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  • 1
    Online Resource
    Online Resource
    Flexible Tools for Gene Expression and Silencing in Tomato    
    Oxford University Press (OUP) ; 2009
    In:  Plant Physiology Vol. 151, No. 4 ( 2009-12-04), p. 1729-1740
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 151, No. 4 ( 2009-12-04), p. 1729-1740
    Abstract: As a genetic platform, tomato (Solanum lycopersicum) benefits from rich germplasm collections and ease of cultivation and transformation that enable the analysis of biological processes impossible to investigate in other model species. To facilitate the assembly of an open genetic toolbox designed to study Solanaceae, we initiated a joint collection of publicly available gene manipulation tools. We focused on the characterization of promoters expressed at defined time windows during fruit development, for the regulated expression or silencing of genes of interest. Five promoter sequences were captured as entry clones compatible with the versatile MultiSite Gateway format: PPC2, PG, TPRP, and IMA from tomato and CRC from Arabidopsis (Arabidopsis thaliana). Corresponding transcriptional fusions were made with the GUS gene, a nuclear-localized GUS-GFP reporter, and the chimeric LhG4 transcription factor. The activity of the promoters during fruit development and in fruit tissues was confirmed in transgenic tomato lines. Novel Gateway destination vectors were generated for the transcription of artificial microRNA (amiRNA) precursors and hairpin RNAs under the control of these promoters, with schemes only involving Gateway BP and LR Clonase reactions. Efficient silencing of the endogenous phytoene desaturase gene was demonstrated in transgenic tomato lines producing a matching amiRNA under the cauliflower mosaic virus 35S or PPC2 promoter. Lastly, taking advantage of the pOP/LhG4 two-component system, we found that well-characterized flower-specific Arabidopsis promoters drive the expression of reporters in patterns generally compatible with heterologous expression. Tomato lines and plasmids will be distributed through a new Nottingham Arabidopsis Stock Centre service unit dedicated to Solanaceae resources.
    Type of Medium: Online Resource
    ISSN: 1532-2548
    URL: Article
    DOI: 10.1104/pp.109.147546
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2009
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Recombinational Cloning with Plant Gateway Vectors
    Oxford University Press (OUP) ; 2007
    In:  Plant Physiology Vol. 145, No. 4 ( 2007-12-04), p. 1144-1154
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 145, No. 4 ( 2007-12-04), p. 1144-1154
    Type of Medium: Online Resource
    ISSN: 1532-2548
    URL: Article
    DOI: 10.1104/pp.107.106989
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2007
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Modular cloning in plant cells
    Elsevier BV ; 2005
    In:  Trends in Plant Science Vol. 10, No. 3 ( 2005-3), p. 103-105
    Details
    In: Trends in Plant Science, Elsevier BV, Vol. 10, No. 3 ( 2005-3), p. 103-105
    Type of Medium: Online Resource
    ISSN: 1360-1385
    URL: Article
    DOI: 10.1016/j.tplants.2005.01.008
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2005
    detail.hit.zdb_id: 2011003-0
    SSG: 12
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  • 4
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    Online Resource
    Efficient mouse transgenesis using Gateway-compatible ROSA26 locus targeting vectors and F1 hybrid ES cells
    Oxford University Press (OUP) ; 2009
    In:  Nucleic Acids Research Vol. 37, No. 7 ( 2009-04-01), p. e55-e55
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 37, No. 7 ( 2009-04-01), p. e55-e55
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkp112
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2009
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 5
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    Online Resource
    A Role for AtWRKY23 in Feeding Site Establishment of Plant-Parasitic Nematodes
    Oxford University Press (OUP) ; 2008
    In:  Plant Physiology Vol. 148, No. 1 ( 2008-09-04), p. 358-368
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 148, No. 1 ( 2008-09-04), p. 358-368
    Abstract: During the interaction between sedentary plant-parasitic nematodes and their host, complex morphological and physiological changes occur in the infected plant tissue, finally resulting in the establishment of a nematode feeding site. This cellular transformation is the result of altered plant gene expression most likely induced by proteins injected in the plant cell by the nematode. Here, we report on the identification of a WRKY transcription factor expressed during nematode infection. Using both promoter-reporter gene fusions and in situ reverse transcription-polymerase chain reaction, we could show that AtWRKY23 is expressed during the early stages of feeding site establishment. Knocking down the expression of WRKY23 resulted in lower infection of the cyst nematode Heterodera schachtii. WRKY23 is an auxin-inducible gene and in uninfected plants WRKY23 acts downstream of the Aux/IAA protein SLR/IAA14. Although auxin is known to be involved in feeding site formation, our results suggest that, during early stages, auxin-independent signals might be at play to activate the initial expression of WRKY23.
