Biology subjects

Duan, B.

Publications and source records attributed to Duan, B..

28 records · Page 2Linked to original sources

bioRxiv2022

Privacy-preserving integration of multiple institutional data for single-cell type identification with scPrivacy

The rapid accumulation of large-scale single-cell RNA-seq datasets from multiple institutions presents remarkable opportunities for automatically cell annotations through integrative analyses. However, the privacy issue has existed but being ignored, since we are limited to access and utilize all the reference datasets distributed in different institutions globally due to the prohibited data transmission across institutions by data regulation laws. To this end, we present scPrivacy, which is the first and generalized automatically single-cell type identification prototype to facilitate single cell annotations in a data privacy-preserving collaboration manner. We evaluated scPrivacy on a comprehensive set of publicly available benchmark datasets for single-cell type identification to stimulate the scenario that the reference datasets are rapidly generated and distributed in multiple institutions, while they are prohibited to be integrated directly or exposed to each other due to the data privacy regulations, demonstrating its effectiveness, time efficiency and robustness for privacy-preserving integration of multiple institutional datasets in single cell annotations.

bioinformatics↗

bioRxiv2022

A Spinal Circuit That Transmits Innocuous Cool Sensations

Temperature information is precisely processed in the nervous system. While progress has been made in identifying molecular thermosensors in the periphery, the neural circuits that process temperature information in the central nervous system remain unknown. Here we have identified an essential node in the neural circuitry for innocuous cool sensations. We found that a population of excitatory interneurons co-expressing Calbindin1 and Lbx1 (Calb1Lbx1) in the dorsal horn of the spinal cord is activated by innocuous cool temperatures. Genetic ablation or silencing of spinal Calb1Lbx1 neurons causes loss of innocuous cool but not noxious cold sensations. Further Brainbow labeling with expansion microscopy and electrophysiology showed that a small cluster of spinal Calb1Lbx1 interneurons in lamina I and the outer layer of lamina II represents the cooling-transmission neurons. These neurons receive monosynaptic connections from TRPM8+ primary sensory neurons and amplify the activity of cool-sensitive spinoparabrachial projection neurons. Our findings reveal a microcircuit in the dorsal spinal cord that specifically transmits innocuous cool sensations.

neuroscience↗

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↗

bioRxiv2021

Engineered human brown adipocyte microtissues improved glucose and insulin homeostasis in high fat diet-induced obese and diabetic mice

A large population of people is affected by obesity (OB) and its associated type 2 diabetes mellitus(T2DM). There are currently no safe and long-lasting anti-OB/T2DM therapies. Clinical data and preclinical transplantation studies show that transplanting metabolically active brown adipose tissue (BAT) is a promising approach to prevent and treat OB and its associated metabolic and cardiovascular diseases. However, most transplantation studies used mouse BAT, and it is uncertain whether the therapeutic effect would be applied to human BAT since human and mouse BATs have distinct differences. Here, we report the fabrication of three-dimensional (3D) human brown adipose microtissues, their survival and safety, and their capability to improve glucose and insulin homeostasis and manage body weight gain in high-fat diet (HFD)-induced OB and diabetic mice. Methods3D BA microtissues were fabricated and transplanted into the kidney capsule of Rag1-/- mice. HFD was initiated to induce OB 18 days after transplantation. A low dose of streptozotocin (STZ) was administrated after three months HFD to induce diabetes. The body weight, fat and lean mass, plasma glucose level, glucose tolerance and insulin sensitivity were recorded regularly. In addition, the levels of human and mouse adipokines in the serum were measured, and various tissues were harvested for histological and immunostaining analyses. ResultsWe showed that 3D culture promoted BA differentiation and uncoupling protein-1 (UCP-1) protein expression, and the microtissue size significantly influenced the differentiation efficiency and UCP-1 protein level. The optimal microtissue diameter was about 100 {micro}m. Engineered 3D BA microtissues survived for the long term with angiogenesis and innervation, alleviated body weight and fat gain, and significantly improved glucose tolerance and insulin sensitivity. They protected the endogenous BAT from whitening and reduced mouse white adipose tissue (WAT) hypertrophy and liver steatosis. In addition, the microtissues secreted soluble factors and modulated the expression of mouse adipokines. We also showed that scaling up the microtissue production could be achieved using the 3D suspension culture or a 3D thermoreversible hydrogel matrix. Further, these microtissues can be preserved at room temperature for 24 hours or be cryopreserved for the long term without significantly sacrificing cell viability. ConclusionOur study showed that 3D BA microtissues could be fabricated at large scales, cryopreserved for the long term, and delivered via injection. BAs in the microtissues had higher purity, and higher UCP-1 protein expression than BAs prepared via 2D culture. In addition, 3D BA microtissues had good in vivo survival and tissue integration, and had no uncontrolled tissue overgrowth. Furthermore, they showed good efficacy in preventing OB and T2DM with a very low dosage compared to literature studies. Thus, our results show engineered 3D BA microtissues are promising anti-OB/T2DM therapeutics. They have considerable advantages over dissociated BAs or BAPs for future clinical applications in terms of product scalability, storage, purity, quality, and in vivo safety, dosage, survival, integration, and efficacy.

