Biology subjects

Jiang, T.

Publications and source records attributed to Jiang, T..

At least 163 records · Page 9Linked to original sources

bioRxiv2019

Experimental study of lumbar ligamentum flavum hypertrophy induced in bipedal mice

Lumbar spinal stenosis (LSS) is a common degenerative disease among the elderly. The role that mechanical stress-induced hypertrophic ligamentum flavum (HLF) plays in patients with LSS remains unclear. Here, we used a finite element analysis to investigate the stress characteristics on the ligamentum flavum (LF) and evaluate the feasibility of a mouse model of HLF. First, we induced a bipedal posture in mice by taking advantage of their hydrophobia. A micro-CT scan was performed to examine their spinal change during bipedal posture. A finite element analysis showed that the stress and strain on the upright posture were significantly increased compared with those on the sprawling posture. Tissue staining showed that the degeneration degree of the LF in bipedal standing group gradually increased over the modeling period. The amount of elastic fibers decreased under HLF, whereas the amount of collagen fibers, the number of the LF cells, and the expression of fibrosis-related factors increased. Compared with aged group, LF degeneration was more severe in the bipedal standing group. Our findings demonstrate that the increased stress caused by a posture change causes HLF and that a bipedal mouse model can be used to study HLF in vivo.

biophysics↗

bioRxiv2019

Branched-Chain Amino Acid Metabolic Reprogramming Orchestrates Drug Resistance to EGFR Tyrosine Kinase Inhibitors

Drug resistance is a significant hindrance to effective cancer treatment. Although resistance mechanisms of epidermal growth factor receptor (EGFR)-mutant cancer cells to lethal EGFR tyrosine kinase inhibitors (TKI) treatment have been investigated intensively, how cancer cells orchestrate adaptive response under sublethal drug challenge remains largely unknown. Here we find that 2-hour sublethal TKI treatment elicits a transient drug-tolerant state in EGFR-mutant lung cancer cells. Continuous sublethal treatment reinforces this tolerance and eventually establishes long-term TKI resistance. This adaptive process involves H3K9 demethylation-mediated epigenetic upregulation of branched-chain amino acid aminotransferase 1 (BCAT1) and subsequent metabolic reprogramming, which promotes TKI resistance through attenuating reactive oxygen species (ROS) accumulation. Combinational treatment with TKI and ROS-inducing reagents overcomes this drug resistance in preclinical mouse models. Clinical information analyses support the correlation of BCAT1 expression with EGFR TKI response. Collectively, our findings reveal the importance of epigenetically regulated BCAT1-engaged metabolism reprogramming in TKI resistance in lung cancer.\n\nHIGHLIGHTSSublethal EGFR TKI treatment induces transient drug-tolerant state and long-term resistance in EGFR-mutant lung cancer cells\n\nEpigenetically regulated BCAT1-mediated metabolic reprogramming orchestrates EGFR TKI-induced drug resistance\n\nCombinational treatment with TKI and ROS-inducing agents overcomes the drug resistance induced by EGFR TKI treatment

cancer biology↗

bioRxiv2019

A Network of Phosphatidylinositol 4,5-bisphosphate Binding Sites Regulate Gating of the Ca2+-activated Cl- Channel ANO1 (TMEM16A)

