Biology subjects

Huang, Y.

Publications and source records attributed to Huang, Y..

At least 739 records · Page 41Linked to original sources

bioRxiv2021

Striking Antibody Evasion Manifested by the Omicron Variant of SARS-CoV-2

The Omicron (B.1.1.529) variant of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) was only recently detected in southern Africa, but its subsequent spread has been extensive, both regionally and globally1. It is expected to become dominant in the coming weeks2, probably due to enhanced transmissibility. A striking feature of this variant is the large number of spike mutations3 that pose a threat to the efficacy of current COVID-19 (coronavirus disease 2019) vaccines and antibody therapies4. This concern is amplified by the findings from our study. We found B.1.1.529 to be markedly resistant to neutralization by serum not only from convalescent patients, but also from individuals vaccinated with one of the four widely used COVID-19 vaccines. Even serum from persons vaccinated and boosted with mRNA-based vaccines exhibited substantially diminished neutralizing activity against B.1.1.529. By evaluating a panel of monoclonal antibodies to all known epitope clusters on the spike protein, we noted that the activity of 17 of the 19 antibodies tested were either abolished or impaired, including ones currently authorized or approved for use in patients. In addition, we also identified four new spike mutations (S371L, N440K, G446S, and Q493R) that confer greater antibody resistance to B.1.1.529. The Omicron variant presents a serious threat to many existing COVID-19 vaccines and therapies, compelling the development of new interventions that anticipate the evolutionary trajectory of SARS-CoV-2.

microbiology↗

bioRxiv2021

Isolation and comparative analysis of antibodies that broadly neutralize sarbecoviruses

The devastation caused by SARS-CoV-2 has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses and thus its promise as an agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses, but also uncovered a new antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine. One sentence summaryA monoclonal antibody that neutralizes or binds all sarbecoviruses tested and represents a reproducible antibody class.

microbiology↗

bioRxiv2021

Cell transcriptomic atlas of the non-human primate Macaca fascicularis

Studying tissue composition and function in non-human primates (NHP) is crucial to understand the nature of our own species. Here, we present a large-scale single-cell and single-nucleus transcriptomic atlas encompassing over one million cells from 43 tissues from the adult NHP Macaca fascicularis. This dataset provides a vast, carefully annotated, resource to study a species phylogenetically close to humans. As proof of principle, we have reconstructed the cell-cell interaction networks driving Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases and intersected our data with human genetic disease orthologous coordinates to identify both expected and unexpected associations. Our Macaca fascicularis cell atlas constitutes an essential reference for future single-cell studies in human and NHP.

cell biology↗

bioRxiv2021

Production of novel Spike truncations in Chinese hamster ovary cells

SARS-CoV-2 Spike is a key protein that mediates viral entry into cells and elicits antibody responses. Its importance in infection, diagnostics, and vaccinations has created a large demand for purified Spike for clinical and research applications. Spike is difficult to express, prompting modifications to the protein and expression platforms to improve yields. Alternatively, Spike receptor binding domain (RBD) is commonly expressed with higher titers, though it has lower sensitivity in serological assays. Here, we improve transient Spike expression in Chinese hamster ovary (CHO) cells. We demonstrate that Spike titers increase significantly over the expression period, maximizing at 14 mg/L at day 7. In comparison, RBD titers peak at 54 mg/L at day 3. Next, we develop 8 Spike truncations (T1-T8) in pursuit of a truncation with high expression and antibody binding. The truncations T1 and T4 express at 130 mg/L and 73 mg/L, respectively, which are higher than our RBD titers. Purified proteins were evaluated for binding to antibodies raised against full-length Spike. T1 has similar sensitivity as Spike against a monoclonal antibody and even outperforms Spike for a polyclonal antibody. These results suggest T1 is a promising Spike alternative for use in various applications.

bioengineering↗

bioRxiv2021

Comparing management strategies for conserving communities of climate-threatened species with a stochastic metacommunity model

Many species are shifting their ranges to keep pace with climate change, but habitat fragmentation and limited dispersal could impede these range shifts. In the case of climate-vulnerable foundation species such as tropical reef corals and temperate forest trees, such limitations might put entire communities at risk of extinction. Restoring connectivity through corridors, stepping-stones, or enhanced quality of existing patches could prevent the extinction of several species, but dispersal-limited species might not benefit if other species block their dispersal. Alternatively, managers might relocate vulnerable species between habitats through assisted migration, but this is generally a species-by-species approach. To evaluate the relative efficacy of these strategies, we simulated the climate-tracking of species in randomized competitive metacommunities with alternative management interventions. We found that corridors and assisted migration were the most effective strategies at reducing extinction. Assisted migration was especially effective at reducing the extinction likelihood for short-dispersing species, but it often required moving several species repeatedly. Assisted migration was more effective at reducing extinction in environments with higher stochasticity, and corridors were more effective at reducing extinction in environments with lower stochasticity. We discuss the application of these approaches to an array of systems ranging from tropical corals to temperate forests.

