Biology subjects

Zhu, M.

Publications and source records attributed to Zhu, M..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Ethylene modulates cell wall mechanics for root responses to compaction

Soil stresses impact crop yields, presenting global agricultural challenges. Soil compaction triggers root length reduction and radial expansion driven by the plant hormone ethylene. We report how ethylene controls cell wall properties to promote root radial expansion. We demonstrate how soil compaction stress, via ethylene, upregulates Auxin Response Factor1 in the root cortex, which represses Cellulose Synthase (CESA) genes. CESA repression drives radial expansion of root cortical cells by modifying the thickness and mechanics of their cell walls, which result in a "stiff epidermis-soft cortex" contrast. Our research thus connects ethylene signaling with root mechanics via cell wall strength, and reveals how dynamic regulation of cellulose synthesis crucially controls root growth in compacted soil.

plant biology↗

bioRxiv2025

Cryo-ET of IgG bivalent binding on SARS-CoV-2 provides structural basis for antibody avidity

The bivalent nature of IgG enhances its neutralization potency against enveloped viruses; however, on-virion structural details of IgG bivalent binding with antigens remain elusive. Here we used cryo-ET to investigate how two potent IgGs P17 and S309 interact with S-trimers on the SARS-CoV-2 surface. We found that these antibodies exploit the mobility of S-trimers to form diverse bivalent binding patterns. P17 stabilizes S-trimers in a one-RBD-up conformation and gathers S-trimer into linear multimers within minutes, whereas S309 primarily forms circular S-trimer assemblies that extend into lattice-like structures. Additionally, both IgGs can facilitate inter-virion coupling through bivalent binding of opposing S-trimers. These findings provide a structural basis for understanding IgG avidity and offer insights for antibody engineering and vaccine design.

biophysics↗

bioRxiv2025

Virus-host interactome reveals host cellular pathways perturbed by tick-borne encephalitis virus infection

Tick-borne encephalitis virus (TBEV) poses an increasingly significant threat to public health. Here, we delved into the virus-host interactome and discovered that TBEV has a profound impact on multiple host cellular pathways. Viral pre-membrane protein (prM), non-structural proteins NS1, NS2B3, NS4A, and NS5 remodel the hosts innate immune responses. PrM and NS2B3 are involved in autophagy, NS4A is associated with neurodegenerative diseases, and NS5 participates in spliceosome dynamics, ribosomal biogenesis, cell cycle regulation, and DNA damage response. Notably, TBEV infection causes G0/G1 cell cycle arrest in host cells. NS5 interacts with histone acetyltransferase P300 to upregulate P16 expression, suppressing CDK4 and resulting in cell cycle arrest. Elevated P16 and reduced CDK4 levels were observed in TBEV-infected brain organoids. The P300 inhibitors and CDK4 agonist can reverse virus-induced cell cycle arrest and inhibit viral replication. Further analysis uncovered potential antiviral targets like KAT6A, XIAP, and RIOK1/BRD9. These findings provide valuable insights into TBEV pathogenicity and hold promise for antiviral drug development.

microbiology↗

bioRxiv2025

Transcriptomic and spatial GABAergic neuron subtypes in zona incerta mediate distinct innate behaviors

Understanding the anatomical connection and behaviors of transcriptomic neuron subtypes is critical to delineating cell type-specific functions in the brain. Here we integrated single-nucleus transcriptomic sequencing, in vivo circuit mapping, optogenetic and chemogenetic approaches to dissect the molecular identity and function of heterogeneous GABAergic neuron populations in the zona incerta (ZI) in mice, a region involved in modulating various behaviors. By microdissecting ZI for transcriptomic and spatial gene expression analyses, our results revealed two non-overlapping Ecel1- and Pde11a-expressing GABAergic neurons with dominant expression in the rostral and medial zona incerta (ZIrEcel1 and ZImPde11a), respectively. The GABAergic projection from ZIrEcel1 to periaqueductal gray mediates self-grooming, while the GABAergic projection from ZImPde11a to the oral part of pontine reticular formation promotes transition from sleep to wakefulness. Together, our results revealed the molecular markers, spatial organization and specific neuronal circuits of two discrete GABAergic projection neuron populations in segregated subregions of the ZI that mediate distinct innate behaviors, advancing our understanding of the functional organization of the brain.

neuroscience↗

bioRxiv2025

The lower jaw of Devonian ray-finned fishes (Actinopterygii): anatomy, relationships, and functional morphology

