Biology subjects

Yu, Y.

Publications and source records attributed to Yu, Y..

At least 217 records · Page 12Linked to original sources

bioRxiv2024

Chlorobaculum tepidum Outer Membrane Vesicles Are Likely a Significant Route for Biogenic Sulfur Transport.

Outer membrane-derived vesicles (OMVs) have been studied in different phyla of Gramnegative bacteria, most extensively in the Pseudomonadota, where they have been shown to participate in diverse biological and environmental processes. To date, the production of OMVs has not been reported in the Chlorobiaceae within the phylum Chlorobiota. Chlorobaculum. tepidum is the model organism for the Chlorobiaceae that synthesizes and consumes insoluble extracellular sulfur (S(0)) globules by an unknown mechanism. Here, we report evidence implicating outer membrane vesicles in biogenic S(0) globule synthesis. We demonstrate that Cba. tepidum secretes OMVs in the extracellular milieu, and that OMV concentration and size vary with growth conditions, particularly sulfide concentration. A core of 31 proteins involved in diverse biological processes such as cell wall biogenesis, inorganic ion transport and metabolism were found to be shared between OMVs, extracellular S(0) globules and Cba. tepidum intact cells. Multiple analytical methods indicated that OMVs contain S(0) and that OMVs and biogenic S(0) globules share protein and polysaccharide signatures, including lipooligosaccharides. Together these lines of evidence indicate that Cba. tepidums OMVs are one component of sulfur transport between cells and extracellular sulfur globules. IMPORTANCEAll living cells must exchange material with their environment while maintaining cellular integrity. This is a particular challenge for materials that are not water soluble, yet many bacteria utilize insoluble materials for energy conservation and as nutrients for growth. Here we show that Cba. tepidum makes outer membrane vesicles and that these vesicles are likely involved in the exchange of material with extracellular elemental sulfur globules formed and consumed by Cba. tepidum as part of its energy metabolism based on oxidizing reduced sulfur compounds like hydrogen sulfide. These data expand our basic understanding of Cba. tepidums metabolism. As elemental sulfur is an industrial by-product with a limited number of uses, the information here may help enable the use of additional sulfur compounds by Cba. tepidum to drive the synthesis of biomass and/or specialty biochemicals from waste elemental sulfur by this autotrophic bacterium.

microbiology↗

bioRxiv2024

Mechanism of NPC1L1 mediated 27-hydroxycholesterol metabolisms in the occurrence and development of osteoporosis

Cholesterol metabolism is closely related to the occurrence and development of osteoporosis, but the exact mechanism remains unclear. Niemann-Pick C1-like 1 (NPC1L1) is one of the key cholesterol transporter proteins, however, there are few reports on the functions of NPC1L1 besides regulating cholesterol transport, let alone bone homeostasis. Our preliminary research indicated that NPC1L1 may play a negative regulatory role in osteogenic differentiation. In this study, using in vitro osteogenic differentiation experiment and mouse osteoporosis model, we showed here that NPC1L1 expression was downregulated during osteogenesis, and NPC1L1 knockdown significantly enhanced osteogenic differentiation ability of osteoblasts and delayed progress of osteoporosis. Mechanistically, through RNA sequencing, NPC1L1 was found regulate cholesterol metabolism rather than transportation. It increased 27-Hydroxycholesterol (27-OHC) level through activating 27-hydroxylase (Cyp27a1), resulting in 27-OHC accumulation in osteoblasts and inhibition of osteogenesis. Moreover, C/EBP was proved mediated NPC1L1 promotes production of 27-OHC by Cyp27a1. These findings reveal that NPC1L1 inhibits osteogenesis and promotes osteoporosis via regulate cholesterol metabolism. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/615783v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@11a62bforg.highwire.dtl.DTLVardef@148fb9aorg.highwire.dtl.DTLVardef@7e486eorg.highwire.dtl.DTLVardef@c53116_HPS_FORMAT_FIGEXP M_FIG NPC1L1 inhibits osteogenic differentiation and promotes the progression of OP through the C/EBP/Cyp27a1/27-OHC axis. C_FIG

molecular biology↗

bioRxiv2024

CPK3-mediated cytosolic-nuclear translocation of bHLH107 recruits HY5 to regulate the Cu2+-triggered upregulation of ACS8