ecology↗

bioRxiv2021

Genome Assembly and Population Resequencing Reveal the Geographical Divergence of 'Shanmei'(Rubus corchorifolius)

Rubus corchorifolius ( Shanmei or mountain berry, 2n =14) is widely distributed in China, and its fruit has high nutritional and medicinal values. Here, we report a high-quality chromosome-scale genome assembly of Shanmei, with a size of 215.69 Mb and encompassing 26,696 genes. Genome comparisons among Rosaceae species show that Shanmei and Fupenzi (Rubus chingii Hu) are most closely related, and then is blackberry (Rubus occidentalis). Further resequencing of 101 samples of Shanmei collected from four regions in provinces of Yunnan, Hunan, Jiangxi, and Sichuan in South China reveals that the Hunan population of Shanmei possesses the highest diversity and may represent the relatively more ancestral population. Moreover, the Yunnan population undergoes strong selection based on nucleotide diversity, linkage disequilibrium, and the historical effective population size analyses. Furthermore, genes from candidate genomic regions that show strong divergence are significantly enriched in flavonoid biosynthesis and plant hormone signal transduction, indicating the genetic basis of adaptation of Shanmei to the local environments. The high-quality genome sequences and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

genomics↗

bioRxiv2021

NucleoMap: a computational tool for identifying nucleosomes in ultra-high resolution contact maps

1Although poorly positioned nucleosomes are ubiquitous in the prokaryote genome, they are difficult to identify with existing nucleosome identification methods. Recently available enhanced high-throughput chromatin conformation capture techniques such as Micro-C, DNase Hi-C, and Hi-CO characterize nucleosome-level chromatin proximity, probing the positions of mono-nucleosomes and the spacing between nucleosome pairs at the same time, enabling profiling of nucleosomes in poorly positioned regions. Here we develop a novel computational approach, NucleoMap, to identify nucleosome positioning from ultra-high resolution chromatin contact maps. By integrating nucleosome binding preferences, read density, and pairing information, NucleoMap precisely locates nucleosomes in both eukaryotic and prokaryotic genomes and outperforms existing nucleosome identification methods in precision and recall. We rigorously characterize genome-wide association in eukaryotes between the spatial organization of mono-nucleosomes and their corresponding histone modifications, protein binding activities, and higher-order chromatin functions. We also predict two tetra-nucleosome folding structures in human embryonic stem cells using machine learning methods and analysis their distribution at different structural and functional regions. Based on the identified nucleosomes, nucleosome contact maps are constructed, reflecting the inter-nucleosome distances and preserving the original datas contact distance profile.

bioinformatics↗

bioRxiv2021

Low frequency somatic copy number alterations in normal human lymphocytes revealed by large scale single-cell whole genome profiling

Genomic-scale somatic copy number alterations in healthy humans are difficult to investigate because of low occurrence rates and the structural variations stochastic natures. Using a Tn5-transposase assisted single-cell whole genome sequencing method, we sequenced over 20,000 single lymphocytes from 16 individuals. Then, with the scale increased to a few thousand single cells per individual, we found that about 7.5% of the cells had large-size copy number alterations. Trisomy 21 was the most prevalent aneuploid event among all autosomal copy number alterations, while monosomy X occurred most frequently in over-30-year-old females. In the monosomy X single cells from individuals with phased genomes and identified X-inactivation ratios in bulk, the inactive X Chromosomes were lost more often than were the active ones.

genomics↗

bioRxiv2021

The Stickland fermentation precursor trans-4-hydroxyproline differentially impacts the metabolism of Clostridioides difficile and commensal Clostridia