ANO1 (TMEM16A) is a Ca2+-activated Cl- channel that regulates diverse cellular functions including fluid secretion, neuronal excitability, and smooth muscle contraction. ANO1 is activated by elevation of cytosolic Ca2+ and modulated by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). Here we describe a closely concerted experimental and computational study, including electrophysiology, mutagenesis, functional assays, and extended sampling of lipid-protein interactions with molecular dynamics (MD) to characterize PI(4,5)P2 binding modes and sites on ANO1. ANO1 currents in excised inside-out patches activated by 270 nM Ca2+ at +100 mV are increased by exogenous PI(4,5)P2 with an EC50 = 1.24 {micro}M. The effect of PI(4,5)P2 is dependent on membrane voltage and Ca2+ and is explained by a stabilization of the ANO1 Ca2+-bound open state. Unbiased atomistic MD simulations with 1.4 mol% PI(4,5)P2 in a phosphatidylcholine bilayer identified 8 binding sites with significant probability of binding PI(4,5)P2. Three of these sites captured 85% of all ANO1 - PI(4,5)P2 interactions. Mutagenesis of basic amino acids near the membrane-cytosol interface found three regions of ANO1 critical for PI(4,5)P2 regulation that correspond to the same three sites identified by MD. PI(4,5)P2 is stabilized by hydrogen bonding between amino acid sidechains and phosphate/hydroxyl groups on PI(4,5)P2. Binding of PI(4,5)P2 alters the position of the cytoplasmic extension of TM6, which plays a crucial role in ANO1 channel gating, and increases the accessibility of the inner vestibule to Cl-ions. We propose a model consisting of a network of three PI(4,5)P2 binding sites at the cytoplasmic face of the membrane allosterically regulating ANO1 channel gating.\n\nSignificance statementMembrane proteins dwell in a sea of phospholipids that not only structurally stabilize the proteins by providing a hydrophobic environment for their transmembrane segments, but also dynamically regulate protein function. While many cation channels are known to be regulated by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), relatively little is known about anion channel regulation by phosphoinositides. Using a combination of patch clamp electrophysiology and atomistic molecular dynamics simulations, we have identified several PI(4,5)P2 binding sites in ANO1 (TMEM16A), a Cl- channel that performs myriad physiological functions from epithelial fluid secretion to regulation of electrical excitability. These binding sites form a band at the cytosolic interface of the membrane that we propose constitute a network to dynamically regulate this highly allosteric protein.

biophysics↗

bioRxiv2019

Controlling emulsification for organic solvent-based tissue clearing

Organic solvent-based tissue clearing techniques are hampered by the quenching of fluorescent proteins, partially due to routine complete dehydration. Unexpectedly, we discovered that complete dehydration is unnecessary for organic solvents to clear tissues and that the hidden purpose has been to prevent emulsification. After controlling emulsification of organic solvent-cleared but incompletely dehydrated mouse brain, we achieved sufficient tissue transparency that allowed light-sheet imaging while well-preserving the fluorescence of fluorescent proteins.

neuroscience↗

bioRxiv2019

Identification of viruses with the potential to infect human

The virus has caused much mortality and morbidity to humans, and still posed a serious threat to the global public health. The virome with the human-infection potential is far from complete. Novel viruses have been discovered at an unprecedented pace as the rapid development of viral metagenomics. However, there is still a lack of a method for rapidly identifying the virus with the human-infection potential. This study built several machine learning models for discriminating the human-infecting viruses from other viruses based on the frequency of k-mers in the viral genomic sequences. The k-nearest neighbor (KNN) model could predict the human-infecting virus with an accuracy of over 90%. Even for the KNN models built on the contigs as short as 1kb, they performed comparably to those built on the viral genomes, suggesting that the models could be used to identify the human-infecting virus from the viral metagenomic sequences. This work could help for discovery of novel human-infecting virus in metagenomics studies.

bioinformatics↗

bioRxiv2019

Prediction of antiviral drugs against African Swine Fever Viruses based on protein-protein interaction analysis

The African swine fever virus (ASFV) has severely influenced the swine industry of the world. Unfortunately, there is no effective antiviral drug or vaccine against the virus until now. Identification of new anti-ASFV drugs is urgently needed. Here, an up-to-date set of protein-protein interactions (PPIs) between ASFV and swine were curated by integration of PPIs from multiple sources. Thirty-two swine proteins were observed to interact with ASFVs and were defined as AIPs. They were found to play a central role in the swine PPI network, with significant larger degree, betweenness and smaller shortest path length than other swine proteins. Some of AIPs also interacted with several other viruses and could be taken as potential targets of drugs for broad-spectrum effect, such as HSP90AB1. Finally, the antiviral drugs which targeted AIPs and ASFV proteins were predicted. Several drugs with either broad-spectrum effect or high specificity on AIPs were identified, such as Polaprezinc. This work could not only deepen our understanding towards the ASFV-swine interactions, but also help for the development of effective antiviral drugs against the ASFVs.