    Type of Medium: Online Resource
    ISSN: 1532-2548
    URL: Article
    DOI: 10.1104/pp.108.119131
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
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  • 6
    Online Resource
    Online Resource
    Building Blocks for Plant Gene Assembly
    Oxford University Press (OUP) ; 2007
    In:  Plant Physiology Vol. 145, No. 4 ( 2007-12-04), p. 1183-1191
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 145, No. 4 ( 2007-12-04), p. 1183-1191
    Abstract: The MultiSite Gateway cloning system, based on site-specific recombination, enables the assembly of multiple DNA fragments in predefined order, orientation, and frame register. To streamline the construction of recombinant genes for functional analysis in plants, we have built a collection of 36 reference Gateway entry clones carrying promoters, terminators, and reporter genes, as well as elements of the LhG4/LhGR two-component system. This collection obeys simple engineering rules. The genetic elements (parts) are designed in a standard format. They are interchangeable, fully documented, and can be combined at will according to the desired output. We also took advantage of the MultiSite Gateway recombination sites to create vectors in which two or three genes can be cloned simultaneously in separate expression cassettes. To illustrate the flexibility of these core resources for the construction of a wide variety of plant transformation vectors, we generated various transgenes encoding fluorescent proteins and tested their activity in plant cells. The structure and sequence of all described plasmids are accessible online at http://www.psb.ugent.be/gateway/. All accessions can be requested via the same Web site.
    Type of Medium: Online Resource
    ISSN: 1532-2548
    URL: Article
    DOI: 10.1104/pp.107.110411
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2007
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
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  • 7
    Online Resource
    Online Resource
    Qualitative analysis of Adenomatous Polyposis Coli promoter: Hypermethylation, engagement and effects on survival of patients with esophageal cancer in a high risk region of the world, a potential molecular marker
    Springer Science and Business Media LLC ; 2009
    In:  BMC Cancer Vol. 9, No. 1 ( 2009-12)
    Details
    In: BMC Cancer, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2009-12)
    Abstract: Squamous cell carcinoma of esophagus (SCCE) occurs at a high incidence rate in certain parts of the world. This feature necessitates that different aspects of the disease and in particular genetic characteristics be investigated in such regions. In addition, such investigations might lead to achievement of molecular markers helpful for early detection, successful treatment and follow up of the disease. Adenomatous Polyposis Coli ( APC ) promoter hypermethylation has been shown to be a suitable marker for both serum and solid tumors of adenocarcinoma of esophagus. We investigated the status of APC promoter hypermethylation in Iranian patients, compared the results with the former studies, and evaluated its applicability as a candidate molecular marker by examining association between survival of SCCE patients and APC promoter methylation. Methods For evaluating the status of APC promoter hypermethylation and its association with SCCE, a qualitative methylation specific PCR (MSP) was used. DNA was extracted and digested with an appropriate restriction enzyme, treated with sodium bisulfite in agarose beads and amplified in two-step PCR reaction by applying either methylated or unmethylated promoter specific primers. Universally methylated DNA and methylase treated blood DNA of healthy donors were used as positive controls as well. Survival of patients was followed up for two years after treatment and survival rate of patients with methylated APC promoter was compared with that of unmethylated patients. Results Assessment of APC promoter methylation revealed that normal tissues were unmethylated, while twenty out of forty five (44.4%) tumor tissues were hypermethylated either in one or both alleles of APC . Among the tissues in which methylation was detected, seven were hypermethylated in both alleles while the other thirteen were hypermethylated in one of the two alleles of APC . Analyzing two-year survival rate of patients with respect to promoter hypermethylation showed a lower rate of survival for patients with methylated APC promoter following their treatment. Further investigation into the association between promoter hypermethylation and tumor differentiation status indicated that patients with well differentiated tumors were more likely to develop promoter hypermethylation. Conclusion Observing similar level of APC promoter hypermethylation in patients with SCCE in this high risk region and comparing it with other parts of the world could support the hypothesis that a common molecular mechanism might be involved in tumorigenesis of SCCE. In addition, the higher rate of two-year survival for patients with unmethylated APC promoter as well as its relationship with tumor differentiation would suggest that this tumor suppressor could be an appropriate candidate molecular marker for evaluating tumor malignancy and predicting survival of patients subsequent to treatment.
