1.1 3198 info:srw/schema/1/mods-v3.3xml journalArticle A1 Integration of Agrobacterium tumefaciens transfer DNA (T-DNA) involves rearrangements of target plant DNA sequences Godelieve Gheysen aut author ug_LA25 0000-0003-1929-5059 Marc Van Montagu aut author ug_WE09 Patricia Zambryski aut author ug_WE09 eng The transfer DNA (T-DNA) mobilized into plant cells by Agrobacterium tumefaciens seems to integrate rather randomly into the plant genome. We analyzed a target site in the genome of Nicotiana tabacum before and after integration of a T-DNA. Clones presenting right and left T-DNA/plant DNA junctions were used as probes to identify and isolate a unique 1.8-kilobase EcoRI fragment corresponding to the plant DNA target site for a T-DNA insertion event. Comparison of the nucleotide sequences of the plant DNA portions of the T-DNA junction clones with the original plant DNA target revealed that several types of rearrangements resulted from insertion of the T-DNA. The most dramatic alteration was a 158-base-pair direct repeat of target plant sequences at the left and right T-DNA junctions. In addition, there were deletion and insertion events at the ends of the right and left copies of the 158-base-pair repeat. The variety of target-site rearrangements suggests that T-DNA insertion is a multistep process of recombination accompanied by local replicative and repair activities mediated by host-cell enzymes. Biology and Life Sciences http://hdl.handle.net/1854/LU-1902434 10.1073/pnas.84.17.6169 A1987J864900036 0027-8424 1987 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Proc. Natl. Acad. Sci. USA 0027-8424 1987 84 17 6169 6173 1987 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1902434/file/1902440 application/pdf restricted ug 1902434 2011-09-16T16:40:24Z 2018-08-13T14:11:58Z A1 VABB-1 1 info:srw/schema/1/mods-v3.3xml journalArticle A1 Illegitimate recombination in plants : a model for T-DNA integration Godelieve Gheysen aut author ug_LA25 0000-0003-1929-5059 Raimundo Villarroel-Mandiola aut author ug_UGent Marc Van Montagu aut author ug_WE09 eng Agrobacterium tumefaciens is a soil bacterium capable of transferring DNA (the T-DNA) to the genome of higher plants, where it is then stably integrated. Six T-DNA inserts and their corresponding preinsertion sites were cloned from Arabidopsis thaliana and analyzed. Two T-DNA integration events from Nicotiana tabacum were included in the analysis. Nucleotide sequence comparison of plant target sites before and after T-DNA integration showed that the T-DNA usually causes only a small (13-28 bp) deletion in the plant DNA but larger target rearrangements can occur. Short homologies between the T-DNA ends and the target sites, as well as the presence of filler sequences at the junctions, indicate that T-DNA integration is mediated by illegitimate recombination and that these processes in plants are very analogous to events in mammalian cells. We propose a model for T-DNA integration on the basis of limited base-pairing for initial synapsis, followed by DNA repair at the junctions. Variations of the model can explain the formation of filler DNA at the junctions by polymerase slipping and template switching during DNA repair synthesis and the presence of larger plant target DNA rearrangements. Biology and Life Sciences CROWN GALL TUMOR AGROBACTERIUM-TUMEFACIENS BINDING-PROTEIN NONHOMOLOGOUS RECOMBINATION ESCHERICHIA-COLI MAMMALIAN-CELLS VIRD2 PROTEIN SEQUENCES MECHANISMS PLASMID AGROBACTERIUM-TUMEFACIENS REARRANGEMENT RECOMBINATION TARGET T-DNA TRANSGENIC PLANTS http://hdl.handle.net/1854/LU-8514406 10.1101/gad.5.2.287 A1991EX51800013 0890-9369 1991 GENES & DEVELOPMENT Genes Dev. 0890-9369 1991 5 2 287 297 1991 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/8514406/file/8514407 application/unknown restricted ug 8514406 2017-03-15T12:25:49Z 2018-08-16T07:59:18Z A1 VABB-1 2 info:srw/schema/1/mods-v3.3xml journalArticle A1 Orphan gene finding: an exon assembly approach Philippe Blayo aut author Pierre Rouzé aut author ug_UGent Marie-France Sagot aut author eng Biology and Life Sciences gene finding orphan gene exon assembly DNA/DNA and DNA/protein comparison coding DNA comparison models dynamic programming ARABIDOPSIS-THALIANA PROTEIN ALIGNMENT DNA-SEQUENCES LINEAR-SPACE GENOMIC DNA CODING DNA PREDICTION ALGORITHM COMPUTER ERRORS http://hdl.handle.net/1854/LU-215318 10.1016/S0304-3975(02)00043-9 000179441900007 0304-3975 2003 THEORETICAL COMPUTER SCIENCE Theor. Comput. Sci. 0304-3975 2003 290 3 1407 1431 2003 