Biology subjects

Xu, K.

Publications and source records attributed to Xu, K..

At least 145 records · Page 8Linked to original sources

bioRxiv2023

SARS-CoV-2 Omicron BA.2.86: less neutralization evasion compared to XBB sub-variants

The continual emergence and circulation of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have caused a great challenge for the coronavirus disease 2019 (COVID-19) pandemic control. Recently, Omicron BA.2.86 was identified with more than 30 amino acid changes on the spike (S) protein, compared to Omicron BA.2 or XBB.1.5. The immune evasion potential of BA.2.86 is of great concern. In this study, we evaluated the neutralizing activities of sera collected from participants and mice. Participants were divided into five groups according to their vaccination (inactivated vaccine, protein subunit vaccine ZF2001 or ZF2202-A) and infection (Omicron BF.7/BA.5.2) status. ZF2202-A is ZF2001 vaccines next-generation COVID-19 vaccine with updated bivalent Delta-BA.5 RBD-heterodimer immunogen. BALB/c mice were immunized with XBB.1.5 RBD-homodimer, BA.5-BA.2, Delta-XBB.1.5 or BQ.1.1-XBB.1.5 RBD-heterodimers protein vaccine candidates for evaluating the neutralizing responses. We found that Omicron BA.2.86 shows stronger immune evasion than BA.2 due to >30 additional mutations on S protein. Compared to XBB sub-variants, BA.2.86 does not display more resistance to the neutralizing responses induced by ZF2001-vaccination, BF.7/BA.5.2 breakthrough infection or a booster dose of ZF2202-A-vaccination. In addition, the mouse experiment results showed that BQ.1.1-XBB.1.5 RBD-heterodimer and XBB.1.5 RBD-homodimer induced high neutralizing responses against XBB sub-variants and BA.2.86, indicating that next-generation COVID-19 vaccine should be developed to enhance the protection efficacy against the circulating strains in the future.

immunology↗

bioRxiv2023

Immune Evasion, Infectivity, and Fusogenicity of SARS-CoV-2 Omicron BA.2.86 and FLip Variants

Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and the XBB-lineage variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose vaccinated and bivalent vaccinated healthcare workers, XBB.1.5-wave infected first responders, and monoclonal antibody (mAb) S309. We assessed the biology of the variant Spikes by measuring viral infectivity and membrane fusogenicity. BA.2.86 is less immune evasive compared to FLip and other XBB variants, consistent with antigenic distances. Importantly, distinct from XBB variants, mAb S309 was unable to neutralize BA.2.86, likely due to a D339H mutation based on modeling. BA.2.86 had relatively high fusogenicity and infectivity in CaLu-3 cells but low fusion and infectivity in 293T-ACE2 cells compared to some XBB variants, suggesting a potentially differences conformational stability of BA.2.86 Spike. Overall, our study underscores the importance of SARS-CoV-2 variant surveillance and the need for updated COVID-19 vaccines.

microbiology↗

bioRxiv2023

Carotenoid metabolism negatively regulates auxin-mediated root growth

Root development is essential for plant survival. The lack of carotenoid biosynthesis in the phytoene desaturase 3 (pds3) mutant results in short primary roots (PR) and reduced lateral root (LR) formation. In this study, we show that short-term inhibition of PDS by fluridone suppressed PR growth in WT, but to a lesser extent in auxin mutants. Such an inhibition of PDS activity increased endogenous indole-3-acetic acid (IAA) levels, promoted auxin signaling, and partially complemented the PR growth of auxin deficient mutant, YUCCA 3 5 7 8 9 quadruple mutant (yucQ). The exogenous application of retinaldehyde (retinal), an apocarotenoid derived from {beta}-carotene, complemented the fluridone-induced suppression of root growth, as well as the short roots of the pds3 mutant. Retinal also partially complemented the auxin-induced suppression of root growth. These results suggest that retinal may play a role in regulating root growth by modulating endogenous auxin levels. One-sentence summaryThe short-term inhibition of carotenoid biosynthesis mediates the production of {beta}-carotene-derived apocarotenoid retinal which negatively regulates auxin levels and signaling to control root growth.

plant biology↗

bioRxiv2023

Neutralization of SARS-CoV-2 EG.5/EG.5.1 by sera from ZF2001 RBD-dimer and its next-generation vaccines

