Biology subjects

Hu, X.

Publications and source records attributed to Hu, X..

At least 361 records · Page 20Linked to original sources

bioRxiv2019

siRNA containing a unique 5-nucleotide motif acts as a quencher of IFI16-mediated innate immune response

We previously reported that small interfering RNA (siRNA) enhances DNA or DNA virus mediated-interferon (IFN)-{lambda}1 induction through retinoic acid-inducible gene I (RIG-I) and interferon gamma-inducible protein 16 (IFI16) crosstalk-signalling pathway. Here we provide further evidence of a new role for siRNA. siRNA containing a 5-nucleotide (nt) motif sequence suppresses DNA-mediated IFNs and inflammatory cytokines. We determined that motif siRNA inhibits the induction when the motif is located at the 3 or 5-terminus of siRNA. Using THP1-Lucia ISG cells with various DNA stimulants, it is demonstrated that motif siRNA inhibits DNA or DNA virus but not RNA virus-mediated signaling. Motif siRNA specifically interrupts IFI16 binding to DNA and has 2.5-fold higher affinity to IFI16 than that of siRNA without the motif. Collectively, these findings may shed lights on a novel function of siRNA with the 5-nt motif as a quencher of innate immunity and facilitate the development of potential therapeutics to treat diseases in which this pathway is dysregulated.

immunology↗

bioRxiv2019

Parthenolide Covalently Targets and Inhibits Focal Adhesion Kinase in Breast Cancer Cells

Parthenolide, a natural product from the feverfew plant and member of the large family of sesquiterpene lactones, exerts multiple biological and therapeutic activities including anti-inflammatory and anti-cancer effects. Herein, we further study parthenolide mechanism of action using activity-based protein profiling (ABPP)-based chemoproteomic platforms to map additional covalent targets engaged by parthenolide in human breast cancer cells. We find that parthenolide, as well as other related exocyclic methylene lactone-containing sesquiterpenes, covalently modify cysteine 427 (C427) of focal adhesion kinase 1 (FAK1) leading to impairment of FAK1-dependent signaling pathways and breast cancer cell proliferation, survival, and motility. These studies reveal a novel functional target exploited by members of a large family of anticancer natural products.

cancer biology↗

bioRxiv2019

SwiftOrtho: a Fast, Memory-Efficient, Multiple Genome Orthology Classifier

IntroductionGene homology type classification is a requisite for many types of genome analyses, including comparative genomics, phylogenetics, and protein function annotation. A large variety of tools have been developed to perform homology classification across genomes of different species. However, when applied to large genomic datasets, these tools require high memory and CPU usage, typically available only in costly computational clusters. To address this problem, we developed a new graph-based orthology analysis tool, SwiftOrtho, which is optimized for speed and memory usage when applied to large-scale data. ResultsIn our tests, SwiftOrtho is the only tool that completed orthology analysis of 1,760 bacterial genomes on a computer with only 4GB RAM. Using various standard orthology datasets, we also show that SwiftOrtho has a high accuracy. SwiftOrtho enables the accurate comparative genomic analyses of thousands of genomes using low memory computers. Availabilityhttps://github.com/Rinoahu/SwiftOrtho

bioinformatics↗

bioRxiv2019

Effectiveness of Genomic Selection by Response to Selection for Winter Wheat Variety Improvement

