Biology subjects

Chen, G.-Y.

Publications and source records attributed to Chen, G.-Y..

13 recordsLinked to original sources

bioRxiv2026

The circ_0074371/miR-4738-3p/AMPK Signaling Axis Induces M1 Macrophage Polarization and Restricts Intracellular Survival of Mycobacterium tuberculosis

Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis, remains endemic in regions where it is prevalent. Mycobacterium tuberculosis is an intracellular pathogen that can survive within host macrophages; however, the mechanisms governing its long-term persistence and the progression to active pulmonary tuberculosis remain poorly understood. Circular RNAs (circRNAs) have been implicated in the initiation and progression of numerous diseases. In our previous study, circRNA sequencing identified several circRNAs associated with tuberculosis progression. In the present study, sequencing and reverse transcription-polymerase chain reaction (RT-PCR) analyses revealed that Circ_0074371 was significantly downregulated in monocytes from patients with active pulmonary tuberculosis (ATB) and was closely associated with disease onset and progression, exhibiting considerable diagnostic value for ATB. Functional experiments further showed that Circ_0074371 significantly impaired the intracellular survival of Mtb and promoted M1 macrophage polarization. Mechanistically, Circ_0074371 acted as a competing endogenous RNA by sequestering miR-4738-3p, a potent negative regulator of AMP-activated protein kinase (AMPK) activation. Collectively, these findings identify Circ_0074371 as a tuberculosis-associated circRNA that regulates AMPK activity and reveal a novel mechanism through which Circ_0074371 influences macrophage polarization via the AMPK pathway, providing new insights into potential therapeutic targets for ATB.

immunology↗

bioRxiv2026

Integrated Proteo-Metabolomics of Urinary Extracellular Vesicles Reveals Early Molecular Divergence and Temporal Pathogenesis of Sepsis-Associated AKI

BackgroundSepsis-associated acute kidney injury (S-AKI) is a major contributor to morbidity and mortality in critically ill patients. However, the molecular mechanisms underlying its temporal progression remain poorly understood because conventional biomarkers primarily reflect renal dysfunction rather than disease pathogenesis. Urinary extracellular vesicles (uEVs), which carry kidney-derived molecular cargo, provide a promising platform for monitoring renal-specific biological alterations during disease progression. MethodsWe conducted a longitudinal multi-omics study of uEVs collected from 81 patients with sepsis, including 48 patients with S-AKI and 33 sepsis-only controls. Patients were randomly assigned to a discovery cohort (n = 52) and an independent validation cohort (n = 29). Urine samples were collected at Day 1, Day 4, and Day 8 after AKI diagnosis. High-resolution proteomic and metabolomic profiling was performed to characterize temporal molecular alterations. Enriched pathways identified in the discovery cohort were evaluated in the validation cohort using pathway-level concordance analysis. ResultsComparative analysis between S-AKI and sepsis-only patients identified distinct stage-specific molecular alterations throughout disease progression. At the early stage (Day 1), validated pathways included complement and coagulation cascades, ferroptosis, HIF-1 signaling, sphingolipid metabolism, and arachidonic acid metabolism, highlighting coordinated inflammatory, hypoxic, and lipid metabolic responses. During the mid-stage (Day 4), persistent activation of complement and coagulation cascades, ferroptosis, and HIF-1 signaling was accompanied by metabolic reprogramming involving alanine, aspartate and glutamate metabolism and tyrosine metabolism. Although limited sample availability reduced statistical power at Day 8, phenylalanine metabolism remained validated in the metabolomic analysis, suggesting persistent metabolic dysregulation during late-stage disease progression. ConclusionsThis study provides the first longitudinal, independently validated multi-omics characterization of human uEVs in S-AKI. By integrating proteomic and metabolomic profiling, we reveal the temporal evolution of renal-specific molecular pathways from early inflammatory and hypoxic responses to subsequent metabolic reprogramming. These findings establish uEV-based multi-omics as a promising strategy for molecular phenotyping of S-AKI beyond conventional clinical biomarkers and provide a valuable resource for future biomarker discovery and therapeutic target identification.