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/215318/file/4144219 application/pdf restricted ug 215318 2004-05-10T17:59:00Z 2018-08-13T14:15:10Z A1 VABB-1 3 info:srw/schema/1/mods-v3.3xml journalArticle A1 T-DNA integration in Arabidopsis chromosomes: presence and origin of filler DNA sequences Pieter Windels aut author Sylvie De Buck aut author ug_WE09 Erik Van Bockstaele aut author ug_UGent Marc De Loose aut author ug_WE09 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng To investigate the relationship between T-DNA integration and double-stranded break (DSB) repair in Arabidopsis, we studied 67 T-DNA/plant DNA junctions and 13 T-DNA/T-DNA junctions derived from transgenic plants. Three different types of T-DNA-associated joining could be distinguished. A minority of T-DNA/plant DNA junctions were joined by a simple ligation-like mechanism, resulting in a junction without microhomology or filler DNA insertions. For about one-half of all analyzed junctions, joining of the two ends occurred without insertion of filler sequences. For these junctions, microhomology was strikingly combined with deletions of the T-DNA ends. For the remaining plant DNA/T-DNA junctions, up to 51-bp-long filler sequences were present between plant DNA and T-DNA contiguous sequences. These filler segments are built from several short sequence motifs, identical to sequence blocks that occur in the T-DNA ends and/or the plant DNA close to the integration site. Mutual microhomologies among the sequence motifs that constitute a filler segment were frequently observed. When T-DNA integration and DSB repair were compared, the most conspicuous difference was the frequency and the structural organization of the filler insertions. In Arabidopsis, no filler insertions were found at DSB repair junctions. In maize (Zea mays) and tobacco (Nicotiana tabacum), DSB repair-associated filler was normally composed of simple, uninterrupted sequence blocks. Thus, although DSB repair and T-DNA integration are probably closely related, both mechanisms have some exclusive and specific characteristics. Biology and Life Sciences NONHOMOLOGOUS RECOMBINATION STRAND BREAK REPAIR ILLEGITIMATE RECOMBINATION PLANT-CELLS AGROBACTERIUM-TUMEFACIENS GENOME EVOLUTION MAMMALIAN-CELLS LIGASE-IV THALIANA MAIZE http://hdl.handle.net/1854/LU-348784 10.1104/pp.103.027532 000187528700063 0032-0889 2003 PLANT PHYSIOLOGY Plant Physiol. 0032-0889 2003 133 4 2061 2068 2003 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/348784/file/4144327 application/pdf restricted ug 348784 2004-05-10T18:14:00Z 2018-08-13T14:25:25Z A1 VABB-1 4 info:srw/schema/1/mods-v3.3xml book B1 DNA & biotechnologie DNA en biotechnologie Godelieve Gheysen aut author ug_LA25 0000-0003-1929-5059 dut Biology and Life Sciences http://hdl.handle.net/1854/LU-8514849 9789460580178 Antwerpen Luster 2009 52 p. De Essentie 16 published ug 8514849 2017-03-20T11:42:48Z 2017-07-25T14:01:12Z B1 VABB-2 5 info:srw/schema/1/mods-v3.3xml journalArticle A1 Effect of food processing on plant DNA degradation and PCR-based GMO analysis: a review Nicolas Gryson aut author ug_UGent eng The applicability of a DNA-based method for GMO detection and quantification depends on the quality and quantity of the DNA. Important food-processing conditions, for example temperature and pH, may lead to degradation of the DNA, rendering PCR analysis impossible or GMO quantification unreliable. This review discusses the effect of several food processes on DNA degradation and subsequent GMO detection and quantification. The data show that, although many of these processes do indeed lead to the fragmentation of DNA, amplification of the DNA may still be possible. Length and composition of the amplicon may, however, affect the result, as also may the method of extraction used. Also, many techniques are used to describe the behaviour of DNA in food processing, which occasionally makes it difficult to compare research results. Further research should be aimed at defining ingredients in terms of their DNA quality and PCR amplification ability, and elaboration of matrix-specific certified reference materials. Agriculture and Food Sciences PCR analysis DNA quantification GMO detection DNA degradation Food processing GENETICALLY-MODIFIED ORGANISMS POLYMERASE-CHAIN-REACTION REAL-TIME PCR QUANTITATIVE COMPETITIVE PCR DIFFERENT EXTRACTION METHODS MODIFIED SOY BEANS MODIFIED BT MAIZE ZEA-MAYS L. MODIFIED SOYBEANS RECOMBINANT-DNA http://hdl.handle.net/1854/LU-812815 10.1007/s00216-009-3343-2 