Biology subjects

Lin, X.

Publications and source records attributed to Lin, X..

At least 289 records · Page 16Linked to original sources

bioRxiv2020

Neutralizing antibodies induced by first-generation gp41-stabilized HIV-1 envelope trimers and nanoparticles

Antigen-specific B-cell sorting and next-generation sequencing (NGS) were combined to isolate HIV-1 neutralizing antibodies (NAbs) from mice and rabbits immunized with BG505 trimers and nanoparticles. Three mouse NAbs potently neutralize BG505.T332N and recognize a glycan epitope centered at the C3/V4 region, as revealed by electron microscopy (EM), x-ray crystallography, and epitope mapping. Three potent NAbs were sorted from rabbit B cells that target glycan holes on the BG505 envelope glycoprotein (Env) and account for a significant portion of autologous NAb response. We then determined a 3.4[A]-resolution crystal structure for the clade C transmitted/founder Du172.17 Env with a redesigned heptad repeat 1 (HR1) bend. This clade C Env, as a soluble trimer and attached to a ferritin nanoparticle, along with a clade A Q482-d12 Env trimer, elicited distinct NAb responses in rabbits. Our study demonstrates that nanoparticles presenting gp41-stabilized trimers can induce potent NAb responses in mice and rabbits with Env-dependent breadth. TEASERMouse and rabbit NAbs elicited by gp41-stabilized trimers and nanoparticles neutralize autologous HIV-1 by targeting different epitopes

microbiology↗

bioRxiv2020

Computational optical sectioning by phase-space imaging with an incoherent multiscale scattering model

Optical sectioning is essential for fluorescence imaging in thick tissue to extract in-focus information from noisy background. Traditional methods achieve optical sectioning by rejecting the out-of-focus photons at a cost of photon efficiency, resulting in a tradeoff between sectioning capability and detection parallelization. Here, we show phase-space imaging with an incoherent multiscale scattering model can achieve computational optical sectioning with ~20 dB improvement for signal-to-background ratio in scattering medium, while maximizing the detection parallelization by imaging the entire volume simultaneously. We validated the superior performance by imaging various biological dynamics in Drosophila embryos, zebrafish larvae, and mice.

cell biology↗

bioRxiv2020

Cross-tissue eQTL mapping in the presence of missing data via surrogate outcome analysis

Sample sizes vary substantially across tissues in the Genotype-Tissue Expression (GTEx) project, where considerably fewer samples are available from certain inaccessible tissues, such as the substantia nigra (SSN), than from accessible tissues, such as blood. This severely limits power for identifying tissue-specific expression quantitative trait loci (eQTL) in undersampled tissues. Here we propose Surrogate Phenotype Regression Analysis (SO_SCPLOWPRAYC_SCPLOW) for leveraging information from a correlated surrogate outcome (e.g. expression in blood) to improve inference on a partially missing target outcome (e.g. expression in SSN). Rather than regarding the surrogate outcome as a proxy for the target outcome, SO_SCPLOWPRAYC_SCPLOW jointly models the target and surrogate outcomes within a bivariate regression framework. Unobserved values of either outcome are treated as missing data. We describe and implement an expectation conditional maximization algorithm for performing estimation in the presence of bilateral outcome missingness. SO_SCPLOWPRAYC_SCPLOW estimates the same association parameter estimated by standard eQTL mapping and controls the type I error even when the target and surrogate outcomes are truly uncorrelated. We demonstrate analytically and empirically, using simulations and GTEx data, that in comparison with marginally modeling the target outcome, jointly modeling the target and surrogate outcomes increases estimation precision and improves power.

genetics↗

bioRxiv2020

Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised learning

Calcium imaging is inherently susceptible to detection noise especially when imaging with high frame rate or under low excitation dosage. We developed DeepCAD, a self-supervised learning method for spatiotemporal enhancement of calcium imaging without requiring any high signal-to-noise ratio (SNR) observations. Using this method, detection noise can be effectively suppressed and the imaging SNR can be improved more than tenfold, which massively improves the accuracy of neuron extraction and spike inference and facilitate the functional analysis of neural circuits.

