1.1 3222 info:srw/schema/1/mods-v3.3xml journalArticle A1 Characterization of mononucleotide repeats in sequenced prokaryotic genomes Tom Coenye aut author ug_FW02 0000-0002-6407-0601 Peter Vandamme aut author ug_WE10 0000-0002-5581-7937 eng Medicine and Health Sciences http://hdl.handle.net/1854/LU-366006 000242119700001 1340-2838 2005 DNA RESEARCH DNA Res. 1340-2838 Oxford University Press 2005 12 4 221 233 2005 published ug 366006 2007-05-15T11:31:00Z 2018-08-13T14:26:26Z A1 VABB-1 1 info:srw/schema/1/mods-v3.3xml conference C1 Protection of turkeys against Chlamydophila psittaci challenge by DNA and rMOMP vaccination and evaluation of the immunomodulating effect of 1 alpha,25-dihydroxyvitamin D-3 Eric Cox aut author ug_DI04 0000-0003-4281-2990 Bruno Goddeeris aut author ug_UGent D VANROMPAY aut author Medicine and Health Sciences http://hdl.handle.net/1854/LU-378479 2004 DNA vaccines 2004: The gene vaccine conference. 2004 1 1 2004 published ug 378479 2007-10-09T14:29:00Z 2018-08-13T14:27:11Z C1 VABB-5 2 info:srw/schema/1/mods-v3.3xml journalArticle A1 Influence of bacterial age and pH of lysis buffer on type of nucleic acid isolated Mieke Uyttendaele aut author ug_LA23 0000-0002-3134-8929 R Schukkink aut author B van Gemen aut author Johan Debevere aut author ug_UGent eng This study deals with the determination of the factors which influence isolation of RNA using a silica-based nucleic acid isolation protocol. Four bacteria were included in the investigation: Campylobacter jejuni, Escherichia coli, Listeria monocytogenes and Pseudomonas fluorescens. An increase of RNA yield could be obtained with all four strains at the exponential growth phase, reaching a maximum at the beginning of the stationary phase. Later the amount of RNA isolated gradually decreased. At the late stationary phase DNA was also isolated in case of Escherichia coli and Pseudomonas a fluorescens. DNA was only obtained at this stage of the growth curve, probably because RNA contents of the cell decreases in the late stationary phase thus enabling DNA only now to bind to the silica used in the isolation procedure. In the exponential and stationary phase, when there is a competition between RNA and DNA to bind to the silica, there is a preferential binding of RNA over DNA to the silica. It was shown that a pH of 6.0 and 6.5 promoted isolation of RNA. At pH 8.0 and 8.5 large amounts of DNA were obtained from the Gram-negative bacteria. Thus, the silica based nucleic acid isolation method enables isolation of either RNA or DNA when taking into account the appropriate conditions of pH of the buffers and applying the corresponding incubation time of the bacterial culture. A preceding treatment of lysozyme and proteinase K was sufficient to accomplish lysis of the Gram-positive cell. Biology and Life Sciences RNA DNA silica isolation POLYMERASE CHAIN-REACTION EXTRACTION http://hdl.handle.net/1854/LU-189438 10.1016/0167-7012(96)00904-9 A1996VA30600016 0167-7012 1996 JOURNAL OF MICROBIOLOGICAL METHODS J. Microbiol. Methods 0167-7012 1996 26 1-2 133 138 1996 published ug 189438 2004-01-14T13:41:00Z 2018-11-13T14:50:39Z A1 VABB-1 3 info:srw/schema/1/mods-v3.3xml dissertation D1 Electron-nuclear double resonance approach for studying radiation damage in DNA Jevgenij Kusakovskij aut author ug_UGent Henk Vrielinck promoter ug_WE04 0000-0003-4861-9630 Freddy Callens promoter ug_WE04 0000-0002-6504-6945 eng Physics and Astronomy Biology and Life Sciences EPR ESR ENDOR radiation damage radicals DFT DNA http://hdl.handle.net/1854/LU-8532881 Ghent, Belgium Ghent University. Faculty of Sciences 2017 I have transferred the copyright for this publication to the publisher published Gent : Campus Sterre (S2, auditorium 1.008) https://biblio.ugent.be/publication/8532881/file/8532883 application/pdf restricted ug 8532881 2017-10-02T10:01:46Z 2018-11-13T14:55:47Z D1 4 info:srw/schema/1/mods-v3.3xml conference C3 On the transfer and expression of bacterial plasmid DNA in higher plants Jeff Schell aut author 105e Bijeenkomst van de Belgische Vereniging voor Biochemie eng Biology and Life Sciences http://hdl.handle.net/1854/LU-5669383 10.3109/13813457809069536 A1978GH15400057 0003-9799 1978 ARCHIVES INTERNATIONALES DE PHYSIOLOGIE ET DE BIOCHIMIE Arch. Int. Physiol. Biochim. 0003-9799 1978 86 4 901 902 1978 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/5669383/file/5671387 application/pdf restricted ug 5669383 2014-08-06T15:09:26Z 2018-08-13T14:34:47Z C3 5 info:srw/schema/1/mods-v3.3xml conference C1 Genetica (DNA) als hulpwetenschap bij het genealogisch onderzoek. Benedikt Sas aut author ug_LA23 Agriculture and Food Sciences http://hdl.handle.net/1854/LU-426518 2006 Vlaamse ingenieurskamer 2006 1 1 2006 published ug 426518 2008-07-04T13:56:00Z 2016-12-19T15:36:21Z C1 VABB-5 6 info:srw/schema/1/mods-v3.3xml journalArticle A1 Noncoding DNA in lipofection of HeLa cells: a few insights Nathalie Symens aut author ug_UGent Joanna Rejman aut author ug_FW01 Bart Lucas aut author ug_FW01 Jo Demeester aut author ug_FW01 0000-0003-2436-1524 Stefaan De Smedt aut author ug_CA05 ug_FW01 0000-0002-8653-2598 Katrien Remaut aut author ug_FW01 eng In cationic carrier-mediated gene delivery, the disproportional relationship between the quantity of delivered DNA and the amount of encoded protein produced is a well-known phenomenon. The numerous intracellular barriers which need to be overcome by pDNA to reach the nucleoplasm play a major role in it. In contrast to what one would expect, a partial replacement of coding pDNA by noncoding DNA does not lead to a decrease in transfection efficiency. The mechanism underlying this observation is still unclear. Therefore, we investigated which constituents of the transfection process might contribute to this phenomenon. Our data reveal that the topology of the noncoding plasmid DNA plays a major role. Noncoding pDNA can be used only in a supercoiled form to replace coding pDNA in Lipofectamine lipoplexes, without a loss in transfection levels. When noncoding pDNA is linearized or partly digested, it diminishes the transfection potential of coding pDNA, as does noncoding salmon DNA. The difference in transfection efficiencies could not be attributed to diverse physicochemical characteristics of the Lipofectamine lipoplexes containing different types of noncoding DNA or to the extent of their internalization. At the level of endosomal release, however, nucleic acid release from the endosomal compartment proceeds faster when lipoplexes contain noncoding salmon DNA. Since the half-life of pDNA in the cytosol hardly exceeds 90 min, it is conceivable that prolonged release of coding pDNA from complexes carrying supercoiled noncoding pDNA may explain its positive effect on transfection, while this depot effect does not exist when noncoding salmon DNA is used. Medicine and Health Sciences NUCLEAR TOPOLOGY TRANSGENE EXPRESSION MAMMALIAN-CELLS NONLINEAR PHARMACODYNAMICS PLASMID DNA TRANSFECTION EFFICIENCY TRANSPORT IN-VITRO TRANSCRIPTION endosomal depot endosomal release mRNA cationic lipids Lipofectamine NONVIRAL GENE DELIVERY transfection salmon DNA intact coding plasmid DNA http://hdl.handle.net/1854/LU-3197624 10.1021/mp300569j 000315763500028 1543-8384 2013 MOLECULAR PHARMACEUTICS Mol. Pharm. 