Biology subjects

An, R.

Publications and source records attributed to An, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Adjacent Z-DNA contributes to the formation of homologous DNA triplex

Whether the homologous parallel triplex (HP-triplex, formed by dsDNA and a homologous ssDNA) acts as an intermediate prior to DNA recombination remains controversy, owing to the intrinsic instability and lake of experimental data. Here, we report a HP-triplex that is stable at least at 35 oC under protein-free conditions. Two complementary circular ssDNAs were first hybridized at a 1:1 ratio to form an LR-chimera containing both Z-DNA and B-DNA. Then the circular homologous ssDNA (T-rich) was found to easily hybridize with this LR-chimera to form the HP-triplex (strand ratio of 2:1), involving both left- and right-handed triplex parts under the topological constraint. The third strand locates in the major groove and forms hydrogen bonds with both bases in each base pair of dsDNA without obvious strand exchange. Our data indicate that the third-strand ssDNA may first bind to the B-DNA region, followed by association with the Z-DNA region to assemble the full triplex structure. Structural simulations and analyses reveal that topological constraint imposed by the circular architecture raises the energy barrier for strand displacement, thereby stabilizing this triplex. In summary, the dynamic HP triplex can be stabilized via a Z B junction structure that mimics the in vivo one formed by negative supercoiling. These findings demonstrate that HP-triplex may act as an intermediate for DNA recombination, anti-gene strategy, and other interactions between dsDNA and homologous ssDNA or RNA.

molecular biology↗

bioRxiv2026

Lack of ancestral SARS-CoV-2 imprinting promotes BA.3.2.2 infection in children

The ongoing evolution of SARS-CoV-2 is heavily constrained by population-level immune imprinting. Recent genomic surveillance reveals an unexpected demographic shift: the highly mutated BA.3.2.2 sublineage is significantly enriched in paediatric populations globally, unlike concurrent variants XFG and NB.1.8.1. Here, the evidence demonstrates that this paediatric susceptibility arises from the absence of ancestral Wuhan-strain immune imprinting. Serological analyses reveal a profound failure to neutralise BA.3.2.2 in young children with no ancestral strain exposure. Concurrently, single-B-cell sequencing analyses demonstrate that BA.3.2.2 completely evades Omicron-specific Class 1/4 neutralising antibodies, encoded by IGHV2-5 and IGHV5-51, which dominate the repertoires of weakly imprinted individuals such as young children. Conversely, BA.3.2.2 remains uniquely susceptible to broadly cross-reactive Class 1 antibodies, encoded by IGHV3-53/66, typically enriched in adults with strong ancestral imprinting, such as mRNA vaccine recipients. Critically, sustained transmission of BA.3.2.2 in paediatric populations may catalyse the emergence of secondary variants that combine the paediatric-evading features of BA.3.2.2 with adult-evading Class 1 mutations. This could allow the lineage to breach the imprinted immunity of the adult population, potentially driving widespread global transmission. Together, these findings show that legacy immune imprinting paradoxically provides superior protection against a highly divergent saltation variant, directly explaining the age-biased transmission of BA.3.2.2, and informing future paediatric vaccination strategies.

immunology↗

bioRxiv2026

Chromosomal variability in a clonal crop: Somaclonal change follows the emergence of triploid saffron crocus

(1) BackgroundSaffron crocus (Crocus sativus) is the source of saffron, the most expensive spice in the world. It evolved about 3000 years ago as a sterile triploid clone in Greece. Since then, saffron has spread across the globe, where regionally distinct practices of saffron cultivation have developed. Despite differences in morpho-physiological traits, genetic variability is low, if present at all. Here, we aim to resolve chromosomal and sequence-associated variability across saffron crocus cultivars from the crops main cultivation areas in Africa, Asia and Europe. (2) MethodsWe used genome-wide DNA polymorphisms obtained through genotyping-by-sequencing (GBS) of 33 saffron and 14 closely related Crocus accessions, which we place into a phylogenetic context. For karyotyping, we compare nine saffron accessions by multi-color fluorescent in situ hybridisation (FISH) with repetitive DNA probes. (3) Key resultsPhylogenetic analyses confirmed the single origin and clonal nature of all saffron accessions. We detected slight DNA differences among saffron crocus genotypes, which were minor compared with those in wild C. cartwrightianus populations. Still, the Iranian saffron accessions form a genetically very narrow group that differs from the other proveniences in population genetic analyses. However, chromosomes of some saffron accessions display variable FISH signals, likely resulting from gains and losses of tandemly repeated DNA. (4) Main conclusionsBased on the high genetic identity and small karyotypic differences, we confirm the clonal origin of the saffron accessions. Nevertheless, as we detected small and regional chromosomal variability, we conclude that at least four somaclonal saffron lineages emerged after saffrons origin. Societal Impact StatementFor millennia, many cultures developed cultivation practices and regional crop varieties. A notable case is saffron, the worlds most expensive spice that is harvested from stigmas of saffron crocus. This flower crop arose 3000 years ago in a singular genome triplication event and since then spread clonally across the globe. By identifying genetic and chromosomal variability in clonal saffron accessions, we highlight regional diversity, support the preservation of traditional knowledge, and underscore the risk of relying on only one clonal lineage. This informs strategies for saffron cultivation, linking cultural heritage with modern genomics to address biodiversity, evolution, and food security.