Copper serves as a micronutrient for plant growth and development and has been a key component of copper-based antimicrobial compounds (CBACs) for protection against plant diseases for more than 130 years. We previously revealed that nanomolar- to-micromolar concentrations of Cu2+ elicit plant immune responses by activating the expression of the ethylene synthesis rate-limiting enzyme ACS8, which is dependent on the promoter copper response element (CuRE) cis-element. Here, we genetically confirmed that Cu2+-induced resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 is dependent on the CuRE in ACS8. Upon screening for CuRE-binding transcription factors, bHLH107, which is required for Cu2+-triggered activation of ACS8 expression and resistance to Pst DC3000, was identified via DNA-pull-down and mass spectrometry (MS) assays. Calcium-dependent protein kinase 3 (CPK3) interacts with and phosphorylates bHLH107 at Ser62 and Ser72 to mediate bHLH07 translocation from the cytoplasm into the nucleus, where it interacts with Arabidopsis ELONGATED HYPOCOTYL5 (HY5). HY5 directly binds to the G-box and acts as a coactivator to promote bHLH107 binding to the CuRE cis-element and to increase transcription of ACS8 upon Cu2+ treatment. Overall, we revealed a CPK3-bHLH107-HY5 module that regulates the Cu2+-responsive regulatory network upstream of ACS8 that is involved in the cytosolic-nuclear translocation of bHLH107.

plant biology↗

bioRxiv2024

A Unified Theory of Response Sparsity and Variability for Energy-Efficient Neural Coding

Understanding how cortical neurons use dynamic firing patterns to represent sensory signals is a central challenge in neuroscience. Decades of research have shown that cortical neuronal activities exhibit high variance, typically quantified by the coefficient of variation (CV), suggesting intrinsic randomness. Conversely, substantial evidence indicates that cortical neurons display high response sparseness, indicative of efficient encoding. The apparent contradiction between these neural coding properties--stochastic yet efficient--has lacked a unified theoretical framework. This study aims to resolve this discrepancy. We conducted a series of analyses to establish a direct relational function between CV and sparseness, proving they are intrinsically correlated or equivalent across different statistical distributions in neural activities. We further derive a function showing that both irregularity and sparsity in neuronal activities are positive functions of energy-efficient coding capacity, quantified by Information-Cost Efficiency (ICE). This suggests that the observed high irregularity and sparsity in cortical activities result from a shared mechanism optimized for maximizing information encoding capacity while minimizing cost. Furthermore, we introduce a CV-maximization algorithm to generate kernel functions replicating the receptive fields of the primary visual cortex. This finding indicates that the neuronal functions in the visual cortex are optimal energy-efficient coding operators for natural images. Hence, this framework unifies the concepts of irregularity and sparsity in neuronal activities by linking them to a common mechanism of coding efficiency, offering deeper insights into neural coding strategies.

neuroscience↗

bioRxiv2024

Bergeyella cardium variant induces unique cytoplasmic vacuolization cell death

Bacterial pathogens have evolved multiple mechanisms to modulate host cell death, evade host immunity, and establish persistent infection. Here, we show that an emerging pathogen Bergeyella cardium variant (BCV) survives serum killing, inducing unique cytoplasmic vacuolization cell death in the majority of cells and apoptosis in a small number of bystanders. The cytoplasmic vacuolization cell death triggered by BCV is characterized by fused lysosome-associated termination and is inhibited by the sodium channel inhibitor amiloride. Endosomal solute carrier family 9 member A9 (SLC9A9) was identified as a critical regulator in the process of BCV-triggered cytoplasmic vacuolization cell death. Moreover, outer membrane vesicles (OMVs) or transfection of barrel-like membrane proteins lipocalin, {beta}-barrel, and PorV dramatically induced cytoplasmic vacuolization. BCV hijacked SLC9A9 by maintaining its high expression, increasing cytoplasmic vacuolization, and enhancing pathogenicity. These findings contribute to the development of novel approaches to modulate cytoplasmic vacuolization cell death and treat infectious diseases. HighlightsO_LIBCV triggers unique cytoplasmic vacuolization cell death. C_LIO_LISLC9A9 is essential for BCV-induced cytoplasmic vacuolization cell death. C_LIO_LIOMVs and the transfection of barrel-like proteins derived from BCV induce cytoplasmic vacuolization cell death. C_LIO_LIBCV increases pathogenicity via cytoplasmic vacuolization cell death. C_LI

cell biology↗

bioRxiv2024

Constructing a Norm for Children's Scientific Drawing: Distribution Features Based on Semantic Similarity of Large Language Models