bioinformatics↗

bioRxiv2019

Hierarchy of connectivity-function relationship of the human cortex revealed through predicting activity across functional domains

Many studies showed that anatomical connectivity supports both anatomical and functional hierarchies that span across the primary and association cortices in the cerebral cortex. However, it remains unclear whether a hierarchy of connectivity-function relationship (CFR) exists across the human cortex as well as how to characterize the hierarchy of this CFR if it exists. We first addressed whether anatomical connectivity could be used to predict functional activations across different functional domains using multilinear regression models. Then we characterized the CFR by predicting activity from anatomical connectivity throughout the cortex. We found that there is a hierarchy of CFR across the human cortex. Moreover, this CFR hierarchy was correlated to the functional and anatomical hierarchy reflected in functional flexibility, functional variability, and the myelin map. Our results suggest a shared hierarchical mechanism in the cortex, a finding which provides important insights into the anatomical and functional organization of the human brain.

neuroscience↗

bioRxiv2019

OMGS: Optical Map-based Genome Scaffolding

Due to the current limitations of sequencing technologies, de novo genome assembly is typically carried out in two stages, namely contig (sequence) assembly and scaffolding. While scaffolding is computationally easier than sequence assembly, the scaffolding problem can be challenging due to the high repetitive content of eukaryotic genomes, possible mis-joins in assembled contigs and inaccuracies in the linkage information. Genome scaffolding tools either use paired-end/mate-pair/linked/Hi-C reads or genome-wide maps (optical, physical or genetic) as linkage information. Optical maps (in particular Bionano Genomics maps) have been extensively used in many recent large-scale genome assembly projects (e.g., goat, apple, barley, maize, quinoa, sea bass, among others). However, the most commonly used scaffolding tools have a serious limitation: they can only deal with one optical map at a time, forcing users to alternate or iterate over multiple maps. In this paper, we introduce a novel scaffolding algorithm called OMGS that for the first time can take advantages of multiple optical maps. OMGS solves several optimization problems to generate scaffolds with optimal contiguity and correctness. Extensive experimental results demonstrate that our tool outperforms existing methods when multiple optical maps are available, and produces comparable scaffolds using a single optical map. OMGS can be obtained from https://github.com/ucrbioinfo/OMGS

bioinformatics↗

bioRxiv2019

Genetic determinants in Salmonella enterica serotype Typhimurium required for overcoming stressors in the host environment

Salmonella enterica serovar Typhimurium (S. Typhimurium), a non-typhoidal Salmonella (NTS), result in a range of diseases, including self-limiting gastroenteritis, bacteremia, enteric fever, and focal infections representing a major disease burden worldwide. There is still a significant portion of Salmonella genes whose functional basis to overcome host innate defense mechanisms, consequently causing disease in host, largely remains unknown. Here, we have applied a high-throughput transposon sequencing (Tn-seq) method to unveil the genetic factors required for the growth or survival of S. Typhimurium under various host stressors simulated in vitro. A highly saturating Tn5 library of S. Typhimurium 14028s was subjected to selection during growth in the presence of short chain fatty acid (100 mM propionate), osmotic stress (3% NaCl) or oxidative stress (1 mM H2O2) or survival in extreme acidic pH (30 min in pH3) or starvation (12 days in 1X PBS). We have identified an overlapping set of 339 conditionally essential genes (CEGs) required by S. Typhimurium to overcome these host insults. Interestingly, entire eight genes encoding F0F1-ATP synthase subunit proteins were required for fitness in all five stresses. Intriguingly, total 88 genes in Salmonella pathogenicity island (SPI), including SPI-1, SPI-2, SPI-3, SPI-5, SPI-6 and SPI-11 are also required for fitness under the in vitro conditions evaluated in this study. Additionally, by comparative analysis of the genes identified in this study and the genes previously shown to be required for in vivo fitness, we identified novel genes (marBCT, envF, barA, hscA, rfaQ, rfbI and putative proteins STM14_1138, STM14_3334, STM14_4825, and STM_5184) that has compelling potential to be exploited as vaccine development and/or drug target to curb the Salmonella infection.