plant biology↗

bioRxiv2025

Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity

Abstract Imaging-based spatially resolved transcriptomics (imSRT) technologies provide high-throughput molecular-resolution spatial characterization of genes within cells. Conventional analysis methods to identify cell-types and states in imSRT data rely on gene count matrices derived from tallying the number of mRNA molecules detected for each gene per segmented cell, thereby overlooking subcellular heterogeneity that can be useful in defining cell states. To take advantage of the molecular-resolution information in imSRT data and potentially identify cell-states based on subcellular heterogeneity, we developed STARIT (Spatial Transcriptomics As Rasterized Image Tensors). STARIT converts transcripts within segmented cells in imSRT data into an image-based tensor representation that can be combined with deep learning computer vision models for downstream analysis. Using simulated and real imSRT data, we demonstrate that STARIT distinguishes transcriptionally distinct cell-types and further separates cell states based on subcellular transcript localization, which conventional gene count analysis fails to capture. By providing a standardized framework to encode subcellular molecular information in imSRT data, STARIT will enable deeper insights into subcellular heterogeneity and enhance the identification and characterization of cell-types and states that are overlooked by gene count representations.

bioinformatics↗

bioRxiv2025

IGHV3-53 antibody abundance drives divergent SARS-CoV-2 immune imprinting

The mechanisms driving divergent SARS-CoV-2 immune imprinting in populations with distinct SARS-CoV-2 exposure histories remain unclear. However, conventional wild-type mouse models fail to recapitulate severe imprinting, even after potent ancestral-strain mRNA immunization, hindering imprinting-related mechanistic investigation and vaccine evaluation. Here, we surprisingly found that V(D)J-humanized mice could faithfully recapitulate human severe imprinting phenotypes. Comprehensive antibody repertoire analysis and deep mutational scanning-based epitope mapping of 583 monoclonal antibodies from these models revealed that the pre-existing IGHV3-53/66 antibody abundance determine imprinting severity through antibody-mediated masking of Omicron-specific epitopes. Both passive IGHV3-53/66 antibody transfer and IGHV3-53 knock-in were sufficient to induce severe imprinting in wild-type mice. Together, these findings demonstrate that the V(D)J germline repertoire--even a single germline-encoded antibody response--can profoundly shape humoral imprinting severity. Accordingly, we established an IGHV3-53 knock-in mouse model that accurately recapitulates the human antibody landscape, providing a valuable tool for guiding future COVID-19 vaccine updates.

immunology↗

bioRxiv2025

Label invariance: a guiding principle for ecological models

Ecological models, though diverse in form, are strengthened when they obey guiding principles. We formalize and advocate for a foundational principle we call "label invariance", which says that a models dynamics must remain the same when identical individuals are arbitrarily grouped into distinct sub-populations. This principle is a necessary consequence of trait continuity--the observation that ecological interactions change continuously as organisms become more similar. Violation of label invariance often implies a hidden, intrinsic niche differentiation between species, which may obscure the mechanisms of biodiversity maintenance. We provide a general framework for constructing both deterministic and stochastic models that follow label invariance. We further demonstrate its utility as a complementary, non-statistical tool for empirical model selection. In sum, label invariance provides an important test for evaluating existing ecological models and a guide for developing new ones, promoting clarity in model assumptions from the outset.

