Biology subjects

Cao, Y.

Publications and source records attributed to Cao, Y..

11 recordsLinked to original sources

bioRxiv2018

Genome structure and evolution of Antirrhnum majus L.

Snapdragon (Antirrhinum majus L.), a member of Plantaginaceae, is an important model for plant genetics and molecular studies on plant growth and development, transposon biology and self-incompatibility. Here we report a high-quality genome assembly of A. majus cultivated JI7 (A. majus cv.JI7) of a 510 Mb with 37,714 annotated protein-coding genes. The scaffolds covering 97.12% of the assembled genome were anchored on 8 chromosomes. Comparative and evolutionary analyses revealed that Plantaginaceae and Solanaceae diverged from their most recent ancestor around 62 million years ago (MYA). We also revealed the genetic architectures associated with complex traits such as flower asymmetry and self-incompatibility including a unique TCP duplication around 46-49 MYA and a near complete{psi} S-locus of ca.2 Mb. The genome sequence obtained in this study not only provides the first genome sequenced from Plantaginaceae but also bring the popular plant model system of Antirrhinum into a genomic age.

genomics↗

bioRxiv2018

(-)-Epigallocatechin-3-gallate inhibition of Epstein-Barr virus lytic replication involves latent membrane protein 1-mediated MAPK signaling pathways

AbstractEBV lytic replication has been shown to be important for carcinogenesis. Latent membrane protein 1 (LMP1) plays an important role in the viral latent infection and is abundantly expressed after EBV entry into the lytic cycle. However, the biological significance of LMP1 continuous expression in EBV lytic cycle is still not completely understood. We found that LMP1 promotes EBV reactivation by activating the downstream MAPK signaling in both AGS-EBV and B95.8 cells. In AGS-EBV cells, LMP1 induces EBV the initiation of the EBV lytic cycle in a p53 dependent manner. Activation of c-Jun by LMP1 through JNKs appears to be involved in EBV reactivation in p53 mutant B95.8 cells. We also demonstrated that EGCG, an anti-EBV agent, inhibits LMP1 expression and the activation of the downstream MAPK signaling pathways, followed by downregulation of EBV lytic protein expression level. Together, this study provides the first evidence that LMP1 promotes EBV reactivation via activation of the MAPK signaling pathways. Our findings further demonstrate that the mechanisms underlying EGCG inhibition of the EBV lytic replication involve the suppression of LMP1-mediated MAPK signaling pathways.\n\nSummary statementThis study definitely confirms the role of LMP1 in EBV reactivation and further explores the mechanism by which EGCG inhibits EBV lytic replication.

molecular biology↗

bioRxiv2018

A comparative study of machine learning algorithms in predicting severe complication after bariatric surgery

Accurate models to predict severe postoperative complications could be of value in the preoperative assessment of potential candidates for bariatric surgery. Traditional statistical methods have so far failed to produce high accuracy. To find a useful algorithm to predict the risk for severe complication after bariatric surgery, we trained and compared 29 supervised machine learning (ML) algorithms using information from 37,811 patients operated with a bariatric surgical procedure between 2010 and 2014 in Sweden. The algorithms were then tested on 6,250 patients operated in 2015. Most ML algorithms showed high accuracy (>90%) and specificity (>0.9) in both the training and test data. However, none achieved an acceptable sensitivity in the test data. ML methods may improve accuracy of prediction but we did not yet identify one with a high enough sensitivity that can be used in clinical praxis in bariatric surgery. Further investigation on deeper neural network algorithms is needed.

epidemiology↗

bioRxiv2018

Regulatory networks of gene expression in maize (Zea mays) under drought stress and re-watering