neuroscience↗

bioRxiv2020

Investigating the shared genetic architecture between multiple sclerosis and inflammatory bowel diseases

An epidemiological association between multiple sclerosis (MS) and inflammatory bowel disease (IBD) is well-established, but whether this reflects a shared genetic aetiology, and whether consistent genetic relationships exist between MS and the two predominant subtypes of IBD, ulcerative colitis (UC) and Crohns disease (CD), remains unclear. Here, we used genome-wide association study (GWAS) summary data to estimate genetic correlations (rg) between MS and each of IBD, UC and CD, finding that the rg between MS and UC was approximately twice that between MS and CD. On the basis of these genetic correlations, we performed cross-trait meta-analysis of GWAS summary data for MS and each of IBD, UC and CD, identifying a total of 42 novel SNPs shared between MS and IBD (N=19), UC (N=14), and CD (N=18). We then used multiple Mendelian randomization (MR) methods to investigate causal relationships between these diseases, finding suggestive but inconclusive evidence for a causal effect of MS on UC and IBD, and no or weak and inconsistent evidence for a causal effect of IBD or UC on MS. There was also no evidence for causality in bidirectional analyses of MS and CD. We also investigated tissue- and cell-type-specific enrichment of SNP heritability for each disease using stratified LD score regression. At the tissue level, we observed largely consistent patterns of enrichment for all four diseases in immune system-related tissues, including lung, spleen and whole blood, and in contrast to prior studies, small intestine. At the cell-type level, we identified significant enrichment for all diseases in CD4+ T cells in lung, and for MS, IBD and CD in CD8+ cytotoxic T cells in both lung and spleen, and regulatory T cells in lung. Our study sheds new insights into the biological basis of comorbidity between MS and both UC and CD.

genetics↗

bioRxiv2020

Taxonomic description and genome sequence of Christensenella intestinihominis sp. nov., a novel cholesterol-lowering bacterium isolated from human gut

A Gram-staining-negative, non-spore-forming, short, straight rod, non-motile, obligate anaerobic bacterial strain, AF73-05CM02T, was isolated from faecal sample of thirty-years old healthy male. Colonies were approximately 0.2mm in diameter, beige and circular after 4 days of incubation on PYG agar under anaerobic conditions at 37{degrees}C. Strain AF73-05CM02T grew in a temperature range between 30-42{degrees}C and pH range from 6.0 to 8.5, with optimum growth at 37-42{degrees}C and pH 7.0. Base on the 16S rRNA gene sequence analysis, strain AF73-05CM02T belongs to the genus Christensenella and showed the highest level of sequence similarity with Christensenella minuta YIT 12065T. The predominant fatty acids of strain AF73-05CM02T were C10:0 (7.5%), iso-C11:0 (5.6%), C12:0 (7.2%), C14:0 (46.6%), iso-C15:0 (7.4%), C16:0 (9.7%) and C18:1 {omega} 9 c (6.9%). Acetic acid, formic acid, butyric acid and lactic acid were end products of glucose fermentation. The isolate was negative for catalase, indole production and hydrolysis of gelatin. Genomic relatedness analyses based on average nucleotide identity indicated strain AF73-05CM02T significantly differed from other species of the genus Christensenella, showing ANI values under 82.89% with the phylogenetically closest species. The G+C content of the genomic DNA was 52.07 mol% from genome sequence, which differs from that of Christensenella minuta. Several physiological biochemical and genotypic properties differentiated the novel bacterial strain from the related species, indicating that the isolate represent a new species of the genus Christensenella for which the name Christensenella intestinihominis sp. nov. is proposed, with strain AF73-05CM02T (=CGMCC 1.5207T =DSM 103477T) being the type strain. The follow study approached the function of cholesterol-lowering for strains AF73-05CM02T and DSM 22067T revealed the two strains exhibit capacity for removing cholesterol with efficiency of 36.6% and 54.3%. Exopolysaccharide production of two strains were 234 and 271 mg/L, respectively.

