Biology subjects

Fu, Y.

Publications and source records attributed to Fu, Y..

At least 181 records · Page 10Linked to original sources

bioRxiv2023

Genotype, antimicrobial resistance and virulence profiles of livestock-derived enterotoxigenic Escherichia coli (ETEC) in the United States, 1970-2023

Enterotoxigenic Escherichia coli (ETEC) is a significant pathogen in both cattle and pigs, causing diarrhea in these animals and leading to economic losses in the livestock industry. Understanding the dissimilarity in genotype, antimicrobial resistance (AMR), and virulence between bovine and swine ETEC is crucial for development of targeted preventive and therapeutic approaches for livestock. However, a comprehensive study on this area remains lacking. Here, we performed whole-genome sequencing-based analyses of bovine (n = 554) and swine (n = 623) ETEC collected in the US over a 53-year period. We identified distinct ETEC genotypes (fimH type, O antigen, H antigen, sequence type) in cattle and pigs. Further, specific AMR and virulence profiles were associated with bovine and swine ETEC. Compared to swine ETEC, bovine ETEC were less diverse in genotypes, had a significantly (p < 0.001) lower number of AMR genes per isolate but higher co-occurrence of Shiga toxin and enterotoxin genes. Our results provide an overview of the key genomic differences between bovine and swine ETEC in the US, which might be attributed to host adaptation and antibiotic usage practice. Ongoing surveillance and research are essential to monitor the genetic diversity and AMR patterns of ETEC in different host species.

microbiology↗

bioRxiv2023

Systematic comparison of sequencing-based spatial transcriptomic methods

Recent advancements of sequencing-based spatial transcriptomics (sST) have catalyzed significant advancements by facilitating transcriptome-scale spatial gene expression measurement. Despite this progress, efforts to comprehensively benchmark different platforms are currently lacking. The extant variability across technologies and datasets poses challenges in formulating standardized evaluation metrics. In this study, we established a collection of reference tissues and regions characterized by well-defined histological architectures, and used them to generate data to compare six sST methods. We highlighted molecular diffusion as a variable parameter across different methods and tissues, significantly impacting the effective resolutions. Furthermore, we observed that spatial transcriptomic data demonstrate unique attributes beyond merely adding a spatial axis to single-cell data, including an enhanced ability to capture patterned rare cell states along with specific markers, albeit being influenced by multiple factors including sequencing depth and resolution. Our study assists biologists in sST platform selection, and helps foster a consensus on evaluation standards and establish a framework for future benchmarking efforts that can be used as a gold standard for the development and benchmarking of computational tools for spatial transcriptomic analysis.

genomics↗

bioRxiv2023

High-speed Auto-Polarization Synchronization Modulation Three-dimensional Structured Illumination Microscopy

In recent years, notable progress has been achieved in both the hardware and algorithms of structured illumination microscopy (SIM). Nevertheless, the advancement of 3DSIM has been impeded by challenges arising from the speed and intricacy of polarization modulation. In this study, we introduce a high-speed modulation 3DSIM system, leveraging the polarization maintaining and modulation capabilities of a digital micro-mirror device (DMD) in conjunction with an electro-optic modulator. The DMD-3DSIM system yields a 2-fold enhancement in both lateral (133 nm) and axial (300 nm) resolution compared to wide-field imaging, and can acquire a data set comprising 29 sections of 1024x1024 pixels, with 15 ms exposure time and 6.75 s per volume. The versatility of the DMD-3DSIM approach was exemplified through the imaging of various specimens, including fluorescent beads, nuclear pores, microtubules, actin filaments, and mitochondria within cells, as well as plant and animal tissues. Notably, polarized 3DSIM elucidated the orientation of actin filaments. Furthermore, the implementation of diverse deconvolution algorithms further enhances three-dimensional resolution. The DMD-based 3DSIM system presents a rapid and reliable methodology for investigating biomedical phenomena, boasting capabilities encompassing 3D superresolution, fast temporal resolution, and polarization imaging.