bioengineering↗

bioRxiv2021

Dr. Sim: Similarity Learning for Transcriptional Phenotypic Drug discovery

Transcriptional phenotypic drug discovery has achieved great success, and various compound perturbation-based data resources, such as Connectivity Map (CMap) and Library of Integrated Network-Based Cellular Signatures (LINCS), have been presented. Computational strategies fully mining these resources for phenotypic drug discovery have been proposed, and among them, a fundamental issue is to define the proper similarity between the transcriptional profiles to elucidate the drug mechanism of actions and identify new drug indications. Traditionally, this similarity has been defined in an unsupervised way, and due to the high dimensionality and the existence of high noise in those high-throughput data, it lacks robustness with limited performance. In our study, we present Dr. Sim, which is a general learning-based framework that automatically infers similarity measurement rather than being manually designed and can be used to characterize transcriptional phenotypic profiles for drug discovery with generalized good performance. We evaluated Dr. Sim on comprehensively publicly available in vitro and in vivo datasets in drug annotation and repositioning using high-throughput transcriptional perturbation data and indicated that Dr. Sim significantly outperforms the existing methods and is proved to be a conceptual improvement by learning transcriptional similarity to facilitate the broad utility of high-throughput transcriptional perturbation data for phenotypic drug discovery. The source code and usage of Dr. Sim is available at https://github.com/bm2-lab/DrSim/.

bioinformatics↗

bioRxiv2020

An early Cambrian ecdysozoan with a terminal mouth but no anus

The ecdysozoans are the most diverse animal group on Earth1, 2. Molecular clock studies indicate that the ecdysozoans may have diverged and diversified in the Ediacaran Period3, 4, but unambiguous ecdysozoan fossils first appear in the earliest Cambrian and are limited to cycloneuralians5-7. Here we report new material of the early Cambrian microscopic animal Saccorhytus coronarius, which was previously interpreted as a deuterostome8. Saccorhytus coronarius is reconstructed as a millimetric and ellipsoidal meiobenthic animal with a spinose armor and an anterior mouth but no anus. Purported pharyngeal gills in support of the deuterostome hypothesis8 are shown to be taphonomic artifacts. Phylogenetic analyses indicate that Saccorhytus coronarius belongs to the total-group Ecdysozoa, highlighting the morphological and ecological diversity of early Cambrian ecdysozoans.

paleontology↗

bioRxiv2020

Integration of Machine Learning Improves the Prediction Accuracy of Molecular Modelling for M. jannaschii Tyrosyl-tRNA Synthetase Substrate Specificity

Design of enzyme binding pocket to accommodate substrates with different chemical structure is a great challenge. Traditionally, thousands even millions of mutants have to be screened in wet-lab experiment to find a ligand-specific mutant and large amount of time and resources is consumed. To accelerate the screening process, here we propose a novel workflow through integration of molecular modeling and data-driven machine learning method to generate mutant libraries with high enrichment ratio for recognition of specific substrate. M. jannaschii tyrosyl-tRNA synthetase (Mj. TyrRS) is used as an example system to give a proof of concept since the sequence and structure of many unnatural amino acid specific Mj. TyrRS mutants have been reported. Based on the crystal structures of different Mj. TyrRS mutants and Rosetta modeling result, we find D158G/P is the critical residue which influences the backbone disruption of helix with residue 158-163. Our results show that compared with random mutation, Rosetta modeling and score function calculation can elevate the enrichment ratio of desired mutants by 2-fold in a test library having 687 mutants, while after calibration by machine learning model trained using known data of Mj. TyrRS mutants and ligand, the enrichment ratio can be elevated by 11-fold. This molecular modeling and machine learning-integrated workflow is anticipated to significantly benefit to the Mj. tyrRS mutant screening and substantially reduce the time and cost of web-lab experiment. Besides, this novel process will have broad application in the field of computational protein design. CCS Concepts* Applied computing * Life and medical sciences * Computational biology * Molecular structural biology

bioinformatics↗

bioRxiv2020

Unsupervised Neural Tracing in Densely Labeled Multispectral Brainbow Images

Reconstructing neuron morphology is central to uncovering the complexity of the nervous system. That is because the morphology of a neuron essentially provides the physical constraints to its intrinsic electrophysiological properties and its connectivity. Recent advances in imaging technologies generated large quantities of high-resolution 3D images of neurons in the brain. Furthermore, the multispectral labeling technology, Brainbow permits unambiguous differentiation of neighboring neurons in a densely labeled brain, therefore enables for the first time the possibility of studying the connectivity between many neurons from a light microscopy image. However, lack of reliable automated neuron morphology reconstruction makes data analysis the bottleneck of extracting rich informatics in neuroscience. Supervoxel-based neuron segmentation methods have been proposed to solve this problem, however, the use of previous approaches has been impeded by the large numbers of errors which arise in the final segmentation. In this paper, we present a novel unsupervised approach to trace neurons from multispectral Brainbow images, which prevents segmentation errors and tracing continuity errors using two innovations. First, we formulate a Gaussian mixture model-based clustering strategy to improve the separation of segmented color channels that provides accurate skeletonization results for the following steps. Next, a skeleton graph approach is proposed to allow the identification and correction of discontinuities in the neuron tree topology. We find that these innovations allow our approach to outperform current state-of-the-art approaches, which results in more accurate neuron tracing as a tree representation close to human expert annotation.