ecology↗

bioRxiv2025

Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

Evolutionary adaptation to diurnal vision in ground squirrels has led to the development of a cone-dominant retina, in stark contrast to the rod-dominant retinas of most mammals. The molecular mechanisms driving this shift remain largely unexplored. Here, we perform single-cell RNA sequencing (scRNA-Seq) and chromatin accessibility profiling (scATAC-Seq) across developmental retinal neurogenesis in the 13-lined ground squirrel (13LGS) to uncover the regulatory basis of this adaptation. We find that 13LGS cone photoreceptors arise not only from early-stage neurogenic progenitors, as seen in rod-dominant species like mice, but also from late-stage neurogenic progenitors. This extended period of cone generation is driven by a heterochronic shift in transcription factor expression, with cone-promoting factors such as Onecut2, Pou2f1, and Zic3 remaining active in late-stage progenitors, and factors that promote cone differentiation such as Thrb, Rxrg, and Mef2c expressed precociously in late-stage neurogenic progenitors. Functional analyses reveal that Zic3 and Mef2c are sufficient to promote cone and repress rod photoreceptor-specific gene expression, and act through species-specific regulatory elements that drive their expression in late-stage progenitors. These results demonstrate that modifications to gene regulatory networks underlie the development of cone-dominant retinas, and provide insight into mechanisms of sensory adaptation and potential strategies for cone photoreceptor regeneration in vision disorders.

neuroscience↗

bioRxiv2024

Single Cells Signal Non-self from Self via 'XOR' and 'NOT EQUALS' Logic in a Dimer of Dimers

The ciliate Tetrahymena thermophilas seven mating types are defined by unique receptor-ligand pairs (Mta/Mtb). While Mta and Mtb are known to participate in a mating signal complex, how they distinguish between oneself and six non-self cell types remains unknown. AlphaFold3 predictions reveal Mta/Mtb as large glycoproteins likely derived from ancient, unisexual, intercellular adhesion molecules. Since homologous binary-type systems perform XOR by switching mtA expression, we show spectrum (n) types naturally extend XOR to multi-bit NOT EQUALS operations via differential affinities of Mta/Mtb dimers. We model kinetics begetting the n + 1th type, demonstrating self-inhibition by trans-homophilic Mtb-Mtb. A computational approach reconciles recent and classical evidence for mating exclusivity, including selfing failures (same type mating). Binding kinetics enables fast, robust intercellular computation across an intermembrane mating space. Thus, Mta/Mtb families are a model system allowing us to derive a calculus of antigenic variation and inspire synthetic designs of XOR logic underlying self/non-self recognition. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/616003v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@572f8forg.highwire.dtl.DTLVardef@1f386b2org.highwire.dtl.DTLVardef@1104fb1org.highwire.dtl.DTLVardef@1e006a1_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIWithin minutes, swimming cells signal compatible mating types via membrane proteins C_LIO_LIAlphaFold insights reveal Mta/Mtb family as elongate adhesion receptors/ligands C_LIO_LIRelative affinities of two dimers explain multi-bit intercellular signaling capacity C_LIO_LIDimer-of-dimers compute NOT EQUALS via homo-vs. hetero-philic interactions C_LIO_LIIn Brief Free-living ciliates T. thermophila breed only when two cells are different in mating type, out of seven types total. Their mating-type-specific coexpression of a receptor-ligand glycoprotein pair reveals how competitive homophilic vs. heterophilic binding computes self vs. non-self recognition with single-layer intercellular logic. Proteins perform binary XOR gates (with two mating types) that extend to multi-bit NOT EQUALS (with multiple mating types). The work illuminates principles of eXclusivity in molecular recognition and inspires the design of synthetic cellular recognition systems. C_LI

systems biology↗

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

Omicron-specific naive B cell maturation alleviates immune imprinting induced by SARS-CoV-2 inactivated vaccine

SARS-CoV-2 ancestral strain-induced immune imprinting poses great challenges to vaccine updates. Studies showed that repeated Omicron exposures could override immune imprinting induced by inactivated vaccines but not mRNA vaccines, a disparity yet to be understood. Here, we analyzed the underlying mechanism of immune imprinting alleviation in inactivated vaccine (CoronaVac) cohorts. We observed in CoronaVac-vaccinated individuals who experienced BA.5/BF.7 breakthrough infection (BTI), the proportion of Omicron-specific memory B cells (MBCs) substantially increased after an extended period post-Omicron BTI, with their antibodies displaying enhanced somatic hypermutation and neutralizing potency. Consequently, the neutralizing antibody epitope distribution encoded by MBCs post-BA.5/BF.7 BTI after prolonged maturation closely mirrors that in BA.5/BF.7-infected unvaccinated individuals. Together, these results indicate the activation and expansion of Omicron-specific naive B cells generated by first-time Omicron exposure helped to alleviate CoronaVac-induced immune imprinting, and the absence of this process should have caused the persistent immune imprinting seen in mRNA vaccine recipients. HighlightsO_LILongitudinal MBC profiling of CoronaVac-vaccinated individuals following BA.5 BTI C_LIO_LIOmicron-specific MBC proportion rises greatly after extended period post-BA.5 BTI C_LIO_LIOmicron-specific naive B cell maturation reduces ancestral strain immune imprinting C_LI