The genomic revolution opened up the possibility for predicting un-tested phenotypes in schemes commonly referred as genomic selection (GS). Considering the practicality of applying GS in the line development stage of a hard red winter (HRW) wheat variety development program (VDP), effectiveness of GS was evaluated by prediction accuracy, as well as by the response to selection across field seasons that demonstrated challenges for crop improvement under significant climate variability. Important breeding targets for HRW wheat improvement in the southern Great Plains of USA, including Grain Yield, Kernel Weight, Wheat Protein content, and Sodium Dodecyl Sulfate (SDS) Sedimentation Volume as a rapid test for predicting bread-making quality, were used to estimate GSs effectiveness across harvest years from 2014 (drought) to 2016 (normal). In general, nonparametric algorithms RKHS and RF produced higher accuracies in both same-year/environment cross validations and cross-year/environment predictions, for the purpose of line selection in this bi-parental doubled haploid (DH) population. Further, the stability of GS performance was greatest for SDS Sedimentation Volume but least for Wheat Protein content. To ensure long-term genetic gain, our study on selection response suggested that across this sample of environmental variability, and though there are cases where phenotypic selection (PS) might be still preferential, training conducted under drought stress or in suboptimal conditions could still provide an encouraging prediction outcome, when selection decisions were made in normal conditions. However, it is not advisable to use training information collected from a normal field season to predict trait performance under drought conditions. Further, the superiority of response to selection was most evident if the training population can be optimized. Core IdeasO_LIPrediction performance for winter wheat grain yield and end-use quality traits. C_LIO_LIPrediction accuracy evaluated by cross validations significantly overestimated. C_LIO_LINon-parametric algorithms outperform, when considering cross-year predictions. C_LIO_LIStrategically designing training population improves response to selection. C_LIO_LIResponse to selection varied across growing seasons/environments. C_LI

plant biology↗

bioRxiv2019

Endogenous insulin contributes to pancreatic cancer development

Obesity and early-stage type 2 diabetes (T2D) increase the risk for many cancers, including pancreatic ductal adenocarcinoma (PDAC). The mechanisms linking obesity and T2D to cancer have not been established, preventing targeted interventions. Arguments have been made that hyperinsulinemia, hyperglycemia, or inflammation could drive cancer initiation and/or progression1. Hyperinsulinemia is a cardinal feature of obesity and T2D, and is independently associated with PDAC incidence and mortality2-4, even in non-obese people5. Despite ample human epidemiological evidence linking hyperinsulinemia to PDAC, there is no direct in vivo evidence of a causal role for endogenous insulin in cancer in any system. Using mice with reduced insulin gene dosage6, 7, we show here that a modest reduction in endogenous insulin production leads to a ~50% reduction in pancreatic intraepithelial neoplasia (PanIN) pre-cancerous lesions in high fat diet-fed mice expressing the KrasG12D oncogene8. The significant reduction in PanIN lesions occurred in the absence of changes in fasting glucose. Reduced insulin also led to a ~50% reduction in pancreatic fibrosis, suggesting that endogenous insulin drives PanIN development, in part, via its pro-fibrotic effects on the stroma surrounding acinar cells and PanIN. Collectively, our data indicate that endogenous insulin hypersecretion contributes causally to pancreatic cancer development. This suggests a modest reduction in fasting insulin via lifestyle interventions or therapeutics may be useful in cancer prevention.

cancer biology↗

bioRxiv2019

An improved control efficacy against tobacco bacterial wilt by an engineered Pseudomonas mosselii expressing the ripAA gene from phytopathogenic Ralstonia solanacearum

The environmental bacterium Pseudomonas mosselii produces antagonistic secondary metabolites with inhibitory effects on multiple plant pathogens, including Ralstonia solanacearum, the causal agent of bacterial wilt. In this study, an engineered P. mosselii strain was generated to express R. solanacearum ripAA, which determines incompatible interactions with tobacco plants. The ripAA gene together with its native promoter was integrated into the P. mosselii chromosome. The resulting strain showed no difference in antimicrobial activity against R. solanacearum. Promoter-LacZ fusion and RT-PCR experiments demonstrated that the ripAA gene was transcribed in culture media. Compared with that of the wild type, the engineered strain reduced the disease index by 9.1% for bacterial wilt on tobacco plants. A transcriptome analysis was performed to identify differentially expressed genes in tobacco plants, and the results revealed that ethylene-and jasmonate-dependent defense signaling pathways were induced. These data demonstrated that the engineered P. mosselii expressing ripAA enables improved biological control against tobacco bacterial wilt by the activation of host defense responses.\n\nImportanceNowadays, the use of biocontrol agents is more and more popular in agriculture, but they cannot replaced of chemical agents mostly, due to the poorer control effect. So the study about how to improve the efficacy of biocontrol agents become necessary and urgent. We increase the efficacy against plant pathogen through introducing an avirulence gene from plant pathogen into the biocontrol agent based on \"gene to gene\" hypothesis. The new engineered strain can improve the systemic resistance and elicit primary immune response of plants. Our research not only provides a new strategy for genetic modification of biocontrol agent, a number of avirulence gene from pathogen or plant can be tested to be expressed in different biocontrol agents to antagonize plant disease, but also help the study of interaction between phythopathogenic avirulence gene and host.

