Showing papers by "Dabing Zhang published in 2012"

Transcriptional Regulation of Arabidopsis MIR168a and ARGONAUTE1 Homeostasis in Abscisic Acid and Abiotic Stress Responses

Abstract: The accumulation of a number of small RNAs in plants is affected by abscisic acid (ABA) and abiotic stresses, but the underlying mechanisms are poorly understood. The miR168-mediated feedback regulatory loop regulates ARGONAUTE1 (AGO1) homeostasis, which is crucial for gene expression modulation and plant development. Here, we reveal a transcriptional regulatory mechanism by which MIR168 controls AGO1 homeostasis during ABA treatment and abiotic stress responses in Arabidopsis (Arabidopsis thaliana). Plants overexpressing MIR168a and the AGO1 loss-of-function mutant ago1-27 display ABA hypersensitivity and drought tolerance, while the mir168a-2 mutant shows ABA hyposensitivity and drought hypersensitivity. Both the precursor and mature miR168 were induced under ABA and several abiotic stress treatments, but no obvious decrease for the target of miR168, AGO1, was shown under the same conditions. However, promoter activity analysis indicated that AGO1 transcription activity was increased under ABA and drought treatments, suggesting that transcriptional elevation of MIR168a is required for maintaining a stable AGO1 transcript level during the stress response. Furthermore, we showed both in vitro and in vivo that the transcription of MIR168a is directly regulated by four abscisic acid-responsive element (ABRE) binding factors, which bind to the ABRE cis-element within the MIR168a promoter. This ABRE motif is also found in the promoter of MIR168a homologs in diverse plant species. Our findings suggest that transcriptional regulation of miR168 and posttranscriptional control of AGO1 homeostasis may play an important and conserved role in stress response and signal transduction in plants.

Direct reprogramming of human fibroblasts into dopaminergic neuron-like cells.

Abstract: Transplantation of exogenous dopaminergic neuron (DA neurons) is a promising approach for treating Parkinson's disease (PD). However, a major stumbling block has been the lack of a reliable source of donor DA neurons. Here we show that a combination of five transcriptional factors Mash1, Ngn2, Sox2, Nurr1, and Pitx3 can directly and effectively reprogram human fibroblasts into DA neuron-like cells. The reprogrammed cells stained positive for various markers for DA neurons. They also showed characteristic DA uptake and production properties. Moreover, they exhibited DA neuron-specific electrophysiological profiles. Finally, they provided symptomatic relief in a rat PD model. Therefore, our directly reprogrammed DA neuron-like cells are a promising source of cell-replacement therapy for PD.

ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis

Abstract: Protein interactions are fundamental to the molecular processes occurring within an organism and can be utilized in network biology to help organize, simplify, and understand biological complexity. Currently, there are more than 10 publicly available Arabidopsis (Arabidopsis thaliana) protein interaction databases. However, there are limitations with these databases, including different types of interaction evidence, a lack of defined standards for protein identifiers, differing levels of information, and, critically, a lack of integration between them. In this paper, we present an interactive bioinformatics Web tool, ANAP (Arabidopsis Network Analysis Pipeline), which serves to effectively integrate the different data sets and maximize access to available data. ANAP has been developed for Arabidopsis protein interaction integration and network-based study to facilitate functional protein network analysis. ANAP integrates 11 Arabidopsis protein interaction databases, comprising 201,699 unique protein interaction pairs, 15,208 identifiers (including 11,931 The Arabidopsis Information Resource Arabidopsis Genome Initiative codes), 89 interaction detection methods, 73 species that interact with Arabidopsis, and 6,161 references. ANAP can be used as a knowledge base for constructing protein interaction networks based on user input and supports both direct and indirect interaction analysis. It has an intuitive graphical interface allowing easy network visualization and provides extensive detailed evidence for each interaction. In addition, ANAP displays the gene and protein annotation in the generated interactive network with links to The Arabidopsis Information Resource, the AtGenExpress Visualization Tool, the Arabidopsis 1,001 Genomes GBrowse, the Protein Knowledgebase, the Kyoto Encyclopedia of Genes and Genomes, and the Ensembl Genome Browser to significantly aid functional network analysis. The tool is available open access at http://gmdd.shgmo.org/Computational-Biology/ANAP.

PMRD: a curated database for genes and mutants involved in plant male reproduction.

Abstract: Male reproduction is an essential biological event in the plant life cycle separating the diploid sporophyte and haploid gametophyte generations, which involves expression of approximately 20,000 genes. The control of male reproduction is also of economic importance for plant breeding and hybrid seed production. With the advent of forward and reverse genetics and genomic technologies, a large number of male reproduction-related genes have been identified. Thus it is extremely challenging for individual researchers to systematically collect, and continually update, all the available information on genes and mutants related to plant male reproduction. The aim of this study is to manually curate such gene and mutant information and provide a web-accessible resource to facilitate the effective study of plant male reproduction. Plant Male Reproduction Database (PMRD) is a comprehensive resource for browsing and retrieving knowledge on genes and mutants related to plant male reproduction. It is based upon literature and biological databases and includes 506 male sterile genes and 484 mutants with defects of male reproduction from a variety of plant species. Based on Gene Ontology (GO) annotations and literature, information relating to a further 3697 male reproduction related genes were systematically collected and included, and using in text curation, gene expression and phenotypic information were captured from the literature. PMRD provides a web interface which allows users to easily access the curated annotations and genomic information, including full names, symbols, locations, sequences, expression patterns, functions of genes, mutant phenotypes, male sterile categories, and corresponding publications. PMRD also provides mini tools to search and browse expression patterns of genes in microarray datasets, run BLAST searches, convert gene ID and generate gene networks. In addition, a Mediawiki engine and a forum have been integrated within the database, allowing users to share their knowledge, make comments and discuss topics. PMRD provides an integrated link between genetic studies and the rapidly growing genomic information. As such this database provides a global view of plant male reproduction and thus aids advances in this important area.

