Biology subjects

Zou, R.

Publications and source records attributed to Zou, R..

11 recordsLinked to original sources

bioRxiv2026

Multi-omics reveals accumulation mechanisms underlying differences in sesquiterpenoid content across different growth environments of Atractylodes macrocephala rhizome

This study aimed to explore mechanisms driving differential sesquiterpenoid accumulation in Atractylodes macrocephala rhizome (AMR) under different growth environments. Root and rhizosphere soil samples were collected from wild, imitated wild, one- and two-year cultivated AMR. Combined metabolomic, transcriptomic and microbiomic profiling was carried out to investigate alterations in sesquiterpenoid levels, root-associated microbiota, and terpenoid biosynthetic genes under different growth environments. Metabolomics revealed that wild AMR exhibited higher pyruvate consumption and accumulated more atractylone and atractylenolides. Transcriptomic analysis demonstrated that the genes encoding key MEP pathway enzymes (DXS, DXR, MCT, HDS) and the genes encoding the sesquiterpenoid biosynthetic enzyme GDS were significantly upregulated in wild AMR. In contrast, the genes encoding triterpenoid synthetic enzymes (SQS, SQE, {beta}-AS) were downregulated, redirecting metabolic precursors toward sesquiterpenoid synthesis. Microbial community structures differed substantially across groups. Further analysis suggested rhizosphere microorganisms were important contributors to AMR medicinal quality, and sesquiterpenoid metabolites accumulated in AMR roots, together with the rhizosphere microenvironment, jointly shape specific rhizosphere fungal assembly. This study systematically revealed the synergistic regulatory relationships among sesquiterpenoids metabolism, gene expression, growth environment, and root-associated microbes, providing multi-omics evidence for clarifying the mechanism by which these factors coordinately regulate the quality of AMR.

plant biology↗

bioRxiv2026

In silico evaluation of the effects of temperature on the affinity of the SV2C ligand UCB-1A to SV2 isoforms

Synaptic vesicle glycoproteins 2 (SV2) are integral membrane proteins essential for neurotransmitter release and are implicated in neurological disorders including epilepsy and Parkinsons disease. In the attempt to develop a ligand selective for SV2C, and in collaboration with UCB, UCB-F was identified as a potential candidate. However, the affinity of UCB-F to SV2C was found to be temperature dependent, decreasing by about 10-fold from +4 to 37 degrees. UCB1A was subsequently identified as SV2C ligand displaying in vitro a 100-fold selectivity for SV2C compared with SV2A. In this study we investigated whether the binding of UCB-1A to SV2A and SV2C was affected by the temperature. A combination of experimental binding assay data and molecular dynamics (MD) simulations were used. The binding studies revealed that UCB1A affinity for SV2A decreased significantly at 37 {degrees}C compared with 4 {degrees}C, whereas binding to SV2C remained largely unchanged. MD simulations reproduced these observations, namely that ligand RMSD values at 310 K showed that UCB1A binding fluctuated markedly in the SV2A complex, with many trajectories exceeding the 3.0 [A] stability cutoff, whereas UCB1A remained relatively well-anchored in SV2C under the same conditions. Structural analysis showed that, while UCB1A adopts a conserved binding pose across all isoforms stabilized by {pi}- {pi} stacking and a hydrogen bond with Asp, SV2C possesses a unique stabilizing feature. In SV2C, Tyr298 is less exposed to the solvent and engages in a persistent hydrogen bond with Asparagine, a structural feature that reinforces pocket stability and limits temperature-induced destabilization. This interaction is absent in SV2A, consistent with its greater temperature sensitivity. Together, these findings provide a mechanistic explanation for the experimentally observed temperature independence of UCB1A binding to SV2C. More broadly, the results highlight the importance of incorporating physiologically relevant temperatures into SV2 ligand evaluation and demonstrate how combining experiments with simulations can uncover isoform-specific mechanisms of ligand recognition and stability.

biochemistry↗

bioRxiv2026

Discovery and characterization of UCB-1A: the first PET radioligand for imaging synaptic vesicle glycoprotein 2C