microbiology↗

bioRxiv2019

Direct control of shell regeneration by the mantle tissue in the pearl oyster Pinctada fucata via accelerating CaCO3 nucleation

Molluscan bivalves rapidly repair the damaged shells to prevent further injury. However, it remains unclear how this process is precisely controlled. In this study, we applied scanning electronic microscopy, transmission electronic microscopy and histochemical analysis to examine the detailed shell regeneration process of the pearl oyster Pinctada fucata. It was found that the shell damage caused the mantle tissue to retract, which resulted in dislocation of the mantle zones to their correspondingly secreted shell layers. However, the secretory repertoires of the different mantle zones remained unchanged. As a result, the dislocation of the mantle tissue dramatically affected the shell morphology, and the unusual presence of the submarginal zone on the nacreous layers caused de novo precipitation of prismatic layers on the nacreous layers. Real-time PCR revealed that the expression of the shell matrix proteins (SMPs) were significantly upregulated, which was confirmed by the thermal gravimetric analysis (TGA) of the newly formed shell. The increased matrix secretion accelerated CaCO3 nucleation thus promoting shell deposition. Taken together, our study revealed the close relationship between the physiological activities of the mantle tissue and the morphological change of the regenerated shells.

zoology↗

bioRxiv2019

Common functional networks in the mouse brain revealed by multi-centre resting-state fMRI analysis

Preclinical applications of resting-state functional magnetic resonance imaging (rsfMRI) offer the possibility to non-invasively probe whole-brain network dynamics and to investigate the determinants of altered network signatures observed in human studies. Mouse rsfMRI has been increasingly adopted by numerous laboratories world-wide. Here we describe a multi-centre comparison of 17 mouse rsfMRI datasets via a common image processing and analysis pipeline. Despite prominent cross-laboratory differences in equipment and imaging procedures, we report the reproducible identification of several large-scale resting-state networks (RSN), including a murine default-mode network, in the majority of datasets. A combination of factors was associated with enhanced reproducibility in functional connectivity parameter estimation, including animal handling procedures and equipment performance. Our work describes a set of representative RSNs in the mouse brain and highlights key experimental parameters that can critically guide the design and analysis of future rodent rsfMRI investigations.

neuroscience↗

bioRxiv2019

Same-Species Contamination Detection with Variant Calling Information from Next Generation Sequencing

