Biology subjects

Yang, P.

Publications and source records attributed to Yang, P..

At least 127 records · Page 7Linked to original sources

bioRxiv2022

Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events

The current pandemic of COVID-19 is fueled by more infectious emergent Omicron variants. Ongoing concerns of emergent variants include possible recombinants, as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral pathogens. Although recombination events among SARS-CoV-1 and MERS-CoV were well-documented, it has been difficult to detect the recombination signatures in SARS-CoV-2 variants due to their high degree of sequence similarity. In this study, we identified diverse recombination events between two Omicron major subvariants (BA.1 and BA.2) and other variants of concern (VOCs) and variants of interest (VOIs), suggesting that co-infection and subsequent genome recombination play important roles in the ongoing evolution of SARS-CoV-2. Through scanning high-quality completed Omicron spike gene sequences, eighteen core mutations of BA.1 variants (frequency >99%) were identified (eight in NTD, five near the S1/S2 cleavage site, and five in S2). BA.2 variants share three additional amino acid deletions with the Alpha variants. BA.1 subvariants share nine common amino acid mutations (three more than BA.2) in the spike protein with most VOCs, suggesting a possible recombination origin of Omicron from these VOCs. There are three more Alpha-related mutations (del69-70, del144) in BA.1 than BA.2, and therefore BA.1 may be phylogenetically closer to the Alpha variant. Revertant mutations are found in some dominant mutations (frequency >95%) in the BA.1 subvariant. Most notably, multiple additional amino acid mutations in the Delta spike protein were also identified in the recently emerged Omicron isolates, which implied possible recombination events occurred between the Omicron and Delta variants during the on-going pandemic. Monitoring the evolving SARS-CoV-2 genomes especially for recombination is critically important for recognition of abrupt changes to viral attributes including its epitopes which may call for vaccine modifications.

microbiology↗

bioRxiv2022

Single-cell analysis reveals a pathogenic cellular module associated with early allograft dysfunction after liver transplantation

Liver transplantation (LT) is the standard therapy for patients with end-stage liver disease. Although LT technology has markedly progressed in recent decades, early allograft dysfunction (EAD) exacerbates the current organ shortage and impacts the prognosis of recipients. However, understanding of cellular characteristics and molecular events contributing to EAD is limited. Here, a large single-cell transcriptomic atlas of transplanted livers collected from four patients is constructed, including 58,243 cells, which are classified into 14 cell types and 29 corresponding subtypes with known markers, including liver parenchymal cells and non-parenchymal cells with different cell states. Compared to the pre-LT livers, graft remodeling is noted in the post-LT livers, with marked changes in several immune cells in either cell ratios or cell states. More importantly, an EAD-associated pathogenic cellular module is identified, consisting of mucosal-associated invariant T (MAIT) cells, granzyme B (GZMB)+ granzyme K (GZMK)+ natural killer (NK) cells, and S100A12+ neutrophils, all of which are elevated in EAD patient after LT. This cellular module is also verified in two independent datasets. Collectively, these results reveal the cellular characteristics of transplanted livers and the EAD-associated pathogenic cellular module at the single-cell level, offering new insights into the EAD occurrence after LT.

genomics↗

bioRxiv2022

SARS-CoV-2 invades cognitive centers of the brain and induces Alzheimer's-like neuropathology

Major cell entry factors of SARS-CoV-2 are present in neurons; however, the neurotropism of SARS-CoV-2 and the phenotypes of infected neurons are still unclear. Acute neurological disorders occur in many patients, and one-third of COVID-19 survivors suffer from "brain diseases". Here, we show that SARS-CoV-2 invades the brains of five patients with COVID-19 and Alzheimers, autism, frontotemporal dementia or no underlying condition by infecting neurons and other cells in the cortex. SARS-CoV-2 induces or enhances Alzheimers-like neuropathology with manifestations of {beta}-amyloid aggregation and plaque formation, tauopathy, neuroinflammation and cell death. SARS-CoV-2 infects mature but not immature neurons derived from inducible pluripotent stem cells from healthy and Alzheimers individuals through its receptor ACE2 and facilitator neuropilin-1. SARS-CoV-2 triggers Alzheimers-like gene programs in healthy neurons and exacerbates Alzheimers neuropathology. A gene signature defined as an Alzheimers infectious etiology is identified through SARS-CoV-2 infection, and silencing the top three downregulated genes in human primary neurons recapitulates the neurodegenerative phenotypes of SARS-CoV-2. Thus, SARS-CoV-2 invades the brain and activates an Alzheimers-like program.