The synaptic vesicle glycoprotein 2C (SV2C) is a synaptic protein involved in the regulation of dopamine release. It is expressed in striatum, globus pallidus and substantia nigra, regions involved in the regulation of motor function. Genome-wide association studies, animal model and human brain tissue data indicate a strong link between SV2C and Parkinso[n]s disease, suggesting a potential role of SV2C as synaptic marker for Parkinso[n]s disease. We hypothesize that a positron emission tomography (PET) radioligand for SV2C can serve as imaging marker for Parkinso[n]s disease, enabling early diagnosis and assessment of disease progression. This study was therefore designed to develop a PET radioligand for imaging SV2C. UCB-1A was the lead candidate selected from a library of compounds developed by UCB BioPharma. A translational approach was used, including autoradiography and in vitro binding studies with [3H]UCB-1A, and in vivo PET studies with [11C]UCB-1A in non-human primates (NHPs). The KD of [3H]UCB-1A for rat and human SV2C ranged between 6 and 15 nM, with >100-fold selectivity towards SV2A and SV2B. Specific binding of [3H]UCB-1A in rat and NHP brains was observed in substantia nigra, globus pallidus, striatum and brainstem nuclei, consistent with the expression of SV2C, and was decreased in the striatum of 6-hydroxydopamine-lesioned rats and in the putamen of Parkinson donors. UCB-1A was successfully radiolabelled with 11C and PET studies in NHPs demonstrated that [11C]UCB-1A displays suitable pharmacokinetic properties, a brain distribution consistent with the expression of SV2C and is selective for SV2C. [11C]UCB-1A is the first PET radioligand for in vivo imaging of SV2C and a potential synaptic marker for in vivo studies in Parkinso[n]s disease.

neuroscience↗

bioRxiv2026

Imaging Synaptic Vesicle Protein SV2C with 18F-UCB-F: An In Vitro Autoradiography and In Vivo NHP PET Study

The synaptic vesicle protein SV2C, predominantly found in the basal ganglia, has been associated with Parkinsons disease through genetic studies. It plays a crucial role in regulating dopamine release and has been shown to be disrupted in PD animal models and brain tissues from PD patients. In the context of PD-related synaptopathy, SV2C may serve as a potential imaging target for monitoring disease progression and response to treatment. [18F]UCB-F is a radioligand binding to SV2C developed by UCB. Preliminary autoradiography and PET studies in rats showed that [18F]UCB-F displays a brain distribution consistent with the expression of SV2C in vitro but does not display any specific binding in vivo. This study was therefore designed to further investigate the affinity and selectivity of [18F]UCB-F for SV2C and to examine the in vitro and in vivo properties of the radioligand in non-human primates. In vitro binding studies were performed to measure the affinity of UCB-F to SV2A, SV2B, and SV2C. Insilico modeling was used to assess the binding mode and energy of UCB-F. Autoradiography studies on rat and non-human primate (NHP) brain tissues were performed to confirm that [18F]UCB-F showed similar distribution in rat and NHP tissue. Finally, PET studied in NHPs were performed to examine the in vivo pharmacokinetic properties of [18F]UCB-F. [18F]UCB-F was successfully synthesized from the corresponding precursor with high yield. Autoradiography on brain slices from rats and NHPs demonstrated specific binding of [18F]UCB-F in the pallidum, striatum, substantia nigra, and brainstem, consistent with the known brain expression of SV2C. In NHPs, [18F]UCB-F rapidly crossed the blood-brain barrier, reaching peak uptake values of 2.8 %ID in NHP1 and 2.1 %ID in NHP2 at 4 minutes post-injection. The tracer wasrapidly washed out from the brain, with no clear regional distribution. Radiometabolite analysis revealed the formation of only more polar radiometabolites, with approximately 15% of unchanged radioligand remaining in plasma at 15 minutes post-injection. In vitro and in-silico studies demonstrated that the affinity of [18F]UCB-F decreased by approximately one factor of magnitude with increase of temperature from 4{degrees} to 37{degrees} C. This temperature-related decrease of the affinity for SV2C together with rapid in vivo radiometabolism might explain the discrepancy between in vitro and in vivo performance of [18F]UCB-F. Overall, these findings suggest that [18F]UCB-F is not a suitable PET radioligand for imaging SV2C. Further research is needed to identify alternative candidates with improved in vivo stability and brain retention.

neuroscience↗

bioRxiv2024

Molecular basis underlying specific interaction of mammalian melanopsins with an antagonist AA92593

Melanopsin functions in intrinsically photosensitive retinal ganglion cells of mammals to regulate circadian clock and pupil constriction. The opsinamide AA92593 has been reported to specifically inhibit mouse and human melanopsin functions as a competitive antagonist against retinal; however, the molecular mechanisms underlying its specificity have not been resolved. In this study, we attempted to identify amino acid residues responsible for the specific interaction of AA92593 with mammalian melanopsins. Our cell-based assays confirmed that AA92593 effectively inhibited the light-induced cellular responses of mammalian melanopsins, but not those of non-mammalian vertebrate and invertebrate melanopsins. These results suggest that amino acid residues specifically conserved among mammalian melanopsins are important for the antagonistic effect of AA92593, and we noticed Phe-94, Ser-188, and Ser-269 as candidate residues. Substitutions of these residues reduced the antagonistic effect of AA92593. We conducted docking and molecular dynamics simulations based on the AlphaFold-predicted melanopsin structure. The simulations indicated that Phe-94, Ser-188, and Ser-269 are located at the AA92593-binding site, and additionally identified Trp-189 and Leu-207 interacting with the antagonist. Substitutions of Trp-189 and Leu-207 affected the antagonistic effect of AA92593. Furthermore, substitutions of these amino acid residues converted AA92593-insensitive melanopsins susceptible to the antagonist. Based on experiments and molecular simulations, five amino acid residues, at positions 94, 188, 189, 207, and 269, were found to be responsible for the specific interaction with AA92593 in mammalian melanopsins.