The use of childrens drawings to examining their conceptual understanding has been proven to be an effective method, but there are two major problems with previous research: 1. The content of the drawings heavily relies on the task, and the ecological validity of the conclusions is low; 2. The interpretation of drawings relies too much on the subjective feelings of the researchers. To address this issue, this study uses the Large Language Model (LLM) to identify 1420 childrens scientific drawings (covering 9 scientific themes/concepts), and uses the word2vec algorithm to calculate their semantic similarity. The study explores whether there are consistent drawing representations for children on the same theme, and attempts to establish a norm for childrens scientific drawings, providing a baseline reference for follow-up childrens drawing research. The results show that the representation of most drawings has consistency, manifested as most semantic similarity>0.8. At the same time, it was found that the consistency of the representation is independent of the accuracy (of LLMs recognition), indicating the existence of consistency bias. In the subsequent exploration of influencing factors, we used Kendall rank correlation coefficient to investigate the effects of "sample size", "abstract degree", and "focus points" on drawings, and used word frequency statistics to explore whether children represented abstract themes/concepts by reproducing what was taught in class. It was found that accuracy (of LLMs recognition) is the most sensitive indicator, and data such as sample size and semantic similarity are related to it; The consistency between classroom experiments and teaching purpose is also an important factor, many students focus more on the experiments themselves rather than what they explain. In addition, most children tend to use examples they have seen in class to represent more abstract themes/concepts, indicating that they may need concrete examples to understand abstract things.

scientific communication and education↗

bioRxiv2024

Microbial magnetite oxidation via MtoAB porin-multiheme cytochrome complex in Sideroxydans lithotrophicus ES-1

Most of Earths iron is mineral-bound, but it is unclear how and to what extent iron-oxidizing microbes can use solid minerals as electron donors. A prime candidate for studying mineral-oxidizing growth and pathways is Sideroxydans lithotrophicus ES-1, a robust, facultative iron oxidizer with multiple possible iron oxidation mechanisms. These include Cyc2 and Mto pathways plus other multiheme cytochromes and cupredoxins, and so we posit that the mechanisms may correspond to different Fe(II) sources. Here, S. lithotrophicus ES-1 was grown on dissolved Fe(II)-citrate and magnetite. S. lithotrophicus ES-1 oxidized all dissolved Fe2+ released from magnetite, and continued to build biomass when only solid Fe(II) remained, suggesting it can utilize magnetite as a solid electron donor. Quantitative proteomic analyses of S. lithotrophicus ES-1 grown on these substrates revealed global proteome remodeling in response to electron donor and growth state and uncovered potential proteins and metabolic pathways involved in the oxidation of solid magnetite. While the Cyc2 iron oxidases were highly expressed on both dissolved and solid substrates, MtoA was only detected during growth on solid magnetite, suggesting this protein helps catalyze oxidation of solid minerals in S. lithotrophicus ES-1. A set of cupredoxin domain-containing proteins were also specifically expressed during solid iron oxidation. This work demonstrated the iron oxidizer S. lithotrophicus ES-1 utilized additional extracellular electron transfer pathways when growing on solid mineral electron donors compared to dissolved Fe(II). ImportanceMineral-bound iron could be a vast source of energy to iron-oxidizing bacteria, but there is limited physiological evidence of this metabolism, and it has been unknown whether the mechanisms of solid and dissolved Fe(II) oxidation are distinct. In iron-reducing bacteria, multiheme cytochromes can facilitate iron mineral reduction, and here, we link a multiheme cytochrome-based pathway to mineral oxidation, expanding the known functionality of multiheme cytochromes. Given the growing recognition of microbial oxidation of minerals and cathodes, increasing our understanding of these mechanisms will allow us to recognize and trace the activities of mineral-oxidizing microbes. This work shows how solid iron minerals can promote microbial growth, which if widespread, could be a major agent of geologic weathering and mineral-fueled nutrient cycling in sediments, aquifers, and rock-hosted environments.

microbiology↗

bioRxiv2024

In-cell processing enables rapid and in-depth proteome analysis of low-input Caenorhabditis elegans