immunology↗

bioRxiv2024

Humoral immunogenicity comparison of XBB and JN.1 in human infections

The continuous evolution of SARS-CoV-2, particularly the emergence of the BA.2.86/JN.1 lineage replacing XBB lineages, necessitates re-evaluation of current vaccine compositions. Here, we provide a comprehensive analysis of the humoral immune response to XBB and JN.1 human exposures, emphasizing the need for JN.1-lineage-based boosters. We demonstrate the antigenic distinctiveness of XBB and JN.1 lineages in SARS-CoV-2-naive individuals but not in those with prior vaccinations or infections, and JN.1 infection elicits superior plasma neutralization titers against its subvariants. We highlight the strong immune evasion and receptor binding capability of KP.3, supporting its foreseeable prevalence. Extensive analysis of the BCR repertoire, isolating [~]2000 RBD-specific monoclonal antibodies (mAbs) with their targeting epitopes characterized by deep mutational scanning (DMS), underscores the systematic superiority of JN.1-elicited memory B cells (MBCs). Notably, Class 1 IGHV3-53/3-66-derived neutralizing antibodies (NAbs) contribute majorly within wildtype (WT)-reactive NAbs against JN.1. However, KP.2 and KP.3 evade a substantial subset of them, even those induced by JN.1, advocating for booster updates to KP.3 for optimized enrichment. JN.1-induced Omicron-specific antibodies also demonstrate high potency across all Omicron lineages. Escape hotspots of these NAbs have mainly been mutated in Omicron RBD, resulting in higher immune barrier to escape, considering the probable recovery of previously escaped NAbs. Additionally, the prevalence of broadly reactive IGHV3-53/3-66- encoding antibodies and MBCs, and their capability of competing with all Omicron-specific NAbs suggests their inhibitory role on the de novo activation of Omicron-specific naive B cells, potentially explaining the heavy immune imprinting in mRNA-vaccinated individuals. These findings delineate the evolving antibody response to Omicron antigenic shift from XBB to JN.1, and highlight the importance of developing JN.1 lineage, especially KP.3-based vaccine boosters, to enhance humoral immunity against current and future SARS-CoV-2 variants.

immunology↗

bioRxiv2024

A generalized framework to identify SARS-CoV-2 broadly neutralizing antibodies

Monoclonal antibodies (mAbs) targeting the SARS-CoV-2 receptor-binding domain (RBD) are used to treat and prevent COVID-19. However, the rapid evolution of SARS-CoV-2 drives continuous escape from therapeutic mAbs. Therefore, the ability to identify broadly neutralizing antibodies (bnAbs) against future variants is needed. Here, we use deep mutational scanning (DMS) to predict viral RBD evolution and to select for mAbs neutralizing both existing and prospective variants. A retrospective analysis of 1,103 SARS-CoV-2 wildtype-elicited mAbs shows that this method can increase the probability of identifying effective bnAbs against the XBB.1.5 strain from 1% to 40% in an early pandemic setup. Among these bnAbs, BD55-1205 exhibited potent activity against all tested variants. Cryo-EM structural analyses revealed the receptor mimicry of BD55-1205, explaining its broad reactivity. Delivery of mRNA-LNPs encoding BD55-1205-IgG in mice resulted in ~5,000 serum NT50 against XBB.1.5, HK.3.1, and JN.1 variants. Combining bnAb identification using viral evolution prediction with the versatility of mRNA delivery technology can enable rapid development of next-generation antibody-based countermeasures against SARS-CoV-2 and potentially other pathogens with pandemic potential.

immunology↗

bioRxiv2024

Large-scale multi-omics analyses identified root-microbiome associations underlying plant nitrogen nutrition