MotivationSame-species contamination detection is an important quality control step in genetic data analysis. Compared with widely discussed cross-species contamination, same-species contamination is more challenging to detect, and there is a scarcity of methods to detect and correct for this quality control issue. Same-species contamination may be due to contamination by lab technicians or samples from other contributors. Here, we introduce a novel machine learning algorithm to detect same species contamination in next generation sequence data using support vector machines. Our approach uniquely detects such contamination using variant calling information stored in the variant call format (VCF) files (either DNA or RNA), and importantly can differentiate between same species contamination and mixtures of tumor and normal cells. MethodsIn the first stage of our approach, a change-point detection method is used to identify copy number variations or copy number aberrations (CNVs or CNAs) for filtering prior to testing for contamination. Next, single nucleotide polymorphism (SNP) data is used to test for same species contamination using a support vector machine model. Based on the assumption that alternative allele frequencies in next generation sequencing follow the beta-binomial distribution, the deviation parameter {rho} is estimated by maximum likelihood method. All features of a radial basis function (RBF) kernel support vector machine (SVM) are generated using either publicly available or private training data. Lastly, the generated SVM is applied in the test data to detect contamination. If training data is not available, a default RBF kernel SVM model is used. ResultsWe demonstrate the potential of our approach using simulation experiments, creating datasets with varying levels of contamination. The datasets combine, in silico, exome sequencing data of DNA from two lymphoblastoid cell lines (NA12878 and NA10855). We generated VCF files using variants identified in these data, and then evaluated the power and false positive rate of our approach to detect same species contamination. Our simulation experiments show that our method can detect levels of contamination as low as 5% with reasonable false positive rates. Results in real data have sensitivity above 99.99% and specificity at 90.24%, even in the presence of DNA degradation that has similar features to contaminated samples. Additionally, the approach can identify the difference between mixture of tumor-normal cells and contamination. We provide an R software implementation of our approach using the defcon()function in the vanquish: Variant Quality Investigation Helper R package on CRAN.

bioinformatics↗

bioRxiv2018

Genetically distinct clinical subsets, and associations with asthma and eosinophil abundance, within Eosinophilic Granulomatosis with Polyangiitis

Eosinophilic granulomatosis with polyangiitis (EGPA: formerly Churg-Strauss syndrome) is a rare inflammatory disease of unknown cause. 30% of patients have anti-neutrophil cytoplasm antibodies (ANCA) specific for myeloperoxidase (MPO). We performed a genome-wide association study (GWAS) of EGPA, testing 7.5 million genetic variants in 684 cases and 6,838 controls. Case-control analyses were performed for EGPA as a whole, and stratified by ANCA. To increase power, we used a conditional false discovery rate method to leverage findings from GWASs of related phenotypes. In total, 11 variants were associated with EGPA, two specifically with ANCA-negative EGPA, and one (HLA-DQ) with MPO+ANCA EGPA. Many variants were associated with asthma, eosinophilic and immune-mediated diseases and, strikingly, nine were associated with eosinophil count in the general population. Through Mendelian randomisation, we show that a primary tendency to eosinophilia underlies EGPA susceptibility. We demonstrate that EGPA comprises two genetically and clinically distinct syndromes, with ANCA-negative EGPA genetically more similar to asthma. MPO+ ANCA EGPA is an eosinophilic autoimmune disease sharing certain clinical features and an MHC association with MPO+ ANCA-associated vasculitis, while ANCA-negative EGPA may instead have a mucosal/barrier dysfunction origin. Five identified candidate genes are targets of therapies in development, supporting their exploration in EGPA.

genetics↗

bioRxiv2018

Characterization of functional diversity of the human brain based on intrinsic connectivity networks

Spontaneous fluctuations underlying the brain activity can reflect the intrinsic organization of the system, such as the functional brain networks. In large scale, a network perspective has emerged as a new avenue to explore the functional properties of human brain. Here, we studied functional diversity in healthy subjects based on the network perspective. We hypothesized that the patterns of participation of different functional networks were related with the functional diversity of particular brain regions. Independent component analysis (ICA) was adopted to detect the intrinsic connectivity networks (ICNs) based on the data of resting-state functional MRI. An index of functional diversity (FD index) was proposed to quantitatively describe the degree of anisotropic distribution related with participation of various ICNs. We found that FD index continuously varied across the brain, for example, the primary motor cortex with low FD value and the precuneus with significantly high FD value. The FD values indicated the different functional roles of the corresponding brain regions, which were reflected by the various patterns of participation of ICNs. The FD index can be used as a new approach to quantitatively characterize the functional diversity of human brain, even for the changed functional properties caused by the psychiatric disorders.

neuroscience↗

bioRxiv2018

Homologous recombination shapes the genetic diversity and drives the evolution of African swine fever viruses

