Construction of two Gateway vectors for gene expression in fungi

We report the construction of two Gateway fungal expression vectors pCBGW and pGWBF. The pCBGW was generated by introducing an expression cassette, which consists of a Gateway recombinant cassette (attR1-Cmr-ccdB-attR2) under the control of fungal promoter PgpdA and a terminator TtrpC, into the multiple cloning site of fungal vector pCB1004. The pGWBF is a binary vector, which was generated from the plant expression vector pGWB2 by replacing the CaMV35S promoter with PgpdA. The pGWBF can be transformed into fungi efficiently with Agrobacterium-mediated transformation. The applicability of two newly constructed vectors was tested by generating the destination vectors pGWBF-GFP and pCBGW-GFP and examining the expression of GFP gene in Trichoderma viride and Gibberella fujikuroi, respectively. Combining with the advantage of Gateway cloning technology, pCBGW and pGWBF will be useful in fungi for large-scale investigation of gene functions by constructing the interested gene destination/expression vectors in a high-throughput way.     

A Cre-loxP based system for studying horizontal gene transfer

We have previously shown that DNA can be transferred to phagocytosing cells via the uptake of apoptotic cells. We report a model system that facilitates study of antigen presentation of genes transferred specifically via horizontal gene transfer. Constructs were generated encoding the LacZ gene or the influenza A nucleoprotein silenced by a STOP sequence flanked by two loxP sites. These reporter genes were demonstrated to be silent in donor cells and become activated after phagocytosis of Cre-expressing fibroblasts or macrophages. These results provide a model system for studying the influence of horizontally transferred antigens on activation of the immune system.     

Emerging computational tools and models for studying gut microbiota composition and function

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A rapid and scalable system for studying gene function in mice using conditional RNA interference

RNA interference is a powerful tool for studying gene function, however, the reproducible generation of RNAi transgenic mice remains a significant limitation. By combining optimized fluorescence-coupled miR30-based shRNAs with high efficiency ES cell targeting, we developed a fast, scalable pipeline for the production of shRNA transgenic mice. Using this system, we generated eight tet-regulated shRNA transgenic lines targeting Firefly and Renilla luciferases, Oct4 and tumor suppressors p53, p16(INK4a), p19(ARF) and APC and demonstrate potent gene silencing and GFP-tracked knockdown in a broad range of tissues in?vivo. Further, using an shRNA targeting APC, we illustrate how this approach can identify predicted phenotypes and also unknown functions for a well-studied gene. In addition, through regulated gene silencing we validate APC/Wnt and p19(ARF) as potential therapeutic targets in T?cell acute lymphoblastic leukemia/lymphoma and lung adenocarcinoma, respectively. This system provides a cost-effective and scalable platform for the production of RNAi transgenic mice targeting any mammalian gene. PAPERCLIP:     

A new model system for studying the phosphatidylinositol cycle

An early manifestation of the response of WRK-1 rat mammary tumor cells to vasopressin is an increase in incorporation of (³²P)P_i into phospholipids. Incorporation into all classes of phospholipids is stimulated; however, incorporation into phosphatidylinositol (PI) is increased to the greatest degree (3- to 10-fold as compared with 1.3- to 2-fold for the other phosholipids). Furthermore, increased incorporation into PI is accompanied by an increased rate of PI turnover; turnover rates of the other phospholipids are unaffected by vasopressin.     

Analyzing gene regulation in ascidian embryos: new tools for new perspectives

Ascidians are marine protochordates at the evolutionary boundary between invertebrates and vertebrates. Ascidian larvae provide a simple system for unraveling gene regulation networks underlying the formation of the basic chordate body plan. After being used for over a century as a model for embryological studies, ascidians have become, in the past decade, an increasingly popular organism for studying gene regulation. Part of the renewed appeal of this system is the use of electroporation to introduce transgenic DNAs into developing embryos. This method is considerably more efficient than conventional microinjection assays and permits the simultaneous transformation of hundreds of embryos. Electroporation has allowed the identification and characterization of cis-regulatory DNAs that mediate gene expression in a variety of tissues, including the notochord, tail muscles, CNS, and endoderm. Electroporation has also provided a simple method for misexpressing patterning genes and producing dominant mutant phenotypes. Recent studies have used electroporation to create "knock-out" phenotypes by overexpressing dominant negative forms of particular proteins. Here we review the past and present uses of electroporation in ascidian development, and speculate on potential future uses.     