SARS-CoV-2 Omicron EG.5 and EG.5.1 are surging in several areas of the world, including China. Compared with XBB.1, EG.5 contains additional mutations of F456L and S486P in the spike protein receptor binding domain (RBD) and its subvariant EG.5.1 carries a further spike mutation Q52H. The immune escape potential of EG.5/EG.5.1 is of great concern. In this study, we evaluated the neutralization activities of sera from participants who received COVID-19 inactivated vaccines, protein subunit vaccine ZF2001 or a booster vaccination of Delta-BA.5 RBD-heterodimer protein vaccine, and participants who had a breakthrough infection during a wave of BF.7/BA.5.2 circulation in December 2022. Neutralization profiles elicited by bivalent RBD-heterodimer vaccine candidates containing XBB.1.5 antigen were evaluated in a murine model. We found that EG.5 and EG.5.1 displayed similar immune evasion potential to XBB.1 and XBB.1.5. The Delta-BA.5 RBD-heterodimer booster induced higher neutralizing titers against the tested XBB subvariants, including EG.5 and EG.5.1, than breakthrough infection by BF.7 or BA.5.2. In addition, Delta-XBB.1.5 and BQ.1.1-XBB.1.5 RBD-heterodimer vaccines induced high neutralizing activities against XBB sub-variants in a murine model, suggesting that next-generation COVID-19 vaccines with updated components must be developed to enhance the protection efficacy against the circulating SARS-CoV-2 strains.

immunology↗

bioRxiv2023

Immune Evasion and Membrane Fusion of SARS-CoV-2 XBB Subvariants EG.5.1 and XBB.2.3

Immune evasion by SARS-CoV-2 paired with immune imprinting from monovalent mRNA vaccines has resulted in attenuated neutralizing antibody responses against Omicron subvariants. In this study, we characterized two new XBB variants rising in circulation -- EG.5.1 and XBB.2.3, for their ability of neutralization and syncytia formation. We determined the neutralizing antibody in sera of individuals that received a bivalent mRNA vaccine booster, BA.4/5-wave infection, or XBB.1.5-wave infection. Bivalent vaccination-induced antibodies neutralized efficiently ancestral D614G, but to a much less extent, two new EG.5.1 and XBB.2.3 variants. In fact, the enhanced neutralization escape of EG.5.1 appeared to be driven by its key defining mutation XBB.1.5-F456L. Notably, infection by BA.4/5 or XBB.1.5 afforded little, if any, neutralization against EG.5.1, XBB.2.3 and previous XBB variants -- especially in unvaccinated individuals, with average neutralizing antibody titers near the limit of detection. Additionally, we investigated the infectivity, fusion activity, and processing of variant spikes for EG.5.1 and XBB.2.3 in HEK293T-ACE2 and CaLu-3 cells but found no significant differences compared to earlier XBB variants. Overall, our findings highlight the continued immune evasion of new Omicron subvariants and, more importantly, the need to reformulate mRNA vaccines to include XBB spikes for better protection.

immunology↗

bioRxiv2023

Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes

The prion-like spread of protein aggregates is a leading hypothesis for the propagation of neurofibrillary lesions in the brain, including the spread of tau inclusions associated with Alzheimers disease. The mechanisms of cellular uptake of tau seeds and subsequent nucleated polymerization of cytosolic tau are major questions in the field, and the potential for coupling between the entry and nucleation mechanisms has been little explored. We found that in primary astrocytes, endocytosis of tau seeds leads to their accumulation in lysosomes. This in turn leads to lysosomal swelling, deacidification and recruitment of ESCRT proteins, but not Galectin-3, to the lysosomal membrane. These observations are consistent with nanoscale damage of the lysosomal membrane. Using live cell and STORM, imaging, nucleation of cytosolic tau occurs primarily at the lysosome membrane under these conditions. These data suggest that tau seeds escape from lysosomes via nanoscale damage rather than wholesale rupture, and that nucleation of cytosolic tau commences as soon as tau fibril ends emerge from the lysosomal membrane.

cell biology↗

bioRxiv2023

Harnessing extracellular vesicles for efficient siRNA delivery in vitro and in vivo

To fulfill the potential of small interference RNA (siRNA) therapeutics, diverse and efficient delivery platforms for siRNA are urgently needed. Extracellular vesicles (EVs) are endogenous, cell secreted nano-vehicles which have been explored for functional siRNA delivery, yet impurities in EVs preparation and lack of efficient siRNA loading method have been limiting its further development into clinical applications. In this work, we have achieved high quality EVs production and an siRNA loading system via EVs. The prepared EV-siRNA system was able to deliver siRNA cargo to model cell lines to silence the expression of targeted genes with high potency. Furthermore, EV-siRNA administration in a tumor xenograft model significantly inhibited tumor growth. Therefore, this study establishes an innovative and efficient EV-siRNA platform for siRNA delivery in vitro and in vivo.