microbiology↗

bioRxiv2020

HiCAR: a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility, and cis-regulatory chromatin contacts

The long-range interactions of cis-regulatory elements (cREs) play a central role in regulating the spatial-temporal gene expression program of multi-cellular organism. cREs are characterized by the presence of accessible (or open) chromatin, which can be identified at genome-wide scale with assays such as ATAC-seq, DHS-seq, and FAIRE-seq. However, it remains technically challenging to comprehensively identify the long-range physical interactions that occur between cREs, especially in a cost effective manner using low-input samples. Here, we report HiCAR (High-throughput Chromosome conformation capture on Accessible DNA with mRNA-seq co-assay), a method that enables simultaneous assessment of cis-regulatory chromatin interactions and chromatin accessibility, as well as evaluation of the transcriptome, which represents the functional output of chromatin structure and accessibility. Unlike immunoprecipitation-based methods such as HiChIP, PLAC-seq, and ChIA-PET, HiCAR does not require target-specific antibodies and thus can comprehensively capture the cis-regulatory chromatin contacts anchored at accessible regulatory DNA regions and associated with diverse epigenetic modifications and transcription factor binding. Compared to Trac-looping, another method designed to capture interactions between accessible chromatin regions, HiCAR produced a 17-fold greater yield of informative long-range cis- reads at a similar sequencing depth and required 1,000-fold fewer cells as input. Applying HiCAR to H1 human embryonic stem cells (hESCs) revealed 46,792 cis-regulatory chromatin interactions at 5kb resolution. Interestingly, we found that epigenetically poised, bivalent, and repressed cREs exhibit comparable spatial interaction activity to those transcriptionally activated cREs. Using machine learning approaches, we predicated 22 epigenome features that are potentially important for the spatial interaction activity of cREs in H1 hESC. Lastly, we also identified long-range cis-regulatory chromatin interactions in GM12878 and mouse embryonic stem cells with HiCAR. Our results demonstrate that HiCAR is a robust and cost-effective multi-omics assay, which is broadly applicable for simultaneous analysis of genome architecture, chromatin accessibility, and the transcriptome using low-input samples.

genomics↗

bioRxiv2020

An efficient and accurate frailty model approach for genome-wide survival association analysis controlling for population structure and relatedness in large-scale biobanks

With decades of electronic health records linked to genetic data, large biobanks provide unprecedented opportunities for systematically understanding the genetics of the natural history of complex diseases. Genome-wide survival association analysis can identify genetic variants associated with ages of onset, disease progression and lifespan. We developed an efficient and accurate frailty (random effects) model approach for genome-wide survival association analysis of censored time-to-event (TTE) phenotypes in large biobanks by accounting for both population structure and relatedness. Our method utilizes state-of-the-art optimization strategies to reduce the computational cost. The saddlepoint approximation is used to allow for analysis of heavily censored phenotypes (>90%) and low frequency variants (down to minor allele count 20). We demonstrated the performance of our method through extensive simulation studies and analysis of five TTE phenotypes, including lifespan, with heavy censoring rates (90.9% to 99.8%) on ~400,000 UK Biobank participants with white British ancestry and ~180,000 samples in FinnGen, respectively. We further performed genome-wide association analysis for 871 TTE phenotypes in UK Biobank and presented the genome-wide scale phenome-wide association (PheWAS) results with the PheWeb browser.

genomics↗

bioRxiv2020

SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility

During the evolution of SARS-CoV-2 in humans a D614G substitution in the spike (S) protein emerged and became the predominant circulating variant (S-614G) of the COVID-19 pandemic1. However, whether the increasing prevalence of the S-614G variant represents a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains elusive. Here, we generated isogenic SARS-CoV-2 variants and demonstrate that the S-614G variant has (i) enhanced binding to human ACE2, (ii) increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a novel human ACE2 knock-in mouse model, and (iii) markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Collectively, our data show that while the S-614G substitution results in subtle increases in binding and replication in vitro, it provides a real competitive advantage in vivo, particularly during the transmission bottle neck, providing an explanation for the global predominance of S-614G variant among the SARS-CoV-2 viruses currently circulating.