000275454900007 1618-2642 2010 ANALYTICAL AND BIOANALYTICAL CHEMISTRY Anal. Bioanal. Chem. 1618-2642 2010 396 6 2003 2022 2010 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/812815/file/6824118 application/pdf restricted ug 812815 2009-12-16T13:37:59Z 2016-12-19T15:44:45Z A1 VABB-1 6 info:srw/schema/1/mods-v3.3xml journalArticle A1 Comparative evaluation of six extraction methods for DNA quantification and PCR detection in cocoa and cocoa-derived products Viet Ha Lam Thi aut author ug_LA23 Lore Vanlerberghe aut author ug_LA15 Ha Thanh Toan aut author Koen Dewettinck aut author ug_LA23 Kathy Messens aut author ug_LA25 eng Six methologies for extracting DNA in cocoa and cocoa-derived products (cocoa leaves, cocoa beans, cocoa powder, cocoa butter, cocoa mass, and dark chocolate) are described. These DNA extraction methods included 4 commercial kits DNeasy Plant kit, DNeasy Plant kit with polyvinyl polypyrrolidone (PVPP), QIAamp DNA Stool kit, Wizard Genomic DNA kit and 2 CTAB based methods, CTAB-Proteinase K procedure and CTAB-SDS (sodium dodecyl sulfate) procedure. The DNA yield, purity, and quality for 6 different cocoa matrices are discussed. The yield and purity were determined through spectrophotometry. Three different conventional PCR reactions were used to assess the quality of the DNA extracted. The Wizard Genomic DNA kit and the CTAB-Proteinase K method were found to be the best for DNA quality and PCR detection in cocoa leaves. The CTAB-Proteinase K procedure is highly recommended for cocoa beans, while the Wizard Genomic DNA kit revealed the best PCR performance when applied to cocoa powder. The cocoa butter matrix gave the lowest DNA yield, purity, and amplification results for all the examined extraction methods. The QIAamp DNA Stool kit and the CTAB-SDS method showed the best result for PCR detection of cocoa mass. The Wizard Genomic DNA kit and the CTAB-SDS method showed the best PCR performance for dark chocolate. In general, the two CTAB based methods, namely the CTAB-Proteinase K and the CTAB-SDS were suitable for the DNA extraction of all types of cocoa-derived products with the exeption of cocoa butter. This evaluation can be especially useful for the detection of DNA in cocoa derived samples. Biology and Life Sciences AMPLIFICATION THEOBROMA-CACAO POLYMERASE-CHAIN-REACTION Cocoa Polymerase Chain Reaction Deoxyribonucleic Acid extraction Cocoa-derived products http://hdl.handle.net/1854/LU-5938720 10.1080/08905436.2014.996761 000349898400001 0890-5436 2015 FOOD BIOTECHNOLOGY Food Biotechnol. 0890-5436 2015 29 1 1 19 2015 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/5938720/file/5938727 application/pdf restricted ug 5938720 2015-04-21T07:34:03Z 2016-12-19T15:41:51Z A1 VABB-1 7 info:srw/schema/1/mods-v3.3xml journalArticle A1 Base excision repair and its role in maintaining genome stability Joke Baute aut author ug_UGent Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng For all living organisms, genome stability is important, but is also under constant threat because various environmental and endogenous damaging agents can modify the structural properties of DNA bases. As a defense, organisms have developed different DNA repair pathways. Base excision repair (BER) is the predominant pathway for coping with a broad range of small lesions resulting from oxidation, alkylation, and deamination, which modify individual bases without large effect on the double helix structure. As, in mammalian cells, this damage is estimated to account daily for 104 events per cell, the need for BER pathways is unquestionable. The damage-specific removal is carried out by a considerable group of enzymes, designated as DNA glycosylases. Each DNA glycosylase has its unique specificity and many of them are ubiquitous in microorganisms, mammals, and plants. Here, we review the importance of the BER pathway and we focus on the different roles of DNA glycosylases in various organisms. Biology and Life Sciences DNA repair DNA glycosylase DNA damage mutagenesis URACIL-DNA-GLYCOSYLASE COLI ENDONUCLEASE-III CELL NUCLEAR ANTIGEN OXIDATIVELY DAMAGED DNA P53 TUMOR-SUPPRESSOR DOUBLE-STRANDED DNA GUANOSINE LESIONS SPIROIMINODIHYDANTOIN SENSOR RAD9-RAD1-HUS1 INTERACTS HUMAN ALKYLADENINE GLYCOSYLASE BROAD SUBSTRATE-SPECIFICITY http://hdl.handle.net/1854/LU-439471 10.1080/10409230802309905 000258774400001 1040-9238 2008 CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY Crit. Rev. Biochem. Mol. Biol. 1040-9238 2008 43 4 239 276 2008 