster target proteins. Screening of candidate proteins was further refined using PLM-based assessments of solubility and thermal stability. Biochemical experiments showed that 14 of 34 candidates exhibited PET degradation activity across a temperature range of 30-60 {degrees}C. Notably, we identified a PET hydrolase -KbPETase, which possesses a melting temperature 32 {degrees}C higher than that of IsPETase and exhibits the highest PET degradation activity within 30-50 {degrees}C compared to other wild-type PETases. KbPETase also shows higher catalytic efficiency than FastPETase. X-ray crystallography and molecular dynamics simulations further revealed that KbPETase has a conserved catalytic domain and enhanced intramolecular interactions. This work develops a novel deep learning approach to discover natural PETases with enhanced functions.

molecular biology↗

bioRxiv2024

Evidence for transient, uncoupled power and functional connectivity dynamics

There is growing interest in studying the temporal structure in brain network activity, in particular, dynamic functional connectivity (FC), which has been linked in several studies with cognition, demographics and disease states. The sliding window approach is one of the most common approaches to compute dynamic FC. However it cannot detect cognitively relevant and transient temporal changes at the time scales of fast cognition, i.e. on the order 100 milliseconds, which can be identified with model-based methods such as HMM (Hidden Markov Model) and DyNeMo (Dynamic Network Modes) using electrophysiology. These new methods provide time-varying estimates of the "power" (i.e. variance) and of the functional connectivity of the brain activity, under the assumption that they share the same dynamics. But there is no principled basis for this assumption. In this work, we propose Multi-dynamic Network Modes (M-DyNeMo), an extension to DyNeMo, that allows for the possibility that the power and the FC networks have different dynamics. Using this new method on magnetoencephalography (MEG) data, we show intriguingly that the dynamics of the power and the FC networks are uncoupled. Using a (visual) task MEG dataset, we also show that the power and FC network dynamics are modulated by the task, such that the coupling in their dynamics changes significantly during task. This new method reveals novel insights into evoked network responses and ongoing activity that previous methods fail to capture, challenging the assumption that power and FC share the same dynamics. HighlightsO_LIWe show that our proposed model - Multi-dynamic Network Modes (M-DyNeMo) - infers transient, uncoupled dynamics for time-varying variance (i.e. power) and functional connectivity (FC) in MEG data. C_LIO_LIM-DyNeMo infers plausible power and FC networks that are reproducible across different subjects, datasets, and parcellations. C_LIO_LIM-DyNeMo reveals task modulates the dynamics of the power and the FC networks, which induces a coupling between dynamics. C_LIO_LIThe evoked FC network response to a (visual) task is different to the evoked network response in power. C_LIO_LIThe datasets and scripts for performing all the analysis in this paper are made publicly available. C_LI

neuroscience↗

bioRxiv2024

Directed evolution of a sequence-specific covalent protein tag for RNA labeling

Efficient methods for conjugating proteins to RNA are needed for RNA delivery, imaging, editing, interactome mapping, as well as for barcoding applications. Non-covalent coupling strategies using viral RNA binding proteins such as MCP have been applied extensively but are limited by tag size, sensitivity, and dissociation over time. We took inspiration from a sequence-specific, covalent protein-DNA conjugation method based on the Rep nickase of a porcine circovirus called "HUH tag". Though wild-type HUH protein has no detectable activity towards an RNA probe, we engineered an RNA-reactive variant, called rHUH, through 7 generations of yeast display-based directed evolution. Our 13.4 kD rHUH has 12 mutations relative to HUH, and forms a covalent tyrosine-phosphate ester linkage with a 10-nucleotide RNA recognition sequence ("rRS") within minutes. We engineered the sensitivity down to 1 nM of target RNA, shifted the metal ion requirement from Mn2+ towards Mg2+, and demonstrated efficient labeling in mammalian cell lysate. This work paves the way toward a new methodology for sequence-specific covalent protein-RNA conjugation in biological systems.

bioengineering↗

bioRxiv2024

Locus coeruleus activation 'resets' hippocampal event representations and separates adjacent memories