Caenorhabditis elegans is a widely used genetic model organism, however, the worm cuticle complicates extraction of intracellular proteins, a prerequisite for typical bottom-up proteomics. Conventional physical disruption procedures are not only time-consuming, but can also cause significant sample loss, making it difficult to perform proteomics with low-input samples. Here, for the first time, we present an on-filter in-cell (OFIC) processing approach, which can digest C. elegans proteins directly in the cells of the organism after methanol fixation. With OFIC processing and single-shot LCMS analysis, we identified over 9,400 proteins from a sample of only 200 worms, the largest C. elegans proteome reported to date that did not require fractionation or enrichment. We systematically evaluated the performance of the OFIC approach by comparing it with conventional lysis-based methods. Our data suggest equivalent and unbiased performance of OFIC processing for C. elegans proteome identification and quantitation. We further evaluated the OFIC approach with even lower input samples, then used this method to determine how the proteome is impacted by loss of superoxide dismutase sod-1, the ortholog of human SOD-1, a gene associated with amyotrophic lateral sclerosis (ALS). Analysis of 8,800 proteins from only 50 worms as the initial input showed that loss of sod-1 affects the abundance of proteins required for stress response, ribosome biogenesis, and metabolism. In conclusion, our streamlined OFIC approach, which can be broadly applied to other systems, minimizes sample loss while offering the simplest workflow reported to date for C. elegans proteomics analysis.

biochemistry↗

bioRxiv2024

Cortical connectivity supports motoric synchronization to both auditory and visual rhythms in a frontal-temporal network

Synchronizing motoric responses to metrical sensory rhythms is key to social activities, e.g., group singing and dancing. It remains elusive, however, whether there is a common neural network for motoric synchronization to metrical rhythms from different sensory modalities. Here, we separate sensorimotor responses from basic sensory responses by combining a metrical sensorimotor synchronization task with frequency-domain magnetoencephalography (MEG) analysis. A common frontal-temporal network, not including visual cortex, is observed during both visual- and auditory-motor synchronization, and the network remains in congenitally deaf participants during visual-motor synchronization, suggesting the network is formed by intrinsic cortical connections instead of auditory experience. Furthermore, activation of the left and right frontal-temporal areas, as well as the ipsilateral white matter connection, separately predict the precision of auditory and visual synchronization. These results reveal a common but lateralized frontal-temporal network for visual- and auditory-motor synchronization, which is generated based on intrinsic cortical connections.

neuroscience↗

bioRxiv2024

Cross-Tissue Coordination between SLC Nucleoside Transporters Regulates Reproduction in Caenorhabditis elegans

Metabolism is fundamental to organism physiology and pathology. From the intricate network of metabolic reactions, diverse chemical molecules, collectively termed as metabolites, are produced. In multicellular organisms, metabolite communication between different tissues is vital for maintaining homeostasis and adaptation. However, the molecular mechanisms mediating these metabolite communications remain poorly understood. Here, we focus on nucleosides and nucleotides, essential metabolites involved in multiple cellular processes, and report the pivotal role of the SLC29A family of transporters in mediating nucleoside coordination between the soma and the germline. Through genetic analysis, we discovered that two Caenorhabditis elegans homologs of SLC29A transporters, Equilibrative Nucleoside Transporter ENT-1 and ENT-2, act in the germline and the intestine, respectively, to regulate reproduction. Their knockdown synergistically results in sterility. Further single-cell transcriptomic and targeted metabolomic profiling revealed that the ENT double knockdown specifically affects genes in the purine biosynthesis pathway and reduces the ratio of guanosine to adenosine levels. Importantly, guanosine supplementation into the body cavity/pseudocoelom through microinjection rescued the sterility caused by the ENT double knockdown, whereas adenosine microinjection had no effect. Together, these studies support guanosine as a rate limiting factor in the control of reproduction, uncover the previously unknown nucleoside/nucleotide communication between the soma and the germline essential for reproductive success, and highlight the significance of SLC-mediated cell-nonautonomous metabolite coordination in regulating organism physiology. Author SummaryMetabolism is essential for life, involving a complex network of chemical reactions that requires a well-organized system to maintain efficiency. This includes the optimal allocation of resources and the dynamic exchange of metabolic products between various compartments within an organism. Solute carriers (SLCs) are the largest family of transporters for metabolic products across the animal kingdom. In our research, we investigated how specific SLC transporters collaborate to move key metabolic products between different tissues. We identified two SLC transporters, Equilibrative Nucleoside Transporter ENT-1 and ENT-2, which are vital for transporting guanosine, a purine nucleoside, to support successful reproduction in the nematode Caenorhabditis elegans. We discovered that ENT-2 acts in the gut to export guanosine to the surrounding body cavity, while ENT-1 functions in the germline to import guanosine from the body cavity. When both transporters are disrupted, the animals experience significant reproductive defects. Our study underscores the importance of coordinated activity between SLC transporters in different tissues to maintain organism health. A breakdown in this communication can result in metabolic imbalances and physiological dysfunction.

