Biology subjects

Xia, K.

Publications and source records attributed to Xia, K..

31 records · Page 2Linked to original sources

bioRxiv2021

Golgi structural defect impairs glycosaminoglycan synthesis, sulfation, and secretion

Synthesis of glycosaminoglycans such as heparan sulfate (HS) and chondroitin sulfate (CS) occurs in the lumen of the Golgi but the relationship between Golgi structural integrity and glycosaminoglycan synthesis is not clear. In this study, we disrupted the Golgi structure by knocking out GRASP55 and GRASP65 and determined its effect on the synthesis, sulfation, and secretion of HS and CS. We found that GRASP depletion increased HS synthesis while decreasing CS synthesis in cells, altered HS and CS sulfation, and reduced both HS and CS secretion. Using proteomics, RNA-seq and biochemical approaches, we identified EXTL3, a key enzyme in the HS synthesis pathway, whose level is upregulated in GRASP knockout cells; while GalNacT1, an essential CS synthesis enzyme, is robustly reduced. In addition, we found that GRASP depletion decreased HS sulfation via the reduction of PAPSS2, a bifunctional enzyme in HS sulfation. Our study provides the first evidence that Golgi structural defect may significantly alter the synthesis and secretion of glycosaminoglycans.

cell biology↗

bioRxiv2021

Performance Comparison of Computational Prediction Methods for the Function and Pathogenicity of Non-coding Variants

Non-coding variants in the human genome greatly influence some traits and complex diseases by their own regulation and modification effects. Hence, an increasing number of computational methods are developed to predict the effects of variants in the human non-coding sequences. However, it is difficult for users with insufficient knowledge about the performances of computational methods to select appropriate computational methods from dozens of methods. In order to solve this problem, we assessed 12 performance measures of 24 methods on four independent non-coding variant benchmark datasets: (I) rare germline variant from ClinVar, (II) rare somatic variant from COSMIC, (III) common regulatory variant dataset, and (IV) disease associated common variant dataset. All 24 tested methods performed differently under various conditions, indicating that these methods have varying strengths and weaknesses under different scenarios. Importantly, the performance of existing methods was acceptable in the rare germline variant from ClinVar with area under curves (AUCs) of 0.4481 - 0.8033 and poor in the rare somatic variant from COSMIC (AUCs: 0.4984 - 0.7131), common regulatory variant dataset (AUCs: 0.4837 - 0.6472), and disease associated common variant dataset (AUCs: 0.4766 -0.5188). We also compared the prediction performance among 24 methods for non-coding de novo mutations in autism spectrum disorder and found that the CADD and CDTS methods showed better performance. Summarily, we assessed the performances of 24 computational methods under diverse scenarios, providing preliminary advice for proper tool selection and new method development in interpreting non-coding variants.

bioinformatics↗

bioRxiv2021

miR2105 regulates ABA biosynthesis via OsbZIP86-OsNCED3 module to contribute to drought tolerance in rice

Induced abscisic acid (ABA) biosynthesis plays an important role in plant tolerance to abiotic stresses, including drought, cold and salinity. However, regulation pathway of the ABA biosynthesis in response to stresses is unclear. Here, we identified a rice miRNA, osa-miR2105 (miR2105), which plays a crucial role in ABA biosynthesis under drought stress. Analysis of expression, transgenic rice and cleavage site showed that OsbZIP86 is a target gene of miR2105. Subcellular localization and luciferase activity assays showed that OsbZIP86 is a nuclear transcription factor. In vivo and in vitro analyses showed that OsbZIP86 directly binds to the promoter of OsNCED3, and interacts with OsSAPK10, resulting in enhanced-expression of OsNCED3. Transgenic rice plants with knock-down of miR2105 or overexpression of OsbZIP86 showed higher ABA content, more tolerance to drought, a lower rate of water loss, more stomatal closure than wild type rice ZH11 under drought stress. These rice plants showed no penalty with respect to agronomic traits under normal conditions. By contrast, transgenic rice plants with miR2105 overexpression, OsbZIP86 downregulation, or OsbZIP86 knockout displayed less tolerance to drought stress and other phenotypes. Collectively, our results show that a regulatory network of miR2105-OsSAPK10/OsbZIP86-OsNCED3 control ABA biosynthesis in response to drought stress. One-sentence summary miR2105-OsbZIP86-OsNCED3 module plays crucial role in mediating ABA biosynthesis to contribute to drought tolerance with no penalty with respect to agronomic traits under normal conditions.