microbiology↗

bioRxiv2018

Phylogenetic reconstruction and divergence time estimation of Blumea DC. (Asteraceae: Inuleae) in China based on nrDNA ITS and cpDNA trnL-F sequences

The genus Blumea DC. is one of the economically most important genera of Inuleae (Asteraceae) in China. It is particularly diverse in south China, where 30 species occur, more than half of which are used as herbal medicine or in the chemical industry. However, little is known about the phylogenetic relationships and molecular evolution of this genus in China. We used nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) trnL-F sequences to reconstruct the phylogenetic relationship and estimate the divergence time of Blumea DC. in China. Results indicated the genus of Blumea DC. was monophyletic and could be divided into two clades, the two clades were resolved that differ with respect to habitat, morphology, chromosome type and chemical composition, of their members. Furthermore, based on the two root time of Asteraceae, the divergence time of Blumea DC. were compare estimated. Results indicated the most recent common ancestor of Asteraceae maybe originated from 76-66 Ma, and Blumea DC. maybe originated from 72.71-52.42 Ma, and had an explosive expansion during Oligocene and Miocene (30.09-11.44 Ma), two major clades were differentiated during the Palaeocene and Oligocene (66.29-46.72 Ma), also the evidence from paleogeography and paleoclimate also supported Blumea DC. had an differentiation and explosive expansion during Oligocene and Miocene.

systems biology↗

bioRxiv2018

Consensus interpretation of the Met34Thr and Val37Ile variants in GJB2 by the ClinGen Hearing Loss Expert Panel

PURPOSEPathogenic variants in GJB2 are the most common cause of autosomal recessive sensorineural hearing loss. The classification of c.101T>C/p.Met34Thr and c.109G>A/p.Val37Ile in GJB2 are controversial. Therefore, an expert consensus is required for the interpretation of these two variants.\n\nMETHODSThe ClinGen Hearing Loss Expert Panel (HL-EP) collected published data and shared unpublished information from participating laboratories regarding the two variants. Functional, computational, allelic, and segregation data were also obtained.\n\nRESULTSThe panel reviewed the synthesized information, and classified the Met34Thr and Val37Ile variants according to professional variant interpretation guidelines. We found that Met34Thr and Val37Ile are significantly overrepresented in hearing loss patients, compared to the general population. Met34Thr or Val37Ile homozygotes or compound heterozygotes typically manifest mild to moderate hearing loss. Several other types of evidence also support pathogenic roles for those two variants.\n\nCONCLUSIONResolving controversies in variant classification requires coordinated effort among a panel of international multi-institutional experts to share data, standardize classification rules, review evidence, and reach a consensus. The ClinGen HL-EP concluded that Met34Thr and Val37Ile variants in GJB2 are pathogenic for autosomal recessive nonsyndromic hearing loss with variable expressivity and age-dependent penetrance.

genetics↗

bioRxiv2018

A fluorescent reporter enables instantaneous measurement of cell cycle speed in live cells

Cell proliferation changes concomitantly with fate transitions during reprogramming, differentiation, regeneration, and oncogenesis. Methods to resolve cell cycle length heterogeneity in real-time are currently lacking. Here, we describe a genetically encoded fluorescent reporter that captures live cell cycle speed using a single measurement. This reporter is based on the color-changing Fluorescent Timer (FT) protein, which emits blue fluorescence when newly synthesized before maturing into a red fluorescent protein. We generated a mouse strain expressing an H2B-FT fusion reporter from a universally active locus, and demonstrate that faster-cycling cells can be distinguished from slower-cycling ones based on the intracellular fluorescence ratio between the FTs blue and red states. Using this reporter, we reveal the native cell cycle speed distributions of fresh hematopoietic cells, and demonstrate its utility in analyzing cell proliferation in solid tissues. This system is broadly applicable for dissecting functional heterogeneity associated with cell cycle dynamics in complex tissues.