biochemistry↗

bioRxiv2026

Dynamics of Take-off in Bipedal Animals and Robots

Take-off is a fast and energy-efficient strategy for bipedal animals, such as birds, to achieve rapid movement; however, how muscle physiology scales to govern this universal behavior remains unresolved. Research in other species physiologies is not readily applicable. As a result, important questions, whether theropod dinosaurs such as Tyrannosaurus rex were capable of jumping, remain unanswered. In this article, we coupled Lagrangian dynamics with Hills muscle equations and developed new experimental methods to quantify joint rotational stiffness and damping, thereby enabling a systematic description of lower-limb mechanics. The approach establishes a novel kinetic framework that links muscle contractile properties to lower-limb performance without invoking control optimization. Animal observations and tabletop mechanisms validate the framework. The mechanics model reveals that the take-off time of about 0.1 s across body masses of 0.003 to 90 kg is achievable, as heavier birds generate proportionally higher reaction forces. Additionally, Tyrannosaurus rex should be capable of jumping, based on the available physiology data. Beyond evolutionary insights, our framework provides a new methodology for analyzing the mechanical properties of biological joints and informing the design of scalable bio-inspired robots.

biophysics↗

bioRxiv2024

habtools: an R package to calculate 3D metrics for surfaces and objects

O_LITechnological advances in three-dimensional imaging techniques have opened the door to advanced morphological analyses and habitat mapping for biologists and ecologists. C_LIO_LIAt the same time, the challenge of translating complex 3D data into meaningful metrics that can be used in conjunction with biological data currently hinders progress and accessibility. C_LIO_LIWe introduce habtools, an R package that provides R functions to efficiently calculate complexity and shape metrics from DEMs, 3D meshes and 2D shapes as well as some helper functions to facilitate workflow. C_LIO_LIWe expect the functionality of habtools to continue to expand as new metrics and faster methods become available, and welcome new contributions and ideas. C_LI

ecology↗

bioRxiv2024

Conditional Localization Pharmacology Manipulates the Cell Cycle with Spatiotemporal Precision

Traditional pharmacology has limited control of drug activity and localization in space and time. Herein, we described an approach for kinase regulation using conditional localization pharmacology (CLP), where an inactive caged inhibitor is localized to a site of interest in a dormant state using intracellular protein tethering. The activity of the inhibitor can be regulated with spatial and temporal precision in a live cellular environment using light. As a proof of concept, a photocaged MPS1 kinase inhibitor (reversine) bearing a Halo-tag ligand tether was designed to manipulate the cell cycle. We demonstrate that this new caged reversine halo probe (CRH) strategy is capable of efficient localization and exceptional spatiotemporal control over spindle assembly checkpoint (SAC) silencing and mitotic exit. Table of Contents artwork O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/612697v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@cd44f8org.highwire.dtl.DTLVardef@6b14f7org.highwire.dtl.DTLVardef@2d8945org.highwire.dtl.DTLVardef@18f4985_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

The central spindle drives anaphase chromosome segregation

Anaphase chromosome segregation depends on forces exerted by spindle microtubules. Current models propose two mechanisms of force generation: kinetochore microtubules (kMTs) depolymerize to pull chromosomes toward the spindle poles (anaphase A), while antiparallel microtubule sliding in the central spindle further separates the chromosomes by elongating the spindle (anaphase B). Experimental evidence in cells supports the sliding mechanism, but contributions of the depolymerization mechanism remain unclear. Here we show that kMT depolymerization limits spindle elongation rather than moving chromosomes apart. We developed a chemical optogenetic approach to recruit a microtubule depolymerase to kinetochores at anaphase onset, thereby increasing the rate of kMT depolymerization without perturbing earlier stages of mitosis. We find that increased depolymerization slows the velocity at which spindle poles move apart without changing kinetochore separation velocities. Our findings support a model in which kinetochores selectively couple to central spindle microtubules parallel to their kMTs, so that antiparallel sliding drives chromosome segregation while kMT depolymerization pulls poles inward.

cell biology↗

bioRxiv2024

Os-circANK negatively regulates resistance to bacterial blight in rice via Osa-miR398b/OsCSD1/OsCSD2 pathways