The microbiome determines the performance and fitness of the host plant. Nevertheless, the causal interaction between host genetic variation, gene regulation and the impact of the microbiome on the host phenotype remain unknown. Here we generated 1,341 paired root transcriptome, rhizosphere microbiome and root ionome samples and performed a multi-omics analyses of the host-microbe association at the root-soil interface using 175 rapeseeds (Brassica napus L.) resequenced ecotypes at two field environments. We observed the highest statistically explained variance for root nitrogen uptake among natural ionomic variation by overall transcriptome-wide gene expression and microbial abundance variation. Moreover, we identified significant genome-wide associations for 203 highly heritable amplicon sequence variants (ASVs) at multiple genetic loci regulated by eQTL hotspots associated with nitrogen metabolism components. These associations involved a central bacterial genus (Sphingopyxis), which plays a dominant role on gene regulatory effect on its variation regulated by eQTL hotspots. In addition, we performed high-throughput bacterial cultivation from rapeseed roots and subjected Sphingopyxis to whole genome sequencing. Finally, targeted metabolite profiling and confocal imaging assays demonstrated a host-microbiome regulatory effect on Sphingopyxis established by lateral root development and plant nitrogen nutrition. In summary, our integrative approach reveals the genetic basis of host-microbiome trait associations in the transcriptional, nutritional and environmental domains and suggests that the microbiome might have causal effects on root development with implications towards the breeding of nutrient-efficient crops.

plant biology↗

bioRxiv2023

Motion Blur Microscopy

Imaging and characterizing the dynamics of cellular adhesion in blood samples is of fundamental importance in understanding biological function. In vitro microscopy methods are widely used for this task, but typically require diluting the blood with a buffer to allow for transmission of light. However whole blood provides crucial mechanical and chemical signaling cues that influence adhesion dynamics, which means that conventional approaches lack the full physiological complexity of living microvasculature. We propose to overcome this challenge by a new in vitro imaging method which we call motion blur microscopy (MBM). By decreasing the source light intensity and increasing the integration time during imaging, flowing cells are blurred, allowing us to identify adhered cells. Combined with an automated analysis using machine learning, we can for the first time reliably image cell interactions in microfluidic channels during whole blood flow. MBM provides a low cost, easy to implement alternative to intravital microscopy, the in vivo approach for studying how the whole blood environment shapes adhesion dynamics. We demonstrate the methods reproducibility and accuracy in two example systems where understanding cell interactions, adhesion, and motility is crucial--sickle red blood cells adhering to laminin, and CAR-T cells adhering to E-selectin. We illustrate the wide range of data types that can be extracted from this approach, including distributions of cell size and eccentricity, adhesion durations, trajectories and velocities of adhered cells moving on a functionalized surface, as well as correlations among these different features at the single cell level. In all cases MBM allows for rapid collection and processing of large data sets, ranging from thousands to hundreds of thousands of individual adhesion events. The method is generalizable to study adhesion mechanisms in a variety of diseases, including cancer, blood disorders, thrombosis, inflammatory and autoimmune diseases, as well as providing rich datasets for theoretical modeling of adhesion dynamics.

biophysics↗

bioRxiv2023

Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability

Existing single cell bisulfite-based DNA methylation analysis is limited by low DNA recovery, and the measurement of 5hmC at single-base resolution remains challenging. Here we present a bisulfite-free single-cell whole-genome 5mC and 5hmC profiling technique, named Cabernet, which can characterize 5mC and 5hmC at single-base resolution with high genomic coverage. Cabernet utilizes Tn5 transposome for DNA fragmentation, which enables the discrimination between different alleles for measuring hemi-methylation status. Using Cabernet, we revealed the 5mC, hemi-5mC and 5hmC dynamics during early mouse embryo development, uncovering genomic regions exclusively governed by active or passive demethylation. We show that hemi-methylation status can be used to distinguish between pre- and post-replication cells, enabling more efficient cell grouping when integrated with 5mC profile. The property of Tn5 naturally enables Cabernet to achieve high-throughput single-cell methylome profiling, where we probed mouse cortical neurons and embryonic day 7.5 (E7.5) embryos, and constructed the library for thousands of single cells at high efficiency, demonstrating its potential for analyzing complex tissues at substantially low cost. Together, we present a new way of high-throughput methylome and hydroxymethylome detection at single-cell resolution, enabling efficient analysis of epigenetic status of biological systems with complicated nature such as neurons and cancer cells. Significance StatementMost of current methylation profiling techniques rely on bisulfite treatment, which suffers low DNA recovery. The technique proposed in this study, named Cabernet, can be used to measure 5mC and 5hmC at single-base resolution with high genomic coverage. By using Tn5 transposome, hemi-methylation status can be measured and high-throughput methylome profiling can be achieved. Together, it provides an efficient way to analyze the epigenetic landscape of complicated biological systems.