cell biology↗

bioRxiv2018

MLL-AF9 Initiates Transformation From Fast-Proliferating Myeloid Progenitors

Cancer is a hyper-proliferative clonal disease. Whether the proliferative state originates from the cell-of-origin or emerges later remains elusive. By tracking de novo transformation from normal hematopoietic progenitors expressing an acute myeloid leukemia (AML) oncogene MLL-AF9, we reveal that the cell cycle rate heterogeneity among granulocyte-macrophage progenitors (GMPs) determines their probability of transformation. An intrinsic fast cell cycle kinetics at the time of oncogene expression provide permissiveness for transformation, with the fastest cycling 3% of GMPs ([~]0.006% of bone marrow nucleated cells) acquiring malignancy with nearly 100% efficiency. Molecularly, we propose that MLL-AF9 preserves the gene expression of the cellular states in which it is expressed. As such, when expressed in the naturally-existing, rapidly-cycling myeloid progenitors, this cell state is perpetuated, yielding malignancy. Our work elucidates one of the earliest steps toward malignancy and suggests that modifying the cycling state of the cell-of-origin could be an effective approach to prevent malignancy.

cancer biology↗

bioRxiv2018

Non-cell-autonomous promotion of pluripotency induction mediated by YAP

While Yes-associated protein (YAP) antagonizes pluripotency during early embryogenesis, it has also been shown to promote stemness of multiple stem cell types, including pluripotent stem cells. Whether cellular context underlies these distinct functions of YAP in pluripotency remains unclear. Here, we establish that depending on the specific cells in which it is expressed, YAP exhibits opposing effects on pluripotency induction from somatic cells. Specifically, YAP inhibits pluripotency induction cell-autonomously but promotes it non-cell-autonomously. For its non-cell-autonomous role, YAP alters the expression of many secreted and matricellular proteins including CYR61, which recapitulates the promotional effect when added as a recombinant protein. Thus, we define a unique YAP-driven non-cell-autonomous process that enhances pluripotency induction. Our work highlights the importance of considering the distinct contributions from heterologous cell types in deciphering the mechanism of cell fate control and calls for careful re-examination of the co-existing bystander cells in complex cultures or tissues.

cell biology↗

bioRxiv2018

Spatiotemporal expression of FRIGIDA modulate flowering time in Arabidopsis thaliana

FRIGIDA (FRI) as the major regulator of flowering time in Arabidopsis accessions can activate its target FLOWERING LOCUS C (FLC) to delay flowering before vernalization. Besides FLC, other FRI targets also exist in Arabidopsis. Although leaves sense environmental cues to modulate flowering time, it is not known if roots also regulate the floral transition. In this study, we investigated the spatiotemporal effect of FRI on flowering time. Local expression of FRI in the phloem and leaves activated FLC to delay flowering. Furthermore, we found that local expression of FRI in the roots also delayed flowering by activating other targets MADS AFFECTING FLOWERING4 (MAF4) and MAF5 in the roots. Graft and genetic experiments revealed that the spatial expression of FRI in the root might generate a mobile signal, which is transmitted from roots to shoot and antagonizes the FT signal to delay flowering. Specifically expressing FRI in the embryo efficiently delayed flowering, even expressing FRI as early as pro-embryo stage is enough to upregulate FLC expression to delay flowering. Together, our findings confirm the spatiotemporal effect of FRI on delaying flowering, and propose that root tissue also perceives the flowering signal to fine-tune the flowering time through MAF4/5 as novel targets of FRI.\n\nHighlightRoot FRIDIGA activated the novel targets MAF4/5 to delay flowering; Temporal expressing FRIGIDA at as early as pro-embryo stage is efficient to delay flowering.

plant biology↗

bioRxiv2018

LC3 and STRAP regulate actin filament assembly by JMY during autophagosome formation