cancer biology↗

bioRxiv2023

Distinct Microstructural Heterogeneities Underpin Specific Micromechanical Properties in Human ACL Femoral and Tibial Entheses

The anterior cruciate ligament (ACL) is anchored to the femur and tibia by a specialized interface tissue called the enthesis, which transfers forces in multiple directions and magnitudes without accruing fatigue damage during loading cycles over a lifetime. However, the precise structural and mechanical characteristics of the ACL femoral enthesis (FE) and tibial enthesis (TE) and their intricate interplay are unknown. In this study, we identified two ultrathin-graded mineralization regions in the FE ([~]21 m) and TE ([~]14 m), both of which exhibited distinct biomolecular compositions and mineral assembly patterns. FE interface exhibited progressively maturing hydroxyapatites (HAps), whereas minerals at the TE interface region changed from an amorphous phase (ACP) to HAps with increasing crystallinity. The LC-MS/MS results revealed that MGP protein uniquely enriched at the TE interface may be favorable for stabilizing ACP, while CLEC11A enriched at the FE interface could facilitate osteogenesis of the interface. The finite element analysis results indicated that the FE model was more resistant to shearing, while the TE model facilitated tensile resistance. It suggested that the great discrepancy in biomolecular expression and the corresponding mineral assembling heterogeneities together contributed to the superior mechanical properties of both the FE and TE models. These findings provide new perspectives regarding the management of ACL injury and the development of high-performance interface materials.

bioengineering↗

bioRxiv2023

Recombinant Ranpirnase enhances the expression of co-transfected mRNA by modulating cellular metabolic activity

As the worlds first approved prophylactic mRNA vaccine, the development of the Covid-19 mRNA vaccine marks a milestone in mRNA therapeutics. However, achieving efficient transgene expression in therapeutic applications such as protein replacement and cancer therapeutical vaccines remains challenging. This study explores the use of recombinant Ranpirnase, a small ribonuclease, as a novel expression-enhancing tool for mRNA-based therapeutics. In Balb/c mice, co-expression of Ranpirnase significantly increased transgene expression levels by 3-to 6-fold and prolonged expression duration by more than 85%, regardless of mRNA nucleoside modification status. Recombinant Ranpirnase induces a cytostatic state in host cells, stabilizing mRNA and protein transcripts, thereby enhancing transgene expression. Importantly, co-expression of Ranpirnase recombinants did not cause detectable cytotoxicity or alter the tissue distribution of transgene expression, ensuring safety and tolerability at higher translation levels. The compact size of the recombinant Ranpirnase gene allows for seamless fusion with the target gene or co-transfection with existing delivery technologies. Altogether, recombinant Ranpirnase shows promise as an expression-enhancing element in mRNA-based therapeutics, including veterinary applications.

molecular biology↗

bioRxiv2023

EnrichMiner: a biologist-oriented web server for mining biological insights from functional enrichment analysis

Functional enrichment analysis has been widely used to help researchers obtain biological insights from -omics data. However, the results are often redundant and difficult to digest. The key is developing tools to help users explore the relationships between the enriched terms, remove the redundant terms, and finally select representative terms. However, existing tools hardly make a good integration between enrichment analysis and representative terms selection in a biological-friendly manner. Here, we developed a biologist-oriented web server named EnrichMiner to provide a one-stop solution. It is a complete analysis pipeline from a gene list or a ranked gene table to published-style figures. More importantly, it provides user-friendly interfaces and rich interactive operations to help users explore the term relationships and remove redundancy. EnrichMiner has been integrated into the ExpressVis platform, and is freely accessible at https://omicsmining.ncpsb.org.cn/ExpressVis/EnrichMiner and does not require login.

bioinformatics↗

bioRxiv2023

Multidimensional super-resolution microscopy unveils nanoscale surface aggregates in the aging of FUS condensates

The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remain unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here we uncover nanoscale heterogeneities in the aging process of FUS condensates. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SMdM), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating nanoscale structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems.

biophysics↗

bioRxiv2023

An ACE2 decamer viral trap as a durable intervention solution for current and future SARS-CoV