1543-8384 2013 10 3 1070 1079 2013 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/3197624/file/3197660 application/pdf restricted ug 3197624 2013-04-19T15:04:28Z 2018-11-13T14:50:26Z A1 VABB-1 7 info:srw/schema/1/mods-v3.3xml dissertation D1 Design and systematic study of imidazole based DNAzymes : an integrated NMR and molecular dynamics approach Dieter Buyst aut author ug_WE07 José Martins promoter ug_WE07 0000-0001-7350-2253 Annemieke Madder promoter ug_WE07 0000-0003-0179-7608 eng Proteins are known as the workhorses of the cell and fulfill numerous tasks essential for the cell’s survival. One of the most important tasks is their involvement in catalysis. From a thermodynamic point of view, this is made possible by the stabilisation of the transition state, a high-energy reaction state between reactants and products. This stabilization is made possible due to a combination of a wide variety of chemical functionalities inherent to the twenty amino acid building blocks. This variety observed with proteins stands in sharp contrast to the limited structural diversity of DNA and RNA. These biomolecules are optimized for hydrogen bonding and the formation of complementary, predictable helix-like structures. It thus seemed highly unlikely DNA and RNA could ever fulfill the same catalytic functions as proteins. The discovery and subsequent development of natural and synthetic catalytic RNA and DNA (deoxy)ribozymes has overturned this belief. Mainly identified by means of in vitro selection and evolution experiments, RNA/DNA-based catalysts employ a variety of catalytic mechanisms. Nevertheless, despite the numerous successes of the top-down in vitro approach, structural insight in how these RNA- and DNAzymes ultimately achieve catalysis is still lacking and can be considered as one of the main drawbacks for their further development. Inspired by these developments and limitations, the current research project aims to develop DNA-based hydrolases via a more bottom-up approach. Here the stable and predictable nature of the DNA duplex is employed to position one or more imidazole-bearing thymine nucleotide building blocks (TIm) using standard phosphoramidite solid phase chemistry. Via systematic studies using UV-VIS thermal melting experiments, NMR and molecular dynamics simulations, the mutual impact of the modification and the DNA scaffold could be identified. This approach was applied in two major systematic studies focussing on both single and multiple TIm modified DNA systems. In case of the single modified systems a so-called pKaH-regulating motif (figure) has been uncovered where the imidazole modification at position n in the DNA duplex engages in a persistent hydrogen bond interaction with the carbonyl groups of guanine bases at positions n+1 and n+2 residing in the DNA major groove. This interaction in turn contributes in a significant thermal stabilisation of ±6°C and increase of over 1 pKaH unit with respect to other non-interacting modified systems. In addition to its identity and overall features, the possible sequential permutations of this motif were explored as well. Given that a single TIm functionality alone is unlikely to generate any meaningful catalytic activity, the second systematic study focused on the mutual impact of multiple imidazole residues residing in the same system, both in the presence and absence of the interaction motif. Furthermore these systems allowed to confirm that the motif is tolerated when multiple imidazoles are present and relative positioning of the pKaH-regulating motif with respect to the non-interacting imidazole allows to regulate the pKaH value of the second non-interacting imidazole functionality within certain limits as well. The observations and guidelines obtained during these studies should allow to gradually develop more intricate systems that are ultimately able to cleave ester and/or amide bonds in a stereo selective fashion. Chemistry NMR DNA Molecular Dynamics Enzymes Imidazole http://hdl.handle.net/1854/LU-7010798 Ghent, Belgium Ghent University. Faculty of Sciences 2015 I have transferred the copyright for this publication to the publisher published Gent : Aula Universiteit https://biblio.ugent.be/publication/7010798/file/7011244 application/pdf restricted ug 7010798 2015-12-15T11:44:53Z 2018-11-13T14:54:17Z D1 8 info:srw/schema/1/mods-v3.3xml journalArticle A1 Interleukin 6 dependence of anti-DNA antibody production: evidence for two pathways of autoantibody formation in pristane-induced lupus HB Richards aut author M Satoh aut author M Shaw aut author Claude Libert aut author ug_WE14 0000-0001-6408-036X V Poli aut author WH Reeves aut author eng Pristane induces a lupus-like syndrome in nonautoimmune mice characterized by the development of glomerulonephritis and lupus-associated autoantibodies. This is accompanied by overproduction of interleukin (IL)-6, a cytokine linked with autoimmune phenomena. The goal of this study was to evaluate the role of IL-6 in autoantibody production in pristane-induced lupus. BALB/cAn IL-6-deficient (-/-) and -intact (+/+) mice were treated with pristane or phosphate-buffered saline, and autoantibody production was evaluated. Pristane induced high levels of immunoglobulin (Ig)G anti-single-stranded DNA, -double-stranded (ds)DNA, and -chromatin antibodies in IL-6(+/+), but not IL-6(-/-) mice by enzyme-linked immunosorbent assay. High titer IgG anti-dsDNA antibodies also were detected in sera from +/+, but not -/-, mice by Crithidia luciliae kinetoplast staining. The onset of IgG anti-dsDNA antibody production in +/+ mice occurred >5 mo after pristane treatment, well after the onset of nephritis, suggesting that these antibodies are not directly responsible for inducing renal disease. In contrast to anti-DNA, the frequencies of anti-nRNP/Sm and anti-Su antibodies were similar in pristane-treated IL-6(-/-) and IL-6(+/+) mice. However, levels were higher in the +/+ group. These results suggest that IgG anti-DNA and chromatin antibodies in pristane-treated mice are strictly IL-6 dependent, whereas induction of anti-nRNP/Sm and Su autoantibodies is IL-6 independent. The IL-6 dependence of anti-DNA, but not anti-nRNP/Sm, may have implications for understanding the patterns of autoantibody production in lupus. Anti-DNA antibodies are produced transiently, mainly during periods of disease activity, whereas anti-nRNP/Sm antibody levels are relatively insensitive to disease activity. This may reflect the differential IL-6 dependence of the two responses. Biology and Life Sciences antinuclear antibodies interleukin 6 anti-DNA antibodies pristane systemic lupus erythematosus B-CELLS IL-6 IMMUNE-COMPLEX GLOMERULONEPHRITIS T-CELL CLONES BALB/C MICE MURINE LUPUS MRL/LPR MICE LPR/LPR MICE CD40 LIGAND LPR MICE http://hdl.handle.net/1854/LU-1203246 000075929600019 0022-1007 1998 JOURNAL OF EXPERIMENTAL MEDICINE J. Exp. Med. 0022-1007 1998 188 5 985 990 1998 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1203246/file/1203253 application/pdf restricted http://jem.rupress.org/content/188/5/985.abstract ug 1203246 2011-04-06T11:47:16Z 2018-08-13T14:07:25Z A1 VABB-1 9 info:srw/schema/1/mods-v3.3xml journalArticle A1 Synthetic polymers for vectorial delivery of DNA: characterisation of polymer-DNA complexes by photon correlation spectroscopy and stability to nuclease degradation and disruption by polyanions in vitro. PR DASH aut author Veska Toncheva aut author ug_WE07 Etienne Schacht aut author ug_UGent LW SEYMOUR aut author eng Science General http://hdl.handle.net/1854/LU-185150 A1997XX69800017 0168-3659 1997 JOURNAL OF CONTROLLED RELEASE J. Control. Release 0168-3659 1997 48 2-3 269 276 1997 published ug 185150 2004-01-14T13:41:00Z 2018-08-13T14:11:30Z A1 VABB-1 10 info:srw/schema/1/mods-v3.3xml journalArticle A1 The structure of the DNA of bacteriophage φX174, I: the action of exopolynucleotidases Structure of DNA of bacteriophage psiX174, 1 : action of exopolynucleotidases Walter Fiers aut author ug_UGent Robert L