Biology subjects

Zhao, G.

Publications and source records attributed to Zhao, G..

122 records · Page 7Linked to original sources

bioRxiv2019

Copper Induces Zebrafish Central Neural System Myelin Defects: the Regulatory Mechanisms in Wnt/Notch-hoxb5b Signaling and Underlying DNA Methylation

Unbalanced copper (Cu2+) homeostasis is associated with neurological development defects and diseases. However, the molecular mechanisms remain elusive. Here, central neural system (CNS) myelin defects and down-regulated expression of Wnt/Notch signaling and their down-stream mediator hoxb5b were observed in Cu2+ stressed zebrafish larvae. Loss/knockdown-of-function of hoxb5b phenocopied the myelin and axon defects observed in Cu2+ stressed embryos. Meanwhile, activation of Wnt/Notch signaling and ectopic expression of hoxb5b could rescue copper-induced myelin defects, suggesting Wnt&Notch-hoxb5b axis mediated Cu2+ induced myelin and axon defects. Additionally, whole genome DNA methylation sequencing unveiled that a novel gene fam168b, similar to pou3f1/2, exhibited significant promoter hypermethylation and reduced expression in Cu2+ stressed embryos. The hypermethylated locus in fam168b promoter acted pivotally in its transcription, and loss/knockdown of fam168b/pou3f1 also induced myelin defects. Moreover, this study unveiled that fam168b/pou3f1 and hoxb5b axis acted in a seesaw manner during fish embryogenesis, and demonstrated that copper induced the down-regulated expression of the Wnt&Notch-hoxb5b axis dependent of the function of copper transporter cox17, coupled with the promoter methylation of genes fam168b/pou3f1 and their subsequent down-regulated expression dependent of the function of another transporter atp7b, making joint contributions to myelin defects in embryos. Those data will shed some light on the linkage of unbalanced copper homeostasis with specific gene promoter methylation and signaling transduction as well as the resultant neurological development defects and diseases. Author summaryIn this study, we first unveiled that copper induced central neural system (CNS) myelin defects via down-regulating Wnt/Notch-hoxb5b signaling, and parallel with hypermethylating promoters of genes fam168b/pou3f2 and their subsequent down-regulated expression. Additionally, we unveiled that fam168b/pou3f1 and hoxb5b axis acted in a seesaw manner during fish embryogenesis. Genetically, we unveiled that copper was trafficked to mitochondrion via cox17 then led to the down-regulation of Wnt&Notch-hoxb5b axis, and was trafficked to trans-Golgi network via atp7b to induce the hypermethylation and the down-regulated expression of pou3f1/fam168b genes, making joint contributions to myelin defects in embryos.

developmental biology↗

bioRxiv2019

SPOP Promotes Ubiquitination and Degradation of MyD88 to Suppress the Innate Immune Response

As a canonical adaptor for Toll-like receptor (TLR) family, MyD88 has crucial roles in host defence against infection of microbial pathogens and its dysregulation might induce autoimmune diseases. Here we demonstrate that the Cullin 3-based ubiquitin ligase adaptor SPOP recognizes the intermediate domain and degrades chMyD88 through the proteasome pathway. Knockdown or genetic ablation of chSPOP leads to aberrant elevation of the chMyD88 protein. Consequently, ChSPOP negatively regulates the activity of NF-{kappa}B pathway and thus the production of IL-1{beta} and IL-8 upon LPS challenge. Furthermore, SPOP deficiency mice are more susceptible to infection of Salmonella typhimurium. Collectively, these findings demonstrate chMyD88 as a bona fide substrate of chSPOP and uncover a mechanism by which chSPOP suppresses the innate immune signaling.\n\nAuthor SummaryMyD88 is a central adaptor mediating the initiate of innate immune response and production of proinflammatory cytokines that restrain pathogens and activate adaptive immunity. Although MyD88 is crucial for the host to prevent pathogenic infection, misregulation of MyD88 abundance might lead to autoimmune diseases. Thus, degradation of MyD88 is a canonical mechanism to terminate cytokines production. Here we characterized a novel E3 ligase SPOP that target MyD88 for degradation. SPOP attenuated IL1{beta} and IL8 production through K48-linked polyubiquitination and degradation of MyD88 and thus impaired immune responses. SPOP deficient mice show more susceptibility to infection by Salmonella typhimurium. These findings demonstrate that SPOP is a negative regulator of MyD88-dependent pathway activation triggered by LPS and Salmonella typhimurium, which helps the host to maintain immune homeostasis.