neuroscience↗

bioRxiv2022

scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

Recent advances in single-cell technologies enable scientists to measure molecular data at high-resolutions and hold the promise to substantially improve clinical outcomes through personalised medicine. However, due to a lack of tools specifically designed to represent each sample (e.g. patient) from the collection of cells sequenced, disease outcome prediction on the sample level remains a challenging task. Here, we present scFeatures, a tool that creates interpretable molecular representation of single-cell and spatial data using 17 types of features motivated by current literature. The feature types span across six distinct categories including cell type proportions, cell type specific gene expressions, cell type specific pathway scores, cell type specific cell-cell interaction scores, overall aggregated gene expressions and spatial metrics. By generating molecular representation using scFeatures for single-cell RNA-seq, spatial proteomic and spatial transcriptomic data, we demonstrate that different types of features are important for predicting different disease outcomes in different datasets and the downstream analysis of features uncover novel biological discoveries.

bioinformatics↗

bioRxiv2022

Spatially resolved single-cell deconvolution of bulk RNA-seq using Bulk2Space

Uncovering the tissue molecular architecture at single-cell resolution could help better understand organisms biological and pathological processes. However, bulk RNA-seq can only measure gene expression in cell mixtures, without revealing the transcriptional heterogeneity and spatial patterns of single cells. Herein, we introduce Bulk2Space (https://github.com/ZJUFanLab/bulk2space), a deep learning framework-based spatial deconvolution algorithm that can simultaneously disclose the spatial and cellular heterogeneity of bulk RNA-seq data using existing single-cell and spatial transcriptomics references. The use of bulk transcriptomics to validate Bulk2Space unveils, in particular, the spatial variance of immune cells in different tumor regions, the molecular and spatial heterogeneity of tissues during inflammation-induced tumorigenesis, and spatial patterns of novel genes in different cell types. Moreover, Bulk2Space is utilized to perform spatial deconvolution analysis on bulk transcriptome data from two different mouse brain regions derived from our in-house developed sequencing approach termed Spatial-seq. We have not only reconstructed the hierarchical structure of the mouse isocortex but also further annotated cell types that were not identified by original methods in the mouse hypothalamus.

bioinformatics↗

bioRxiv2021

Structural and functional characterizations of altered infectivity and immune evasion of SARS-CoV-2 Omicron variant

The SARS-CoV-2 Omicron with increased fitness is spreading rapidly worldwide. Analysis of cryo-EM structures of the Spike (S) from Omicron reveals amino acid substitutions forging new interactions that stably maintain an "active" conformation for receptor recognition. The relatively more compact domain organization confers improved stability and enhances attachment but compromises the efficiency of viral fusion step. Alterations in local conformation, charge and hydrophobic microenvironments underpin the modulation of the epitopes such that they are not recognized by most NTD- and RBD-antibodies, facilitating viral immune escape. Apart from already existing mutations, we have identified three new immune escape sites: 1) Q493R, 2) G446S and 3) S371L/S373P/S375F that confers greater resistance to five of the six classes of RBD-antibodies. Structure of the Omicron S bound with human ACE2, together with analysis of sequence conservation in ACE2 binding region of 25 sarbecovirus members as well as heatmaps of the immunogenic sites and their corresponding mutational frequencies sheds light on conserved and structurally restrained regions that can be used for the development of broad-spectrum vaccines and therapeutics.

biophysics↗

bioRxiv2021

A subset of Memory B-derived antibody repertoire from 3-dose vaccinees is ultrapotent against diverse and highly transmissible SARS-CoV-2 variants, including Omicron

Omicron, the most heavily mutated SARS-CoV-2 variant so far, is highly resistant to neutralizing antibodies, raising unprecedented concerns about the effectiveness of antibody therapies and vaccines. We examined whether sera from individuals who received two or three doses of inactivated vaccine, could neutralize authentic Omicron. The seroconversion rates of neutralizing antibodies were 3.3% (2/60) and 95% (57/60) for 2- and 3-dose vaccinees, respectively. For three-dose recipients, the geometric mean neutralization antibody titer (GMT) of Omicron was 15, 16.5-fold lower than that of the ancestral virus (254). We isolated 323 human monoclonal antibodies derived from memory B cells in 3-dose vaccinees, half of which recognize the receptor binding domain (RBD) and show that a subset of them (24/163) neutralize all SARS-CoV-2 variants of concern (VOCs), including Omicron, potently. Therapeutic treatments with representative broadly neutralizing mAbs individually or antibody cocktails were highly protective against SARS-CoV-2 Beta infection in mice. Atomic structures of the Omicron S in complex with three types of all five VOC-reactive antibodies defined the binding and neutralizing determinants and revealed a key antibody escape site, G446S, that confers greater resistance to one major class of antibodies bound at the right shoulder of RBD through altering local conformation at the binding interface. Our results rationalize the use of 3-dose immunization regimens and suggest that the fundamental epitopes revealed by these broadly ultrapotent antibodies are a rational target for a universal sarbecovirus vaccine. One sentence summaryA sub-set of antibodies derived from memory B cells of volunteers vaccinated with 3 doses of an inactivated SARS-CoV-2 vaccine work individually as well as synergistically to keep variants, including Omicron, at bay.