Sinsheimer aut author eng Biology and Life Sciences http://hdl.handle.net/1854/LU-1927346 10.1016/S0022-2836(62)80029-1 A19625805B00005 0022-2836 1962 JOURNAL OF MOLECULAR BIOLOGY J. Mol. Biol. 0022-2836 1962 5 4 408 419 1962 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1927346/file/1963091 application/pdf restricted ug 1927346 2011-10-13T11:16:04Z 2018-08-13T14:12:14Z A1 VABB-1 11 info:srw/schema/1/mods-v3.3xml journalArticle A1 Efficient gene tagging in Arabidopsis thaliana using a gene trap approach Elena Babiychuk aut author ug_WE09 Mayuree Fuangthong aut author Marc Van Montagu aut author ug_WE09 Dirk Inzé aut author ug_WE09 0000-0002-3217-8407 Sergei Kushnir aut author ug_WE09 eng Large quantities of DNA sequence information about plant genes are rapidly accumulating in public databases, but to progress from DNA sequence to biological function a mutant allele for each of the genes ideally should be available, Here we describe a gene trap construct that allowed us to disrupt transcribed genes with a high efficiency in Arabidopsis thaliana. In the T-DNA vector used, the expression of a bacterial reporter gene coding for neomycin phosphotransferase II (nptII) depends on the in vivo generation of a translation fusion upon the T-DNA integration into the Arabidopsis genome, Analysis of 20 selected transgenic lines showed that 12 lines are T-DNA insertion mutants, The disrupted genes analyzed encoded ribosomal proteins (three lines), aspartate tRNA synthase, DNA ligase, basic-domain leucine zipper DNA binding protein, ATP-binding cassette transporter, and five proteins of unknown function, Four tagged genes were new for Arabidopsis. The results presented here suggest that gene trapping, using nptII as a reporter gene, can be as high as 80% and opens novel perspectives for systematic gene tagging in A. thaliana. Biology and Life Sciences insertion mutagenesis Agrobacterium tumefaciens T-DNA TRANSPOSABLE ELEMENTS PLANTS TRANSFORMATION RECOMBINATION INTEGRATION DISRUPTION CLONING PROTEIN VECTORS http://hdl.handle.net/1854/LU-185794 10.1073/pnas.94.23.12722 A1997YF39300086 0027-8424 1997 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Proc. Natl. Acad. Sci. USA 0027-8424 1997 94 23 12722 12727 1997 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/185794/file/4173434 application/pdf restricted ug 185794 2004-01-14T13:41:00Z 2018-08-13T14:11:34Z A1 VABB-1 12 info:srw/schema/1/mods-v3.3xml conference C3 Identification of novel DNA stress checkpoint genes Pooneh Kalhorzadeh aut author ug_UGent Lieven De Veylder aut author ug_WE09 2nd International meeting on Plant DNA Repair and Recombination eng Biology and Life Sciences http://hdl.handle.net/1854/LU-4256578 2010 Plant DNA Repair and Recombination, 2nd International meeting, Abstracts 2010 2010 published ug 4256578 2014-01-30T12:11:21Z 2016-12-19T15:36:32Z C3 13 info:srw/schema/1/mods-v3.3xml journalArticle A1 Mechanistic insight into how multidrug resistant Acinetobacter baumannii response regulator AdeR recognizes an intercistronic region Yurong Wen aut author Zhenlin Ouyang aut author Yue Yu aut author Xiaorong Zhou aut author Yingmei Pei aut author Bart Devreese aut author ug_WE10 0000-0002-9764-2581 Paul G Higgins aut author Fang Zheng aut author eng AdeR-AdeS is a two-component regulatory system, which controls expression of the adeABC efflux pump involved in Acinetobacter baumannii multidrug resistance. AdeR is a response regulator consisting of an N-terminal receiver domain and a C-terminal DNA-binding-domain. AdeR binds to a direct-repeat DNA in the intercistronic region between adeR and adeABC. We demonstrate a markedly high affinity binding between unphosphorylated AdeR and DNA with a dissociation constant of 20 nM. In addition, we provide a 2.75 angstrom crystal structure of AdeR DNA-binding-domain complexed with the intercistronic DNA. This structure shows that the alpha 3 and beta hairpin formed by beta 5-beta 6 interacts with the major and minor groove of the DNA, which in turn leads to the introduction of a bend. The AdeR receiver domain structure revealed a dimerization motif mediated by a gearwheel-like structure involving the D108F109-R122 motif through cation pi stack interaction. The structure of AdeR receiver domain bound with magnesium indicated a conserved Glu19Asp20-Asp63 magnesium-binding motif, and revealed that the potential phosphorylation site Asp63(OD1) forms a hydrogen bond with Lys112. We thus dissected the mechanism of how AdeR recognizes the intercistronic DNA, which leads to a diverse mode of response regulation. Unlocking the AdeRS mechanism provides ways to circumvent A. baumannii antibiotic resistance. Biology and Life Sciences 2-COMPONENT SIGNAL-TRANSDUCTION MOLECULAR-REPLACEMENT DNA-BINDING DOMAIN TIGECYCLINE ACTIVATION SYSTEM ADEABC OVEREXPRESSION EPIDEMIOLOGY http://hdl.handle.net/1854/LU-8539032 10.1093/nar/gkx624 000411096400046 0305-1048 1362-4962 2017 NUCLEIC ACIDS RESEARCH Nucleic Acids Res. 0305-1048 1362-4962 2017 45 16 9773 9787 2017 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/8539032/file/8539035 application/pdf ug 8539032 2017-11-27T08:21:18Z 2017-12-19T09:19:39Z A1 VABB-1 14 info:srw/schema/1/mods-v3.3xml journalArticle A1 Strategies for validation and testing of DNA methylation biomarkers C Noehammer aut author W Pulverer aut author MR Hassler aut author M Hofner aut author M Wielscher aut author K Vierlinger aut author T Liloglou aut author D McCarthy aut author TJ Jensen aut author A Nygren aut author H Gohlke aut author Geert Trooskens aut author ug_LA26 M Braspenning aut author Wim Van Criekinge aut author ug_LA26 0000-0003-2971-5539 G Egger aut author A Weinhaeusel aut author eng DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and therapeutic response prediction. Although the advent of genome-wide DNA methylation profiling in primary disease tissue has provided a manifold resource for biomarker development, only a tiny fraction of DNA methylation-based assays have reached clinical testing. Here, we provide a critical overview of different analytical methods that are suitable for biomarker validation, including general study design considerations, which might help to streamline epigenetic marker development. Furthermore, we highlight some of the recent marker validation studies and established markers that are currently commercially available for assisting in clinical management of different cancers. Biology and Life Sciences assay validation biomarker bisulfite-deamination circulating free DNA deep sequencing DNA methylation MALDI qPCR pyrosequencing CELL-FREE DNA REAL-TIME PCR SENSITIVE RESTRICTION ENZYMES BLOOD-PROCESSING PROTOCOLS BASE-SPECIFIC CLEAVAGE COLORECTAL-CANCER HIGH-THROUGHPUT PROMOTER METHYLATION LUNG-CANCER PLASMA DNA http://hdl.handle.net/1854/LU-5936513 10.2217/EPI.14.43 000346665000007 1750-1911 2014 EPIGENOMICS Epigenomics 1750-1911 2014 6 6 603 622 2014 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/5936513/file/8516958 application/pdf https://biblio.ugent.be/publication/5936513/file/8557832 application/pdf restricted ug 5936513 2015-04-17T19:27:38Z 2018-11-13T14:54:24Z A1 VABB-1 15 info:srw/schema/1/mods-v3.3xml journalArticle A1 The structure of the DNA of bacteriophage φX174, III: ultracentrifugal evidence for a ring structure Structure of DNA of bacteriophage psiX174, 3 : ultracentrifugal evidence for a ring structure Walter Fiers aut author ug_UGent Robert L Sinsheimer aut author eng Biology and Life Sciences http://hdl.handle.net/1854/LU-1927352 10.1016/S0022-2836(62)80031-X A19625805B00007 0022-2836 1962 JOURNAL OF MOLECULAR BIOLOGY J. Mol. Biol. 0022-2836 1962 