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/439471/file/3066226 application/pdf restricted ug 439471 2008-11-12T13:58:00Z 2018-08-13T14:32:53Z A1 VABB-1 8 info:srw/schema/1/mods-v3.3xml journalArticle A1 Fate of selectable marker DNA integrated into the genome of Nicotiana tabacum Armin P Czernilofsky aut author Rüdiger Hain aut author Luis Herrera-Estrella aut author Horst Lörz aut author Elisabeth Goyvaerts aut author Barbara J Baker aut author Jeff Schell aut author eng To compare the effects of different transformation methods on the integration behavior and structural stability of integrated foreign genes in plant cells, tobacco protoplasts were transformed with Escherichia coli plasmid pLGV2103neo DNA using the Ca phosphate DNA coprecipitation technique. Parallel transformations were done by cocultivation with Agrobacterium tumefaciens harboring the Ti plasmid derivatives pGV3850::2103neo or pGV3850::1103neo. A comparison of the fine structure of the integrated donor DNA obtained by direct gene transfer and by cocultivation indicates that the donor DNA in cells transformed by the former technique undergoes structural changes and concatemerizations, while the DNA integrated by the latter procedure is often unaltered. The cotransformed nopaline synthase gene, which is present in the donor Ti plasmid DNA, was inactivated in two out of nine cases. Once integrated, the arrays of selectable marker DNA appear to be structurally stable under different cell culture and selection conditions, as well as after genetic transmission. Biology and Life Sciences http://hdl.handle.net/1854/LU-1903293 10.1089/dna.1986.5.101 A1986D177200002 0198-0238 1986 DNA-A JOURNAL OF MOLECULAR & CELLULAR BIOLOGY DNA 0198-0238 1986 5 2 101 113 1986 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1903293/file/1903304 application/pdf restricted ug 1903293 2011-09-19T10:59:25Z 2018-08-13T14:11:58Z A1 VABB-1 9 info:srw/schema/1/mods-v3.3xml journalArticle A1 T-DNA transfer and T-DNA integration efficiencies upon Arabidopsis thaliana root explant cocultivation and floral dip transformation Rim Ghedira aut author ug_UGent Sylvie De Buck aut author ug_WE09 Frédéric Van Ex aut author Geert Angenon aut author Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng T-DNA transfer and integration frequencies during Agrobacterium-mediated root explant cocultivation and floral dip transformations of Arabidopsis thaliana were analyzed with and without selection for transformation-competent cells. Based on the presence or absence of CRE recombinase activity without or with the CRE T-DNA being integrated, transient expression versus stable transformation was differentiated. During root explant cocultivation, continuous light enhanced the number of plant cells competent for interaction with Agrobacterium and thus the number of transient gene expression events. However, in transformation competent plant cells, continuous light did not further enhance cotransfer or cointegration frequencies. Upon selection for root transformants expressing a first T-DNA, 43-69 % of these transformants showed cotransfer of another non-selected T-DNA in two different light regimes. However, integration of the non-selected cotransferred T-DNA occurred only in 19-46 % of these transformants, indicating that T-DNA integration in regenerating root cells limits the transformation frequencies. After floral dip transformation, transient T-DNA expression without integration could not be detected, while stable T-DNA transformation occurred in 0.5-1.3 % of the T1 seedlings. Upon selection for floral dip transformants with a first T-DNA, 8-34 % of the transformants showed cotransfer of the other non-selected T-DNA and in 93-100 % of them, the T-DNA was also integrated. Therefore, a productive interaction between the agrobacteria and the female gametophyte, rather than the T-DNA integration process, restricts the floral dip transformation frequencies. Biology and Life Sciences SELECTION AGROBACTERIUM-MEDIATED TRANSFORMATION RECOMBINATION LIGHT TUMEFACIENS HIGH-FREQUENCY PLANT-CELLS VACUUM-INFILTRATION Transgene expression Transformation efficiency CRE recombinase TARGET GENETIC-TRANSFORMATION Agrobacterium http://hdl.handle.net/1854/LU-4213826 10.1007/s00425-013-1948-3 000327386200003 0032-0935 2013 PLANTA Planta 0032-0935 2013 238 6 1025 1037 2013 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/4213826/file/4213850 application/pdf restricted ug 4213826 2013-12-19T16:46:48Z 2018-08-13T14:30:28Z A1 VABB-1 10 1.1dnasrw.ServerChoicescrdna