cell biology↗

bioRxiv2023

LightMHC: A Light Model for pMHC Structure Prediction with Graph Neural Networks

The peptide-major histocompatibility complex (pMHC) is a crucial protein in cell-mediated immune recognition and response. Accurate structure prediction is potentially beneficial for protein interaction prediction and therefore helps immunotherapy design. However, predicting these structures is challenging due to the sequential and structural variability. In addition, existing pre-trained models such as AlphaFold 2 require expensive computation thus inhibiting high throughput in silico peptide screening. In this study, we propose LightMHC: a lightweight model (2.2M parameters) equipped with attention mechanisms, graph neural networks, and convolutional neural networks. LightMHC predicts full-atom pMHC structures from amino-acid sequences alone, without template structures. The model achieved comparable or superior performance to AlphaFold 2 and ESMFold (93M and 15B parameters respectively), with five-fold acceleration (6.65 seconds/sample for LightMHC versus 36.82 seconds/sample for AlphaFold 2), potentially offering a valuable tool for immune protein structure prediction and immunotherapy design.

bioinformatics↗

bioRxiv2023

FrameDiPT: SE(3) Diffusion Model for Protein Structure Inpainting

Protein structure prediction field has been revolutionised by deep learning with protein folding models such as AlphaFold 2 and ESMFold. These models enable rapid in silico prediction and have been integrated into de novo protein design and protein-protein interaction (PPI) prediction. However, biologically relevant features dependent on conformational distributions cannot be estimated with these models. Diffusion models, a novel class of generative models, have been developed to learn conformational distributions and applied to de novo protein design. Limited work has been done on protein structure inpainting, where a masked section is recovered by simultaneously conditioning on its sequence and the rest of the structure. In this work, we propose FrameDiff inPainTing (FrameDiPT), a generalised model for protein inpainting. This is important for T-cells given the hyper-variability of the complementarity determining region (CDR) loops. We evaluated the model on CDR loop design for T-cell receptors and achieved comparable prediction accuracy to ProteinGenerator and RFdiffusion with limited training data and learnable parameters. Different from deterministic structure prediction models, FrameDiPT captures the conformational distribution at different regions and binding states, highlighting a key advantage of generative models. The model and inference code have been released1.

immunology↗

bioRxiv2023

Microbiome-based correction of nutrient profiles derived from self-reported dietary assessments

Since dietary intake is challenging to directly measure in large-scale cohort studies, we often rely on self-reported instruments (e.g., food frequency questionnaires, 24-hour recalls, and diet records) developed in nutritional epidemiology. Those self-reported instruments are prone to measurement errors, which can lead to inaccuracies in the calculation of nutrient profiles. Currently, few computational methods exist to address this problem. In the present study, we introduce a deep-learning approach --- Microbiome-based nutrient profile corrector (METRIC), which leverages gut microbial compositions to correct random errors in self-reported dietary assessments using 24-hour recalls or diet records. We demonstrate the excellent performance of METRIC in minimizing the simulated random errors, particularly for nutrients metabolized by gut bacteria in both synthetic and three real-world datasets. Further research is warranted to examine the utility of METRIC to correct actual measurement errors in self-reported dietary assessment instruments.

microbiology↗

bioRxiv2023

Connecting Chromatin Structures to Gene Regulation Using Dynamic Polymer Simulations

The transfer of regulatory information between distal loci on chromatin is thought to involve physical proximity, but key biophysical features of these contacts remain unclear. For instance, it is unknown how close and for how long two loci need to be in order to productively interact. The main challenge is that it is currently impossible to measure chromatin dynamics with high spatiotemporal resolution at scale. Polymer simulations provide an accessible and rigorous way to test biophysical models of chromatin regulation, yet there is a lack of simple and general methods for extracting the values of model parameters. Here we adapt the Nelder-Mead simplex optimization algorithm to select the best polymer model matching a given Hi-C dataset, using the MYC locus as an example. The models biophysical parameters predict a compartmental rearrangement of the MYC locus in leukemia, which we validate with single-cell measurements. Leveraging trajectories predicted by the model, we find that loci with similar Hi-C contact frequencies can exhibit widely different contact dynamics. Interestingly, the frequency of productive interactions between loci exhibits a non-linear relationship with their Hi-C contact frequency when we enforce a specific capture radius and contact duration. These observations are consistent with recent experimental observations and suggest that the dynamic ensemble of chromatin configurations, rather than average contact matrices, is required to fully predict productive long-range chromatin interactions.