5 4 424 434 1962 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1927352/file/1963081 application/pdf restricted ug 1927352 2011-10-13T11:16:04Z 2018-08-13T14:12:14Z A1 VABB-1 16 info:srw/schema/1/mods-v3.3xml dissertation D1 Stability and detection of genetically modified soy DNA in processed foods Stabiliteit en detectie van genetisch gewijzigd soja-DNA in verwerkte levensmiddelen Nicolas Gryson aut author ug_UGent Koen Dewettinck promoter ug_LA23 Katthy Messens promoter eng Agriculture and Food Sciences http://hdl.handle.net/1854/LU-469579 90-5989-144-9 Ghent, Belgium Ghent University, Faculty of Bioscience Engineering 2006 I have retained and own the full copyright for this publication published https://biblio.ugent.be/publication/469579/file/1878922 application/pdf http://lib.ugent.be/fulltxt/RUG01/001/041/902/RUG01-001041902_2010_0001_AC.pdf ug 469579 2007-04-06T08:36:10Z 2017-01-02T09:54:47Z D1 17 info:srw/schema/1/mods-v3.3xml journalArticle A1 Performance of 16s rDNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies Bram Beckers aut author Michiel Op De Beeck aut author Sofie Thijs aut author Sascha Truyens aut author Nele Weyens aut author Wout Boerjan aut author ug_WE09 0000-0003-1495-510X Jaco Vangronsveld aut author eng Next-generation sequencing technologies have revolutionized the methods for studying microbial ecology by enabling high resolutioncommunity profiling. However, the use of these technologies in unraveling the plant microbiome remains challenging. Many bacterial 16S rDNA primer pairs also exhibit high affinity for non-target DNA such as plastid (mostly chloroplast) DNA and mitochondrial DNA. Therefore, we experimentally tested a series of commonly used primers for the analysis of plant associated bacterial communities using 454 pyrosequencing. We evaluated the performance of all selected primer pairs in the study of the bacterial microbiomes present in the rhizosphere soil, root, stem and leaf endosphere of field-grown poplar trees (Populus tremula x Populus alba) based on (a) co-amplification of non-target DNA, (b) low amplification efficiency for pure chloroplast DNA (real-time PCR), (c) high retrieval of bacterial 16S rDNA, (d) high operational taxonomic unit (OTU) richness and Inverse Simpson diversity and (e) taxonomic assignment of reads. Results indicate that experimental evaluation of primers provide valuable information that could contribute in the selection of suitable primer pairs for 16S rDNA metabarcoding studies in plant-microbiota research. Furthermore, we show that primer pair 799F-1391R outperforms all other primer pairs in our study in the elimination of non target DNA and retrieval of bacterial OTUs. Biology and Life Sciences DNA COMMUNITIES DIVERSITY RARE BIOSPHERE ROOT MICROBIOTA ONLINE RESOURCE LIGNIN BIOSYNTHESIS RIBOSOMAL-RNA POLYMERASE-CHAIN-REACTION RNA GENE DATABASE endophytes chloroplast DNA plant microbiome 454 pyrosequencing 16S rDNA metabarcoding http://hdl.handle.net/1854/LU-7756487 10.3389/fmicb.2016.00650 000375998700001 1664-302X 650 2016 FRONTIERS IN MICROBIOLOGY Front. Microbiol. 1664-302X 2016 7 2016 I have retained and own the full copyright for this publication published https://biblio.ugent.be/publication/7756487/file/7763475 application/pdf ug 7756487 2016-06-27T11:52:33Z 2018-11-13T14:54:23Z A1 VABB-1 18 info:srw/schema/1/mods-v3.3xml journalArticle A1 Validation of a sensitive DNA walking strategy to characterise unauthorised GMOs using model food matrices mimicking common rice products Marie-Alice Fraiture aut author ug_UGent Philippe Herman aut author Isabel Taverniers aut author Marc De Loose aut author ug_WE09 Filip Van Nieuwerburgh aut author ug_FW01 Dieter Deforce aut author ug_FW01 0000-0002-0635-661X Nancy H. Roosens aut author eng To identify unauthorised GMOs in food and feed matrices, an integrated approach has recently been developed targeting pCAMBIA family vectors, highly present in transgenic plants. Their presence is first assessed by qPCR screening and is subsequently confirmed by characterising the transgene flanking regions, using DNA walking. Here, the DNA walking performance has been thoroughly tested for the first time, regarding the targeted DNA quality and quantity. Several assays, on model food matrices mimicking common rice products, have allowed to determine the limit of detection as well as the potential effects of food mixture and processing. This detection system allows the identification of transgenic insertions as low as 10 HGEs and was not affected by the presence of untargeted DNA. Moreover, despite the clear impact of food processing on DNA quality, this method was able to cope with degraded DNA. Given its specificity, sensitivity, reliability, applicability and practicability, the proposed approach is a key detection tool, easily implementable in enforcement laboratories. Agriculture and Food Sciences FOODSTUFFS GENETICALLY-MODIFIED ORGANISMS PROMOTER PLANTS GENES MAIZE PCR Rice food Sensitivity DNA walking Transgene flanking region Detection Unauthorised GMO http://hdl.handle.net/1854/LU-5912308 10.1016/j.foodchem.2014.09.148 000347755800165 0308-8146 2015 FOOD CHEMISTRY Food Chem. 0308-8146 2015 173 1259 1265 2015 I have retained and own the full copyright for this publication published https://biblio.ugent.be/publication/5912308/file/6874110 application/pdf ug 5912308 2015-03-25T10:14:16Z 2018-11-13T14:53:40Z A1 VABB-1 19 info:srw/schema/1/mods-v3.3xml journalArticle A1 Comparison of digital PCR platforms and semi-nested qPCR as a tool to determine the size of the HIV reservoir Kobus J Bosman aut author Monique Nijhuis aut author Petra M Van Ham aut author Annemarie MJ Wensing aut author KAREN VERVISCH aut author ug_UZGent Linos Vandekerckhove aut author ug_GE32 ug_GE35 ug_UZGent Ward De Spiegelaere aut author ug_DI03 0000-0003-2097-8439 eng HIV persists in latently infected cells of patients on antiretroviral therapy (ART). This persistent proviral DNA reservoir is an important predictor of viral rebound upon therapy failure or interruption and forms a major obstacle towards cure. Accurate quantification of the low levels of persisting HIV DNA may aid patient monitoring and cure research. Digital PCR is a promising tool that enables direct absolute quantification with high sensitivity. With recent technological advances, several platforms are available to implement digital PCR in a clinical setting. Here, we compared two digital PCR platforms, the Quantstudio 3D (Life Technologies) and the QX100 (Bio-Rad) with a semi-nested qPCR on serial HIV DNA dilutions and DNA isolated from PBMCs of ART-suppressed patients. All three methods were able to detect target to the lowest levels of 2.5 HIV DNA copies. The QX100 excelled in having the least bias and highest precision, efficiency and quantitative linearity. Patient sample quantifications by the QX100 and semi-nested qPCR were highly agreeable by Bland-Altman analysis (0.01 ± 0.32 log10). Due to the observation of false-positive signals with current digital PCR platforms however, semi-nested qPCR may still be preferred in a setup of low quantity detection to discriminate between presence or absence of HIV DNA. Biology and Life Sciences HIV DNA Quantstudio3D digital PCR seminested qPCR QX100 ddPCR POLYMERASE-CHAIN-REACTION DNA COPY NUMBER ABSOLUTE QUANTIFICATION DISEASE PROGRESSION LATENT RESERVOIR QUANTITATION INFECTION REPLICATION LEVEL CELLS http://hdl.handle.net/1854/LU-6929096 10.1038/srep13811 000360898600001 2045-2322 13811 2015 SCIENTIFIC REPORTS Sci. Rep. 2045-2322 2015 5 2015 I have retained and own the full copyright for this publication published