molecular biology↗

bioRxiv2021

p57Kip2 regulates embryonic haematopoietic stem cell numbers by controlling the size of the sympathoadrenal progenitor pool

Haematopoietic stem cells (HSCs) are of major clinical importance, and finding methods for their in vitro generation is a prime research focus. We demonstrate that the cell cycle inhibitor p57Kip2/Cdkn1c limits HSC numbers by restricting the size of the sympathetic nervous system (SNS) and the amount of HSC-supportive catecholamines secreted by these cells, specifically in the aorta-gonads-mesonephros (AGM) region via {beta}2-adrenergic receptor signalling. This regulation occurs at the SNS progenitor level and is in contrast to the cell-intrinsic function of p57Kip2 in maintaining adult HSCs. Using single-cell RNA-Seq we dissect the differentiation pathway of neural crest cells into SNS cells in the AGM and reveal that they are able to take an alternative differentiation pathway, giving rise to a subset of mesenchymal cells expressing HSC-supportive factors. Neural crest cells thus appear to contribute to the AGM HSC niche via two different mechanisms: SNS-mediated catecholamine secretion and HSC-supportive mesenchymal cell production.

developmental biology↗

bioRxiv2021

AAV-mediated gene therapy produces fertile offspring in the Lhcgr-deficient mouse model of Leydig cell failure

Leydig cell failure (LCF) caused by gene mutation results in testosterone deficiency and infertility. Serum testosterone levels can be recovered via testosterone replacement; however, established therapies have shown limited success in restoring fertility. Here, we used a luteinizing hormone/choriogonadotrophin receptor (Lhcgr)-deficient mouse model of genetic LCF to investigate the feasibility of gene therapy for restoring testosterone production and fertility. We screened several adeno-associated virus (AAV) serotypes and identified AAV8 as an efficient vector to drive exogenous Lhcgr expression in progenitor Leydig cells through interstitial injection. We observed considerable testosterone recovery and Leydig cell maturation after AAV8-Lhcgr treatment in pubertal Lhcgr-/- mice. This gene therapy substantially recovered sexual development, partially restored spermatogenesis and effectively produced fertile offspring. Furthermore, these favorable effects could be reproduced in adult Lhcgr-/- mice. Our proof-of-concept experiments in this mouse model demonstrate that AAV-mediated gene therapy may represent a promising therapeutic approach for patients with genetic LCF.

developmental biology↗

bioRxiv2021

The plastid genome characteristics of a moth orchid (Phalaenopsis wilsoniii, Orchidaceae)

Phalaenopsis wilsonii is a typical deciduous species in the horticulturally well-known genus, Phalaenopsis. Tshi species is belonging to the section Aphyllae in moth orchid, and is endemic to South China. Although the Aphyllae section display the deciduous feature that is unique in this genus, their genetic information is still insufficient and limited them as breeding parent in moth orchid. Here, we reported and characterized the complete chloroplast genome for Phalaenopsis wilsonii. We found the total size of the chloroplast genome was 145,373 bp, constituting of a large single copy (LSC) region (84,996 bp), a small single-copy region (10,668 bp) and two inverted repeats (IRs) regions (24,855 bp). Based on homologous searching on database, we annotated 76 protein-coding genes, 38 tRNA, and 8 rRNA. The phylogenetic reconstruction revealed that P. wilsonii show the closest relationship with P. lowii within subgenus Parishianae.

genomics↗

bioRxiv2021

Customized de novo mutation detection for any variant calling pipeline: SynthDNM

MotivationAs sequencing technologies and analysis pipelines evolve, DNM calling tools must be adapted. Therefore, a flexible approach is needed that can accurately identify de novo mutations from genome or exome sequences from a variety of datasets and variant calling pipelines. ResultsHere, we describe SynthDNM, a random-forest based classifier that can be readily adapted to new sequencing or variant-calling pipelines by applying a flexible approach to constructing simulated training examples from real data. The optimized SynthDNM classifiers predict de novo SNPs and indels with robust accuracy across multiple methods of variant calling. AvailabilitySynthDNM is freely available on Github (https://github.com/james-guevara/synthdnm) Contactjsebat@ucsd.edu Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