CircRNAs are widely present in plants, yet there have been no reports on the role of circRNA in the regulatory mechanisms of interactions between rice and pathogenic bacteria. As the sequence of circRNAs matches the parent gene except for the back splicing site, there is no feasible way to specifically knockdown circRNAs in plants. We identified a circRNA, named Os-circANK, derived from an ankyrin repeat protein, which was significantly downregulated post Xanthomonas oryzae pv. oryzae (Xoo) inoculation. We have created a CRISPR-Cas13d system to specifically knockdown a plant circular RNA, resulting in genetically edited rice with a targeted decrease in Os-circANK expression. Os-circANK was found to function as a sponge for Osa-miR398b, suppressing the cleavage of OsCSD1/OsCSD2 by Osa-miR398b, leading to a reduction in ROS levels following Xoo infection and a negative regulation of resistance to bacterial blight in rice. Our findings demonstrate that Os-circANK inhibits the resistance to bacterial blight in rice via the Osa-miR398b/OsCSD1/OsCSD2 pathways.

microbiology↗

bioRxiv2022

Decreasing photosystem antenna size: a double-edged sword for canopy photo-synthetic efficiency

Optimization of antenna size of photosynthetic systems is one strategy to increase plant canopy photosynthesis and crop yield potential. The relationship between antenna size and photosynthesis rate has been extensively studied recently. However, conflicting results have been obtained. Here we show that the extent of decrease in antenna size is a major factor determining the consequences of decreasing antenna on photosynthesis and growth-related parameters. Specifically, we constructed transgenic rice lines with artificial microRNA (amiRNA) targeting to Chlorophyll Synthesis (YGL1) to generate transgene heterozygous and homozygous lines with different leaf chlorophyll contents and antenna sizes. We found that canopy photosynthesis (Ac), biomass and grain yield of the heterozygote were not significantly different from those of WT while the Ac, biomass and grain yield of the homozygote were lower than those of WT. Further, when the maximal quantum yield of photosystem II (Fv/Fm) was larger than 0.8, decreasing antenna size by reducing chlorophyll biosynthesis did not affect leaf photosynthesis; but when Fv/Fm was lower than 0.8, there is a positive relationship between antenna size and leaf photosynthesis. There is large variation in both leaf chlorophyll content and antenna size in elite rice cultivars, suggesting that there is a large scope to decrease leaf chlorophyll content to increase nitrogen use efficiency as long as the quantum yield of PSII is not compromised.

systems biology↗

bioRxiv2020

A non-enzymatic acetylation of lysine residues adversely affects the Rubisco activase protein stability

The post-translational modifications of non-histone (PTMs) proteins functions are crucial for the plant adaption to the changing environment. The Rubisco activase (RCA) plays a key role in the CO2 fixation through the Rubisco activation process. We reported that the RCA from tobacco leaf could be acetylated at several lysine residues including K126 and K164. The acetylation level changes under different light conditions (night and day) as well as under heat stress (45 {degrees}C). We further showed that the RCA can be non-enzymatically acetylated in vitro, especially by the acetyl-CoA (Ac-CoA) through direct interaction between them. Our results of the in vitro assay with deuterium labeled Ac-CoA (D2-Ac-CoA) show that the two conserved RCA lysine residues (K126 and K164) were acetylated by Ac-CoA, entraining a dramatic decline in its ATPase activity and a slight effect on the Rubisco activation process. Furthermore, we revealed that the higher RCA acetylation level induced its faster degradation in the chloroplast, which was not a direct consequence of ubiquitination. Eventually, our findings unraveled a new prominent role for the protein acetylation in modulating the RCA stability, which could certainly regulate the carbon assimilation efficiency towards a different energy status of the plants.

plant biology↗

bioRxiv2020

The discovery of potential natural products for targeting SARS-CoV-2 spike protein by virtual screening