microbiology↗

bioRxiv2021

The first sheep graph pan-genome reveals the spectrum of structural variations and their effects on different tail phenotypes

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here, we assembled 26 haplotype-resolved genome assemblies from 13 genetically diverse sheep using PacBio HiFi sequencing. We constructed a graph-based ovine pan-genome and discovered 142,422 biallelic insertions and deletions, 7,028 divergent alleles and 13,419 multiallelic variations. We then used a graph-based approach to genotype the biallelic SVs in 684 individuals from 45 domestic breeds and two wild species. Integration with RNA-seq data allows to identify candidate expression-associated SVs. We demonstrate a direct link of SVs and phenotypes by localizing the putative causative insertion in HOXB13 gene responsible for the long-tail trait and identifying multiple large SVs associated with the fat-tail. Beyond generating a benchmark resource for ovine structural variants, our study highlights that animal genetic research will greatly benefit from using a pan-genome graph rather than a single reference genome.

genomics↗

bioRxiv2021

Reciprocity between retrograde signal and putative metalloprotease reconfigures plastidial metabolism and structure

Reconfiguration of the plastidial proteome in response to environmental inputs is central to readjustment of its metabolic and structural states. This is necessary for the functionality of this metabolic hub, and the maintenance of organismal integrity. This report establishes the role of the plastidial retrograde signaling metabolite, MEcPP, in increasing the abundance of the putative plastidial metalloprotease (VIR3), and the ensuing decline of VIR3 target enzymes, ascorbate peroxidase and glyceraldehyde 3-phophate dehydrogenase B. The decreased abundance of these enzymes is linked to increased levels of their substrates: H2O2, an elicitor of salicylic acid production and stromule formation; and G3P the substrate for MEcPP synthesis. High-light treatment of wild type plants recapitulated the VIR3-associated reconfiguration of the plastidial metabolic and structural states. These results identify a previously unrecognized link between the stress-induced plastidial retrograde signaling metabolite and a putative zinc-binding metalloprotease. Moreover, the data reveal that the reciprocity between these two components, results in the reconfiguration of the metabolic and structural states of the plastid, deemed necessary to maintain cellular integrity and to shape adaptive responses.

plant biology↗

bioRxiv2021

pGlycoQuant with a deep residual network for precise and minuscule-missing-value quantitative glycoproteomics enabling the functional exploration of site-specific glycosylation

Interpreting large-scale glycoproteomic data for intact glycopeptide identification has been tremendously advanced by software tools. However, software tools for quantitative analysis of intact glycopeptides remain lagging behind, which greatly hinders exploring the differential expression and functions of site-specific glycosylation in organisms. Here, we report pGlycoQuant, a generic software tool for accurate and convenient quantitative intact glycopeptide analysis, supporting both primary and tandem mass spectrometry quantitation for multiple quantitative strategies. pGlycoQuant enables intact glycopeptide quantitation with very low missing values via a deep residual network, thus greatly expanding the quantitative function of several powerful search engines, currently including pGlyco 2.0, pGlyco3, Byonic and MSFragger-Glyco. The pGlycoQuant-based site-specific N-glycoproteomic study conducted here quantifies 6435 intact N-glycopeptides in three hepatocellular carcinoma cell lines with different metastatic potentials and, together with in vitro molecular biology experiments, illustrates core fucosylation at site 979 of the L1 cell adhesion molecule (L1CAM) as a potential regulator of HCC metastasis. pGlycoQuant is freely available at https://github.com/expellir-arma/pGlycoQuant/releases/. We have demonstrated pGlycoQuant to be a powerful tool for the quantitative analysis of site-specific glycosylation and the exploration of potential glycosylation-related biomarker candidates, and we expect further applications in glycoproteomic studies.

systems biology↗

bioRxiv2021

De novo assembly of 20 chickens reveals the undetectable phenomenon for thousands of core genes on sub-telomeric regions