    Type of Medium: Online Resource
    ISSN: 1471-2407
    URL: Article
    DOI: 10.1186/1471-2407-9-24
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2009
    detail.hit.zdb_id: 2041352-X
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  • 8
    Online Resource
    Online Resource
    Systematic analysis of cell‐cycle gene expression during Arabidopsis development
    Wiley ; 2009
    In:  The Plant Journal Vol. 59, No. 4 ( 2009-08), p. 645-660
    Details
    In: The Plant Journal, Wiley, Vol. 59, No. 4 ( 2009-08), p. 645-660
    Abstract: The steady‐state distribution of cell‐cycle transcripts in Arabidopsis thaliana seedlings was studied in a broad in situ survey to provide a better understanding of the expression of cell‐cycle genes during plant development. The 61 core cell‐cycle genes analyzed were expressed at variable levels throughout the different plant tissues: 23 genes generally in dividing and young differentiating tissues, 34 genes mostly in both dividing and differentiated tissues and four gene transcripts primarily in differentiated tissues. Only 21 genes had a typical patchy expression pattern, indicating tight cell‐cycle regulation. The increased expression of 27 cell‐cycle genes in the root elongation zone hinted at their involvement in the switch from cell division to differentiation. The induction of 20 cell‐cycle genes in differentiated cortical cells of etiolated hypocotyls pointed to their possible role in the process of endoreduplication. Of seven cyclin‐dependent kinase inhibitor genes, five were upregulated in etiolated hypocotyls, suggesting a role in cell‐cycle arrest. Nineteen genes were preferentially expressed in pericycle cells activated by auxin that give rise to lateral root primordia. Approximately 1800 images have been collected and can be queried via an online database. Our in situ analysis revealed that 70% of the cell‐cycle genes, although expressed at different levels, show a large overlap in their localization. The lack of regulatory motifs in the upstream regions of the analyzed genes suggests the absence of a universal transcriptional control mechanism for all cell‐cycle genes.
    Type of Medium: Online Resource
    ISSN: 0960-7412 , 1365-313X
    URL: Issue
    URL: Article
    DOI: 10.1111/tpj.2009.59.issue-4
    DOI: 10.1111/j.1365-313X.2009.03893.x
    Language: English
    Publisher: Wiley
    Publication Date: 2009
    detail.hit.zdb_id: 2020961-7
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  • 9
    Online Resource
    Online Resource
    Exploration of jasmonate signalling via automated and standardized transient expression assays in tobacco cells
    Wiley ; 2005
    In:  The Plant Journal Vol. 44, No. 6 ( 2005-12), p. 1065-1076
    Details
    In: The Plant Journal, Wiley, Vol. 44, No. 6 ( 2005-12), p. 1065-1076
    Abstract: Although sequence information and genome annotation are improving at an impressive pace, functional ontology is still non‐existent or rudimentary for most genes. In this regard, transient expression assays are very valuable for identification of short functional segments in particular pathways, because they can be performed rapidly and at a scale unattainable in stably transformed tissues. Vectors were constructed and protocols developed for systematic transient assays in plant protoplasts. To enhance throughput and reproducibility, protoplast treatments were performed entirely by a liquid‐handling robot in multiwell plates, including polyethylene glycol/Ca 2+ cell transfection with plasmid mixtures, washes and lysis. All transcriptional readouts were measured using a dual firefly/ Renilla luciferase assay, in which the former was controlled by a reporter promoter and the latter by the 35S CaMV promoter, which served as internal normalization standard. The automated protocols were suitable for transient assays in protoplasts prepared from cell cultures of Nicotiana tabacum Bright Yellow‐2 and Arabidopsis thaliana . They were implemented in a screen to discover potential regulators of genes coding for key enzymes in nicotine biosynthesis. Two novel tobacco transcription factors were found, NtORC1 and NtJAP1, that positively regulate the putrescine N ‐methyltransferase ( PMT ) promoter. In addition, combinatorial tests showed that these two factors act synergistically to induce PMT transcriptional activity. The development and use of high‐throughput plant transient expression assays are discussed.
    Type of Medium: Online Resource
    ISSN: 0960-7412 , 1365-313X
    URL: Issue
    URL: Article
    DOI: 10.1111/tpj.2005.44.issue-6
    DOI: 10.1111/j.1365-313X.2005.02586.x
    Language: English
    Publisher: Wiley
    Publication Date: 2005
    detail.hit.zdb_id: 2020961-7
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  • 10
    Online Resource
    Online Resource
    Leader sequence of a plant ribosomal protein gene with complementarity to the 18S rRNA triggers in vitro cap-independent translation
    Wiley ; 2006
    In:  FEBS Letters Vol. 580, No. 11 ( 2006-05-15), p. 2630-2636
    Details
    In: FEBS Letters, Wiley, Vol. 580, No. 11 ( 2006-05-15), p. 2630-2636
    Type of Medium: Online Resource
    ISSN: 0014-5793
    URL: Article
    DOI: 10.1016/j.febslet.2006.04.012
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2006
    detail.hit.zdb_id: 1460391-3
    SSG: 12
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