Drought can severely limit plant growth and production. However, few studies have investigated gene expression profiles in maize during drought/re-watering. We compared drought-treated and water-sufficient maize plants by measuring their leaf relative water content, superoxide dismutase and peroxidase activities, proline content, and leaf gas exchange parameters (photosynthetic rates, stomatal conductance, and transpiration rates). We conducted RNA sequencing analyses to elucidate gene expression profiles and identify miRNAs that might be related to drought resistance. A GO enrichment analysis showed that the common DEGs (differently expressed genes) between drought-treated and control plants were involved in response to stimulus, cellular process, metabolic process, cell part, and binding and catalytic activity. Analyses of gene expression profiles revealed that 26 of the DEGs under drought encoded 10 enzymes involved in proline synthesis, suggesting that increased proline synthesis was a key part of the drought response. We also investigated cell wall-related genes and transcription factors regulating abscisic acid-dependent and -independent pathways. The expression profiles of the miRNAs miR6214-3p, miR5072-3p, zma-miR529-5p, zma-miR167e-5p, zma-miR167f-5p, and zma-miR167j-5p and their relevant targets under drought conditions were analyzed. These results provide new insights into the molecular mechanisms of drought tolerance, and may identify new targets for breeding drought-tolerant maize lines.\n\nAbbreviationsleaf relative water content: RWC, superoxide dismutase activity: SOD, peroxidase activity: POD, proline content: Pro, photosynthetic rates: Pn, stomatal conductance: Cond, transpiration rates: Tr.; quantitative real-time polymerase chain reaction: qPCR; abscisic acid; ABA; polyethylene glycol :PEG; Principal component analysis :PCA; polyacrylamide gel electrophoresis :PAGE\n\nHighlightThe study of physiology and molecular mechanism of maize laid a theoretical foundation for drought resistance breeding under drought stress and re-watering.

genomics↗

bioRxiv2018

Structural variability and functional association in the epiphytic bacteria assemblies of freshwater macrophytes (Myriophyllum spicatum)

The underlying principles influencing bacteria community assembly have long been of interest in the field of microbial ecology. Environmental heterogeneity is believed to be important in controlling the uniqueness and variability of communities. However, little is known about the influence of the host macrophytes on epiphytic bacteria assembly processe. Here, we produced two contrasting artificial water environments (eutrophic and oligotrophic) for reciprocal transplant experiment of Myriophyllum spicatum, to recover the colonization of epiphytic bacteria accompanied with plants growth. Comparative analysis addressed a higher species diversity in epiphytic bacteria than in bacterioplankton, and the highest microbiome richness in sediment. Our data revealed that the organization of epiphytic bacterial community was interfered by both plant status (i.e. branch number, net photosynthesis rate etc.) and water bodies (i.e. total phosphate, total nitrogen, pH etc.) while plant status effected the assembly in priority to water. 16S rRNA sequencing further indicated that the epiphytic assemblies were motivated by functionalization and interplay with hosts as a whole. The results complemented new evidences for the lottery process in the epiphytic bacteria assembly traits and shed insights into the assembly patterns referring to functional adaptation across epiphytic bacteria and macrophytes.\n\nImportanceA robust understanding of inter-adaptation between microbiome and the host plants have been established basing on vast majority of researches. However, great efforts were made mostly on rhizosphere microbiome. By contrast, referring to another representative group, macrophytes who composed of the freshwater ecosystem were relatively less investigated on such issue. Our study pioneered the experimental operation to interrogate the triadic relationship among macrophytes, epiphytic bacteria and water body. The research present here showed significant exemplar on discussion of plant associate bacteria adaptation taking account of host colonization as well as the epiphytes. The results expand the hypotheses of bacteria assembly principle and provides potential leads on understanding of plant - microbe interactions.

microbiology↗

bioRxiv2018

Colonization of phosphate-solubilizing Pseudomonas sp. strain P34-L in the wheat rhizosphere and its effects on wheat growth and the expression of phosphate transporter gene TaPT4 in wheat