https://biblio.ugent.be/publication/6929096/file/6929098 application/pdf ug 6929096 2015-09-14T09:12:40Z 2018-11-13T14:54:44Z A1 VABB-1 20 info:srw/schema/1/mods-v3.3xml journalArticle A1 Coadministration of a plasmid encoding HIV-1 Gag enhances the efficacy of cancer DNA vaccines Laure Lambricht aut author Kevin Vanvarenberg aut author Ans De Beuckelaer aut author ug_UGent Lien Van Hoecke aut author ug_WE14 Johan Grooten aut author ug_WE14 Bernard Ucakar aut author Pascale Lipnik aut author Niek Sanders aut author ug_DI07 0000-0003-4585-0343 Stefan Lienenklaus aut author Véronique Préat aut author Gaëlle Vandermeulen aut author eng DNA vaccination holds great promise for the prevention and treatment of cancer and infectious diseases. However, the clinical ability of DNA vaccines is still controversial due to the limited immune response initially observed in humans. We hypothesized that electroporation of a plasmid encoding the HIV-1 Gag viral capsid protein would enhance cancer DNA vaccine potency. DNA electroporation used to deliver plasmids in vivo, induced type I interferons, thereby supporting the activation of innate immunity. The coadministration of ovalbumin (OVA) and HIV-1 Gag encoding plasmids modulated the adaptive immune response. This strategy favored antigen-specific Th1 immunity, delayed B16F10-OVA tumor growth and improved mouse survival in both prophylactic and therapeutic vaccination approaches. Similarly, a prophylactic DNA immunization against the melanoma-associated antigen gp100 was enhanced by the codelivery of the HIV-1 Gag plasmid. The adjuvant effect was not driven by the formation of HIV-1 Gag virus-like particles. This work highlights the ability of both electroporation and the HIV-1 Gag plasmid to stimulate innate immunity for enhancing cancer DNA vaccine immunogenicity and demonstrates interesting tracks for the design of new translational genetic adjuvants to overcome the current limitations of DNA vaccines in humans. Biology and Life Sciences DENDRITIC CELLS ELECTROPORATION IMMUNE-RESPONSES GENETIC ADJUVANTS DELIVERY INNATE VACCINATION PARTICLES ACTIVATION MELANOMA http://hdl.handle.net/1854/LU-8132712 10.1038/mt.2016.122 000384962300020 1525-0016 2016 MOLECULAR THERAPY Mol. Ther. 1525-0016 2016 24 9 1686 1696 2016 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/8132712/file/8132744 application/pdf restricted ug 8132712 2016-11-03T15:44:07Z 2016-12-19T15:40:47Z A1 VABB-1 21 info:srw/schema/1/mods-v3.3xml conference C3 CpG motifs as adjuvant in DNA vaccination against Chlamydophila psittaci in turkeys Karolien Loots aut author Marnix Van Loock aut author Daisy Vanrompay aut author ug_LA22 Bruno Goddeeris aut author ug_UGent DNA vaccines 2004 : the gene vaccine conference eng Biology and Life Sciences http://hdl.handle.net/1854/LU-808148 2004 DNA vaccines : the gene vaccine conference, Abstracts 2004 2004 published ug 808148 2009-12-11T13:52:40Z 2016-12-19T15:35:58Z C3 22 info:srw/schema/1/mods-v3.3xml journalArticle A1 A two-dimensional electrophoretic procedure for the separation of DNA restriction fragments 2-Dimensional electrophoretic procedure for separation of DNA restriction fragments Rik Derynck aut author Walter Fiers aut author ug_UGent eng Biology and Life Sciences http://hdl.handle.net/1854/LU-1927025 10.1016/S0022-2836(77)80078-8 A1977DC70900011 0022-2836 1977 JOURNAL OF MOLECULAR BIOLOGY J. Mol. Biol. 0022-2836 1977 110 2 387 404 1977 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1927025/file/1929087 application/pdf; charset=binary restricted ug 1927025 2011-10-13T11:16:04Z 2018-08-13T14:12:13Z A1 VABB-1 23 info:srw/schema/1/mods-v3.3xml journalArticle A1 Is AFLP fingerprinting a true alternative to the DNA-DNA pairing method to assess genospecies in the genus Aeromonas? Reply. Geert Huys aut author ug_UGent P JANSSEN aut author Karel Kersters aut author ug_UGent eng Science General http://hdl.handle.net/1854/LU-181572 A1997WC10600044 0020-7713 1997 INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY Int. J. Syst. Bacteriol. 0020-7713 1997 47 1 245 246 1997 published ug 181572 2004-01-14T13:41:00Z 2018-08-13T14:11:17Z A1 VABB-1 24 info:srw/schema/1/mods-v3.3xml misc U Wizard( DNA clean-up system in action. The use of molecular techniques to analyse the structure of soil microbial communities is based on purified total soil DNA. Said El Fantroussi aut author S MAERTENS aut author Eva Top aut author eng Agriculture and Food Sciences http://hdl.handle.net/1854/LU-120258 1999 Benelux News 1999 19 1999 published ug 120258 2004-01-14T13:35:00Z 2016-12-19T15:42:00Z U 25 info:srw/schema/1/mods-v3.3xml journalArticle A1 DNA-DNA hybridization and chemotaxonomic studies of Thermus-scotoductus. S TENREIRO aut author MF NOBRE aut author Bart Hoste aut author ug_WE10 Monique Gillis aut author ug_UGent JK KRISTJANSSON aut author MS DACOSTA aut author eng Science General http://hdl.handle.net/1854/LU-194082 A1995RC25800005 0923-2508 1995 RESEARCH IN MICROBIOLOGY Res. Microbiol. 0923-2508 1995 146 4 315 324 1995 published ug 194082 2004-01-14T13:42:00Z 2018-08-13T14:12:26Z A1 VABB-1 26 info:srw/schema/1/mods-v3.3xml journalArticle A1 The structure of the DNA of bacteriophage φX174, II: thermal inactivation Structure of DNA of bacteriophage psiX174, 2 : thermal inactivation Walter Fiers aut author ug_UGent Robert L Sinsheimer aut author eng Biology and Life Sciences http://hdl.handle.net/1854/LU-1927349 10.1016/S0022-2836(62)80030-8 A19625805B00006 0022-2836 1962 JOURNAL OF MOLECULAR BIOLOGY J. Mol. Biol. 0022-2836 1962 5 4 420 423 1962 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1927349/file/1963086 application/pdf restricted ug 1927349 2011-10-13T11:16:04Z 2018-08-13T14:12:14Z A1 VABB-1 27 info:srw/schema/1/mods-v3.3xml journalArticle A1 RNF4 is required for DNA double-strand break repair in vivo R Vyas aut author R Kumar aut author F Clermont aut author A Helfricht aut author P Kalev aut author P Sotiropoulou aut author IA Hendriks aut author E Radaelli aut author Tino Hochepied aut author ug_WE14 C Blanpain aut author A Sablina aut author H van Attikum aut author JV Olsen aut author AG Jochemsen aut author ACO Vertegaal aut author J-C Marine aut author eng Unrepaired DNA double-strand breaks (DSBs) cause genetic instability that leads to malignant transformation or cell death. Cells respond to DSBs with the ordered recruitment of signaling and repair proteins to the sites of DNA lesions. Coordinated protein SUMOylation and ubiquitylation have crucial roles in regulating the dynamic assembly of protein complexes at these sites. However, how SUMOylation influences protein ubiquitylation at DSBs is poorly understood. We show herein that Rnf4, an E3 ubiquitin ligase that targets SUMO-modified proteins, accumulates in DSB repair foci and is required for both homologous recombination (HR) and non-homologous end joining repair. To establish a link between Rnf4 and the DNA damage response (DDR) in vivo, we generated an Rnf4 allelic series in mice. We show that Rnf4-deficiency causes persistent ionizing radiation-induced DNA damage and signaling, and that Rnf4-deficient cells and mice exhibit increased sensitivity to genotoxic stress. Mechanistically, we show that Rnf4 targets SUMOylated MDC1 and SUMOylated BRCA1, and is required for the loading of Rad51, an enzyme required for HR repair, onto sites of DNA damage. Similarly to inactivating mutations in other key regulators of HR repair, Rnf4 deficiency leads to age-dependent impairment in spermatogenesis. These findings identify Rnf4 as a critical component of the DDR in vivo and support the possibility that Rnf4 controls protein localization at DNA damage sites by integrating SUMOylation and ubiquitylation events. Biology and Life Sciences spermatogenesis Rad51 MDC1 BRCA1 RNF4 homologous recombination DNA damage UBIQUITIN E3 LIGASE DAMAGE RESPONSE HISTONE H2AX SUMO MODIFICATION MAMMALIAN-CELLS STABILITY PROTEINS MICE SUMOYLATION http://hdl.handle.net/1854/LU-3211010 10.1038/cdd.2012.145 000317264100011 1350-9047 2013 CELL DEATH AND DIFFERENTIATION Cell Death Differ. 