The capacity of SARS-CoV-2 to evolve poses challenges to conventional prevention and treatment options such as vaccination and monoclonal antibodies, as they rely on viral receptor binding domain (RBD) sequences from previous strains. Additionally, animal CoVs, especially those of the SARS family, are now appreciated as a constant pandemic threat. We present here a new antiviral approach featuring inhalation delivery of a recombinant viral trap composed of ten copies of angiotensin-converting enzyme 2 (ACE2) fused to the IgM Fc. This ACE2 decamer viral trap is designed to inhibit SARS-CoV-2 entry function, regardless of viral RBD sequence variations as shown by its high neutralization potency against all known SARS-CoV-2 variants, including Omicron BQ.1, BQ.1.1, XBB.1 and XBB.1.5. In addition, it demonstrates potency against SARS-CoV-1, human NL63, as well as bat and pangolin CoVs. The multivalent trap is effective in both prophylactic and therapeutic settings since a single intranasal dosing confers protection in human ACE2 transgenic mice against viral challenges. Lastly, this molecule is stable at ambient temperature for more than twelve weeks and can sustain physical stress from aerosolization. These results demonstrate the potential of a decameric ACE2 viral trap as an inhalation solution for ACE2-dependent coronaviruses of current and future pandemic concerns.

microbiology↗

bioRxiv2023

Class I histone deacetylase complex: structure and functional correlates

Schizosaccharomyces pombe Clr6S, a class I histone deacetylase complex, functions as a zinc-dependent enzyme to remove acetyl groups from lysine residues in histone tails. We report here the cryo-EM structures of Clr6S alone and in a complex with a nucleosome. The active center, revealed at near atomic resolution, includes features important for catalysis - a water molecule coordinated by zinc, the likely nucleophile for attack on the acetyl-lysine bond, and a loop that may position the substrate for catalysis. The cryo-EM map in the presence of a nucleosome reveals multiple Clr6S-nucleosome contacts, and a high degree of relative motion of Clr6S and the nucleosome. Such flexibility may be attributed to interaction at a site in the flexible histone tail, and is likely important for function of the deacetylase, which acts at multiple sites in other histone tails.

biophysics↗

bioRxiv2023

A single amino acid substitution in MdLAZY1A dominantly impairs shoot gravitropism in Malus

Plant architecture is one of the most important factors that determines crop yield potential and productivity. In apple (Malus), genetic improvement of tree architecture has been challenging due to a long juvenile phase and their growth as complex trees composed of a distinct scion and a rootstock. To better understand the genetic control of apple tree architecture, the dominant weeping growth phenotype was investigated. We report the identification of MdLAZY1A (MD13G1122400) as the genetic determinant underpinning the Weeping (W) locus that largely controls weeping growth in Malus. MdLAZY1A is one of the four paralogs in apple that are most closely related to AtLAZY1 involved in gravitropism in Arabidopsis. The weeping allele (MdLAZY1A-W) contains a single nucleotide mutation c.584T>C that leads to a leucine to proline (L195P) substitution within a predicted transmembrane domain that co-localizes with Region III, one of the five conserved regions in LAZY1-like proteins. Subcellular localization revealed that MdLAZY1A localizes to the plasma membrane and nucleus in plant cells. Over-expressing the weeping allele in apple cultivar Royal Gala (RG) with standard growth habit impaired its gravitropic response and altered the growth to weeping-like. Suppressing the standard allele (MdLAZY1A-S) by RNA interference (RNAi) in RG similarly changed the branch growth direction to downward. Overall, the L195P mutation in MdLAZY1A is genetically causal for weeping growth, underscoring not only the crucial roles of residue L195 and Region III in MdLAZY1A-mediated gravitropic response, but also a potential DNA base editing target for tree architecture improvement in Malus and other crops.

plant biology↗

bioRxiv2023

Improving mRNA vaccine safety and efficiency with cationized lipid nanoparticle formula

The widespread use of Covid-19 mRNA vaccines has highlighted the need to address rare but concerning side effects. Systemic off-target gene expression has been identified as a primary cause of acute adverse reactions and side effects associated with nucleoside-modified mRNA vaccines. In this study, we incorporated the permanent cationic lipid Dotap component into the mRNA-LNP formula associated with the FDA-approved mRNA vaccine Comirnaty to create a novel positively charged LNP carrier for mRNA vaccine delivery. Using the optimized LNP formula to prepare SARS-Cov-2 Spike mRNA vaccines for immunogenicity testing, Balb/c mice exhibited improved immunogenicity kinetics with initial antibody titers being lower but showing a continuous upward trend, ultimately reaching levels comparable to those of control mRNA vaccines 8 weeks after boost immunization. The mRNA vaccines encapsulated in the modified LNPs have demonstrated a superior safety profile in respect to systemic delivery of LNP constituents, off-target gene expression, and the systemic pro-inflammatory stimulation. Consequently, it may represent a safer alternative of conventional mRNA-LNP vaccines.