immunology↗

bioRxiv2019

AsCRISPR: a web server for allele-specific sgRNA design in precision medicine

Allele-specific genomic targeting by CRISPR provides a point of entry for personalized gene therapy of dominantly inherited diseases, by selectively disrupting the mutant alleles or disease-causing single nucleotide polymorphisms (SNPs), ideally while leaving normal alleles intact. Moreover, the allele-specific engineering has been increasingly exploited not only in treating inherited diseases and mutation-driven cancers, but also in other important fields such as genome imprinting, haploinsufficiency, genome loci imaging and immunocompatible manipulations. Despite the tremendous utilities of allele-specific targeting by CRISPR, very few bioinformatic tools have been implemented for the allele-specific purpose. We thus developed AsCRISPR (Allele-specific CRISPR), a web tool to aid the design of guide RNA (gRNA) sequences that can discriminate between alleles. It provides users with limited bioinformatics skills to analyze both their own identified variants and heterozygous SNPs deposited in the dbSNP database. Multiple CRISPR nucleases and their engineered variants including newly-developed Cas12b and CasX are included for users choice. Meanwhile, AsCRISPR evaluates the on-target efficiencies, specificities and potential off-targets of gRNA candidates, and also displays the allele-specific restriction enzyme sites that might be disrupted upon successful genome edits. In addition, AsCRISPR analyzed with dominant single nucleotide variants (SNVs) retrieved from ClinVar and OMIM databases, and generated a Dominant Database of candidate discriminating gRNAs that may specifically target the alternative allele for each dominant SNV site. A Validated Database was also established, which manually curated the discriminating gRNAs that were experimentally validated in the mounting literatures. AsCRISPR is freely available at http://www.genemed.tech/ascrispr.

bioinformatics↗

bioRxiv2019

HMGB1 mediates the development of tendinopathy due to mechanical overloading

Mechanical overloading is a major cause of tendinopathy, but the underlying pathogenesis of tendinopathy is unclear. Here we report that high mobility group box1 (HMGB1) is released to the tendon extracellular matrix and initiates an inflammatory cascade in response to mechanical overloading in a mouse model. Moreover, administration of glycyrrhizin (GL), a naturally occurring triterpene and a specific inhibitor of HMGB1, the tendons inflammatory reactions. Also, while prolonged mechanical overloading in the form of long-term intensive treadmill running induces Achilles tendinopathy in mice, administration of GL completely blocks the tendinopathy development. Additionally, mechanical overloading of tendon cells in vitro induces HMGB1 release to the extracellular milieu, thereby eliciting inflammatory and catabolic responses as marked by increased production of prostaglandin E2 (PGE2) and matrix metalloproteinase-3 (MMP-3) in tendon cells. Application of GL abolishes the cellular inflammatory/catabolic responses. Collectively, these findings point to HMGB1 as a key molecule that is responsible for the induction of tendinopathy due to mechanical overloading placed on the tendon.

cell biology↗

bioRxiv2019

Ctf4 organizes sister replisomes and Pol α into a replication factory

The current view is that eukaryotic replisomes are independent. Here we show that Ctf4 tightly dimerizes CMG helicase, with an extensive interface involving Psf2, Cdc45, and Sld5. Interestingly, Ctf4 binds only one Pol -primase. Thus, Ctf4 may have evolved as a trimer to organize two helicases and one Pol -primase into a replication factory. In the 2CMG-Ctf43-1Pol -primase factory model, the two CMGs nearly face each other, placing the two lagging strands toward the center and two leading strands out the sides. The single Pol -primase is centrally located and may prime both sister replisomes. The Ctf4-coupled-sister replisome model is consistent with cellular microscopy studies revealing two sister forks of an origin remain attached and are pushed forward from a protein platform. The replication factory model may facilitate parental nucleosome transfer during replication.