genetics↗

bioRxiv2024

Leveraging Multi-Modal Feature Learning for Predictions of Antibody Viscosity

The shift towards the subcutaneous administration route for biologics therapeutics has gained momentum due to its patient-friendly nature, convenience, reduced healthcare burden, and improved compliance compared to traditional intravenous infusions. However, one of the potentially significant challenges with this transition is managing the viscosity of the administered solutions. High viscosity can pose substantial development and manufacturability challenges, directly impacting the patient by increasing injection time and pain at the injection site. Moreover, high viscosity formulations can prolong residence time at the injection site, affecting absorption kinetics and potentially altering the intended pharmacological profile and therapeutic efficacy of the biologic candidate. This publication explores the application of a multimodal feature learning workflow for predicting the viscosity of antibodies in therapeutics discovery, integrating multiple data sources such as sequence, structural, physicochemical properties, and embeddings from a language model. This approach enables the model to learn from various underlying rules, including physicochemical rules from molecular simulations and molecular protein evolutionary rules by large, pre-trained deep learning foundation models. By comparing the effectiveness of this approach against other selected published viscosity prediction methods, this study offers insights on their intrinsic viscosity predictive potential and usability in therapeutics antibody early development pipelines.

bioinformatics↗

bioRxiv2024

SERS Analysis Of Sialic Acid In Single Dendritic Cells Within The Tumor Microenvironment

The crucial role of Dendritic Cells (DCs) in anti-tumor immune responses depends on surface Sialic Acid (SA). The regulation of DC surface sialic acid in the Tumor Microenvironment (TME) remains underexplored. Current methods struggle to provide highly sensitive, multiplex analyses of SA and other immune protein changes in single DCs within the tumor microenvironment. Here, we employed a SERS tags method for specific and highly sensitive analysis of SA, MHCII, CD86, and CD40 in DCs using a single DC analysis microfluidic platform. We also explored the differential regulatory effects of various immune-modulating drugs and tumor supernatant on multiple immunophenotypes of DCs in different immune states. The expanded two-cell microfluidic system further allows for phenotypic analysis of DCs at different time points within the tumor microenvironment. Given this method enables highly sensitive single-cell analysis of DCs, further development of this technology for tumor microenvironment applications will aid in deeply understanding the tumor-induced suppression of DC immune function, providing valuable insights for DC-mediated tumor immunotherapy research.

immunology↗

bioRxiv2024

δ-α cell-to-cell interactions modulate pancreatic islet Ca2+ oscillation modes

Glucose-induced pancreatic islet hormone release is tightly coupled with oscillations in cytoplasmic free Ca2+ concentration of islet cells, which is regulated by a complex interplay between intercellular and intracellular signaling. {delta} cells, which entangle with cells located at the islet periphery, are known to be important paracrine regulators. However, the role of {delta} cells in regulating Ca2+ oscillation pattern remains unclear. Here we show that {delta}- cell-to-cell interactions are the source of variability in glucose-induced Ca2+ oscillation pattern. Somatostatin secreted from {delta} cells prolonged the islets oscillation period in an cell mass-dependent manner. Pharmacological and optogenetic perturbations of {delta}- interactions led islets to switch between fast and slow Ca2+ oscillations. Continuous adjustment of {delta}- coupling strength caused the fast oscillating islets to transition to mixed and slow oscillations. We developed a mathematical model, demonstrating that the fast-mixed-slow oscillation transition is a Hopf bifurcation. Our findings provide a comprehensive understanding of how {delta} cells modulate islet Ca2+ dynamics and reveal the intrinsic heterogeneity of islets due to the structural composition of different cell types. HighlightsO_LISomatostatin slows down islet Ca2+ oscillations in an cell mass-dependent manner. C_LIO_LIPharmacological and optogenetic perturbations of {delta}- interaction cause islet Ca2+ oscillation mode switching. C_LIO_LIContinuous tuning of {delta}- interaction strength induces fast-mixed-slow oscillation transition successively. C_LIO_LIMathematical modeling shows the fast-mixed-slow oscillation transition as a Hopf bifurcation. C_LI