Actinopterygii is a major extant vertebrate group, but limited data are available for its earliest members. Here we investigate the morphology of Devonian actinopterygians, focusing on the lower jaw. We use X-Ray Computed Tomography (XCT) to provide comprehensive descriptions of the mandibles of 19 species, which span the whole of the Devonian and represent roughly two thirds of all taxa known from more than isolated or fragmentary material. Our findings corroborate previous reports in part but reveal considerable new anatomical data and represent the first detailed description for roughly half of these taxa. The mandibles display substantial variation in size, spanning more than an order of magnitude. Although most conform to a generalized pattern of a large dentary and one or two smaller infradentaries, XCT data reveal significant differences in the structure of the jaw and arrangement of teeth that may be of functional relevance. We report the presence of a rudimentary coronoid process in several taxa, contributed to by the dentary and/or infradentaries, as well a raised articular region, resulting in a mandible with an offset bite and that functions as a bent level arm. Among the most striking variation is that of tooth morphology: several taxa have heterodont dentary teeth that vary in size and orientation, and multiple variations on enlarged, whorl-like and posteriorly-oriented anterior coronoid dentition are observed. We use these new data to revise morphological characters that may be of phylogenetic significance and consider the possible functional implications of these traits. The observed variation in mandible form and structure suggests previously unappreciated functional diversity among otherwise morphologically homogenous Devonian ray-finned fishes.

paleontology↗

bioRxiv2025

40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion

During eukaryotic translation initiation, the small (40S) ribosomal subunit is recruited to the 5' cap and subsequently scans the 5' untranslated region (5' UTR) of mRNA in search of the start codon. The molecular mechanism of mRNA scanning remains unclear. Here, using GFP reporters in Saccharomyces cerevisiae cells, we show that order-of-magnitude variations in the lengths of unstructured 5' UTRs have a modest effect on protein synthesis. These observations indicate that mRNA scanning is not rate limiting in yeast cells. Conversely, the presence of secondary structures in the 5' UTR strongly inhibits translation. Loss-of-function mutations in translational RNA helicases eIF4A and Ded1, as well as mutations in other initiation factors implicated in mRNA scanning, namely eIF4G, eIF4B, eIF3g and eIF3i, produced a similar decrease in translation of GFP reporters with short and long unstructured 5' UTRs. As expected, mutations in Ded1, eIF4B and eIF3i severely diminished translation of the reporters with structured 5' UTRs. Evidently, while RNA helicases eIF4A and Ded1 facilitate 40S recruitment and secondary structure unwinding, they are not rate-limiting for the 40S movement along the 5' UTR. Hence, our data indicate that, instead of helicase-driven translocation, one-dimensional diffusion predominately drives mRNA scanning by the 40S subunits in yeast cells.

genetics↗

bioRxiv2024

Enterobactin carries iron into C. elegans and mammalian intestinal cells by a mechanism independent of divalent metal transporter DMT1

The diverse microbiota of the intestine is expected to benefit the host, yet the beneficial metabolites derived from the microbiota are still poorly understood. Enterobactin (Ent) is a well- known secreted iron-scavenging siderophore made by bacteria to fetch iron from the host or environment. Little was known about a positive role of Ent until a recent discovery in the nematode C. elegans indicated a beneficial role of Ent in promoting mitochondrial iron level in the animal intestine. To solidify this new paradigm, we further tested this role in C. elegans and multiple mammalian cell models and its relationship with the primary iron transporter DMT1/SMF-3 and several other iron-related genes. Here we show that ferric enterobactin (FeEnt) supplementation promotes whole organism development in C. elegans, increases iron uptake in caco-2 human intestinal epithelial cells, and supports iron-dependent differentiation of murine erythroid progenitor cells, indicating that the FeEnt complex can effectively enter these cells and be bioavailable. Our data in multiple models demonstrate that FeEnt-mediated iron transport is independent of all tested iron transporters. In addition, FeEnt supplementation robustly suppresses the developmental defects of a hif-1 mutant under low iron condition, suggesting the critical role in iron homeostasis for this well-known hypoxia regulator. These results suggest that FeEnt can effectively enter animal cells and their mitochondria through a previously unknown mechanism that may be leveraged as a therapeutic ferric iron carrier for the treatment of DMT1- or HIF-1-related iron deficiency and anemia.