1350-9047 2013 20 3 490 502 2013 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/3211010/file/3211028 application/pdf restricted ug 3211010 2013-05-13T09:15:42Z 2018-08-13T14:23:13Z A1 VABB-1 28 info:srw/schema/1/mods-v3.3xml journalArticle A1 Ornithine decarboxylase activity and incorporation of thymidine-H-3 into DNA in estrogen-treated male xenopus-laevis ORNITHINE DECARBOXYLASE ACTIVITY AND INCORPORATION OF THYMIDINE-H-3 INTO DNA IN ESTROGEN-TREATED MALE XENOPUS-LAEVIS Anthony Capuco aut author ug_DI01 MT TSENG aut author eng Veterinary Sciences http://hdl.handle.net/1854/LU-932611 A1979HV03300003 0305-6708 1979 IRCS MEDICAL SCIENCE. BIOCHEMISTRY IRCS med. sci., Biochem. 0305-6708 1979 7 11 547 547 1979 published ug 932611 2010-04-20T10:28:06Z 2016-12-19T15:40:16Z A1 VABB-1 29 info:srw/schema/1/mods-v3.3xml journalArticle A1 Bcl-2 and accelerated DNA repair mediates resistance of hair follicle bulge stem cells to DNA-damage-induced cell death Panagiota A Sotiropoulou aut author Aurelie Candi aut author Guilhem Mascre aut author Sarah De Clercq aut author ug_UGent Khalil Kass Youssef aut author Gaelle Lapouge aut author Ellen Dahl aut author Claudio Semeraro aut author Geertrui Denecker aut author ug_GE31 0000-0002-2515-2911 Jean-Christophe Marine aut author ug_WE14 Cedric Blanpain aut author eng Adult stem cells (SCs) are at high risk of accumulating deleterious mutations because they reside and self-renew in adult tissues for extended periods. Little is known about how adult SCs sense and respond to DNA damage within their natural niche. Here, using mouse epidermis as a model, we define the functional consequences and the molecular mechanisms by which adult SCs respond to DNA damage. We show that multipotent hair-follicle-bulge SCs have two important mechanisms for increasing their resistance to DNA-damage-induced cell death: higher expression of the anti-apoptotic gene Bcl-2 and transient stabilization of p53 after DNA damage in bulge SCs. The attenuated p53 activation is the consequence of a faster DNA repair activity, mediated by a higher non-homologous end joining (NHEJ) activity, induced by the key protein DNA-PK. Because NHEJ is an error-prone mechanism, this novel characteristic of adult SCs may have important implications in cancer development and ageing. Biology and Life Sciences STRAND BREAK REPAIR RADIATION-INDUCED APOPTOSIS SMALL-INTESTINE SCID MUTATION P53 MICE SKIN MOUSE MECHANISMS IRRADIATION http://hdl.handle.net/1854/LU-998269 10.1038/ncb2059 000278213400009 1465-7392 2010 NATURE CELL BIOLOGY Nat. Cell Biol. 1465-7392 2010 12 6 572 582 2010 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/998269/file/2937355 application/pdf restricted ug 998269 2010-06-30T14:12:16Z 2016-12-19T15:40:16Z A1 VABB-1 30 info:srw/schema/1/mods-v3.3xml conference C3 Temperature responsive magnetic polymer particles for nucleic acids (DNA/RNA) separation Md. Mahbubor Rahman aut author ug_UGent Abdelhamid Elaissari aut author Conference on Advanced Materials for Biomedical Applications (AMBA 2014) eng Chemistry DNA RNA Magnetic polymer Temperature responsive adsorption desorption http://hdl.handle.net/1854/LU-7064740 2014 AMBA 2014 : advanced materials for biomedical applications 2014 2014 published ug 7064740 2016-02-01T12:23:13Z 2016-12-19T15:37:14Z C3 31 info:srw/schema/1/mods-v3.3xml dissertation D1 Cellulaire internalisering van penetratin peptiden en toepassing voor DNA-transfecties Cellular internalisation of penetratin peptides and application for DNA-transfections Bart Christiaens aut author ug_CA30 Joël Vandekerckhove promoter Maryvonne Rosseneu promoter dut Biology and Life Sciences http://hdl.handle.net/1854/LU-539789 Gent Universiteit Gent. Faculteit Geneeskunde en Gezondheidswetenschappen 2004 published Gent : Faculteit Geneeskunde en Gezondheidswetenschappen http://lib.ugent.be/fulltxt/RUG01/000/843/471/RUG01-000843471_2010_0001_AC.pdf ug 539789 2004-10-12T09:26:00Z 2018-11-13T14:53:30Z D1 32 info:srw/schema/1/mods-v3.3xml dissertation D1 DNA adduct formation due to the gastrointestinal digestion of red meat Vorming van DNA-adducten ten gevolge van de vertering van rood vlees Lieselot Hemeryck aut author ug_DI06 0000-0002-2451-3375 Lynn Vanhaecke promoter ug_DI06 eng Agriculture and Food Sciences Medicine and Health Sciences Biology and Life Sciences http://hdl.handle.net/1854/LU-8522814 Merelbeke, Belgium Ghent University. Faculty of Veterinary Medicine 2017 I have transferred the copyright for this publication to the publisher published Merelbeke : Faculteit Diergeneeskunde (auditorium D) https://biblio.ugent.be/publication/8522814/file/8522821 application/pdf restricted(changes to open on 2020-05-23) ug 8522814 2017-06-08T11:44:44Z 2018-11-13T14:55:32Z D1 33 info:srw/schema/1/mods-v3.3xml journalArticle A1 Characterisation of the Roundup Ready soybean insert Pieter Windels aut author Isabel Taverniers aut author Anna Depicker aut author ug_WE09 0000-0003-0105-7407 Erik Van Bockstaele aut author ug_UGent Marc De Loose aut author ug_WE09 eng In this article we describe the isolation and characterisation of the junction between insert DNA and plant DNA in the transgenic Roundup Ready soybean line event 40-3-2. Our results establish that during integration of the insert DNA several rearrangements occurred at the 3' NOS junction and that the genomic plant DNA at the pre-integration site may have been rearranged. These findings highlight the utility of characterising junction regions to fulfil the request for information regarding which DNA sequences have been incorporated in commercialised transgenic lines. Furthermore, the characterisation of junction regions is, in our opinion, the method of choice to support method development for detection and identification of plant biotechnology-derived products. Biology and Life Sciences junction fragment Roundup Ready soybean rearrangements GMO identification QUANTITATIVE COMPETITIVE PCR DNA PLANTS CORN http://hdl.handle.net/1854/LU-138834 10.1007/s002170100336 000170605100006 1438-2377 2001 EUROPEAN FOOD RESEARCH AND TECHNOLOGY Eur. Food Res. Technol. 