biophysics↗

bioRxiv2023

Live soil ameliorated the negative effects of biodegradable but not non-biodegradable microplastics on the growth of plant communities

O_LIPlastic pollution has become a global environmental problem. Alternative use of biodegradable plastics has been proposed to mitigate the pollution problem caused by the traditional non-biodegradable plastics but the relative impacts of both types of microplastics on plant community productivity and diversity remain unknown. Microplastics can affect growth of individual plants directly by altering plant physiological processes and indirectly by altering soil biota that in turn influence plant growth. However, it remains unknown whether soil biota can mediate impact of biodegradable and non-biodegradable microplastics on plant community productivity and diversity due to a lack of studies on the topic. C_LIO_LIHere, we performed a greenhouse experiment with six plant communities and five biodegradable and five non-biodegradable microplastics to test whether: 1) biodegradable microplastics have a less negative effect on plant community biomass production and diversity than non-biodegradable microplastics, and 2) soil microorganisms differentially mediate the effects of non-biodegradable and biodegradable microplastics on plant community biomass production and diversity. We employed a fully crossed factorial design to grow the six plant communities in the presence vs. absence of the 10 microplastics individually and in live soil vs. sterilized soil. C_LIO_LIResults show that live soil ameliorated the negative effects of biodegradable microplastics on shoot biomass of the plant communities, but microplastics suppressed plant community diversity more strongly in live soil than in sterilized soil regardless of microplastics types under averaged across all treatments. Furthermore, the specific microplastics polymers were the main drivers of these results. C_LIO_LISynthesis and applications: Overall, our findings indicate that even biodegradable microplastics, e.g. PBS, which are considered environmentally friendly, still pose significant ecological risks to the structure and productivity of plant communities with potential implications for functioning of terrestrial ecosystems. Future studies may identify the specific taxa of soil microorganisms that may have degraded the microplastics that we studied, their rates of biodegradation, and the effects thereof on plant community structure and productivity under more natural field conditions in contrasting climatic conditions. C_LI

ecology↗

bioRxiv2023

A synthetic Notch (synNotch) system linking intratumoral immune-cancer cell communication to a synthetic blood biomarker assay

IntroductionCellular immunotherapy has greatly improved cancer treatment in recent years. For instance, chimeric antigen receptor (CAR) T-cell therapy has been proven highly effective in treating hematological malignancies, and many CAR cell designs are being explored for solid tumors. However, many questions remain why responses differ across patients and some tumor types are resistant. Improved and relatively inexpensive ways to monitor these cells could provide some answers. Clinically, blood tests are regularly used to monitor these therapies, but blood signals often do not reflect the activity of immune cells within the tumor(s). Here, using the synthetic Notch (synNotch) receptor that tethers antigen binding to customized transgene expression, we linked intratumoral immune-cancer cell communication to a simple secreted reporter blood test. Specifically, we engineered immune cells with a CD19-targeted synNotch receptor and demonstrate that binding to CD19 on cancer cells in vivo resulted in the production of secreted embryonic alkaline phosphatase (SEAP) at levels that are readily detected in the blood. Methods and ResultsJurkat T cells were engineered via sequential lentiviral transduction of two components: an anti-CD19 synNotch receptor and asynNotchresponse element encoding SEAP. Co-culture of engineered cells with CD19+, but not CD19-, Nalm6 cells, resulted in significantly elevated SEAP in media. Nod-scid-gamma (NSG) mice were subcutaneously injected with either CD19+ or CD19- Nalm6 cells. Intratumoral injection of engineered T cells (1x107) resulted significantly elevated blood SEAP activity in mice bearing CD19+ tumors (n=7), but not CD19- tumors (n=5). DiscussionOur synNotch reporter system allows for the monitoring of antigen-dependent intratumoral immune-cancer cell interactions through a simple and convenient blood test. Continued development of this system for different target antigens of interest should provide a broadly applicable platform for improved monitoring of many cell-based immunotherapies during their initial development and clinical translation, ultimately improving our understanding of design considerations and patient-specific responses.