The ability to colonize the rhizosphere is an important basics requirement for field application of plant growth-promoting rhizobacteria (PGPR) strains. There are complex signal exchanges and mutual recognition between microbes and plants. In this study, phosphate-solubilizing Pseudomonas sp. P34, a PGPR strain with affinity to wheat, was isolated from the wheat rhizosphere by wheat germ agglutinin (WGA). The plasmid pTR102 harboring the luciferase luxAB gene was transferred into P34 to create P34-L. The labeled strain was used to track the temporal and spatial characteristics of colonization in wheat rhizosphere and its effects on wheat development. The transcript level of phosphate transporter gene TaPT4, a phosphorus deficiency indicator gene, in wheat roots was monitored by quantitative reverse-transcription PCR. The experimental results indicated that there was a high density of stain P34-L within the top 8-cm depth of the wheat rhizosphere on day 36 of wheat growth. The strain could survive in the wheat rhizosphere for a long time, and colonize new spaces in wheat rhizosphere following the extension of wheat roots. Compared with uninoculated wheat plants, those inoculated with P34-L showed significantly increased phosphorus accumulation in leaves, seedling fresh and dry weight, root fresh and dry weight, total root length, and number of root tips, forks, crossings, which showed a great value of application of the strain on wheat production by promoting the root growth and dry matter accumulation. Strain P34-L down-regulated the transcript level of TaPT4 in wheat roots, which means a well phosphorus supplementation environment was established by P34-L.\n\nImportanceMany PGPR strains often failed to achieve the desired effects when applied in the field. One major reason for the failure is lack of a special affinity between a certain strain and the target host plant, so those strains have low competitive ability with the indigenous microorganism, and unable to survive constantly in rhizosphere. In this work, a new technique to isolate wheat-specific phosphate-solubilizing PGPR strain by WGA was established. The isolate P34 was confirmed can colonize the wheat rhizosphere, and have significantly ability in promoting phosphorus absorption and wheat growth by luminescence labeling techniques. Furthermore, the phosphate-solubilizing ability of this affinity PGPR strain was verified in gene level by quantitative reverse-transcription PCR. These results lay a firm foundation for further research on the relationships between PGPR and their host plants. Meanwhile, this work supplied a potential ideal biofertilizer producing strain for sustainable agriculture.

microbiology↗

bioRxiv2018

Bradyrhizobium diazoefficiens USDA 110-Glycine max interactome provides candidate proteins associated with symbiosis

Although the legume-rhizobium symbiosis is a most important biological process, there is a limited knowledge about the protein interaction network between host and symbiont. Using interolog and domain-based approaches, we constructed an inter-species protein interactome with 5115 protein-protein interactions between 2291 Glycine max and 290 Bradyrhizobium diazoefficiens USDA 110 proteins. The interactome was validated by expression pattern analysis in nodules, GO term semantic similarity, and co-expression analysis. One sub-network was further confirmed using luciferase complementation image assay. In the G. max-B. diazoefficiens interactome, bacterial proteins are mainly ion channel and transporters of carbohydrates and cations, while G. max proteins are mainly involved in the processes of metabolism, signal transduction, and transport. We also identified the top ten highly interacting proteins (hubs) for each of the two species. KEGG pathway analysis for each hub showed that two 14-3-3 proteins (SGF14g and SGF14k) and five heat shock proteins in G. max are possibly involved in symbiosis, and ten hubs in B. diazoefficiens may be important symbiotic effectors. Subnetwork analysis showed that 18 symbiosis-related SNARE proteins may play roles in regulating bacterial ion channels, and SGF14g and SGF14k possibly regulate the rhizobium dicarboxylate transport protein DctA. The predicted interactome and symbiosis proteins provide a valuable basis for understanding the molecular mechanism of root nodule symbiosis in soybean.

bioinformatics↗

bioRxiv2018

Femtomolar and selective dopamine detection by a gold nanoparticle enhanced surface plasmon resonance aptasensor