biochemistry↗

bioRxiv2019

Crl activates transcription by stabilizing the active conformation of the master stress factor σS

{sigma}S is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses and antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of {sigma}S-mediated transcription requires a {sigma}S-specific activator, Crl. In this study, we determined a 3.80 [A] cryo-EM structure of an E. coli transcription activation complex (E. coli Crl-TAC) comprising E. coli {sigma}S-RNAP holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with the domain 2 of {sigma}S ({sigma}S2), sharing no interaction with promoter DNA. Subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) results indicate that Crl stabilizes key structural motifs of {sigma}S2 to promote the assembly of {sigma}S-RNAP holoenzyme and also to facilitate formation of the RNA polymerase-promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells.

biochemistry↗

bioRxiv2019

The biosynthetic gene cluster of the C-nucleoside antibiotic pyrazomycin with a rare pyrazole moiety

Pyrazomycin is a rare C-nucleoside antibiotic with a naturally occurring pyrazole ring, whose biosynthetic origin has remained obscure for decades. In this study, we report the identification of the gene cluster responsible for pyrazomycin biosynthesis in Streptomyces candidus NRRL 3601, revealing that StrR-family regulator PyrR is the cluster-situated transcriptional activator governing pyrazomycin biosynthesis. Furthermore, our results from in vivo reconstitution and stable-isotope feeding experiments support that PyrN is a new nitrogen-nitrogen bond forming enzyme linking the {varepsilon}-NH2 nitrogen of O_SCPLOWLC_SCPLOW-N6-OH-lysine and -NH2 nitrogen of O_SCPLOWLC_SCPLOW-glutamate. This study lays the foundation for further genetic and biochemical characterization of pyrazomycin pathway enzymes constructing the characteristic pyrazole ring.

biochemistry↗

bioRxiv2019

Dysfunction of ventral tegmental area GABA neurons causes mania-like behavior

The ventral tegmental area (VTA), an important source of dopamine, regulates goal- and reward-directed and social behaviors, wakefulness and sleep. Hyperactivation of dopamine neurons generates behavioral pathologies. But any roles of non-dopamine VTA neurons in psychiatric illness have been little explored. Lesioning or chemogenetically inhibiting VTA GABAergic (VTAVgat) neurons generated persistent wakefulness with mania-like qualities: locomotor activity was increased; sensitivity to D-amphetamine was heightened; immobility times decreased on the tail suspension and forced swim tests; and sucrose preference increased. Furthermore, after sleep deprivation, mice with lesioned VTAVgat neurons did not catch up on the lost NREM sleep, even though they were starting from an already highly sleep-deprived baseline, suggesting that the sleep homeostasis process was bypassed. The mania-like behaviors, including the sleep loss, were reversed by the mood-stabilizing drug valproate, and re-emerged when valproate treatment was stopped. Lithium salts, however, had no effect. The mania like-behaviors partially depended on dopamine, because giving D1/D2/D3 receptor antagonists partially restored the behaviors, but also on VTAVgat projections to the lateral hypothalamus (LH). Optically or chemogenetically inhibiting VTAVgat terminals in the LH elevated locomotion and decreased immobility time during the tail suspension and forced swimming tests. VTAVgat neurons are centrally positioned to help set an animals (and humans) level of mental and physical activity. Inputs that inhibit VTAVgat neurons intensify wakefulness (increased activity, enhanced alertness and motivation), qualities useful for acute survival. Taken to the extreme, however, decreased or failed inhibition from VTAVgat neurons produces mania-like qualities (hyperactivity, hedonia, decreased sleep).