microbiology↗

bioRxiv2020

Fast-Bonito: A Faster Basecaller for Nanopore Sequencing

Oxford Nanopore Technologies (ONT) is a promising sequencing technology that could generate relatively longer sequencing reads compared to the next generation sequencing (NGS) technology. The base calling process is very important for TGS. It translates the original electrical signals from the sequencer to the nucleotide sequence. By doing that, the base calling could significantly influence the accuracy of downstream analysis. Bonito is a recently developed basecaller based on deep neuron network, the neuron network architecture of which is composed of a single convolutional layer followed by three stacked bidirectional GRU layers. Although Bonito achieved the state-of-the-art accuracy, its speed is so slow that it is not likely to be used in production. We therefore implement Fast-Bonito, which introduces systematic optimization to speed up Bonito. Fast-Bonito archives 53.8% faster than the original version on NVIDIA V100 and could be further speed up by HUAWEI Ascend 910 NPU, achieving 565% faster than the original version. The accuracy of Fast-Bonito is also slightly higher than the original Bonito.

bioinformatics↗

bioRxiv2020

Momilactone B inhibits Arabidopsis growth and development via disruption of ABA and auxin signaling

In competition for limited resources, many plants release allelochemicals to inhibit the growth of neighboring plants. Momilactone B (MB) is a major allelochemical produced by rice (Oryza sativa), however its mode of action is currently unknown. We used Arabidopsis (Arabidopsis thaliana) as a model system to evaluate potential mechanisms underlying the inhibitory effects of MB on seed germination, seedling establishment and root growth through the use of confocal microscopy and the examination of transcriptional responses in MB-treated seedlings. In response to MB treatment, transcript levels for genes encoding several key ABA biosynthetic enzymes and signaling components, including the transcription factor ABA-INSENSITIVE 4 (ABI4), were dramatically increased. Additionally, ABA insensitive 4 (abi4) mutant seedlings exhibited reduced susceptibility to exogenously-provided MB. Although the transcript levels of DELLA genes, which negatively regulate GA signaling, were significantly increased upon MB exposure, exogenous GA application did not reverse the inhibitory effects of MB on Arabidopsis germination and seedling development. Moreover, a reduction in seedling root meristematic activity, associated with reduced expression of auxin biosynthetic genes and efflux transporters, and apparent lowered auxin content, was observed in MB-treated root tips. Exogenous auxin applications partially rescued the inhibitory effects of MB observed in root growth. Our results indicate that MB suppresses Arabidopsis seed germination and root growth primarily via disruption of ABA and auxin signaling. These findings underscore the crucial roles played by phytohormones in mediating responses to allelochemical exposure. One-sentence summaryMomilactone B, the key allelochemical of rice, inhibits Arabidopsis growth and development via disruption of ABA and auxin signaling, suggesting the crucial roles of phytohormones in plant allelopathy

plant biology↗

bioRxiv2020

Self-assembling nanoparticles presenting receptor binding domain and stabilized spike as next-generation COVID-19 vaccines