neuroscience↗

bioRxiv2020

Chikungunya Virus Infection Impairs The Function Of Osteogenic Cells

Chikungunya virus (CHIKV) is a positive-sense, single-stranded RNA virus, spread by the Aedes species (sp.) mosquitoes. Chikungunya virus (CHIKV) causes a condition characterized by high fever, headache, rash, and joint pain. Recent investigations reveal presence of bone lesions and erosive arthritis in the joints of CHIKV infected patients, indicating an association of bone pathology with CHIKV infection. However, the molecular mechanism underlying CHIKV-induced bone pathology remains poorly defined. Bone marrow derived mesenchymal stem cells (BMSCs) contribute to bone homeostasis by differentiating into osteogenic cells which later mature to form the bone. Disruption of osteogenic differentiation and function of BMSCs lead to bone pathologies. Studies show that virus infections can alter the properties and function of BMSCs. However, to date, pathogenesis of CHIKV infection in this context has not been studied. In the current study, we investigated the susceptibility of BMSCs and osteogenic cells to CHIKV and studied the effect of infection on these cells. To our knowledge, for the first time we report that CHIKV can productively infect BMSCs and osteogenic cells. We also observed a decreased gene expression of the major regulator of osteogenic differentiation, RUNX2 in CHIKV infected osteogenic cells. Furthermore, impaired functional properties of osteogenic cells i.e. decreased production and activity of alkaline phosphatase (ALP) and matrix mineralization were observed in the presence of CHIKV infection. Thus, we conclude that CHIKV likely impairs osteogenic differentiation of BMSCs indicating a possible role of BMSCs in altering bone homeostasis during CHIKV infection. ImportancePresently, no vaccines or treatment options are available for CHIKV infection. Joint pain is one of the major concerns. Although studies have shown an association between bone pathology and infection, the molecular pathogenesis in context of bone pathology is poorly defined. Here, we demonstrate for the first time that BMSCs and BMSC-derived osteogenic cells are susceptible to CHIKV infection and infection likely alters function of the osteogenic cells. This study highlights altered osteogenic differentiation as a possible mechanism for causing the bone pathology observed in CHIKV pathogenesis.

microbiology↗

bioRxiv2019

Chikungunya virus infection impairs osteogenic differentiation of bone marrow-derived mesenchymal stem cells

Chikungunya virus (CHIKV) is a positive-sense, single-stranded RNA virus, belonging to the genus alphavirus in the family Togaviridae. The virus is spread by the Aedes species (sp.) mosquitoes in tropical and subtropical regions of the world. CHIKV causes Chikungunya fever (CHIKF), where the acute stage of infection is characterized by high fever, headache, rash, and polyarthralgia. In 30-40% of cases, patients develop a chronic stage with debilitating joint pain persisting for months to years imposing a burden on the population in terms of disability adjusted life years (DALY). Presently, no vaccines or treatment options are available for this infection. Prior investigations reveal that CHIKV infection is associated with bone pathology; however, the molecular mechanism underlying CHIKV-induced bone pathology remains poorly defined. Studies show that disruption of osteogenic differentiation and function of bone marrow-derived mesenchymal stem cells (BMMSCs) can lead to bone pathologies. However, to date pathogenesis of CHIKV infection in this context has not been studied. In the current study, we investigated the susceptibility of BMMSCs to CHIKV and studied the effect of infection on BMMSCs-derived osteogenic cells. To our knowledge, for the first time we report that CHIKV can productively infect BMMSCs. We observed a decrease in the intracellular and extracellular alkaline phosphatase (ALP) activity and reduction in calcium phosphate deposition in infected cells compared to mock-infected control. Thus, we conclude that CHIKV infects BMMSCs and disrupts function of osteogenic cells.\n\nImportanceAlthough studies have shown association of bone pathology and CHIKV infection, the pathogenesis of infection causing altered bone homeostasis is not fully understood. Here, we demonstrate for the first time that BMMSCs are susceptible to CHIKV infection. Furthermore, we observe that infection causes disruption in the function of BMMSC- derived osteogenic cells. Impaired function of these osteogenic cells will likely lead to a disruption in bone homeostasis and in part, provides a mechanism for the observed bone pathology associated with CHIKV pathogenesis.

microbiology↗