The gene numbers and evolutionary rates of birds were assumed to be much lower than that of mammals, which in sharp contrast to the huge species number and morphological diversity of birds. It is very necessary to construct a complete avian genome and analyze its evolution.We constructed a chicken pan-genome from 20 de novo genome assemblies with high sequencing depth, newly identified 1,335 protein-coding genes and 3,011 long noncoding RNAs. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were accidentally measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal sub-telomeric regions, surrounded with extremely high proportions of tandem repeats, and strongly blocked DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had three-fold elevated substitution rates than known ones, updating the evolutionary rates of birds. Our study provides a framework for constructing a better chicken genome, which will contribute towards the understanding of avian evolution and improvement of poultry breeding.

genomics↗

bioRxiv2021

Chlamydomonas ARMC2/PF27 is an obligate cargo adapter for IFT of radial spokes

Intraflagellar transport (IFT) carries proteins into flagella but how IFT trains interact with the large number of diverse proteins required to assemble flagella remains largely unknown. Here, we show that IFT of radial spokes in Chlamydomonas requires ARMC2/PF27, a conserved armadillo repeat protein associated with male infertility and reduced lung function. Chlamydomonas ARMC2 was highly enriched in growing flagella and tagged ARMC2 and the spoke protein RSP3 comigrated on anterograde trains. In contrast, a cargo and an adapter of inner and outer dynein arms moved independently of ARMC2, indicating that unrelated cargoes distribute stochastically onto the IFT trains. After concomitant unloading at the flagellar tip, RSP3 attached to the axoneme whereas ARMC2 diffused back to the cell body. In armc2/pf27 mutants, IFT of radial spokes was abolished and the presence of radial spokes was limited to the proximal region of flagella. We conclude that ARMC2 is a cargo adapter required for IFT of radial spokes to ensure their assembly along flagella. ARMC2 belongs to a growing class of cargo-specific adapters that enable flagellar transport of preassembled axonemal substructures by IFT.

cell biology↗

bioRxiv2021

On the use of facial and neck cooling to improve indoor occupant thermal comfort in warm conditions

Face and neck cooling has been found effective to improve thermal comfort during exercise in the heat despite the surface area of human face and neck regions accounts for only 5.5% of the entire body. Presently, very limited work in the literature has been reported on face and neck cooling to improve indoor thermal comfort. In this work, two energy-efficient wearable face and neck cooling fans were used to enhance occupants thermal comfort in two warm indoor conditions (30 & 32 {degrees}C). Local skin temperatures and perceptual responses while using those two wearable cooling fans were examined and compared. Results showed that both cooling fans could largely reduce local skin temperatures at the forehead, face and neck regions up to 2.1 {degrees}C. Local thermal sensation votes at the face and neck were decreased by 0.82-1.21 scale unit at two studied temperatures. Overall TSVs dropped by 1.03-1.14 and 1.34-1.66 scale unit at 30 and 32 {degrees}C temperatures, respectively. Both cooling fans could extend the acceptable HVAC temperature setpoint to 32.0 {degrees}C, resulting in an average energy saving of 45.7% as compared to the baseline HVAC setpoint of 24.5 {degrees}C. Further, the free-control cooling mode is recommended to occupants for further improving thermal comfort while using those two types of wearable cooling fans indoors. Lastly, it is concluded that those two wearable cooling fans could greatly improve thermal comfort and save HVAC energy despite some issues on dry eyes and dry lips associated with those wearable cooling fans were noted.

biophysics↗

bioRxiv2021

Aggregation pheromone 4-vinylanisole promotes the synchrony of sexual maturation in female locusts

Reproductive synchrony generally occurs in various group-living animals; however, the underlying mechanisms remain largely unexplored. Here, we report that aggregation pheromone, 4-vinylanisole, plays a key role in promoting sexual maturation synchrony of female adults in the migratory locust, Locusta migratoria, a worldwide agricultural pest species that can form huge swarms with millions of individuals. Gregarious female locusts display significant synchrony of sexual maturation and oviposition whereas solitarious females and olfactory deficiency mutants do not. Only the presence of gregarious male adults can stimulate sexual maturation synchrony of female adults. Of the volatiles emitted abundantly by gregarious male adults, only 4-vinylanisole induces female sexual maturation synchrony, whereas this effect is abolished in mutants of 4- vinylanisole receptor. Interestingly, 4-vinylanisole mainly accelerates oocyte maturation of young females aged at middle developmental stages (3-4 days post adult eclosion). Juvenile hormone/vitellogenin pathway mediates female sexual maturation triggered by 4-vinylanisole. Our results highlight a "catch-up" strategy by which gregarious females synchronize their oocyte maturation and oviposition by time-dependent endocrinal response to 4-vinylanisole.