Vaccination against SARS-CoV-2 provides an effective tool to combat the COIVD-19 pandemic. Here, we combined antigen optimization and nanoparticle display to develop vaccine candidates for SARS-CoV-2. We first displayed the receptor-binding domain (RBD) on three self-assembling protein nanoparticle (SApNP) platforms using the SpyTag/SpyCatcher system. We then identified heptad repeat 2 (HR2) in S2 as the cause of spike metastability, designed an HR2-deleted glycine-capped spike (S2G{Delta}HR2), and displayed S2G{Delta}HR2 on SApNPs. An antibody column specific for the RBD enabled tag-free vaccine purification. In mice, the 24-meric RBD-ferritin SApNP elicited a more potent neutralizing antibody (NAb) response than the RBD alone and the spike with two stabilizing proline mutations in S2 (S2P). S2G{Delta}HR2 elicited two-fold-higher NAb titers than S2P, while S2G{Delta}HR2 SApNPs derived from multilayered E2p and I3-01v9 60-mers elicited up to 10-fold higher NAb titers. The S2G{Delta}HR2-presenting I3-01v9 SApNP also induced critically needed T-cell immunity, thereby providing a promising vaccine candidate. ONE-SENTENCE SUMMARYThe SARS-CoV-2 receptor binding domain and S2G{Delta}HR2 spike elicited potent immune responses when displayed on protein nanoparticles as vaccine candidates.

microbiology↗

bioRxiv2020

Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines

Ebola virus (EBOV) glycoprotein (GP) can be recognized by neutralizing antibodies (NAbs) and is the main target for vaccine design. Here, we first investigate the contribution of the stalk and heptad repeat 1-C (HR1C) regions to GP metastability. Specific stalk and HR1C modifications in a mucin-deleted form (GP{Delta}muc) increase trimer yield, whereas alterations of HR1C exert a more complex effect on thermostability. Crystal structures are determined to validate two rationally designed GP{Delta}muc trimers in their unliganded state. We then display a modified GP{Delta}muc trimer on reengineered nanoparticles that encapsulate a layer of locking domains (LD) and a cluster of helper T-cell epitopes. In mice and rabbits, GP trimers and nanoparticles elicit cross-ebolavirus NAbs, as well as non-NAbs that enhance pseudovirus infection. Repertoire sequencing reveals quantitative profiles of vaccine-induced B-cell responses. This study demonstrates a promising vaccine strategy for filoviruses, such as EBOV, based on GP stabilization and nanoparticle display.

microbiology↗

bioRxiv2020

Optimized gene expression from bacterial chromosome by high-throughput integration and screening

Chromosomal integration of recombinant genes is desirable compared to expression from plasmids due to increased stability, reduced cell-to-cell variability, and the elimination of antibiotics for plasmid maintenance. Here, we present a new approach for tuning pathway gene expression levels via random integrations and high-throughput screening. We demonstrate multiplexed gene integration and expression-level optimization for isobutanol production in Escherichia coli. The integrated strains could, with significantly lower expression levels than plasmid-based expression, produce high titers (10.0 {+/-} 0.9 g/L isobutanol in 48 h) and yields (69 % of the theoretical maximum). Close examination of pathway expression in the top-performing, as well as other isolates, reveals the complexity of cellular metabolism and regulation, underscoring the need for precise optimization while integrating pathway genes into the chromosome. This new method for multiplexed pathway gene integration and expression optimization could be readily extended to a wide range of pathways and chassis to create robust and efficient production strains.

synthetic biology↗

bioRxiv2020

Protein Structure Refinement Guided by Atomic Packing Frustration Analysis

1Recent advances in machine learning, bioinformatics and the understanding of the folding problem have enabled efficient predictions of protein structures with moderate accuracy, even for targets when there is little information from templates. All-atom molecular dynamics simulations provide a route to refine such predicted structures, but unguided atomistic simulations, even when lengthy in time, often fail to eliminate incorrect structural features that would allow the structure to become more energetically favorable owing to the necessity of making large scale motions and overcoming energy barriers for side chain repacking. In this study, we show that localizing packing frustration at atomic resolution by examining the statistics of the energetic changes that occur when the local environment of a site is changed allows one to identify the most likely locations of incorrect contacts. The global statistics of atomic resolution frustration in structures that have been predicted using various algorithms provide strong indicators of structural quality when tested over a database of 20 targets from previous CASP experiments. Residues that are more correctly located turn out to be more minimally frustrated than more poorly positioned sites. These observations provide a diagnosis of both global and local quality of predicted structures, and thus can be used as guidance in all-atom refinement simulations of the 20 targets. Refinement simulations guided by atomic packing frustration turn out to be quite efficient and significantly improve the quality of the structures.