systems biology↗

bioRxiv2024

Visualizing Single V-ATPase Rotation Using Janus Nanoparticles

Understanding the function of rotary molecular motors, such as the rotary ATPases, relies on our ability to visualize the single-molecule rotation. Traditional imaging methods often involve tagging those motors with nanoparticles (NPs) and inferring their rotation from translational motion of NPs. Here, we report an approach using "two-faced" Janus NPs to directly image the rotation of single V-ATPase from Enterococcus hirae, an ATP-driven rotary ion pump. By employing a 500-nm silica/gold Janus NP, we exploit its asymmetric optical contrast - silica core with a gold cap on one hemisphere - to achieve precise imaging of the unidirectional counter-clockwise rotation of single V-ATPase motors immobilized on surfaces. Despite the added viscous load from the relatively large Janus NP probe, our approach provides accurate torque measurements of single V-ATPase. This study underscores the advantages of Janus NPs over conventional probes, establishing them as powerful tools for single-molecule analysis of rotary molecular motors.

biophysics↗

bioRxiv2024

Machine learning reveals signatures of promiscuous microbial amidases for micropollutant biotransformations

Organic micropollutants - including pharmaceuticals, personal care products, pesticides and food additives - are prevalent in the environment and have unknown and potentially toxic effects. Humans are a direct source of micropollutants as the majority of pharmaceuticals are primarily excreted through urine. Urine contains its own microbiota with the potential to catalyze micropollutant biotransformations. Amidase signature (AS) enzymes are known for their promiscuous activity in micropollutant biotransformations, but the potential for AS enzymes from the urinary microbiota to transform micropollutants is not known. Moreover, characterization of AS enzymes to identify key chemical and enzymatic features predictive of biotransformation profiles is critical for developing benign-by-design chemicals and micropollutant removal strategies. In this study, we biochemically characterized a new AS enzyme with arylamidase activity from a urine isolate, Lacticaseibacillus rhamnosus, and demonstrated its capability to hydrolyze pharmaceuticals and other micropollutants. To uncover the signatures of AS enzyme-substrate specificity, we then designed a targeted enzyme library consisting of 40 arylamidase homologs from diverse urine isolates and tested it against 17 structurally diverse compounds. We found that 16 out of the 40 enzymes showed activity on at least one substrate and exhibited diverse substrate specificities, with the most promiscuous enzymes active on nine different substrates. Using an interpretable gradient boosting machine learning model, we identified chemical and amino acid features predictive of arylamidase biotransformations. Key chemical features from our substrates included the molecular weight of the amide carbonyl substituent and the number of charges in the molecule. Important amino acid features were found to be located on the protein surface and four predictive residues were located in close proximity of the substrate tunnel entrance. Overall, this work highlights the understudied role of urine-derived microbial arylamidases and contributes to enzyme sequence-structure-substrate-based predictions of micropollutant biotransformations.

biochemistry↗

bioRxiv2024

Pressorum Sensing: Growth-induced Compression Activates cAMP Signaling in Pseudomonas aeruginosa

Bacteria employ various strategies to coordinate population-level behaviors, with quorum sensing being a well-established mechanism. Here, we report a novel population-level regulatory mechanism in Pseudomonas aeruginosa, which we term pressorum sensing. This mechanism allows bacteria to modulate their collective behavior in response to growth-induced mechanical compression in confined spaces. Using a highly sensitive cAMP biosensor in combination with microfluidics, we demonstrate that when compressive forces reach approximately 30 nN, P. aeruginosa cells rapidly increases intracellular cAMP levels via the Pil-Chp chemosensory system. This response leads to up-regulation of the Type III Secretion System, a key virulence factor. Unlike quorum sensing, which relies on diffusible chemical signals, pressorum sensing utilizes mechanical cues to gauge population density and spatial confinement. In bacterial colonies, this mechanism generates striking spatial patterns of cAMP signaling, including traveling rings that coincide with step-like structures in colony morphology. Our findings reveal a previously unknown link between mechanical compression and bacterial virulence, providing new insights into how P. aeruginosa coordinates population-level responses in confined environments. This work also expands our knowledge of mechanogenetics and opens up new possibilities in synthetic biology and bioengineering applications.