synthetic biology↗

bioRxiv2023

Comparison of the three-dimensional chromatin structures of adolescent and adult peripheral blood B cells: implications for the study of pediatric autoimmune diseases

Background/PurposeKnowledge of the 3D genome is essential to elucidate genetic mechanisms driving autoimmune diseases. The 3D genome is distinct for each cell type, and it is uncertain whether cell lines faithfully recapitulate the 3D architecture of primary human cells or whether developmental aspects of the pediatric immune system require use of pediatric samples. We undertook a systematic analysis of B cells and B cell lines to compare 3D genomic features encompassing risk loci for juvenile idiopathic arthritis (JIA), systemic lupus (SLE), and type 1 diabetes (T1D). MethodsWe isolated B cells from healthy individuals, ages 9-17. HiChIP was performed using CTCF antibody, and CTCF peaks were identified. CTCF loops within the pediatric were compared to three datasets: 1) self-called CTCF consensus peaks called within the pediatric samples, 2) ENCODEs publicly available GM12878 CTCF ChIP-seq peaks, and 3) ENCODEs primary B cell CTCF ChIP-seq peaks from two adult females. Differential looping was assessed within the pediatric samples and each of the three peak datasets. ResultsThe number of consensus peaks called in the pediatric samples was similar to that identified in ENCODEs GM12878 and primary B cell datasets. We observed <1% of loops that demonstrated significantly differential looping between peaks called within the pediatric samples themselves and when called using ENCODE GM12878 peaks. Significant looping differences were even less when comparing loops of the pediatric called peaks to those of the ENCODE primary B cell peaks. When querying loops found in juvenile idiopathic arthritis, type 1 diabetes, or systemic lupus erythematosus risk haplotypes, we observed significant differences in only 2.2%, 1.0%, and 1.3% loops, respectively, when comparing peaks called within the pediatric samples and ENCODE GM12878 dataset. The differences were even less apparent when comparing loops called with the pediatric vs ENCODE adult primary B cell peak datasets.The 3D chromatin architecture in B cells is similar across pediatric, adult, and EBVtransformed cell lines. This conservation of 3D structure includes regions encompassing autoimmune risk haplotypes. ConclusionThus, even for pediatric autoimmune diseases, publicly available adult B cell and cell line datasets may be sufficient for assessing effects exerted in the 3D genomic space.

genomics↗

bioRxiv2023

Cep290 is cooperatively maintained at basal body by Cep131-Cep162 and Cby-Fam92 modules

Cilia play critical roles in cell signal transduction and organ development. Defects in cilia function result in a variety of genetic disorders. Cep290 is an evolutionarily conserved ciliopathy protein that bridges the ciliary membrane and axoneme at the basal body and plays critical roles in the initiation of ciliogenesis and TZ assembly. How Cep290 is maintained at basal body and whether axonemal and ciliary membrane localized cues converge to determine the localization of Cep290 remain unknown. Here, we report that the Cep131-Cep162 module near the axoneme and the Cby-Fam92 module close to the membrane synergistically control the basal body localization of Cep290 and the subsequent initiation of ciliogenesis. Concurrent deletion of any protein of the Cep131-Cep162 module and of the Cby-Fam92 module leads to a complete loss of Cep290 from basal body and blocks ciliogenesis at its initiation stage. Our results reveal that the first step of ciliogenesis strictly depend on cooperative and retroactive interactions between Cep131-Cep162, Cby-Fam92 and Cep290, which may contribute to the complex pathogenesis of Cep290-related ciliopathies.

cell biology↗

bioRxiv2023

Genomic locus of lncRNA-Gm26793 forms an inter-chromosomal molecular lock with Cubn to ensure proper stem cell differentiation and mouse embryogenesis