An intact gut microbiota confers colonization resistance against Clostridioides difficile through a variety of mechanisms, likely including competition for nutrients. Recently, proline was identified as an important environmental amino acid that C. difficile uses to support growth and cause significant disease. A post-translationally modified form, trans-4-hydroxyproline, is highly abundant in collagen, which is degraded by host proteases in response to C. difficile toxin activity. The ability to dehydrate trans-4-hydroxyproline via the HypD glycyl radical enzyme is wide-spread amongst gut microbiota, including C. difficile and members of the commensal Clostridia, suggesting that this amino acid is an important nutrient in the host environment. Therefore, we constructed a C. difficile {Delta}hypD mutant and found that it was modestly impaired in fitness in a mouse model of infection, and was associated with an altered microbiota when compared to mice challenged with the wild type strain. Changes in the microbiota between the two groups were largely driven by members of the Lachnospiraceae family and the Clostridium genus. We found that C. difficile and type strains of three commensal Clostridia had significant alterations to their metabolic gene expression in the presence of trans-4-hydroxyproline in vitro. The proline reductase (prd) genes were elevated in C. difficile, consistent with the hypothesis that trans-4-hydroxyproline is used by C. difficile to supply proline for fermentation. Similar transcripts were also elevated in some commensal Clostridia tested, although each strain responded differently. This suggests that the uptake and utilization of other nutrients by the commensal Clostridia may be affected by trans-4-hydroxyproline metabolism, highlighting how a common nutrient may be a signal to each organism to adapt to a unique niche. Further elucidation of the differences between them in the presence of hydroxyproline and other key nutrients will be important to determining their role in nutrient competition against C. difficile.

microbiology↗

bioRxiv2021

Effects of tendon viscoelasticity in the distribution of forces over sutures in a model tendon-to-bone repair

Tears to the rotator cuff often require surgical repair. These repairs often culminate in re-tearing when sutures break through the tendon in the weeks following repair. Although numerous studies have been performed to identify suturing strategies that reduce this risk by balancing forces across sutures, none have accounted for how the viscoelastic nature of tendon influences load sharing. With the aim of providing insight into this problem, we studied how tendon viscoelasticity, tendon stiffness, and suture anchor spacing affect this balancing of forces across sutures. Results from a model of a three-row sutured re-attachment demonstrated that optimized distributions of suture stiffnesses and of the spacing of suture anchors can balance the forces across sutures to within a few percent, even when accounting for tendon viscoelasticity. Non-optimized distributions resulted in concentrated force, typically in the outermost sutures. Results underscore the importance of accounting for viscoelastic effects in the design of tendon to bone repairs.

bioengineering↗

bioRxiv2021

Salmonella Outer Membrane Vesicles contain tRNA Fragments (tRFs) that Inhibit Bacteriophage P22 infection

Salmonella Outer Membrane Vesicles (OMVs) were recently shown to inhibit P22 bacteriophage infection. Furthermore, despite there being several published reports now independently describing (1) the marked prevalence of tRFs within secreted vesicle transcriptomes and (2) roles for specific tRFs in facilitating/inhibiting viral replication, there have been no examinations of the effects of vesicle-secreted tRFs on viral infection reported to date. Notably, while specific tRFs have been reported in a number of bacteria, the tRFs expressed by salmonellae have not been previously characterized. As such, we recently screened small RNA-seq datasets for the presence of recurrent, specifically excised tRFs and identified 31 recurrent, relatively abundant tRFs expressed by Salmonella enterica serovar Typhimurium (SL1344). Whats more, we find S. Typhimurium OMVs contain significant levels of tRFs highly complementary to known Salmonella enterica-infecting bacteriophage with 17 of 31 tRFs bearing marked complementarity to at least one known Salmonella enterica-infecting phage (averaging 97.4% complementarity over 22.9 nt). Most notably, tRNA-Thr-CGT-1-1, 44-73, bears 100% sequence complementary over its entire 30 nt length to 29 distinct, annotated Salmonella enterica-infecting bacteriophage including P22. Importantly, we find inhibiting this tRF in secreted OMVs improves P22 infectivity in a dose dependent manner whereas raising OMV tRF levels conversely inhibits P22 infectivity. Furthermore, we find P22 phage pre-incubation with OMVs isolated from naive, control SL1344 S. Typhimurium, successfully rescues the ability of S. Typhimurium transformed with a specific tRNA-Thr-CGT-1-1, 44-73 tRF inhibitor to defend against P22. Collectively, these experiments confirm tRFs secreted in S. Typhimurium OMVs are directly involved with and required for the ability of OMVs to defend against bacteriophage predation. As we find the majority of OMV tRFs are highly complementary to an array of known Salmonella enterica-infecting bacteriophage, we suggest OMV tRFs may primarily function as a broadly acting, previously uncharacterized innate antiviral defense.