Memories reflect the ebb and flow of experiences, capturing distinct events from our lives. Using a combination of functional magnetic resonance imaging (fMRI), neuromelanin imaging, and pupillometry, we show that arousal and locus coeruleus (LC) activation segment continuous experiences into discrete memories. As sequences unfold, encountering a context shift, or event boundary, triggers pupil-linked arousal and LC processes that predict later memory separation. Boundaries furthermore promote temporal pattern separation within left hippocampal dentate gyrus, which correlates with heightened LC responses to those same transition points. Unlike transient LC effects, indirect structural and functional markers of elevated background LC activation correlate with reduced arousal-related LC and pupil responses at boundaries, suggesting that hyperarousal disrupts event segmentation. Our findings support the idea that arousal mechanisms initiate a neural and memory reset in response to significant changes, fundamentally shaping the episodes that define episodic memory.

neuroscience↗

bioRxiv2024

Permissive and instructive Hox codes govern limb positioning

The positioning of limbs along the anterior-posterior axis varies widely across vertebrates. The mechanisms controlling this feature remain to be fully understood. For over 30 years, it has been speculated that Hox genes play a key role in this process but evidence supporting this hypothesis has been largely indirect. In this study, we employed loss- and gain-of-function Hox gene variants in chick embryos to address this issue. Using this approach, we found that Hox4/5 genes are necessary but insufficient for forelimb formation. Within the Hox4/5 expression domain, Hox6/7 genes are sufficient for reprogramming of neck lateral plate mesoderm to form an ectopic limb bud, thereby inducing forelimb formation anterior to the normal limb field. Our findings demonstrate that the forelimb program depends on the combinatorial actions of these Hox genes. We propose that during the evolutionary emergence of the neck, Hox4/5 provide permissive cues for forelimb formation throughout the neck region, while the final position of the forelimb is determined by the instructive cues of Hox6/7 in the lateral plate mesoderm. Impact statementElucidation of the Hox code defining forelimb positioning provides novel insights in lateral plate mesoderm patterning and the integration of vertebrate column structure and limb positioning.

developmental biology↗

bioRxiv2024

Vaccine-elicited and naturally elicited antibodies differ in their recognition of the HIV-1 fusion peptide

Broadly neutralizing antibodies have been proposed as templates for HIV-vaccine design, but it has been unclear how similar vaccine-elicited antibodies are to their naturally elicited templates. To provide insight, here we compare the recognition of naturally elicited and vaccine-elicited antibodies targeting the HIV-1-fusion peptide, which comprises envelope (Env) residues 512-526, with the most common sequence being AVGIGAVFLGFLGAA. Naturally elicited antibodies bound peptides with negative-charge substitutions around residues 517-520 substantially better than the most common sequence, despite these substitutions rarely appearing in HIV; by contrast, vaccine-elicited antibodies were less tolerant of sequence variation, with no substitution of residues 512-516 showing increased binding. Molecular dynamics analysis and cryo-EM structure of the naturally elicited ACS202 antibody in complex with HIV-Env trimer with A517E suggested enhanced binding to result from electrostatic interactions with positively charged antibody residues. Overall, vaccine-elicited antibodies appeared to be more fully optimized to bind the most common fusion peptide sequence. HIGHLIGHTSPeptide substitution scan reveals naturally elicited antibodies against fusion peptide (FP) can bind select non-canonical FP sequences with high affinity. Peptide substitution scan data for FP antibodies correlates significantly with their differential selection indicating variation in binding relates to neutralization tolerance. Structure and energetic analysis of naturally elicited ACS202 with HIV-Env trimer reveals basis for improved recognition of A517E mutant. Atomic level interactions from MD simulation analysis corroborate trends observed with peptide substitutions. verall, peptide substitution scans reveal vaccine-elicited antibodies against FP to be less permissive to FP-sequence variability than naturally elicited antibodies.

immunology↗

bioRxiv2024

Enhancing Phylogenetic Analysis: Integrating Nonparametric Methods for Addressing Abrupt Evolutionary Shifts