biochemistry↗

bioRxiv2024

Crystal structure and catalytic mechanism of PL35 family glycosaminoglycan lyases with an ultrabroad substrate spectrum

Recently, a new class of glycosaminoglycan (GAG) lyases (GAGases) belonging to PL35 family has been discovered with an ultrabroad substrate spectrum that can degrade three types of uronic acid-containing GAGs (hyaluronic acid, chondroitin sulfate and heparan sulfate) or even alginate. In this study, the structures of GAGase II from Spirosoma fluviale and GAGase VII from Bacteroides intestinalis DSM 17393 were determined at 1.9 and 2.4 [A] resolution, respectively, and their catalytic mechanism was investigated by the site-directed mutant of their crucial residues and molecular docking assay. Structural analysis showed that GAGase II and GAGase VII consist of an N-terminal (/)6 toroid multidomain and a C-terminal two-layered {beta}-sheet domain with Mn2+. Notably, although GAGases share similar folds and catalytic mechanisms with some GAG lyases and alginate lyases, they exhibit higher structural similarity with alginate lyases than GAG lyases, which may present a crucial structural evidence for the speculation that GAG lyases with (/)n toroid and antiparallel {beta}-sheet structures arrived by a divergent evolution from alginate lyases with the same folds. Overall, this study not only solved the structure of PL35 GAG lyases for the first time and investigated their catalytic mechanism, especially the reason why GAGase III can additionally degrade alginate, but also provided a key clue in the divergent evolution of GAG lyases that originated from alginate lyases.

biochemistry↗

bioRxiv2024

Enhanced Salt Tolerance in Synechocystis sp. PCC 6803 Through Adaptive Evolution: Mechanisms and Applications for Environmental Bioremediation

Salt stress is common in natural environments, where elevated salt levels in brackish water and saline soil can hinder the growth of organisms, thereby exacerbating environmental challenges. Developing salt-tolerant organisms not only uncovers novel mechanisms of salt tolerance but also lays the groundwork for managing and utilizing saline environments. Cyanobacteria, which are widely distributed in hydrosphere and soil, serve as ideal models for studying salt stress. In this study, the model cyanobacterium Synechocystis sp. PCC 6803 was selected, whose salt (NaCl) tolerance improved from 4.0% to 6.5% (m/v) through adaptive laboratory evolution. Genome re-sequencing and mutant analysis identified six key genes associated with salt tolerance. Notably, the deletion of slr1670, which encodes glycerol glucoside hydrolase, improved the strains salt tolerance. In addition, slr1753 encodes a membrane protein that may enhance salt tolerance by facilitating ion transport to the extracellular space. Further analysis revealed that overexpression of slr1753 significantly accumulates Na+ on the cell surface, enabling effective seawater treatment using the engineered strain, resulting in a 6.35% reduction of Na+ in the seawater. Moreover, the adapted bacteria can be used for the remediation of saline soil samples, leading to a 184.2% and 43.8% increase in the germination rate and average height of Brassica rapa chinensis, respectively, along with a 25.3% rise in total organic carbon content and reductions in both total salt content by 1.82% and pH by 1.91% in soil. This study provides novel insights into salt tolerance mechanisms and the bioremediation of high-salinity environments. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/610226v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@cde16aorg.highwire.dtl.DTLVardef@8a27ccorg.highwire.dtl.DTLVardef@3af9bforg.highwire.dtl.DTLVardef@1e29cfb_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Freestanding rGO electrodes with tunable porous structures for improved neural recording

Invasive neural electrodes prepared from materials with miniaturized geometrical size could improve the longevity of implants by reducing the chronic inflammatory response. Graphene-based microfibers with tunable porous structures have a large electrochemical surface area (ESA)/geometrical surface area (GSA) ratio that has been reported to possess low impedance and high charge injection capacity (CIC), yet the control of the porous structure remains to be fully investigated. In this study, we introduce wet-spun graphene-based electrodes with pores tuned by sucrose concentrations in the coagulation bath. The electrochemical properties of thermally reduced rGO were optimized by adjusting the ratio of rGO to sucrose, resulting in significantly lower impedance, higher CIC, and higher charge storage capacity (CSC) than platinum microwires. Tensile and insertion tests confirmed that optimized electrodes had sufficient strength to ensure a 100% insertion success rate with low angle shift, thus allowing precise implantation without the need for additional mechanical enhancement. Acute in-vivo recordings from the auditory cortex found low impedance benefits from the recorded amplitude of spikes, leading to an increase in the signal-to-noise ratio (SNR). Ex-vivo recordings from hippocampal brain slices demonstrate that it is possible to record and/or stimulate with graphene-based electrodes with good fidelity compared with conventional electrodes.