synthetic biology↗

bioRxiv2023

Cell-type specific EWAS identifies genes involved in HIV pathogenesis andoncogenesis among people with chronic HIV infection

Epigenome-wide association studies (EWAS) of heterogenous blood cells have identified CpG sites associated with chronic HIV infection, which offer limited knowledge of cell-type specific methylation patterns associated with HIV infection. Applying a computational deconvolution method validated by capture bisulfite DNA methylation sequencing, we conducted a cell type-based EWAS and identified differentially methylated CpG sites specific for chronic HIV infection among five immune cell types in blood: CD4+ T-cells, CD8+ T-cells, B cells, Natural Killer (NK) cells, and monocytes in two independent cohorts (Ntotal=1,134). Differentially methylated CpG sites for HIV-infection were highly concordant between the two cohorts. Cell-type level meta-EWAS revealed distinct patterns of HIV-associated differential CpG methylation, where 67% of CpG sites were unique to individual cell types (false discovery rate, FDR <0.05). CD4+ T-cells had the largest number of HIV-associated CpG sites (N=1,472) compared to any other cell type. Genes harboring statistically significant CpG sites are involved in immunity and HIV pathogenesis (e.g. CX3CR1 in CD4+ T-cells, CCR7 in B cells, IL12R in NK cells, LCK in monocytes). More importantly, HIV-associated CpG sites were overrepresented for hallmark genes involved in cancer pathology (FDR<0.05) (e.g. BCL family, PRDM16, PDCD1LGD, ESR1, DNMT3A, NOTCH2). HIV-associated CpG sites were enriched among genes involved in HIV pathogenesis and oncogenesis such as Kras-signaling, interferon- and -{gamma}, TNF-, inflammatory, and apoptotic pathways. Our findings are novel, uncovering cell-type specific modifications in the host epigenome for people with HIV that contribute to the growing body of evidence regarding pathogen-induced epigenetic oncogenicity, specifically on HIV and its comorbidity with cancers.

cancer biology↗

bioRxiv2023

The role of self-fertilization in plant colony establishment

Increased rates of self-fertilization are often found in plant colonies, but the factors driving the observed higher selfing rates remain unclear. Specifically, the higher selfing rates in colonist populations may be due to 1) source populations with a higher selfing rate being more likely to successfully establish colonies (a filter effect), 2) the in situ evolution of selfing rate or a plastic selfing rate increase rescuing the colony from extinction, 3) selfing rate evolution post establishment. Using individual-based simulations and eco-evo models, we show that under both single and multiple dispersal, colony establishment may often be driven by a filter effect, due to a higher initial selfing rate and lower genetic load, which are correlated since selfing can purge deleterious mutations. Moreover, the role of the filter effect is weaker under multiple dispersal than single dispersal. The evolution of a higher selfing rate is unlikely to contribute directly to colony establishment. Although selfing rate evolution occurs during the colonization process, most of the selfing rate evolution may occur post establishment. Plasticity in selfing rates is more effective in facilitating colony establishment than the evolution of selfing.

evolutionary biology↗

bioRxiv2023

Effects of selfing on speciation through the accumulation of Dobzhansky-Muller incompatibilities

Phylogenetic analyses suggest that self-compatible lineages have higher speciation rates than self-incompatible lineages. However, the effects of selfing on speciation remain unclear. Although a selfing population can resist gene flow from other populations, selfing may increase gene flow from a focal population to other populations. This study investigates the effects of selfing rates of two populations on the waiting time to speciation through the accumulation of Dobzhansky-Muller incompatibilities (DMI). Generally, a higher mean selfing rate of two populations facilitates speciation when incompatibility-controlling alleles are recessive and are weakly selected, and when gene flow is mainly through pollen dispersal instead of seed dispersal. However, the selfing rate difference between two populations can retard speciation, especially when the selfing rate of immigrants remains unchanged after migration. When the selfing rates of two populations differ, speciation may be fastest when the mean selfing rate is intermediate. Given that selfing rates often vary among conspecific populations in plant species, the results indicate that lineages with higher mean selfing rates may not necessarily have higher rates of speciation through the accumulation of DMI, and also call for an estimation of the dependency of speciation rates on selfing rates.

evolutionary biology↗