Traditional phylogenetically aware correlation methods perform well under gradual evolutionary processes. However, abrupt evolutionary shifts--or macroevolutionary jumps, characteristic of punctuated evolution--can produce extreme phylogenetically independent contrasts (PIC), leading to inflated false positives or increased false negatives in trait correlation analyses. We introduce O(D)GC (Outlier-and Distribution-Guided Correlation), a flexible workflow that identifies outliers in PICs using a distribution-free boxplot criterion and applies Spearman correlation whenever influential outliers are detected. If no outliers are detected, Pearson correlation is used--automatically for large datasets (n [≥] 30), or guided by normality testing in smaller samples. We systematically compared PIC-O(D)GC with five widely applied phylogenetic correlation methods--PIC-Pearson, PIC-MM, PGLS (phylogenetic generalized least squares), MR-PMM (multi-response phylogenetic mixed model), and Corphylo--on 322,000 simulated datasets spanning five evolutionary scenarios (two shift settings: single-trait shifts and dual-trait co-directional jumps; and three no-shift gradual evolution settings), including both fixed-depth and randomly located shifts, tested across 11 shift or noise gradients, three tree sizes (16, 128, 256 tips), and both balanced and random topologies. Overall, PIC-O(D)GC achieved error rates comparable to--or noticeably higher than--those of PIC-MM, while yielding substantially lower error rates than most alternative methods. Under no-shift conditions, it retained power similar to other methods. Analyses of three empirical datasets likewise showed that PIC-O(D)GC and PIC-MM corrected shift-induced distortions that misled conventional methods. Moreover, PIC-O(D)GC offers a conceptually simple framework and incurs markedly lower computational cost. By design, its correlation-only output provides less mechanistic detail than regression-based approaches like PGLS. However, when paired with PIC diagnostics, this outlier-guided strategy highlights evolutionary jumps, distinguishes coupled from decoupled shifts, and--via clade partitioning or tip pruning--recovers background correlations, offering biologically informative insights into how punctuated events interact with gradual trends in trait evolution.

evolutionary biology↗

bioRxiv2024

Phylogenetic Analysis of the Impact of CRISPR Array Characteristics on Spacer Number Evolution

CRISPR-Cas systems in prokaryotes utilize spacers, segments of DNA acquired from invading phages, to guide immune defense mechanisms. This study investigates the evolution of CRISPR repertoire size by examining its relationships with repeat length, terminal repeat polymorphism, and structural stability in 1,958 bacterial genomes, identifying 5,465 CRISPR arrays. Using CRISPRCasFinder for annotation and RNAfold for predicting RNA secondary structures, we found significant variation in array characteristics. Long-repeat arrays ([≥]38 bp) showed a significant positive correlation between terminal repeat polymorphism and CRISPR spacer number, a correlation absent in short-repeat arrays (<38 bp), suggesting longer repeats facilitate recombination and spacer loss. Additionally, a negative correlation between repeat length and spacer number across all arrays indicates that longer repeats may accelerate spacer loss. Furthermore, our results show that immune demand significantly influences the evolution of spacer number. Larger CRISPR repertoires correlate with conserved repeat sequences and stable secondary structures, vital for functional arrays under continuous selective pressure. Comparing functional and obsolete CRISPR arrays (orphan arrays in genomes lacking Cas genes) revealed that obsolete arrays have fewer spacers and lower repeat consistency, indicating a degenerative state. By elucidating the factors that shape CRISPR memory size evolution, this research offers strategies to enhance bacterial defenses, mitigate resistance, and improve applications in gene editing and therapeutics.

microbiology↗

bioRxiv2024

Single-cell and spatiotemporal profile of ovulation in the mouse ovary

Ovulation is a spatiotemporally coordinated process that involves several tightly controlled events, including oocyte meiotic maturation, cumulus expansion, follicle wall rupture and repair, and ovarian stroma remodeling. To date, no studies have detailed the precise window of ovulation at single-cell resolution. Here, we performed parallel single-cell RNA-seq and spatial transcriptomics on paired mouse ovaries across an ovulation time course to map the spatiotemporal profile of ovarian cell types. We show that major ovarian cell types exhibit time-dependent transcriptional states enriched for distinct functions and have specific localization profiles within the ovary. We also identified gene markers for ovulation-dependent cell states and validated these using orthogonal methods. Finally, we performed cell-cell interaction analyses to identify ligand-receptor pairs that may drive ovulation, revealing previously unappreciated interactions. Taken together, our data provides a rich and comprehensive resource of murine ovulation that can be mined for discovery by the scientific community.

bioinformatics↗