During autophagy actin filament networks move and remodel cellular membranes to form autophagosomes that enclose and metabolize cytoplasmic contents. Two actin regulators, WHAMM and JMY, participate in autophagosome formation, but the signals linking autophagy to actin assembly are poorly understood. We show that, in non-starved cells, cytoplasmic JMY co-localizes with STRAP, a regulator of JMYs nuclear functions, on non-motile vesicles with no associated actin networks. Upon starvation, JMY shifts to motile, LC3-containing membranes that move on actin comet tails. LC3 enhances JMYs de novo actin nucleation activity via a cryptic actin-binding sequence near JMYs N-terminus, and STRAP inhibits JMYs ability to nucleate actin and activate the Arp2/3 complex. Cytoplasmic STRAP negatively regulates autophagy. Finally, we use purified proteins to reconstitute LC3- and JMY-dependent actin network formation on membranes, and inhibition of network formation by STRAP. We conclude that LC3 and STRAP regulate JMYs actin assembly activities in trans during autophagy.\n\neTOC BlurbThe actin regulator JMY creates filament networks that move membranes during autophagy. We find that, in unstarved cells, JMY is inhibited by interaction with the STRAP protein, but upon starvation JMY is recruited away from STRAP and activated by LC3.

cell biology↗

bioRxiv2018

Harnessing the Anti-Cancer Natural Product Nimbolide for Targeted Protein Degradation

Nimbolide, a terpenoid natural product derived from the Neem tree, impairs cancer pathogenicity across many types of human cancers; however, the direct targets and mechanisms by which nimbolide exerts its effects are poorly understood. Here, we used activity-based protein profiling (ABPP) chemoproteomic platforms to discover that nimbolide reacts with a novel functional cysteine crucial for substrate recognition in the E3 ubiquitin ligase RNF114. Nimbolide impairs breast cancer cell proliferation by disrupting RNF114 substrate recognition, leading to inhibition of ubiquitination and degradation of the tumor-suppressor p21, resulting in its rapid stabilization. We further demonstrate that nimbolide can be harnessed to recruit RNF114 as an E3 ligase in targeted protein degradation applications and show that synthetically simpler scaffolds are also capable of accessing this unique reactive site. Our study highlights the utility of ABPP platforms in uncovering unique druggable modalities accessed by natural products for cancer therapy and drug discovery applications.

cancer biology↗

bioRxiv2018

The Histone Demethylase KDM4D Promotes Hepatic Fibrogenesis by Modulating Toll-Like Receptor 4 Signaling Pathway

Accumulating evidence has revealed the pivotal role of epigenetic regulation in the pathogenesis of liver disease. However, the epigenetic mechanism that accounts for hepatic stellate cells (HSCs) activation in liver fibrosis remains largely unknown. In this study, primary HSCs were used to screen the differentially expressed histone H3 lysine methyltransferases and demethylases during HSC activation. KDM4D was identified as a remarkable up-regulated histone H3 demethylase during HSC activation. The overexpression profile of KDM4D was further confirmed in three fibrosis animal models and human fibrotic liver tissues. In vitro genetic silencing of Kdm4d impaired the collagen gel contraction and migration capacity of primary HSCs. In established CCl4-induced mice model, Kdm4d knockdown inhibited fibrosis progression, and promoted fibrosis reversal, with enhanced thinning and splitting of fibrotic septa, as well as a dramatic decrease in collagen area. Whole gene transcriptome analysis showed the regulatory role of KDM4D in Toll-Like Receptor (TLR) signaling pathway. Mechanistically, KDM4D catalyzed histone 3 on lysine 9 (H3K9) di-, and tri-demethylation, which promoted TLR4 expression, and subsequently prompted liver fibrogenesis by activating NF-{kappa}B signaling pathways. KDM4D facilitates TLR4 transcription through demethylation of H3K9, thus activating TLR4/NF-{kappa}B signaling pathways in HSCs, contributing to HSC activation and collagen crosslinking, further, hepatic fibrosis progression.

cell biology↗

bioRxiv2018

Wheat avenin-like protein and its significant Fusarium Head Blight resistant functions