Recent outbreaks of African swine fever virus (ASFV) in China severely influenced the swine industry of the country. Currently, there is no effective vaccine or drugs against ASFVs. How to effectively control the virus is challenging. In this study, we have analyzed all the publicly available ASFV genomes and demonstrated that there was a large genetic diversity of ASFV genomes. Interestingly, the genetic diversity was mainly caused by extensive genomic insertions and/or deletions (indels) instead of the point mutations. The genomic diversity of the virus resulted in proteome diversity. Over 250 types of proteins were inferred from the ASFV genomes, among which only 144 were observed in all analyzed viruses. Further analyses showed that the homologous recombination may contribute much to the indels, as supported by significant associations between the occurrence of extensive recombination events and the indels in the ASFV genomes. Repeated elements of dozens of nucleotides in length were observed to widely distribute and cluster in the adjacent positions of ASFV genomes, which may facilitate the occurrence of homologous recombination. Moreover, two enzymes, which were possibly related to the homologous recombination, i.e., a Lambda-like exonuclease with a YqaJ-like viral recombinase domain, and a DNA topoisomerase II, were found to be conservative in all the analyzed ASFVs. This work highlighted the importance of the homologous recombination in the evolution of the ASFVs, and helped with the strategy development of the prevention and control of the virus.

microbiology↗

bioRxiv2018

rMETL: sensitive and fast mobile element insertion detection with long read realignment

SummaryMobile element insertion (MEI) is a major category of structure variations (SVs). The rapid development of long read sequencing provides the opportunity to sensitively discover MEIs. However, the signals of MEIs implied by noisy long reads are highly complex, due to the repetitiveness of mobile elements as well as the serious sequencing errors. Herein, we propose Realignment-based Mobile Element insertion detection Tool for Long read (rMETL). rMETL takes advantage of its novel chimeric read re-alignment approach to well handle complex MEI signals. Benchmarking results on simulated and real datasets demonstrated that rMETL has the ability to more sensitivity discover MEIs as well as prevent false positives. It is suited to produce high quality MEI callsets in many genomics studies.\n\nAvailability and Implementation: rMETL is available from https://github.com/hitbc/rMETL.\n\nContact: ydwang@hit.edu.cn\n\nSupplementary information: Supplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2018

Identification of genome-wide nucleotide sites associated with mammalian virulence in influenza A viruses

MotivationThe virulence of influenza viruses is a complex multigenic trait. Previous studies about the virulence determinants of influenza viruses mainly focused on amino acid sites, ignoring the influence of nucleotide mutations.\n\nResultsWe collected more than 200 viral strains from 21 subtypes of influenza A viruses with virulence in mammals and obtained over 100 mammalian virulence-related nucleotide sites across the genome by computational analysis. Interestingly, 50 of these nucleotide sites only experienced synonymous mutations. Further experiments showed that synonymous mutations in the top two of these nucleotide sites, i.e., PB1-2031 and PB1-633, enhanced the pathogenicity of the viruses in mice. Finally, machine-learning models with accepted accuracy for predicting mammalian virulence of influenza A viruses were built. Overall, this study highlighted the importance of nucleotide mutations, especially synonymous mutations in viral virulence, and provided rapid methods for evaluating the virulence of influenza A viruses. It could be helpful for early warning of newly emerging influenza A viruses.

microbiology↗

bioRxiv2018

Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity

Since its outbreak in 2007, Zika virus (ZIKV) has become a global health threat that causes severe neurological conditions. Here we perform a comparative in vivo structural analysis of the RNA genomes of two ZIKV strains to decipher the regulation of their infection at the RNA level. Our analysis identified both known and novel functional RNA structural elements. We discovered a functional long-range intramolecular interaction specific for the Asian epidemic strains, which contributes to their infectivity. Our findings illuminate the structural basis of ZIKV regulation and provide a rich resource for the discovery of RNA structural elements that are important for ZIKV infection.

molecular biology↗