developmental biology↗

bioRxiv2024

Mechanical force regulates the inhibitory function of PD-1

The immune checkpoint molecule, programmed cell death 1 (PD-1), plays a pivotal role in regulating T-cell function. Upon binding to its ligands, PD-L1 or PD-L2, PD-1 suppresses T-cell receptor signaling, thereby preventing T-cell activation, making it a critical target in cancer immunotherapy. Although extensively studied, the molecular mechanism of PD-1s inhibitory function is still not fully understood, especially at the atomic level. Using the biomembrane force probe (BFP), we discovered that interactions between PD-1 and PD-L1/PD-L2 exhibit catch-slip bond behavior under force. At lower forces, catch bonds are observed, transitioning to slip bond as the force increases. Steered molecular dynamics (SMD) simulations revealed a force-induced bond state between PD-1 and its ligands, distinct from the force-free state observed in solved complex structures. Disrupting interactions that stabilize either state weakens the catch bond and diminishes PD-1s inhibitory function. Interestingly, soluble forms of PD-L1 and PD-L2 compete with their surface-bond counterparts, attenuating PD-1s suppression of T-cell activation. This suggests that soluble PD-1 ligands could potentially serve as anti-PD-1 drugs. Tumor growth studies in mice confirmed the anti-cancer activity of soluble PD-L1. Our findings highlight the critical role of mechanical force in PD-1s inhibitory function, suggesting that PD-1 may act as a mechanical sensor in suppressing T-cell activation. These insights indicate that mechanical regulation should be considered when designing PD-1 blocking inhibitors and other PD-1 related cancer immunotherapies. TeaserThis study shows that the interaction between PD-1 and its ligands is force-dependent, and soluble forms of PD-1 ligands can potentially serve as PD-1 blockers in cancer immunotherapy.

biophysics↗

bioRxiv2024

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

Biogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, it is hypothesized that these sites must be in proximity. Inverted repeat sequences, such as Alu elements, in the upstream and downstream introns are predicted to base-pair and represent one mechanism for inducing proximity. Here, we investigate the pre-mRNA structure of the human HIPK3 gene at exon 2, which forms a circular RNA via backsplicing. We leverage multiple chemical probing techniques, including the recently developed SHAPE- JuMP strategy, to characterize secondary and tertiary interactions in the pre- mRNA that govern backsplicing. Our data confirm that the antisense Alu elements, AluSz(-) and AluSq2(+) in the upstream and downstream introns, form a highly- paired interaction. Circularization requires formation of long-range Alu-mediated base pairs but does not require the full-length AluSq2(+). In addition to confirming long-range base pairs, our SHAPE-JuMP data identified multiple long-range interactions between non-pairing nucleotides. Genome-wide analysis of inverted repeats flanking circular RNAs confirm that their presence favors circularization, but the overall effect is modest. Together these results suggest that secondary structure considerations alone cannot fully explain backsplicing and additional interactions are key.

molecular biology↗

bioRxiv2024

Multimodal single-cell analyses reveal molecular markers of neuronal senescence in human drug-resistant epilepsy

The histopathological neurons in the brain tissue of drug-resistant epilepsy exhibit aberrant cytoarchitecture and imbalanced synaptic circuit function. However, the gene expression changes of these neurons remain unknown, making it difficult for the diagnosis or to dissect the mechanism of drug-resistant epilepsy. By integrating whole-cell patch clamp recording and single-cell RNA sequencing approaches, we identified a transcriptionally distinct subset of cortical pyramidal neurons. These neurons highly expressed genes CDKN1A (P21), CCL2 and NFKBIA that associated with mTOR pathway, inflammatory response and cellular senescence. We confirmed the expression of senescent marker genes in a subpopulation of cortical pyramidal neurons with enlarged soma size in the brain tissue of drug-resistant epilepsy. We further revealed the expression of senescent cell markers P21, P53, COX2, {gamma}-H2AX, {beta}-Gal and reduction of nuclear integrity marker Lamin B1 in histopathological neurons in the brain tissue of drug-resistant epilepsy patients with different pathologies, but not in control brain tissue with no history of epilepsy. Additionally, chronic, but not acute, epileptic seizures induced senescent markers expression in cortical neurons in mouse models of drug-resistant epilepsy. These results provide important molecular markers for histopathological neurons and new insights into the pathophysiological mechanisms of drug-resistant epilepsy.

neuroscience↗

bioRxiv2024

Long-lasting, subtype-specific regulation of somatostatin interneurons during sensory learning