A human antibody with blocking activity to RBD proteins of multiple SARS-CoV-2 variants including B.1.351 showed potent prophylactic and therapeutic efficacy against SARS-CoV-2 in rhesus macaques

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which causes coronavirus disease-2019 (COVID-19), interacts with the host cell receptor angiotensin-converting enzyme 2 (hACE2) via its spike 1 protein for infection. After the virus sequence was published, we identified two potent antibodies against SARS-CoV-2 RBD from antibody libraries using a phage-to-yeast (PtY) display platform in only 10 days. Our lead antibody JMB2002, now in a phase I clinical trial, showed broad-spectrum in vitro blocking activity against hACE2 binding to the RBD of multiple SARS-CoV-2 variants including B.1.351 that was reportedly much more resistant to neutralization by convalescent plasma, vaccine sera and some clinical stage neutralizing antibodies. Furthermore, JMB2002 has demonstrated complete prophylactic and potent therapeutic efficacy in a rhesus macaque disease model. Prophylactic and therapeutic countermeasure intervention of SARS-CoV-2 using JMB2002 would likely slow down the transmission of currently emerged SARS-CoV-2 variants and result in more efficient control of the COVID-19 pandemic.

microbiology↗

bioRxiv2020

Efficient Multiplex Genome Editing Tools Identified by Protoplast Technology in Phalaenopsis

Phalaenopsis orchids are popular ornamental plants worldwide. The application of the efficient multiplex genome editing tools in Phalaenopsis, will greatly accelerate the development of orchid gene function and breeding research. In this study, we establish a fast and convenient Phalaenopsis protoplast platform for the identification of functional genome editing tools. Two multiplex genome editing tools, PTG-Cas9 (PTG, polycistronic tRNA gRNA) system and PTGm-Cas9 (PTG-Cas9 system with modified sgRNA structure) system are designed to edit PDS gene of commercial Phalaenopsis ST166 at four target sites. We find that both PTG-Cas9 and PTGm-Cas9 system are functional in Phalaenopsis, and the PTGm-Cas9 system with modified sgRNA has a higher editing efficiency than PTG-Cas9 system. Further, we design another multiplex genome editing tool, termed as DPII-Cpf1 system (dual Pol II promoter to drive the expression of Cpf1 endonuclease and crRNA), to edit PDS gene of Phalaenopsis at four target sites likewise. All the four targets are efficiently edited by DPII-Cpf1 system, and the total mutation rate is about 3 times higher than that of PTGm-Cas9 system. Taken together, using the Phalaenopsis protoplast platform, we successfully establish two efficient multiplex genome editing tools for Phalaenopsis research, PTGm-Cas9 and DPII-Cpf1. The multiplex genome editing tools established in this study have great application potentials in efficiently constructing large-scale knockout mutant libraries of orchid and speeding up orchid precise breeding.

plant biology↗

bioRxiv2020

Inhibiting proBDNF to mature BDNF conversion leads to autism-like phenotypes in vivo

Autism spectrum disorders (ASD) comprise a range of early age-onset neurodevelopment disorders with genetic heterogeneity. Most ASD related genes are involved in synaptic function, which is oppositely regulated by brain-derived neurotrophic factor (BDNF): the precursor proBDNF inhibits while mature BDNF (mBDNF) potentiates synapses. Here we generated a knock-in mouse line (BDNFmet/leu) in which the conversion of proBDNF to mBDNF is inhibited. Biochemical experiments revealed residual mBDNF but excessive proBDNF in the brain. Similar to other ASD mouse models, the BDNFmet/leu mice showed decreased brain volumes, reduced dendritic arborization, altered spines, and impaired synaptic transmission and plasticity. They also exhibited ASD-like phenotypes, including stereotypical behaviors, deficits in social interaction, hyperactivity, and elevated stress response. Interestingly, the plasma level of proBDNF, but not mBDNF, was significantly elevated in ASD patients. These results suggest that proBDNF level, but not Bdnf gene, is associated with autism-spectrum behaviors, and identify a potential blood marker and therapeutic target for ASD.