microbiology↗

bioRxiv2021

Integrated analyses of the single-cell ATAC-seq and RNA-seq reveal the epigenetic landscape of human ovarian aging

Studying the molecular mechanisms of ovarian aging is crucial for understanding the age-related fertility issues in females. Recently, a single-cell transcriptomic roadmap of ovarian aging based on non-human primates revealed the molecular signatures of the oocytes at different developmental stages. Herein, we present the first epigenetic landscape of human ovarian aging, through an integrated analysis of the single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) and single-cell RNA-seq. We depicted the transcriptional profiles and chromatin accessibility of the ovarian tissues isolated from old (n=4) and young (n=2) donors. The unsupervised clustering of data revealed seven distinct cell populations in the ovarian tissues and six subtypes of oocytes, which could be distinguished by age difference. Further analysis of the scATAC-seq data from the young and old oocytes revealed that the interaction between the Notch signaling pathway and AP-1 family transcription factors may crucially determine oocyte aging. Finally, a machine-learning algorithm was applied to calculate the optimal model based on the single-cell dataset for predicting oocyte aging, which exhibited excellent accuracy with a cross-validated area under the receiver operating characteristics score of 0.99. In summary, this study provides a comprehensive understanding of human ovarian aging at both the transcriptomic and epigenetic levels, based on an integrated analysis of large-scale single-cell datasets. We believe our results will shed light on the discovery of potential therapeutic targets or diagnostic markers for age-related ovarian disorders.

genetics↗

bioRxiv2021

Domestic pigs experimentally infected with Mycobacterium bovis and Mycobacterium tuberculosis exhibit different disease outcomes

Domestic pigs share many similarities with humans in their pulmonary anatomy, physiology, and immunology. Accordingly, pigs have been shown to be valuable models to study human tuberculosis (TB). Here we examined the outcome of disease in domestic pigs challenged via two different routes with either the human-adapted TB bacillus Mycobacterium tuberculosis or the zoonotic bovine TB bacillus M. bovis in head-to-head comparisons. We found that pigs challenged intravenously with M. bovis AF2122/97 exhibited severe morbidity and rapid onset of mortality, accompanied by higher tissue bacterial burden and necrosis compared to pigs challenged similarly with M. tb Erdman. Concordantly, pigs challenged with aerosolized M. bovis AF2122/97 exhibited reduced weight gain and more severe pathology than pigs challenged similarly with M. tb Erdman. Moreover, pigs aerosol-challenged with M. bovis AF2122/97 exhibited a spectrum of granulomatous lesions ranging from small well-contained granulomas to caseous-necrotic lesions mimicking active TB disease in humans. In contrast, pigs aerosol-challenged with M. tb Erdman exhibited arrested granuloma development. Irrespective of challenge dose and pathological outcome however, peripheral IFN-{gamma} responses were similar in both M. bovis AF2122/97 and M. tb Erdman challenged pigs. This study demonstrates domestic pigs can support infections with M. bovis and M. tb and develop pathology similar to what is observed in humans. And although M. bovis AF2122/97 appears to be more virulent than M. tb Erdman, both strains can be used to model TB in domestic pigs, depending on whether one wishes to recapitulate either acute and active TB or latent TB infections.

pathology↗

bioRxiv2021

Prevalent sex ratio bias in Caenorhabditis nematodes

Although equal sex ratio is ubiquitous and represents an equilibrium in evolutionary theory, biased sex ratios are predicted for certain local conditions. Cases of sex ratio bias have been mostly reported for single species, but little is known about its evolution above the species level. Here, we surveyed progeny sex ratios in 23 species of the nematode genus Caenorhabditis, including 19 for which we tested multiple strains. For the species with multiple strains, 5 species had female-biased and 2 had non-biased sex ratios in all strains, respectively. The other 12 species showed polymorphic sex ratios across strains. Female-biased sex ratios could be due to sperm competition whereby X-bearing sperm outcompete nullo-X sperm during fertilization. In this model, when sperm are limited allowing all sperm to be used, sex ratios are expected to be equal. However, in assays limiting mating to a few hours, most strains showed similarly biased sex ratios compared to unlimited mating experiments, except that one C. becei strain showed significantly reduced female bias compared to unlimited mating. Our study shows frequent polymorphism in sex ratios within Caenorhabditis species and that sperm competition alone cannot explain the sex ratio bias.