neuroscience↗

bioRxiv2019

Pan-genome analysis reveals the molecular basis of niche adaptation of Staphylococcus epidermidis strains

Staphylococcus epidermidis is the most commonly isolated species from human skin and the second leading cause of bloodstream infections. Here, we performed a large-scale comparative study without any pre-assigned reference to identify genomic determinants associated with their diversity and adaptation as a \"double-side spy\", a skin dominant colonization, and a successful pathogen. The pan-genome of S. epidermidis is open with 435 core proteins and a pan-genome size of 8034 proteins. Genome-wide phylogenetic tree shows that whole genome sequence is a powerful tool to analyze the complex evolutionary process of S. epidermidis and investigate the source of infection. Comparative genome analyses demonstrate the high diversity of antimicrobial resistances, especially mobile genetic elements. The complicated relationships of host-bacterium and bacterium-bacterium help S. epidermidis to play a vital role in balancing the epithelial microflora. The highly variable and dynamic nature of the S. epidermidis genome may be the result of its success in adapting to broad habitats, which is necessary to deal with complex environments. This study gives the general landscape of S. epidermidis pan-genome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible species.

microbiology↗

bioRxiv2018

Spatio-temporal variability of soil nutrients and the responses of growth during growth stages of winter wheat in the north of China

Study on soil nutrient variability and its effect on the growth and development of crop under traditional tillage mode is the foundation to comprehensively implement the precision agriculture policy on the field scale and crop excellent management. In this paper, a winter wheat field of 28.5 hm2 under traditional cultivation model in Tianzhuang town of Huantai county was selected as the research area. Sampling by mesh point method (60x60m), the variation characteristics of soil available nitrogen (AN), available phosphorus (AP) and available potassium (AK) in the before sowing, reviving stage, jointing stage, filling stage of winter wheat were analyzed by the method of geostatistics and GIS. At the same time, Pearson correlation analysis was used to study the response of wheat growth and development to soil nutrient variation. As the growth period goes by, 1) each nutrient showed low-high-low and moderate variability. AN and AK had the highest content at reviving stage, while AP at jointing stage, as turning point. The order of variability of each nutrient was AN>AP>AK. 2) The difference of nutrient variation first increased and then decreased, and showed medium to strong spatial correlation.\n\nThree nutrients in the before sowing stage were strong spatial correlation, and the reviving stage was medium spatial correlation, to the jointing and filling stages, AN was medium spatial correlation, AP and AK were strong spatial correlation. The spatial correlation of each nutrients was the weakest in the reviving stage, and AN was the strongest in the before sowing stage, while AP and AK were strongest in the jointing stage. The spatial correlation of each soil nutrients decreased from before sowing to reviving stage, jointing stage to filling stage, and the spatial correlation increased from reviving stage to jointing stage. 3) Soil nutrient content first increased and then decreased, and the grade of nutrient gradually decreased. 4) The correlation between soil nutrients and wheat growth was gradually increasing. AN had the highest correlation with wheat growth, followed by AK and AP lowest. The effect of soil nutrients on the growth of wheat at the reviving stage was higher than that of the current nutrient, and the growth of wheat at jointing stage was mainly influenced by the current nutrient, while the growth of wheat at the filling period was both influenced by the nutrient content of the last and the current period; the date to supplement fertilizer should be postponed properly. In this study, the soil nutrient dynamics and its influence on the growth of wheat during the winter wheat growth period under the traditional field model were well understood, which could provide a theoretical basis for the precision management of soil nutrients in the northern winter wheat area with relatively uniform planting environment and cultivation management.