Ultrasensitive and selective detection and quantification of dopamine (DA) plays a key role in monitoring neurodegenerative diseases. However, the detection limit reported for DA detection is typically in the lower nM range. Pushing the detection limit to pM or lower for this particular target to cover the physiological levels (< 130 pM) is significant. Herein, DA DNA aptamer (DAAPT) gold nanoparticle (AuNP) conjugate is utilized to enhance the surface plasmon resonance (SPR) signal, which enables to detect and quantify DA in the femtomolar (200 fM) to picomolar range. To the best of our knowledge, this is the lowest detection limit achieved for SPR sensing of dopamine. The as-prepared 10 nm DAAPT-AuNP conjugate demonstrates strong binding affinity (Kd = 3.1 {+/-} 1.4 nM) to the complementary DNA (cDNA) probe on gold chip. The cDNA probe is immobilized to the chip via polydopamine surface chemistry, which allows the Michael addition of any primary amine-terminated biomolecules. By adjusting the concentration of the DAAPT-AuNP conjugate, two calibration curves are generated with dynamic ranges from 100 {micro}M to 2 mM, and from 200 fM to 20 nM, respectively. Both calibration curves have negative slopes, showing good agreement to a dose-response curve in an enzyme inhibition assay. In addition, the sensing strategy is evaluated to be specific for DA detection using a series of DA analogs and other metabolites as potential interferences.

biochemistry↗

bioRxiv2017

Genome-wide homology analysis reveals new insights into the origin of the wheat B genome

Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The ancestors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a candidate for the ancestor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure, which has puzzled the wheat research community for nearly a century. In the present study, the genome-wide homology analysis identified perceptible homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was identified on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome in wheat species. Thereby, we conclude that Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive ancestor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings provide significant insights into the origin and evolution of the wheat B genome, and will facilitate polyploid genome studies in wheat and other plants as well.

genetics↗

bioRxiv2017

Non-latching positive feedback enables robust bimodality by de-coupling expression noise from the mean

Fundamental to biological decision-making is the ability to generate bimodal expression patterns where two alternate expression states simultaneously exist. Here, we use a combination of single-cell analysis and mathematical modeling to examine the sources of bimodality in the transcriptional program controlling HIVs fate decision between active replication and viral latency. We find that the HIV Tat protein manipulates the intrinsic toggling of HIVs promoter, the LTR, to generate bimodal ON-OFF expression, and that transcriptional positive feedback from Tat shifts and expands the regime of LTR bimodality. This result holds for both minimal synthetic viral circuits and full-length virus. Strikingly, computational analysis indicates that the Tat circuits non-cooperative non-latching feedback architecture is optimized to slow the promoters toggling and generate bimodality by stochastic extinction of Tat. In contrast to the standard Poisson model, theory and experiment show that non-latching positive feedback substantially dampens the inverse noise-mean relationship to maintain stochastic bimodality despite increasing mean-expression levels. Given the rapid evolution of HIV, the presence of a circuit optimized to robustly generate bimodal expression appears consistent with the hypothesis that HIVs decision between active replication and latency provides a viral fitness advantage. More broadly, the results suggest that positive-feedback circuits may have evolved not only for signal amplification but also for robustly generating bimodality by decoupling expression fluctuations (noise) from mean expression levels.

systems biology↗

bioRxiv2017

scRNASeqDB: a database for gene expression profiling in human single cell by RNA-seq

Summary: Single-cell RNA sequencing (scRNA-Seq) is quickly becoming a powerful tool for high-throughput transcriptomic analysis of cell states and dynamics. Both the number and quality of scRNA-Seq datasets have dramatically increased recently. So far, there is no database that comprehensively collects and curates scRNA-Seq data in humans. Here, we present scRNASeqDB, a database that includes almost all the currently available human single cell transcriptome datasets (n= 36) covering 71 human cell lines or types and 8910 samples. Our online web interface allows user to query and visualize expression profiles of the gene(s) of interest, search for genes that are expressed in different cell types or groups, or retrieve differentially expressed genes between cell types or groups. The scRNASeqDB is a valuable resource for single cell transcriptional studies.\n\nAvailability: The database is available at https://bioinfo.uth.edu/scrnaseqdb/.\n\nContact: zhongming.zhao@uth.tmc.edu

bioinformatics↗