microbiology↗

bioRxiv2024

Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain

A multitude of functional mutations continue to emerge on the N-terminal domain (NTD) of the spike protein in SARS-CoV-2 Omicron subvariants. Understanding the immunogenicity of Omicron NTD and the properties of antibodies elicited by it is crucial for comprehending the impact of NTD mutations on viral fitness and guiding vaccine design. In this study, we find that most of NTD-targeting antibodies isolated from individuals with BA.5/BF.7 breakthrough infection (BTI) are ancestral (wildtype or WT)-reactive and non-neutralizing. Surprisingly, we identified five ultra-potent neutralizing antibodies (NAbs) that can only bind to Omicron but not WT NTD. Structural analysis revealed that they bind to a unique epitope on the N1/N2 loop of NTD and interact with the receptor-binding domain (RBD) via the light chain. These Omicron-specific NAbs achieve neutralization through ACE2 competition and blockage of ACE2-mediated S1 shedding. However, BA.2.86 and BA.2.87.1, which carry insertions or deletions on the N1/N2 loop, can evade these antibodies. Together, we provided a detailed map of the NTD-targeting antibody repertoire in the post-Omicron era, demonstrating their vulnerability to NTD mutations enabled by its evolutionary flexibility, despite their potent neutralization. These results highlighted the importance of considering the immunogenicity of NTD in vaccine design. Author SummaryCOVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a major global public health concern four years after its emergence. The N-terminal domain (NTD) is a critical component of the spike glycoprotein, which is pivotal for SARS-CoV-2 cellular entry and serves as a primary target for antibody therapeutics and vaccine development. Characterizing the properties of antibodies elicited by NTD of Omicron sublineages is crucial for understanding viral evolution and guiding vaccine design. Here, we show that Omicron infection after vaccination induces majorly non-neutralizing NTD antibodies. Still, we identified a class of ultra-potent neutralizing antibodies (NAbs) which specifically bind to the NTD of Omicron sublineages. These NAbs neutralize the virus by competing with ACE2 and blocking ACE2-mediated S1 shedding. Structural analyses reveal that these antibodies target a unique epitope on the N1/N2 loop of NTD, and intriguingly interact with the receptor-binding domain (RBD) of spike glycoprotein. This class of NAbs with the special binding pattern, are escaped by BA.2.86 and BA.2.87.1 sublineages, shedding light on the role of recently emerged mutations in the N1/N2 loop of NTD. Our findings provide fresh insights into the immunogenicity of Omicron NTD, highlighting its capacity for antibody evasion due to its evolutionary flexibility. This underscores the importance of carefully considering the NTD component in vaccine design.

immunology↗

bioRxiv2024

Structural insights into the in situ assembly of clustered protocadherin γB4

Clustered protocadherins (cPcdhs) belong to the cadherin superfamily and play important roles in neural development. cPcdhs can mediate homophilic adhesion and lead to self-avoidance and tiling by giving neurons specific identities in vertebrates. Structures and functions of cPcdhs have been studied extensively in the past decades, but the mechanisms behind the functions have not been fully understood. Here we investigate the in situ assembly of cPcdh-{gamma}B4, a member in the {gamma} subfamily of cPcdhs, by electron tomography and find that the full length cPcdh-{gamma}B4 does not show regular organization at the adhesion interfaces. By contrast, cPcdh-{gamma}B4 lacking the intracellular domain can generate an ordered zigzag pattern between cells and the cis interacting mode is different from the crystal packing of the ectodomain. We also identify the residues on the ectodomain that might be important for the zigzag pattern formation by mutagenesis. Furthermore, truncation mutants of the intracellular domain of cPcdh-{gamma}B4 reveal different assembly patterns between cell membranes, suggesting that the intracellular domain plays a crucial role in the intermembrane organization of cPcdh-{gamma}B4. Taken together, these results suggest both ectodomain and intracellular domain regulate the in situ assembly of cPcdh-{gamma}B4 at the adhesion interfaces, thereby providing mechanistic insights into the functional roles of cPcdhs during neuronal wiring.

biophysics↗