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters into the cells through its spike proteins binding to human angiotensin-converting enzyme 2 (ACE2) protein and causes virus infection in host cells. Until now, there are no available antiviral drugs have been reported that can effectively block virus infection. The study aimed to discover the potential compounds to prevent viral spike proteins to bind to the human ACE2 proteins from Taiwan Database of Extracts and Compounds (TDEC) by structure-based virtual screening. In this study, to rapidly discover potential inhibitors against SARS-CoV-2 spike proteins, the molecular docking calculation was performed by AutoDock Vina program. Herein, we found that 39 potential compounds may have good binding affinities and can respectively bind to the viral receptor-binding domain (RBD) of spike protein in the prefusion conformation and spike-ACE2 complex protein in silico. Among those compounds, especially natural products thioflexibilolide A and candidine that were respectively isolated from the soft corals Sinularia flexibilis and Phaius mishmensis may have better binding affinity than others. This study provided the predictions that these compounds may have the potential to prevent SARS-CoV-2 spike protein from entry into cells.

bioinformatics↗

bioRxiv2020

Tension promotes kinetochore-microtubule release in response to Aurora B activity

Aurora B kinase regulates kinetochore-microtubule interactions to ensure accurate chromosome segregation in cell division. Tension provides a signal to discriminate attachment errors from bi-oriented kinetochores with sisters correctly attached to opposite spindle poles. Current models focus on tension as an input to locally regulate Aurora B activity. Here we show that the outcome of Aurora B activity depends on tension. Using an optogenetic approach to manipulate Aurora B at individual kinetochores, we find that kinase activity promotes microtubule release when tension is high. Conversely, when tension is low, Aurora B activity promotes depolymerization of kinetochore-microtubule bundles while maintaining attachment. We propose that tension is a signal inducing distinct error-correction mechanisms, with release or depolymerization advantageous for typical errors characterized by high or low tension, respectively.

cell biology↗

bioRxiv2019

Kinesin-5 promotes microtubule nucleation and assembly by stabilizing a lattice-competent conformation of tubulin

Besides sliding apart antiparallel microtubules during spindle elongation, the mitotic kinesin-5, Eg5 promotes microtubule polymerization, emphasizing its importance in mitotic spindle length control. Here, we characterize the Eg5 microtubule polymerase mechanism by assessing motor-induced changes in the longitudinal and lateral tubulin-tubulin bonds that form the microtubule lattice. Isolated Eg5 motor domains promote microtubule nucleation, growth and stability. Eg5 binds preferentially to microtubules over free tubulin, and colchicine-like inhibitors that stabilize the bent conformation of tubulin allosterically inhibit Eg5 binding, consistent with a model in which Eg5 induces a curved-to-straight transition in tubulin. Domain swap experiments establish that the family-specific Loop11, which resides near the nucleotide-sensing Switch-II domain, is necessary and sufficient for the polymerase activity of Eg5. Thus, we propose a microtubule polymerase mechanism in which Eg5 at the plus-end promotes a curved-to-straight transition in tubulin that enhances lateral bond formation and thereby promotes microtubule growth and stability.

biophysics↗

bioRxiv2017

Motor reattachment kinetics play a dominant role in multimotor-driven cargo transport

Kinesin-based cargo transport in cells frequently involves the coordinated activity of multiple motors, including kinesins from different families that move at different speeds. However, compared to the progress at the single-molecule level, mechanisms by which multiple kinesins coordinate their activity during cargo transport are poorly understood. To understand these multi-motor coordination mechanisms, defined pairs of kinesin-1 and kinesin-2 motors were assembled on DNA scaffolds and their motility examined in vitro. Although less processive than kinesin-1 at the single-molecule level, addition of kinesin-2 motors more effectively amplified cargo run lengths. By applying the law of total expectation to cargo binding durations in ADP, the kinesin-2 microtubule reattachment rate was shown to be 4-fold faster than that of kinesin-1. This difference in microtubule binding rates was also observed in solution by stopped-flow. High-resolution tracking of gold-nanoparticle-labeled cargo with 1 ms and 2 nm precision revealed that kinesin-2 motors detach and rebind to the microtubule much more frequently than do kinesin-1. Finally, cargo transported by kinesin-2 motors more effectively navigated roadblocks on the microtubule track. These results highlight the importance of motor reattachment kinetics during multi-motor transport and suggest a coordinated transport model in which kinesin-1 motors step effectively against loads while kinesin-2 motors rapidly unbind and rebind to the microtubule. This dynamic tethering by kinesin-2 maintains the cargo near the microtubule and enables effective navigation along crowded microtubules.

biophysics↗