Applicability of plasmid calibrant pTC1507 in quantification of TC1507 maize: an interlaboratory study.

Abstract: To enforce the labeling regulations of genetically modified organisms (GMOs), the application of DNA plasmids as calibrants is becoming essential for the practical quantification of GMOs. This stud...

Assessment of the ex vivo biomechanical properties of porcine cornea with inflation test for corneal xenotransplantation.

Abstract: Objective: This study aims to obtain the biomechanical properties of porcine cornea so as to provide necessary biomechanical experimental basis for pig-to-human corneal xenotransplantation. Methods: Seventeen fresh porcine corneal specimens obtained from pigs aged 4–6 months were examined under inflation conditions to determine the constitutive relationships of the material through dynamic loading conditions (pressure range: 1.47–42.66 mmHg). The forward deflection of porcine anterior corneal apex was measured by the laser displacement sensor. The pressure deformation results were analysed on the basis of shell theory to estimate Young’s modulus of the cornea and derive its relationship with intraocular pressure (IOP). Results: The porcine corneas showed a nonlinear corneal forward displacement/IOP and stress/strain relationship with an initial low stiffness stage and a later high stiffness stage. In spite of the nonlinearity between the internal pressure and apex forward deflection, the relationship betw...

Simultaneous Laccase Production and Color Removal by Culturing Fungus Pycnoporus sp. SYBC-L3 in a Textile Wastewater Effluent Supplemented with a Lignocellulosic Waste Phragmites australis

Abstract: We conducted experiments to culture Pycnoporus sp. SYBC-L3 in a medium comprising an industrial waste (dye-containing textile effluent) and a lignocellulosic waste (Phragmites australis) that achieved laccase production while having the color removed from the wastewater. Our experimental results showed that the fungus grew well in liquid submerged cultivation with the diluted textile effluent as the sole culture medium, but relatively low extracellular laccase activity (1.8 U/mL) was produced. Addition of the lignocellulosic biomass enhanced laccase production and color removal. The highest laccase activity was found to be 6.5 U/mL in the presence of Phragmites australis stem. Under this condition, 70 % color removal occurred in the culture medium. This study provided an alternative novel scheme to remove color in textile wastewater while having an economic value added by producing laccase.

Establishment of an isotope dilution LC-MS/MS method revealing kinetics and distribution of co-occurring mycotoxins in rats

Abstract: An isotope dilution liquid chromatography-tandem mass spectrometry (LC-MS/MS) method with a fast sample preparation using homemade clean-up cartridges was developed for simultaneous determination of co-occurring mycotoxins exemplified with aflatoxin B1 (AFB1) and T-2 toxin (T-2) in representative biomatrices of rat plasma, heart, liver, kidney, spleen, lung and brain in a total run time of 7 min. The established approach using stable internal standards of [13C17]-AFB1 and [13C24]-T-2 was extensively validated by determining the specificity, linearity (R2 ≥ 0.9990), sensitivity (lower limit of quantitation at 0.05 ng mL−1), accuracy (70.9–107.7%), precision (RSD ≤ 14.2%) and stability (≥70.8%). Based on this methodological advance, the subsequent kinetics and tissue distribution after oral administration of 0.5 mg kg−1 b.w. of both AFB1 and T-2 in rats were thoroughly studied. As revealed, both AFB1 and T-2 were rapidly eliminated with the half-life time (t1/2) in plasma of 8.44 ± 4.02 h and 8.12 ± 4.05 h, respectively. Moreover, AFB1 accumulated in all organs where the highest concentration was observed in liver (1.34 μg kg−1), followed by kidney (0.76 μg kg−1). Notably, only low levels of T-2 were observed in spleen (0.70 μg kg−1) and in liver (0.15 μg kg−1). The achieved data as supporting evidence would substantially promote the practical application of the proposed LC-MS/MS method for in vivo toxicokinetics and toxicity studies of co-occurring mycotoxins imitating natural incidence in rat system.

Fabrication and characterization of transparent Tm,Ho:YAG ceramic

Abstract: Transparent Tm,Ho:YAG ceramic with excellent optical properties was fabricated by solid-state reaction method using high-purity commercial powders as raw materials. Optical absorption and 2.0 μm emission spectra of the ceramic specimen have been studied. The strongest emission corresponds to 5I7 → 5I8 transition of Ho3+ centered at 2.06 μm. As a result, Tm,Ho:YAG ceramic shows potential application in 2.0 μm laser devices.