Biology subjects

Duan, B.

Publications and source records attributed to Duan, B..

5 recordsLinked to original sources

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↗