evolutionary biology↗

bioRxiv2021

A hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis

How cell size and number are determined during organ development remains a fundamental question in cell biology. Here, we identified a GRAS family transcription factor, called SCARECROW-LIKE28 (SCL28), with a critical role in determining cell size in Arabidopsis. SCL28 is part of a transcriptional regulatory network downstream of the central MYB3Rs that regulate G2 to M phase cell cycle transition. We show that SCL28 forms a dimer with the AP2-type transcription factor, AtSMOS1, which defines the specificity for promoter binding and directly activates transcription of a specific set of SIAMESE-RELATED (SMR) family genes, encoding plant-specific inhibitors of cyclin-dependent kinases and thus inhibiting cell cycle progression at G2 and promoting the onset of endoreplication. Through this dose-dependent regulation of SMR transcription, SCL28 quantitatively sets the balance between cell size and number without dramatically changing final organ size. We propose that this hierarchical transcriptional network constitutes a cell cycle regulatory mechanism that allows to adjust cell size and number to attain robust organ growth.

plant biology↗

bioRxiv2021

A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses

The repeated emergence of highly pathogenic human coronaviruses as well as their evolving variants highlight the need to develop potent and broad-spectrum antiviral therapeutics and vaccines. By screening monoclonal antibodies (mAbs) isolated from COVID-19-convalescent patients, we found one mAb, 2-36, with cross-neutralizing activity against SARS-CoV. We solved the cryo-EM structure of 2-36 in complex with SARS-CoV-2 or SARS-CoV spike, revealing a highly conserved epitope in the receptor-binding domain (RBD). Antibody 2-36 neutralized not only all current circulating SARS-CoV-2 variants and SARS-COV, but also a panel of bat and pangolin sarbecoviruses that can use human angiotensin-converting enzyme 2 (ACE2) as a receptor. We selected 2-36-escape viruses in vitro and confirmed that K378T in SARS-CoV-2 RBD led to viral resistance. Taken together, 2-36 represents a strategic reserve drug candidate for the prevention and treatment of possible diseases caused by pre-emergent SARS-related coronaviruses. Its epitope defines a promising target for the development of a pan-sarbecovirus vaccine.

microbiology↗

bioRxiv2021

Intercellular alignment of apical-basal polarity coordinates tissue homeostasis and growth

Maintaining apicobasal polarity (ABP) is crucial for epithelial integrity and homeostasis during tissue development. Although recent studies have greatly advanced our understanding of intracellular mechanisms underlying ABP establishment, it remains largely unknown how the ABP is regulated at the tissue level. Here, we address intercellular mechanisms coordinating ABP using the Drosophila wing imaginal disc. By studying Scribble, a key ABP determinant, we show that ABP is regulated through intercellular alignment, which takes place either progressively or regressively in a context-dependent manner. Cells expressing wild type scribble progressively restore ABP in scribble hypomorphic mutant cells. In contrast, cells with conditional scribble knockdown instigate the regressive loss of polarity in abutting wild type cells. Our data reveal that genetic and physical interactions between Scribble, Septate junction complex and -Catenin appear to be key for sustaining intercellular network of ABP. Taken together, our findings indicate that the intercellular relay of the status of ABP contributes to the robustness of polarity across the tissue.

developmental biology↗

bioRxiv2021

Neural mechanisms underlying anxiety-related deficits of attentional inhibition: direct ERP evidence from the Pd component

Behavioral evidence shows that anxious individuals tend to be distracted by irrelevant stimulation not only for threat-related stimuli but also for non-emotional neutral stimuli. These findings suggest that anxious individuals may have a general impairment of attentional control, especially inhibition function. However, the neural mechanism underlying the anxiety-related impairment in attentional control is unclear. Here, in a visual search task with geometric stimuli, we examined attentional processing of the non-emotional neutral distractor on participants with different levels of anxiety, using the event-related-potential (ERP) indices of attentional selection (N2 posterior contralateral [N2pc]) and top-down inhibition (distractor positivity [Pd]). We found that distractor-evoked Pd amplitudes were negatively correlated with trait-anxiety scores, i.e., the higher the level of anxiety, the worse the ability of attentional inhibition. In contrast, the amplitudes of distractor-evoked N2pc did not vary with anxiety levels, suggesting that trait-anxiety level does not affect stimulus-driven attentional capture. We also observed attentional processing of target stimuli and found that the peak latency of target-evoked N2pc was delayed as anxiety levels rise, suggesting that anxiety impairs the efficiency of top-down attentional selection of the target. The present study provides direct neurophysiological evidence for general anxiety-related impairment of attentional control.

neuroscience↗