neuroscience↗

bioRxiv2020

Sorting liposomes of distinct sizes by DNA-brick assisted centrifugation

The "tiny bubbles of fluid" wrapped by lipid-bilayer membranes, termed vesicles, are abundant in cells and extracellular space, performing critical tasks including nutrient uptake, cargo transport, and waste confinement. Vesicles on different missions and transport routes are often distinct both in size and in chemical composition, which confers specificity to their interactions with other membranous compartments. Therefore, to accurately recapitulate the vesicles structure and behavior, it is important to use homogeneous liposomes (vesicles made of synthetic components) with precisely defined attributes as model membranes. Although existing methods can generate liposomes of selected sizes with reasonable homogeneity, the scalable production of uniformly-sized liposomes across a wide range of dimensions and compositions remains challenging. Here we report a streamlined, high-throughput sorting technique that uses cholesterol-modified "nanobricks" made of a few DNA oligonucleotides to differentiate hetero-sized liposomes by their buoyant densities. After DNA-brick coating, milligrams of liposomes of different origins (e.g., produced via extrusion or sonication, and reconstituted with membrane proteins) can be separated by centrifugation into six to eight homogeneous populations with mean diameters from 30 to 130 nm. In proof of concept experiments, we show that these uniform, leak-free liposomes are ideal substrates to study, with an unprecedented resolution, how membrane curvature influences the activity of peripheral (ATG3) and integral (SNARE) membrane proteins. We anticipate that our sorting technique will facilitate the quantitative understanding of membrane curvature in vesicular transport. Furthermore, adding a facile and standardized separation step to the conventional liposome preparation pipeline may benefit the formulation and prototyping of liposomal drug-carrying vehicles.

biophysics↗

bioRxiv2019

Magnus Representation of Genome Sequences

We introduce an alignment-free method, the Magnus Representation, to analyze genome sequences. The Magnus Representation captures higher-order information in genome sequences. We combine our approach with the idea of k-mers to define an effectively computable Mean Magnus Vector. We perform phylogenetic analysis on three datasets: mosquito-borne viruses, filoviruses, and bacterial genomes. Our results on ebolaviruses are consistent with previous phylogenetic analyses, and confirm the modern viewpoint that the 2014 West African Ebola outbreak likely originated from Central Africa. Our analysis also confirms the close relationship between Bundibugyo ebolavirus and Tai Forest ebolavirus. For bacterial genomes, our method is able to classify relatively well at the family and genus level, as well as at higher levels such as phylum level. The bacterial genomes are also separated well into Gram-positive and Gram-negative subgroups.

genomics↗

bioRxiv2018

Flexibility and rigidity index for chromosome packing, flexibility and dynamics analysis

MotivationThe packing of genomic DNA from double string into highly-order hierarchial assemblies has great impact on chromosome flexibility, dynamics and functions. The open and accessible regions of chromosome are the primary binding positions for regulatory elements and are crucial to nuclear processes and biological functions.\n\nResultsMotivated by the success of flexibility-rigidity index (FRI) in biomolecular flexibility analysis and drug design, we propose a FRI based model for quantitatively characterizing the chromosome flexibility. Based on the Hi-C data, a flexibility index for each locus can be evaluated. Physically, the flexibility is tightly related to the packing density. Highly compacted regions are usually more rigid, while loosely packed regions are more flexible. Indeed, a strong correlation is found between our flexibility index and DNase and ATAC values, which are measurements for chromosome accessibility. Recently, Gaussian network model (GNM) is applied to analyze the chromosome accessibility and a mobility profile has been proposed to characterize the chromosome flexibility. Compared with GNM, our FRI is slightly more accurate (1% to 2% increase) and significantly more efficient in both computational time and costs. For a 5kb resolution Hi-C data, the flexibility evaluation process only takes FRI a few minutes on a single-core processor. In contrast, GNM requires 1.5 hours on 10 CPUs. Moreover, interchromosome information can be easily incorporated into the flexibility evaluation, thus further enhance the accuracy of our FRI. In contrast, the consideration of interchromosome information into GNM will significantly increase the size of its Laplacian matrix, thus computationally extremely challenging for the current GNM.\n\nAvailabilityThe software is available at https://github.com/jiajiepeng/FRI_chrFle.\n\nContactxiakelin@ntu.edu.sg; jiajiepeng@nwpu.edu.cn

bioinformatics↗