Somatostatin (SST)-expressing inhibitory neurons are a major class of neocortical {gamma}-amino butyric acid (GABA) neurons, where morphological, electrophysiological, and transcriptomic analyses indicate more than a dozen different subtypes. However, whether this diversity is related to specific roles in cortical computations and plasticity remains unclear. Here we identify learning-dependent, subtype-specific plasticity in layer 2/3 SST neurons of the mouse somatosensory cortex. Martinotti-type, SST neurons expressing calbindin-2 show a selective decrease in excitatory synaptic input and stimulus-evoked calcium responses as mice learn a stimulus-reward association. Using these insights, we develop a label-free classifier using basal activity from in vivo imaging that accurately predicts learning-associated response plasticity. Our data indicate that molecularly-defined SST neuron subtypes play specific and highly-regulated roles in sensory information processing and learning.

neuroscience↗

bioRxiv2024

Reduction of DNA Topoisomerase Top2 reprograms the epigenetic landscape and extends health and life span across species

DNA topoisomerases are essential molecular machines that manage DNA topology in the cell and play important roles in DNA replication and transcription. We find that knocking down the enzyme Topoisomerase Top2 or its mammalian homolog Top2b increases the life span of S. cerevisiae, C. elegans, and mice. Top2b reduction also extends the health span of mice and alleviates the pathologies of aging in multiple tissues. At the cellular/molecular level, Top2b reduction attenuates the major hallmarks of aging, such as cellular senescence, de-regulated nutrient sensing, epigenetic alteration, and lysosomal biogenesis. We observed that Top2b reduction significantly changes the epigenetic landscape in various mouse tissues toward those of the young animals, and differentially down-regulates genes with active promoter and high expression. Our observations suggest that Top2 reduction confers longevity effect across species via a conserved mechanism, and may be used as a novel therapeutic strategy for countering aging.

biochemistry↗

bioRxiv2024

Frem2 Knockout Mice Exhibit Fraser Syndrome Phenotypes and Neonatal Lethality Due to Bilateral Renal Agenesis

Fraser syndrome is a rare autosomal recessive disorder characterized by multiple congenital malformations, including cryptophthalmos, syndactyly, and renal agenesis, which can lead to severe complications beginning at the embryonic stage. Mutations in genes encoding extracellular matrix proteins such as FRAS1, FREM1, FREM2, and the associated trafficking protein GRIP1, are implicated in Fraser syndrome. These proteins are critical for maintaining epithelial integrity during embryogenesis, with deficiencies leading to tissue detachment and blistering phenotypes in mouse models. The FREM2 protein is a single-pass membrane protein of 3169 amino acids. While Frem2-deficient mouse models encoding missense variants found in patients, or a truncated FREM2 protein product were previously reported, it has not been studied in a constitutive knockout (KO) mouse model. Here, we developed constitutive Frem2-KO mice exhibiting neonatal lethality, mainly due to bilateral renal agenesis, along with blood-filled blisters, cryptophthalmos, and syndactyly. Only one mouse survived to adulthood exhibiting unilateral renal agenesis and Fraser syndrome-like phenotypes. These findings confirm FREM2s crucial role in the development of the kidneys, skin, and eyes and provide an animal model for further studies of FREM2-related developmental disorders.

developmental biology↗

bioRxiv2024

Shifts in embryonic oxygen levels cue heterochrony in limb initiation

Heterochrony, or the alteration of developmental timing, is an important mechanism of evolutionary change. Avian species display synchronized growth of the forelimbs and hindlimbs, while mammalian species show delayed hindlimb development. We find that mammalian limb heterochrony is evident from the start of limb bud formation, and is associated with heterochronic expression of T-box transcription factors. This heterochronic shift is not due to changes in cis-regulatory sequences controlling T-box gene expression, but unexpectedly, is dependent upon differential oxygen levels to which avian and mammalian embryos are exposed prior to limb initiation. This is mediated, at least partially, by an NFKB transcription factor, cRel, and by the oxygen-sensing transcription factor hypoxia inducible factor alpha (Hif1a). Together, these results provide mechanistic understanding of an important example of developmental heterochrony and exemplify how the maternal environment regulates timing during embryonic development.

developmental biology↗

bioRxiv2024

Dendritome Mapping Unveils Spatial Organization of Striatal D1/D2-Neuron Morphology