biophysics↗

bioRxiv2020

Inter-determination of blood metabolite levels and gut microbiome supported by Mendelian randomization

The gut microbiome has been implicated in a variety of physiological states, but controversy over causality remains unresolved. Here, we performed bidirectional Mendelian randomization (MR) analyses on 3,432 Chinese individuals with whole genome, whole metagenome, anthropometric, and blood metabolic trait data. We identified 58 causal relationships between the gut microbiome and blood metabolites, and replicated 43 of them. Increased relative abundances of fecal Oscillibacter and Alistipes were causally linked to decreased triglyceride concentration. Conversely, blood metabolites such as glutamic acid appeared to decrease fecal Oxalobacter, and members of Proteobacteria were influenced by metabolites such as 5-methyltetrahydrofolic acid, alanine, glutamate, and selenium. Two-sample MR with data from Biobank Japan partly corroborated results with triglyceride and with uric acid, and also provided causal support for published fecal bacterial markers for cancer and cardiovascular diseases. This study illustrates the value of human genetic information to help prioritize gut microbial features for mechanistic and clinical studies.

genetics↗

bioRxiv2020

Single-cell Transcriptomics Identifies Gene Expression Networks Driving Differentiation and Tumorigenesis in the Human Fallopian Tube

The human fallopian tube harbors the cell-of-origin for the majority of high-grade serous ovarian cancers (HGSCs), but its cellular composition, particularly the epithelial component, is poorly characterized. We performed single-cell transcriptomic profiling in 12 primary fallopian specimens from 8 patients, analyzing around 53,000 individual cells to map the major immune, fibroblastic and epithelial cell types present in this organ. We identified 10 epithelial sub-populations, characterized by diverse transcriptional programs including SOX17 (enriched in secretory epithelial cells), TTF3 and RFX3 (enriched in ciliated cells) and NR2F2 (enriched in early, partially differentiated secretory cells). Based on transcriptional signatures, we reconstructed a trajectory whereby secretory cells differentiate into ciliated cells via a RUNX3high intermediate. Computational deconvolution of the cellular composition of advanced HGSCs based on epithelial subset signatures identified the early secretory population as a likely precursor state for the majority of HGSCs. The signature of this rare population of cells comprised both epithelial (EPCAM, KRT) and mesenchymal (THY1, ACTA2) features, and was enriched in mesenchymal-type HGSCs (P = 6.7 x 10-27), a group known to have particularly poor prognoses. This cellular and molecular compendium of the human fallopian tube in cancer-free women is expected to advance our understanding of the earliest stages of fallopian epithelial neoplasia.

genomics↗

bioRxiv2020

One enzyme many faces: alkaline phosphatase-based phosphorus-nutrient strategies and the regulatory cascade revealed by CRISPR/Cas9 gene knockout

Phosphorus (P) is an essential macronutrient for marine phytoplankton responsible for [~]50% of global carbon fixation. As P availability is variable and likely will decrease in future warming oceans, phytoplankton growth will be constrained by their strategies to scavenge dissolved organophosphate. To enhance our mechanistic understanding of these strategies, here we employ CRISPR/Cas9 to create mutants of alkaline phosphatase (AP) PhoA and PhoD and a putative regulator in the diatom model Phaeodactylum tricornutum, coupled with transcriptomic profiling to interrogate their modes of function and P- regulatory network. Results indicate that these two AP isoforms are differentiated in subcellular localization and substrate specialization, and are mutually compensatory and replaceable. Further analyses reveal a regulatory cascade of P scavenging and potential roles of AP in iron and ammonium uptake as well as diverse metabolic pathways. These findings have important implications in how phytoplankton community will respond to future changing microenvironments of global oceans.

ecology↗