ecology↗

bioRxiv2021

scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model

Cell reprogramming offers a potential treatment to many diseases, by regenerating specialized somatic cells. Despite decades of research, discovering the transcription factors that promote cell reprogramming has largely been accomplished through trial and error, a time-consuming and costly method. A computational model for cell reprogramming, however, could guide the hypothesis formulation and experimental validation, to efficiently utilize time and resources. Current methods often cannot account for the heterogeneity observed in cell reprogramming, or they only make short-term predictions, without modelling the entire reprogramming process. Here, we present scREMOTE, a novel computational model for cell reprogramming that leverages single cell multiomics data, enabling a more holistic view of the regulatory mechanisms at cellular resolution. This is achieved by first identifying the regulatory potential of each transcription factor and gene to uncover regulatory relationships, then a regression model is built to estimate the effect of transcription factor perturbations. We show that scREMOTE successfully predicts the long-term effect of overexpressing two key transcription factors in hair follicle development by capturing higher-order gene regulations. Together, this demonstrates that integrating the multimodal processes governing gene regulation creates a more accurate model for cell reprogramming with significant potential to accelerate research in regenerative medicine.

bioinformatics↗

bioRxiv2021

WUSCHEL-Related Homeobox Genes Cooperate with Cytokinin Signalling to Promote Bulbil Formation in Lilium lancifolium

The bulbil is an important vegetative reproductive organ in triploid Lilium lancifolium. Based on our previously obtained transcriptome data, we screened two WUSCHCEL-related homeobox (WOX) genes closely related to bulbil formation, LlWOX9 and LlWOX11. However, the biological functions and regulatory mechanisms of LlWOX9 and LlWOX11 are unclear. In this study, we cloned the full-length coding sequences of LlWOX9 and LlWOX11. Transgenic Arabidopsis showed increased branch numbers, and the overexpression of LlWOX9 and LlWOX11 in stem segments promoted bulbil formation, while the silencing of LlWOX9 and LlWOX11 inhibited bulbil formation, indicating that LlWOX9 and LlWOX11 are positive regulators of bulbil formation. Cytokinins acting through type-B response regulators (type-B RRs) could bind to the promoters of LlWOX9 and LlWOX11 and promote their transcription. LlWOX11 could enhance cytokinin pathway signalling by inhibiting the transcription of type-A LlRR9. Our study enriches the understanding of the regulation of plant development by the WOX gene family and lays a foundation for further research on the molecular mechanism of bulbil formation in lily.

developmental biology↗

bioRxiv2021

Identification and expression analysis of Shaker K+ channel genes in millet (Setaria italica) under abiotic stresses

Potassium (K+) is one of the essential nutrients for plant, which is involved in plant growth and development and abiotic stress tolerance. The absorption and transport of K+ depends on Shaker K+ channels. Foxtail millet is a Poaceae crop with strong drought stress-tolerant. In this study, we identified ten Shaker K+ channel genes in foxtail millet. Phylogenetic analysis, prediction of conserved motif, and gene structure analysis classified these genes into five groups. The transcription level of these genes under different abiotic stress treatments (cold, heat, NaCl, PEG) and ABA treatment were analyzed by quantitative real-time PCR. Each gene displayed its own regulation pattern under different treatments, suggests these channels play important role in plant adaptation to different environment conditions.

plant biology↗

bioRxiv2021

A deep learning-based iterative digital pathology annotation tool

Well-annotated exemplars are an important prerequisite for supervised deep learning schemes. Unfortunately, generating these annotations is a cumbersome and laborious process, due to the large amount of time and effort needed. Here we present a deep-learning-based iterative digital pathology annotation tool that is both easy to use by pathologists and easy to integrate into machine vision systems. Our pathology image annotation tool greatly reduces annotation time from hours to a few minutes, while maintaining high fidelity with human-expert manual annotations. Here we demonstrate that our active learning tool can be used for a variety of pathology annotation tasks including masking tumor, stroma, and lymphocyte-rich regions, among others. This annotation automation system was validated on 90 unseen digital pathology images with tumor content from the CAMELYON16 database and it was found that pathologists gold standard masks were re-produced successfully using our tool. That is, an average of 2.7 positive selections (mouse clicks) and 8.0 negative selections (mouse clicks) were sufficient to generate tumor masks similar to pathologists gold standard in CAMELYON16 test WSIs. Furthermore, the developed image annotation tool has been used to build gold standard masks for hundreds of TCGA digital pathology images. This set was used to train a convolutional neural network for identification of tumor epithelium. The developed pan-cancer deep neural network was then tested on TCGA and internal data with comparable performance. The validated pathology image annotation tool described herein has the potential to be of great value in facilitating accurate, rapid pathological analysis of tumor biopsies.

pathology↗