Morphology is a cardinal feature of a neuron and mediates its functions, but profiling neuronal morphologies at scale remains a formidable challenge. Here we describe a generalizable pipeline for large-scale brainwide profiling of dendritic morphology of genetically-defined single neurons in the mouse brain. We generated a dataset of 3,762 3D-reconstructed and reference-atlas mapped striatal D1- and D2-medium spiny neurons (MSNs). Integrative morphometric analyses reveal distinct impacts of D1/D2 and anatomical locations on MSN morphology. To analyze striatal regional features of MSN dendrites without prior anatomical constraints, we assigned MSNs to a lattice of cubic boxes in the reference brain atlas, and summarized morphometric representation ("eigen-morph") for each box and clustered boxes with shared morphometry. This analysis reveals 6 modules with characteristic dendritic features and spanning contiguous striatal territories, each receiving distinct corticostriatal inputs. Finally, we found aging confers robust and concordant dendritic length and branching defects in D1/D2-MSNs, while Huntingtons disease (HD) mice exhibit MSN-subtype and striatal regional specific pathology. Together, our study demonstrates a systems-biology approach to profile dendritic morphology of genetically-defined single-neurons; and defines novel striatal D1/D2-MSN morphological territories and aging- or HD-associated pathologies.

neuroscience↗

bioRxiv2024

DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences

MotivationRNA structure is essential for the function of many non-coding RNAs. Using multiple homologous sequences, which share structure and function, secondary structure can be predicted with much higher accuracy than with a single sequence. It can be difficult, however, to establish a set of homologous sequences when their structure is not yet known. We developed a method to identify sequences in a set of putative homologs that are in fact non-homologs. ResultsPreviously, we developed TurboFold to estimate conserved structure using multiple, unaligned RNA homologs. Here, we report that the positive predictive value of TurboFold is significantly reduced by the presence of contamination by non-homologous sequences, although the reduction is less than 1%. We developed a method called DecoyFinder, which applies machine learning trained with features determined by TurboFold, to detect sequences that are not homologous with the other sequences in the set. This method can identify approximately 45% of non-homologous sequences, at a rate of 5% misidentification of true homologous sequences. AvailabilityDecoyFinder and TurboFold are incorporated in RNAstructure, which is provided for free and open source under the GPL V2 license. It can be downloaded at http://rna.urmc.rochester.edu/RNAstructure.html

bioinformatics↗

bioRxiv2024

C-Reactive Protein Drives Potent Clearance of Blood Bacteria in the Liver by Activating the Complement System

Plasma C-reactive protein (CRP) is widely used as a biomarker for bacterial infections due to its massive induction during infections, however, the precise function of CRP in bacterial infections remains undefined. Here we show that CRP enables Kupffer cells (liver macrophages) to capture and eliminate a wide range of encapsulated bacteria from the bloodstream of mice and thereby provides rapid and effective immunity. Mechanistically, CRP binds to the structurally diverse capsular polysaccharides of major Gram-positive and -negative pathogens, and thereby activates complement C3 at the bacterial surface. The C3-opsonized microbes are in turn captured by C3 receptors on the surface of Kupffer cells, and eliminated in the liver sinusoids. Since CRP principally shares the functional features of antibodies in pathogen recognition/execution, CRP-based defense combines the broad spectrum of the innate immunity with the swiftness, potency and specificity of the adaptive immunity, which helps explain massive rise of CRP during systemic bacterial infections.

immunology↗

bioRxiv2024

Stochastic Gene Expression in Auxin Signaling in the Floral Meristem of Arabidopsis thaliana

Cells display striking stochasticity in gene expression, which plays an important role in development, disease, and regeneration. Previous studies have found stochastic gene expression in bacteria, yeast, and from constitutive promoters in Arabidopsis. However, most promoters are non-constitutive. Stochastic gene expression from non-constitutive promoters in a multicellular organism, especially those with key developmental roles, remains largely uncharacterized. Here, we report stochastic expression of auxin responsive genes in the Arabidopsis floral meristem, using promoter reporters of DR5, ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN6 (AHP6), and DNA BINDING WITH ONE FINGER5.8 (DOF5.8). We found highly variable DR5 expression patterns among younger meristems. Such variability is not attributed to heterogeneity in auxin perception, but to downstream stochastic expression of DR5, mainly influenced by cell-intrinsic molecular noise. Expression of AHP6 and DOF5.8 is also noisy, although their noise is lower and has distinct spatiotemporal patterns unlike DR5. Finally, we propose spatial averaging as a mechanism that buffers cellular gene expression noise, allowing the formation of robust global expression patterns. Our study reveals stochastic gene expression downstream of auxin signaling, a key developmental player. Thus, stochastic gene expression from non-constitutive promoters, including those involved in hormone signaling, is an ordinary part of multicellular life.

developmental biology↗