1438-2377 2001 213 2 107 112 2001 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/138834/file/4148399 application/pdf restricted ug 138834 2004-01-14T13:37:00Z 2018-08-13T14:09:04Z A1 VABB-1 34 info:srw/schema/1/mods-v3.3xml journalArticle A1 The TL-DNA in octopine crown-gall tumours codes for seven well-defined polyadenylated transcripts The TL-DNA in octopine crown-gall tumors codes for 7 well-defined polyadenylated transcripts Lothar Willmitzer aut author Gisela Simons aut author Jeff Schell aut author eng Seven polyadenylated transcripts of significantly different relative abundance were detected in octopine crown-gall tissue after gel electrophoretic separation and subsequent transfer to diazobenzyloxymethyl paper. The transcripts range from 670 to 2700 bases long. The different transcripts were located using 19 different fragments of the TL-region as probes. By hybridizing labelled RNA to separated complementary strands of the T-DNA, and parallel determination of the chemical polarity of the strands, the 5' - 3' orientations of six of the seven transcripts was identified. Both strands of the T-DNA code RNA. Hybridization of octopine TL-DNA against poly A RNA's present in two nopaline tumour-lines C58-S1 and BT37, and vice versa, reveals a minimum of two and possibly four transcripts common to both octopine and nopaline tumours. These transcripts originate from corresponding parts of the conserved region of the T-DNA and are of similar size Biology and Life Sciences common T-region crown-gall Northern analysis transcripts http://hdl.handle.net/1854/LU-5918859 A1982NP37600023 0261-4189 1982 EMBO JOURNAL Embo J. 0261-4189 1982 1 1 139 146 1982 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/5918859/file/5919990 application/pdf restricted http://www.ncbi.nlm.nih.gov/pmc/articles/PMC553008/ ug 5918859 2015-03-31T15:17:26Z 2016-12-19T15:43:18Z A1 VABB-1 35 info:srw/schema/1/mods-v3.3xml conference C1 The active microbial community more accurately reflects the anaerobic digestion process : 16S rRNA (gene) sequencing as a predictive tool Jo De Vrieze aut author ug_LA25 0000-0001-9365-8896 Ameet J Pinto aut author William T Sloan aut author Nico Boon aut author ug_LA25 0000-0002-7734-3103 Umer Z Ijaz aut author 15th IWA World Conference on Anaerobic Digestion (AD15) eng Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterise amplicons, but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants was evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing. A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet, the differentiating effect between DNA and RNA was much stronger for archaea. In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion. Earth and Environmental Sciences Biology and Life Sciences Biogas Illumina sequencing microbiome methane methanogenesis http://hdl.handle.net/1854/LU-8542587 2017 Anaerobic Digestion, 15th World conference, Papers 2017 2017 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/8542587/file/8542588 application/pdf ug 8542587 2017-12-19T15:20:50Z 2018-11-13T14:55:57Z C1 VABB-5 36 info:srw/schema/1/mods-v3.3xml dissertation D1 DNA stress checkpoint control in Arabidopsis thaliana by WEE1 Toon Cools aut author ug_UGent Lieven De Veylder promoter ug_WE09 Dirk Inzé promoter ug_WE09 0000-0002-3217-8407 eng The WEE1 kinase is a conserved cell cycle inhibitor that, together with CDC25, controls CDK activity and consequently the G2/M progression in yeast and animals. The same control mechanism is utilized by the DNA damage checkpoint to induce a cell cycle arrest upon DNA stress. In plants, a homolog of the WEE1 gene is present and is also responsible for phosphorylation of CDKs, although only during DNA damage. Plants that not contain a functional WEE1 gene develop normally during normal growth circumstances, but show a hypersensitive growth response to replication stress. To understand this, a transcriptomics analysis was performed, indicating prolonged S-phase duration. A role for WEE1 during S phase was substantiated by its specific accumulation in replicating nuclei that suffered from DNA stress. Besides an extended replication phase, WEE1 knockout plants accumulated dead cells that were associated with the onset of premature vascular differentiation. Furthermore, a new synchronization method for Arabidopsis roots was presented and the initial research on the posttranslational control of plant WEE1 was executed, both providing intriguing results. Biology and Life Sciences vascular differentiation synchronization checkpoints DNA damage WEE1 cell cycle http://hdl.handle.net/1854/LU-1216535 Ghent, Belgium Ghent University. Faculty of Sciences 2011 I have transferred the copyright for this publication to the publisher published Zwijnaarde : Technologiepark (FSVM building) https://biblio.ugent.be/publication/1216535/file/4335544 application/pdf restricted ug 1216535 2011-05-03T17:26:36Z 2018-08-13T14:07:36Z D1 37 info:srw/schema/1/mods-v3.3xml journalArticle A1 Ti plasmid vector for the introduction of DNA into plant cells without alteration of their normal regeneration capacity Patricia Zambryski aut author ug_WE09 Henk Joos aut author Christiane Genetello aut author ug_WE09 Jan Leemans aut author Marc Van Montagu aut author ug_WE09 Jeff Schell aut author eng A Ti plasmid mutant was constructed in which all the on-cogenic functions of the T-DNA have been deleted and replaced by pBR322. This Ti plasmid, pGV3850, still mediates efficient transfer and stabilization of its truncated T-DNA into infected plant cells. Moreover, integration and expression of this minimal T-DNA in plant cells does not interfere with normal plant cell differentiation. A DNA fragment cloned in a pBR vector can be inserted in the pGV3850 T-region upon a single recombination event through the pBR322 region of pGV3850 producing a co-integrate useful for the transformation of plant cells. Based upon these properties, pGV3850 is proposed as an extremely versatile vector for the introduction of any DNA of interest into plant cells. Biology and Life Sciences http://hdl.handle.net/1854/LU-6889680 A1983RV10200008 0261-4189 1983 EMBO JOURNAL EMBO J. 0261-4189 1983 2 12 2143 2150 1983 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/6889680/file/6891268 application/pdf restricted http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555426/ ug 6889680 2015-07-29T17:21:44Z 2016-12-19T15:46:14Z A1 VABB-1 38 info:srw/schema/1/mods-v3.3xml journalArticle A1 Protection of budgerigars (Melopsittacus undulatus) against Chlamydophila psittaci challenge by DNA vaccination Taher Harkinezhad aut author Katelijn Schautteet aut author ug_UGent Daisy Vanrompay aut author ug_LA22 eng Plasmid DNA (pcDNA1::MOMP A) expressing the major outer membrane protein (MOMP) of Chlamydophila psittaci genotype A strain 89/1051 has been tested for its ability to induce protective immunity against Cp. psittaci challenge in budgerigars. Eight pairs of male and female budgerigars were housed in eight separate bird cages placed in two negative pressure isolators, four cages per group. All budgerigars were immunised twice intramuscularly with 100 mu g plasmid DNA. Both groups received a primary DNA inoculation at day 0 followed by a booster inoculation 3 weeks later. Group 1 received pcDNA1:: MOMP A, while group 2 received the placebo vaccine pcDNA1. Budgerigars were challenged by aerosol 2 weeks following the booster vaccination. The challenge consisted of 10(8) TCID50 of the homologous Cp. psittaci genotype A strain. Cloacal and pharyngeal swabs of all budgerigars, taken prior to the experimental infection were negative in both PCR and culture. However, all budgerigars showed low pre-existing serum antibody titres. This indicates that animals were previously infected. Nevertheless, DNA immunisation could significantly reduce clinical signs, macroscopic lesions, pharyngeal and cloacal excretion as well as chlamydial replication, even in the presence of pre-existing serum antibodies, as compared to the placebo-vaccinated controls. Veterinary Sciences GENOTYPE OUTER-MEMBRANE PROTEIN PARROTS CHLAMYDIA-PSITTACI TURKEYS INFECTION HUMANS ANTIBODIES TRANSMISSION PET BIRDS Chlamydophila psittaci DNA vaccination MOMP budgerigar (Melopsittacus undulatus) http://hdl.handle.net/1854/LU-806798 10.1051/vetres/2009044 000272039500010 0928-4249 2009 VETERINARY RESEARCH Vet. Res. 0928-4249 2009 40 6 2009 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/806798/file/823686 application/pdf restricted ug 806798 2009-12-10T18:03:56Z 2016-12-19T15:44:47Z A1 VABB-1 39 info:srw/schema/1/mods-v3.3xml journalArticle A1 One-tube cell lysis and DNA extraction procedure for PCR-based detection of Mycobacterium ulcerans in aquatic insects, molluscs and fish R Kotlowski