Inter-chromosomal interactions play a crucial role in 3D genome organization, yet the organizational principles and functional significances remain elusive. In general, long non-coding RNA (lncRNA) loci and transcripts are frequently associated with transcriptional programs modulated by long-range chromatin interactions. Here, we identified a novel lncRNA named Gm26793, which is abundantly distributed in the primitive streak and mesodermal cells of E7.5 mouse gastrula. Through genetic ablation of Gm26793, we observed a preferential responsiveness to primitive endoderm lineage during stem cell differentiation, as well as enhanced occurrence of transient and degenerative state cells in early mouse embryos when the cell fate segregates between epiblast and primitive endoderm. Mechanistically, we revealed the genomic locus of Gm26793, rather than the lncRNA transcript or adjacent gene governs the cell fate preference towards primitive endoderm. Concretely, Gm26793 locus (Chr 7) forms an inter-chromosomal molecular lock with Cubn (Chr 2), restraining the expression of Cubn and maintaining a natural epigenetic landscape, thus ensuring the proper lineage specification in vitro and in vivo. In order to reinforce this lock, CTCF and cohesin complex serves as a ring to fasten the inter-chromosomal contact. Overall, our study provides a clear paradigm that inter-chromosomal interaction collaborates with architectural factors to stabilize nuclear conformation and guarantee faithful gene expression during stem cell differentiation and mammalian embryogenesis.

developmental biology↗

bioRxiv2023

Duhuo Jisheng Decoction Regulates Intracellular Zinc Homeostasis by Enhancing Autophagy via PTEN/Akt/mTOR to Improve Knee Cartilage Degeneration

BackgroundArticular cartilage degeneration as well as cartilage matrix degradation is one of the key pathological changes in the early stage of knee osteoarthritis (KOA). However, currently, there are limited early prevention and treatment options available. Duhuo Jisheng Decoction (DHJSD) is a formula from Bei Ji Qian jin Yao Fang compiled by Sun Simiao in the Tang Dynasty of China. As a complementary therapy, it is widely used to treat early-stage KOA in China, but its mechanism has not been fully elucidated. ObjectiveThis study is aiming at investigating the potential role and mechanism of DHJSD in protecting cartilage from degradation. MethodsThe mechanism of DHJSD in alleviating OA was explored by gene silencing technology combined with a series of functional experiments in primary rat chondrocytes. Next, 25 wistar rats were used to validate the results obtained in vitro. The PTEN, Akt, mTOR, MMP13, Zn, collagen II, autophagy and apoptosis were determined. ResultsDHJSD reduced the phosphorylation of Akt and mTOR and the expression of zinc, MMP13, Bax and Bcl2. DHJSD increased the level of autophagy and the expression of autophagy proteins LC3 and Beclin1. After silencing PTEN gene, the phosphorylation levels of Akt and mTOR and the effects of Bax, Bcl2, LC3 and Beclin1 were weakened by DHJSD. DHJSD increased the formation of autophagosomes in chondrocytes. Histopathological staining revealed that DHJSD had a protective effect on cartilage. ConclusionDHJSD inhibits Akt/mTOR signaling pathway by targeting PTEN to promote autophagy in chondrocytes, which may be closely to repress the formation of MMP-13 by regulating the level of zinc in chondrocytes.

pharmacology and toxicology↗

bioRxiv2023

Massively Parallel Reporter Assay Confirms Regulatory Potential of hQTLs and Reveals Important Variants in Lupus and Other Autoimmune Diseases

ObjectiveTo systematically characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate gene expression in an allele dependent manner. MethodsWe designed a massively parallel reporter assay (MPRA) containing [~]32K variants and transfected it into an Epstein-Barr virus transformed B cell line generated from an SLE case. ResultsOur study expands our understanding of hQTLs, illustrating that epigenetic QTLs are more likely to contribute to functional mechanisms than eQTLs and other variant types, and a large proportion of hQTLs overlap transcription start sites (TSS) of noncoding RNAs. In addition, we nominate 17 variants (including 11 novel) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies primary and immortalized B cells. ConclusionWe uncover important insights into the mechanistic relationships between genotype, epigenetics, gene expression, and SLE and AI disease phenotypes.

genomics↗

bioRxiv2023

EagleC Explorer: A desktop application for interactively detecting and visualizing SVs and enhancer hijacking on Hi-C contact maps