neuroscience↗

bioRxiv2020

Sequencing of clinical samples reveals that adaptation keeps establishing during H7N9 virus infection in humans

The H7 subtype avian influenza viruses (AIV) have a much longer history and their adaptation through evolution pose continuous threat to humans 1. Since 2013 March, the novel reasserted H7N9 subtype have transmitted to humans through their repeated assertion in the poultry market. Through repeated transmission, H7N9 gradually became the second AIV subtype posing greater public health risk after H5N1 2,3. After infection, how the virus tunes its genome to adapt and evolve in humans remains unknown. Through direct amplification of H7N9 and high throughput (HT) sequencing of full genomes from the swabs and lower respiratory tract samples collected from infected patients in Shenzhen, China, we have analyzed the in vivo H7N9 mutations at the level of whole genomes and have compared with the genomes derived by in vitro cultures. These comparisons and frequency analysis against the H7N9 genomes in the public database, 40 amino acids were identified that play potential roles in virus adaptation during H7N9 infection in humans. Various synonymous mutations were also identified that might be crucial to H7N9 adaptation in humans. The mechanism of these mutations occurred in a single infection are discussed in this study.

microbiology↗

bioRxiv2018

Recovered and dead outcome patients caused by influenza A (H7N9) virus infection show different pro-inflammatory cytokine dynamics during disease progress and its application in real-time prognosis

The persistent circulation of influenza A(H7N9) virus within poultry markets and human society leads to sporadic epidemics of influenza infections. Severe pneumonia and acute respiratory distress syndrome (ARDS) caused by the virus lead to high morbidity and mortality rates in patients. Hyper induction of pro-inflammatory cytokines, which is known as \"cytokine storm\", is closely related to the process of viral infection. However, systemic analyses of H7N9 induced cytokine storm and its relationship with disease progress need further illuminated. In our study we collected 75 samples from 24 clinically confirmed H7N9-infected patients at different time points after hospitalization. Those samples were divided into three groups, which were mild, severe and fatal groups, according to disease severity and final outcome. Human cytokine antibody array was performed to demonstrate the dynamic profile of 80 cytokines and chemokines. By comparison among different prognosis groups and time series, we provide a more comprehensive insight into the hypercytokinemia caused by H7N9 influenza virus infection. Different dynamic changes of cytokines/chemokines were observed in H7N9 infected patients with different severity. Further, 33 cytokines or chemokines were found to be correlated with disease development and 11 of them were identified as potential therapeutic targets. Immuno-modulate the cytokine levels of IL-8, IL-10, BLC, MIP-3a, MCP-1, HGF, OPG, OPN, ENA-78, MDC and TGF-{beta} 3 are supposed to be beneficial in curing H7N9 infected patients. Apart from the identification of 35 independent predictors for H7N9 prognosis, we further established a real-time prediction model with multi-cytokine factors for the first time based on maximal relevance minimal redundancy method, and this model was proved to be powerful in predicting whether the H7N9 infection was severe or fatal. It exhibited promising application in prognosing the outcome of a H7N9 infected patients and thus help doctors take effective treatment strategies accordingly.

immunology↗

bioRxiv2018

Activity of Antimicrobial Peptides Decreases with Increased Cell Membrane Crossing Free Energy Cost

Antimicrobial peptides (AMPs) are a promising alternative to mitigating bacterial infections in light of increasing bacterial resistance to antibiotics. However, predicting, understanding, and controlling the antibacterial activity of AMPs remains a significant challenge. While peptide intramolecular interactions are known to modulate AMP antimi-crobial activity, peptide intermolecular interactions remain elusive in their impact on peptide bioactivity. Herein, we test the relationship between AMP intermolecular interactions and antibacterial efficacy by controlling AMP intermolecular hydrophobic and hydrogen bonding interactions. Molecular dynamics simulations and Gibbs free energy calculations in concert with experimental assays show that increasing intermolecular interactions via inter-peptide aggregation increases the energy cost for the peptide to cross the bacterial cell membrane, which in turn decreases the AMP antibacterial activity. Our findings provide a route for predicting and controlling the antibacterial activity of AMPs against Gramnegative bacteria via reductions of intermolecular AMP interactions.

biophysics↗