scientific communication and education↗

bioRxiv2018

tmap: topological analysis of population-scale microbiome data

Population-scale microbiome study poses specific challenges in data analysis, from enterotype analysis, identification of driver species, to microbiome-wide association of host covariates. Application of advanced data mining techniques to high-dimensional complex dataset is expected to meet the rapid advancement in large scale and integrative microbiome research. Here, we present tmap, a topological data analysis framework for population-scale microbiome study. This framework can capture complex shape of large scale microbiome data into a compressive network representation. We also develop network-based statistical analysis for driver species identification and microbiome-wide association analysis. tmap can be used for exploring variations in a population-scale microbiome landscape to study host-microbiome association.\n\nAvailability and implementationtmap is available at GitHub (https://github.com/GPZ-Bioinfo/tmap), accompanied with online documentation and tutorial (http://tmap.readthedocs.io).\n\nContacthttp://hk.zhou@siat.ac.cn

bioinformatics↗

bioRxiv2018

Development of photoactivatable drugs enables nicotinic optopharmacology

Photoactivatable ( caged) pharmacological agents have revolutionized neuroscience but the palette of available ligands is limited. We describe a general method for caging tertiary amines using an unconventional quaternary ammonium linkage that is chemically stable and elicits a desirable red-shift in activation wavelength. A photoactivatable nicotine (PA-Nic) prepared using this strategy could be uncaged via 1- or 2-photon excitation, making it useful for optopharmacology experiments to study nicotinic acetylcholine receptors (nAChRs) in different experimental preparations and spatiotemporal scales.

neuroscience↗

bioRxiv2018

Proteasome Substrate Capture and Gate Activation by Mycobacterium tuberculosis PafE

In all domains of life, proteasomes are gated chambered proteases that require opening by activators in order to facilitate protein degradation. Twelve proteasome accessory factor E (PafE) monomers assemble into a single, dodecameric ring to promote proteolysis that is required for the full virulence of the human bacterial pathogen Mycobacterium tuberculosis. While the best characterized proteasome activators use ATP to deliver proteins into a proteasome, PafE does not require ATP. In order to understand the mechanism of PafE-mediated protein targeting and proteasome activation, we studied the interactions of PafE with native substrates, including a newly identified proteasome substrate, Rv3213c, and with proteasome core particles. We characterized the function of a highly conserved feature conserved in bacterial proteasome activator proteins: a glycine-glutamine-tyrosine-leucine or \"GQYL\" motif at their carboxyl-termini that is essential to stimulate proteolysis. Using cryo-electron microscopy, we found that the GQYL motif of PafE interacts with specific residues in the -subunits of the proteasome core particle to trigger gate opening and degradation. Finally, we found that PafE rings have 40-[A] openings lined with hydrophobic residues that form a chamber for capturing substrates prior to the onset of degradation. This result suggests PafE has a previously unrecognized chaperone activity. Collectively, our data provide new insights on the mechanistic understanding of ATP-independent proteasome degradation in bacteria.

biochemistry↗

bioRxiv2017

Using eDNA to Detect the Distribution and Density of Invasive Crayfish in the Honghe-Hani Rice Terrace World Heritage Site

The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish Procambarus clarkii. Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report crayfish and are issued pesticide, but this strategy is not expected to eradicate the crayfish nor to prevent their spread since farmers are not able to detect small numbers of crayfish. Thus, we tested whether environmental DNA (eDNA) from paddy-water samples could provide a sensitive detection method. In an aquarium experiment, Real-time Quantitative polymerase chain reaction (qPCR) successfully detected crayfish, even at a simulated density of one crayfish per average-sized paddy (with one false negative). In a field test, we tested eDNA and bottle traps against direct counts of crayfish. eDNA successfully detected crayfish in all 25 paddies where crayfish were observed and in none of the 7 paddies where crayfish were absent. Bottle-trapping was successful in only 68% of the crayfish-present paddies. eDNA concentrations also correlated positively with crayfish counts. In sum, these results suggest that single samples of eDNA are able to detect small crayfish populations, but not perfectly. Thus, we conclude that a program of repeated eDNA sampling is now feasible and likely reliable for measuring crayfish geographic range and for detecting new invasion fronts in the Honghe Hani landscape, which would inform regional control efforts and help to prevent the further spread of this invasive crayfish.

ecology↗