Wheat Avenin-like proteins (TaALP) are atypical storage proteins belonging to the Prolamin superfamily. Previous studies on ALPs have focused on the proteins positive effects on dough strength, whilst no correlation has been made between TaALPs and the plant immune system. Here, we performed genome-wide characterization of ALP encoding genes in bread wheat. In silico analyses indicated the presence of critical peptides in TaALPs that are active in the plant immune system. Pathogenesis-related nucleotide motifs were also identified in the putative promoter regions of TaALP encoding genes. RT-PCR was performed on TaALP and previously characterised pathogenesis resistance genes in developing wheat caryopses under control and Fusarium graminearum infection conditions. The results showed that TaALP and NMT genes were upregulated upon F. graminearum inoculation. mRNA insitu hybridization showed that TaALP genes were expressed in the embryo, aleurone and sub-aleurone layer cells. Seven TaALP genes were cloned for the expression of recombinant proteins in Escherichia coli, which displayed significant inhibitory function on F. graminearum under anti-fungal tests. In addition, FHB index association analyses showed that allelic variations of two ALP genes on chromosome 7A were significantly correlated with FHB symptoms. Over-expression of an ALP gene on chromosome 7A showed an enhanced resistance to FHB. Yeast two Hybridization results revealed that ALPs have potential proteases inhibiting effect on metacaspases and beta-glucosidases. A vital infection process related pathogen protein, F. graminearum Beta-glucosidase was found to interact with ALPs. Our study is the first to report a class of wheat storage protein or gluten protein with biochemical functions. Due to its abundance in the grain and the important multi-functions, the results obtained in the current study are expected to have a significant impact on wheat research and industry.

molecular biology↗

bioRxiv2018

Changes in Microorganisms in the Rhizosphere of Mulberry Genotypes with Differing Resistance to Bacterial Wilt

A close relationship between soil-borne diseases, soil microbial community structure, and functional diversity has been described in the mulberry plant. In the present study, microbial abundance, community structure, and functional diversity in the soil rhizosphere were compared in resistant (Kangqing10) and susceptible (Guisang12) mulberry genotypes using the dilution plate method, micro-ecology technology, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The goal of this study was to develop better management methods for mulberry cultivation and preventing and controlling bacterial wilt. Rhizosphere soil microorganisms were more abundant in the resistant normal mulberry genotype than in the susceptible normal mulberry genotype. Carbon source utilization was better in the susceptible normal mulberry genotype. These properties were lower in the resistant sickly mulberry genotype than in the susceptible sickly mulberry genotype. PCR-DGGE indicated that the bacterial and fungal community structures of the resistant genotypes were more stable than those of the susceptible genotypes. Correlation regression analysis implicated mulberry bacterial wilt in the loss of soil nutrients, particularly organic matter and nitrogen, which can disrupt the balance of the soil microbial community. Loss of soil organic matter and nitrogen had a lower impact on resistant genotype plants than on susceptible genotype plants. Therefore, resistant genotype plants displayed some resistance to bacterial wilt. Further insights into the soil rhizosphere microbial diversities of resistant and susceptible genotypes will help in the control and prevention of mulberry bacterial wilt.

microbiology↗

bioRxiv2018

A divergent kinase lacking the glycine-rich loop regulates membrane ultrastructure of the Toxoplasma parasitophorous vacuole

Apicomplexan parasites replicate within a protective organelle called the parasitophorous vacuole (PV). The Toxoplasma gondii PV is filled with a network of tubulated membranes, which are thought to facilitate trafficking of effectors and nutrients. Despite being critical to parasite virulence, there is scant mechanistic understanding of the networks functions. Here, we identify the parasite secreted kinase WNG1 as a critical regulator of tubular membrane biogenesis. WNG1 family members adopt an atypical protein kinase fold lacking the glycine rich ATP-binding loop that is required for catalysis in canonical kinases. Unexpectedly, we find that WNG1 is an active protein kinase that localizes to the PV lumen and phosphorylates PV-resident proteins, several of which are essential for the formation of a functional intravacuolar network. Moreover, we show that WNG1-dependent phosphorylation of these proteins is required for their membrane association, and thus their ability to tubulate membranes. Consequently, WNG1 knockout parasites have an aberrant PV membrane ultrastructure. Collectively, our results describe a unique family of Toxoplasma kinases and implicate phosphorylation of secreted proteins as a mechanism of regulating PV formation during parasite infection.

cell biology↗