New tools for the genetic manipulation of filamentous fungi

Filamentous fungi have a long-standing tradition as industrial producers of primary and secondary metabolites. Initially, industrial scientists selected production strains from natural isolates that fulfilled both microbiological and technical requirements for economical production processes. Subsequently, genetically modified strains with novel properties were obtained through traditional strain improvement programs relying mostly on random mutagenesis. In recent years, however, recombinant technologies have contributed significantly to improve the capacities of production and have also allowed the design of genetically manipulated strains. These major advances were only made possible by basic research bringing deeper and novel insights into cellular and molecular fungal processes, thus allowing the design of genetically manipulated strains. This better understanding of fundamental genetic processes in model organisms has resulted in the design and generation of new experimental transformation strategies to manipulate specifically gene expression and function in diverse filamentous fungi, including those having a biotechnical significance. In this review, we summarize recent developments in the application of homologous DNA recombination and RNA interference to manipulate fungal recipients for further improvement of physiology and development in regards to biotechnical and pharmaceutical applications.     

Experimental and analytical tools for studying the human microbiome

The human microbiome substantially affects many aspects of human physiology, including metabolism, drug interactions and numerous diseases. This realization, coupled with ever-improving nucleotide sequencing technology, has precipitated the collection of diverse data sets that profile the microbiome. In the past 2 years, studies have begun to include sufficient numbers of subjects to provide the power to associate these microbiome features with clinical states using advanced algorithms, increasing the use of microbiome studies both individually and collectively. Here we discuss tools and strategies for microbiome studies, from primer selection to bioinformatics analysis.     

Technology advancement for studying gene expression and gene function: a workshop report

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Technology advancement for studying gene expression and gene function: a workshop reportSponsored by National Institute of Child Health and Human Development, National Institute of General Medical Sciences, National Center for Human Genome Research, National Center for Research Resources, National Institutes of Health, Bethesda, Maryland 20892, USA     

Development of a homologous transformation system for Aspergillus niger based on the pyrG gene

Summary The development of a homologous transformation system for Aspergillus niger is described. The system is based on the use of an orotidine-5-phosphate decarboxylase deficient mutant (pyrG) and a vector, pAB4-1, which contains the functional A. niger pyrG gene as a selection marker. Transformation of the A. niger pyrG mutant with pAB4-1 resulted in the appearance of stable Pyr⁺ transformants at a frequency of 40 transformants per g of DNA. In 90% of these transformants integration had occurred at the resident pyrG locus, resulting either in replacement of the mutant allele by the wild-type allele (60%) or in insertion of one or two copies of the vector (40%). The A. niger pyrG mutant could also be transformed with the vector pDJB2 containing the pyr4 gene of Neurospora crassa, at a frequency of 2 transformants per g of DNA. Integration at the resident pyrG locus was not found with this vector. The vector pAB4-1 is also capable of transforming an Aspergillus nidulans pyrG mutant to Pyr⁺. The pyrG transformation system was used for the introduction of a non-selectable gene into A. niger.     

Establishment of the expression system for studying the function of active caspase-3 in zebrafish

Caspase-3, a key molecule in apoptosis, has been extensively studied in cell culture system; however, it has been less well characterized in vivo because certain mediators are required for the proteolytic activation of effector caspases, including caspase-3. In this study, various forms of caspase-3 with the C-terminal GFP tag were inserted into the pCS2+ plasmid, and the expression patterns of caspase-3 proteins were characterized in a zebrafish model system using microinjection of nucleic acids into zebrafish embryos. We have verified that active caspase-3 was generated by its autocatalytic activity under the condition of caspase-2 prodomain (C2P)-caspase-3-GFP overexpression, indicating that the C2P domain is crucial for the activation of caspase-3. We also confirmed that the C2P domain plays an important role in regulating the nuclear localization of the C2P-caspase-3 chimeric protein. We used this expression system to establish an animal model system suitable for the investigation of the functional characteristics of caspase-3 in vivo. Thus, our study provides a useful and specific tool for investigating the molecular mechanisms by which active caspase-3 regulates apoptosis during embryonic development.     

Molecular tools for the identification of ectomycorrhizal fungi — taxon-specific oligonucleotide probes for suilloid fungi

Five taxon-specific oligonucleotide probes are described that can be used to help identify the fungal components of ectomycorrhizae. Comparisons among partial sequence from the mitochondrial large subunit rRNA gene (mt-LrRNA) were used to select the probes, which were intended to be specific to several taxa within the suilloid group of the Boletales (Basidiomycota). Probes S1, R1, and G1 were targeted at the genera Suillus, Rhizopogon and Gomphidius ; probe G2 was designed to recognize the family, Gomphidiaceae, and probe US1 was designed to recognize all of these taxa and any other members of the suilloid group. The specificity of each probe was determined empirically by testing their ability to hybridize to PCR amplified fragments derived from 84 species of basidiomycetes. Although none of the probes exhibited their intended specificity, all specifically hybridized to useful subsets of taxa, and collectively they can be used to identify many suilloid taxa to the generic level or below. The probes were also tested for their ability to identify field collected mycorrhizae and were found to perform well.