It has been shown that Hi-C can be used as a powerful tool to detect structural variations (SVs) and enhancer hijacking events. However, there has been no existing programs that can directly visualize and detect such events on a personal computer, which hinders the broad adaption of the technology for intuitive discovery in cancer studies. Here, we introduce the EagleC Explorer, a desktop software that is specifically designed for exploring Hi-C and other chromatin contact data in cancer genomes. EagleC Explorer has a set of unique features, including 1) conveniently visualizing global and local Hi-C data; 2) interactively detecting SVs on a Hi-C map for any user-selected region on screen within seconds, using a deep-learning model; 3) reconstructing local Hi-C map surrounding user-provided SVs and generating publication-quality figures; 4) detecting enhancer hijacking events for any user-suggested regions on screen. In addition, EagleC Explorer can also incorporate other genomic tracks such as RNA-Seq or ChIP-Seq to facilitate scientists for integrative data analysis and making novel discoveries.

bioinformatics↗

bioRxiv2023

ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images

MotivationSingle cell segmentation is critical in the processing of spatial omics data to accurately perform cell type identification and analyze spatial expression patterns. Segmentation methods often rely on semi-supervised annotation or labeled training data which are highly dependent on user expertise. To ensure the quality of segmentation, current evaluation strategies quantify accuracy by assessing cellular masks or through iterative inspection by pathologists. While these strategies each address either the statistical or biological aspects of segmentation, there lacks an unified approach to evaluating segmentation accuracy. ResultsIn this paper, we present ESQmodel, a Bayesian probabilistic method to evaluate single cell segmentation using expression data. By using the extracted cellular data from segmentation and a prior belief of cellular composition as input, ESQmodel computes per cell entropy to assess segmentation quality by how consistent cellular expression profiles match with cell type expectations. Availability and implementationSource code is available on Github at: https://github.com/Roth-Lab/ESQmodel under the MIT license.

bioinformatics↗

bioRxiv2023

Microbiota produced indole metabolites disrupt host cell mitochondrial energy production and inhibit Cryptosporidium parvum growth

Cryptosporidiosis is a leading cause of life-threatening diarrhea in young children in resource-poor settings. Susceptibility rapidly declines with age, associated with changes in the microbiota. To explore microbial influences on susceptibility, we screened 85 microbiota- associated metabolites enriched in the adult gut for their effects on C. parvum growth in vitro. We identified eight inhibitory metabolites in three main classes: secondary bile salts/acids, a vitamin B6 precursor, and indoles. Growth restriction of C. parvum by indoles did not depend on the host aryl hydrocarbon receptor (AhR) pathway. Instead, treatment impaired host mitochondrial function and reduced total cellular ATP, as well as directly reduced the membrane potential in the parasite mitosome, a degenerate mitochondria. Oral administration of indoles, or reconstitution of the gut microbiota with indole producing bacteria, delayed life cycle progression of the parasite in vitro and reduced severity of C. parvum infection in mice. Collectively, these findings indicate that microbiota metabolites contribute to colonization resistance to Cryptosporidium infection.

microbiology↗

bioRxiv2023

Ferroptosis induced by phenolic compound-iron complex

Phenolic compounds are the most ubiquitously distributed pollutants, and are highly toxic to living organisms, however the detailed mechanism how phenols exert toxic effects remains elusive. Here,Escherichia coli and phloroglucinol are adapted as proxy to elucidate the molecular mechanism of phenols toxicity. We demonstrated that phloroglucinol complexed with iron and promoted the generation of hydroxyl radicals in Fenton reaction, leading to reducing power depletion and lipid peroxidation, and further leading to ferroptosis-like cell death ofE. coli. This ferroptotic death can be triggered by various phenols in diverse organisms, from bacteria to mammalian cells. Furthermore, we demonstrated that phloroglucinol-induced ferroptosis suppressed tumor growth in mice effectively, indicating phloroglucinol as promising drug for therapy-resistant cancers. Its also discovered that repression of this ferroptosis-like cell death benefited microbial degradation or production of desired phenolic compounds, showing great application potential in biotechnology field.

microbiology↗