genomics↗

bioRxiv2023

Antigenicity and infectivity characterization of SARS-CoV-2 BA.2.86

The recently identified SARS-CoV-2 variant, BA.2.86, which carries a substantial number of Spike mutations, has raised a global alarm. An immediate assessment of its antigenic properties and infectivity is necessary. Here, we reveal the distinct antigenicity of BA.2.86 compared with previous variants including XBB.1.5. BA.2.86 significantly evades convalescent plasma from XBB breakthrough infection (BTI) and reinfections. Key mutations that mediate the enhanced resistance include N450D, K356T, L452W, A484K, V483del, and V445H on the RBD, while BA.2.86s NTD mutations and E554K on SD1 also largely contribute. However, we found that BA.2.86 pseudovirus exhibits compromised efficiency of infecting HEK293T-hACE2 cells compared to XBB.1.5 and EG.5, which may be caused by K356T, V483del, and E554K, and could potentially limit BA.2.86s transmissibility. In sum, it appears that BA.2.86 has traded its infectivity for higher immune evasion during long-term host-viral evolution. Close attention should be paid to monitoring additional mutations that could improve BA.2.86s infectivity.

immunology↗

bioRxiv2023

Repeated Omicron infection alleviates SARS-CoV-2 immune imprinting

The continuous emergence of highly immune evasive SARS-CoV-2 variants, like XBB.1.51,2 and XBB.1.163,4, highlights the need to update COVID-19 vaccine compositions. However, immune imprinting induced by wildtype (WT)-based vaccination would compromise the antibody response to Omicron-based boosters5-9. Vaccination strategies that can counter immune imprinting are critically needed. In this study, we investigated the degree and dynamics of immune imprinting in mouse models and human cohorts, especially focusing on the role of repeated Omicron stimulation. Our results show that in mice, the efficacy of single Omicron-boosting is heavily limited by immune imprinting, especially when using variants antigenically distinct from WT, like XBB, while the concerning situation could be largely mitigated by a second Omicron booster. Similarly, in humans, we found that repeated Omicron infections could also alleviate WT-vaccination-induced immune imprinting and generate high neutralizing titers against XBB.1.5 and XBB.1.16 in both plasma and nasal mucosa. By isolating 781 RBD-targeting mAbs from repeated Omicron infection cohorts, we revealed that double Omicron exposure alleviates immune imprinting by generating a large proportion of highly matured and potent Omicron-specific antibodies. Importantly, epitope characterization using deep mutational scanning (DMS) showed that these Omicron-specific antibodies target distinct RBD epitopes compared to WT-induced antibodies, and the bias towards non-neutralizing epitopes observed in single Omicron exposures due to imprinting was largely restored after repeated Omicron stimulation, together leading to a substantial neutralizing epitope shift. Based on the DMS profiles, we identified evolution hotspots of XBB.1.5 RBD and demonstrated the combinations of these mutations could further boost XBB.1.5s immune-evasion capability while maintaining high ACE2 binding affinity. Our findings suggest the WT component should be abandoned when updating COVID-19 vaccine antigen compositions to XBB lineages, and those who havent been exposed to Omicron yet should receive two updated vaccine boosters.

immunology↗

bioRxiv2022

Extinction drives a discontinuous temporal pattern of species-area relationships in a microbial microcosm system

The species area relationship (SAR) can be a general law in ecology only if its formation mechanisms are clarified. Essentially, the SAR addresses the relationship between regional area and biodiversity, which is shaped by processes of speciation, extinction and dispersal. Since those three processes has temporal dynamics, we propose the hypothesis that the occurrence of SAR should also have temporal dynamics. Here, we designed independent closed microcosm systems, in which dispersal/speciation can be excluded/neglected, to reveal the role of extinction in shaping the temporal dynamics pattern of SAR. We find that extinction can shape SAR in this system independently. Due to the temporal dynamics of the extinction, SAR was temporally discontinuous. We also observe that small-scale extinctions modified community structure to promote ecosystem stability and shaped SAR, while mass extinction pushed the microcosm system into the next successional stage and dismissed SAR. Our result suggested that SAR could serve as an indicator of ecosystem stability; moreover, temporal discontinuity can be the explaination for many controversies in SAR studies.

ecology↗