aut author Anandi Martin aut author ug_UGent A Ablordey aut author K Chemlal aut author PA Fonteyne aut author F Portaels aut author eng The purpose of this study was to develop a simple procedure for cell lysis and DNA extraction for direct detection of Mycobacterium ulcerans in aquatic insects, gills and intestinal contents of fish, molluscs and human tissue samples using a nested PCR method specific for the insertion sequence IS2404. The simultaneous action of sodium N-lauroyl sarcosine, guanidinium isothiocyanate, chloroform and Tris-saturated phenol on mycobacteria, followed by a DNA purification method using mini-columns fitted with silica-cellulose membranes was successfully employed to extract DNA from cultured bacteria, environmental and human tissue samples. All specimens were collected from Buruli ulcer endemic regions. M. ulcerans DNA was detected in 11 of 57 aquatic insects, one of six molluscs and three of 15 fish, supporting the hypothesis that the fauna of major Buruli ulcer endemic foci in swampy terrain of tropical and subtropical regions can be a source of M. ulcerans infection. Biology and Life Sciences GENOMIC DNA NUCLEIC-ACIDS TUBERCULOSIS INFECTION PURIFICATION CHLOROFORM PROTEINS ALCOHOL SAMPLES PHENOL http://hdl.handle.net/1854/LU-7187256 10.1099/jmm.0.45593-0 000223965600015 0022-2615 2004 JOURNAL OF MEDICAL MICROBIOLOGY J. Med. Microbiol. 0022-2615 2004 53 9 927 933 2004 published ug 7187256 2016-04-18T12:50:28Z 2016-12-19T15:45:33Z A1 VABB-1 40 info:srw/schema/1/mods-v3.3xml journalArticle A1 DNA methylation, bacteria and airway inflammation: latest insights Claudina Perez Novo aut author ug_UGent Claus Bachert aut author ug_GE34 ug_UZGent 0000-0003-4742-1665 eng Purpose of review : DNA methylation is an epigenetic mechanism that has been implicated in the pathogenesis of chronic inflammatory diseases by regulating differentiation, proliferation, apoptosis, and activation of immune cells. Changes in the methylation status of relevant genes have been linked to the origin, perpetuation, and severity of airway diseases. The DNA methylation profile can be also modified by the action of viral and bacterial colonization. Bacteria and specially Staphylococcus aureus toxins are recognized inflammatory amplifying factors in both lower and upper airway chronic diseases. This review summarizes the existent knowledge about the role of DNA methylation changes in chronic airway diseases and the contribution of bacterial infection on this event. Recent findings : It has been demonstrated that changes in DNA methylation, either intrinsic or induced by allergen or infection, may be linked to the pathogenesis of asthma and allergy. These changes in methylation may suppress the production of anti-inflammatory mediators and increase the survival and activation of pro-inflammatory cells, as well as modify the immune response in response to bacterial infection, increasing their survival and pathogenicity within the infected organism. Summary : Understanding the intrinsic epigenetic mechanisms, as well as the effect of environment - for example, bacterial infection in the pathogenesis of airways diseases - will greatly improve the management and the diagnosis of these diseases. Medicine and Health Sciences bacterial infection airway diseases chronic rhinosinusitis DNA methylation Staphylococcus aureus CPG-BINDING-PROTEIN CHRONIC RHINOSINUSITIS BRONCHIAL-ASTHMA SINUS DISEASE EXPRESSION GENES LUNG TRANSCRIPTION PATHWAYS MONOCYTES http://hdl.handle.net/1854/LU-6862684 10.1097/ACI.0000000000000130 000347258500004 1528-4050 2015 CURRENT OPINION IN ALLERGY AND CLINICAL IMMUNOLOGY Curr. Opin. Allergy Clin. Immunol. 1528-4050 2015 15 1 27 32 2015 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/6862684/file/6862751 application/pdf restricted ug 6862684 2015-07-03T15:14:06Z 2016-12-19T15:39:11Z A1 VABB-1 41 info:srw/schema/1/mods-v3.3xml journalArticle A1 A synthetic oligonucleotide model for evaluating the oxidation and crosslinking propensities of natural furan-modified DNA Lieselot Carrette aut author ug_GE31 Annemieke Madder aut author ug_WE07 0000-0003-0179-7608 eng We have previously developed a crosslinking methodology for oligonucleotides based on the incorporation of furan moieties, which can be selectively oxidised to reactive intermediates that will quickly react with the opposite bases in DNA, forming toxic interstrand crosslinks (ICLs). Furan moieties also occur in natural DNA, as a result of oxidative stress. Moreover, the furan-containing degradation product of this modified DNA—kinetin—has been found to display beneficial anti-ageing effects. To investigate the apparent discrepancy between the effects of the synthetic and the natural furan modifications in DNA, a quick and easy postsynthetic method providing access to the natural modification in short synthetic oligonucleotides was developed. On checking for potential crosslinking propensity, we found that the furan moiety does indeed undergo oxidation, in this way functioning as an important scavenger for oxidative stress. The reactive intermediate, however, was shown to degrade without producing toxic crosslinked products. Chemistry kinetin oligonucleotides DNA damage antioxidants biomimetic synthesis DAMAGE PRODUCT KINETIN CYTOKININ N-6-FURFURYLADENINE PROTECTS http://hdl.handle.net/1854/LU-4293585 10.1002/cbic.201300612 000328682000013 1439-4227 2014 CHEMBIOCHEM ChemBioChem 1439-4227 2014 15 1 103 107 2014 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/4293585/file/4293601 application/pdf restricted ug 4293585 2014-02-17T13:52:56Z 2018-08-13T14:31:37Z A1 VABB-1 42 info:srw/schema/1/mods-v3.3xml journalArticle A1 Site-specific T-DNA integration in Arabidopsis thaliana mediated by the combined action of CRE recombinase and φC31 integrase Site-specific T-DNA integration in Arabidopsis thaliana mediated by the combined action of CRE recombinase and phi C31 integrase Annelies De Paepe aut author ug_GE31 Sylvie De Buck aut author ug_WE09 Jonah Nolf aut author ug_WE09 0000-0002-4393-0852 Els Van Lerberge aut author ug_WE09 0000-0002-8407-7413 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng Random T-DNA integration into the plant host genome can be problematic for a variety of reasons, including potentially variable transgene expression as a result of different integration positions and multiple T-DNA copies, the risk of mutating the host genome and the difficulty of stacking well-defined traits. Therefore, recombination systems have been proposed to integrate the T-DNA at a pre-selected site in the host genome. Here, we demonstrate the capacity of the phi C31 integrase (INT) for efficient targeted T-DNA integration. Moreover, we show that the iterative site-specific integration system (ISSI), which combines the activities of the CRE recombinase and INT, enables the targeting of genes to a pre-selected site with the concomitant removal of the resident selectable marker. To begin, plants expressing both the CRE and INT recombinase and containing the target attP site were constructed. These plants were supertransformed with a T-DNA vector harboring the loxP site, the attB sites, a selectable marker and an expression cassette encoding a reporter protein. Three out of the 35 transformants obtained (9%) showed transgenerational site-specific integration (SSI) of this T-DNA and removal of the resident selectable marker, as demonstrated by PCR, Southern blot and segregation analysis. In conclusion, our results show the applicability of the ISSI system for precise and targeted Agrobacterium-mediated integration, allowing the serial integration of transgenic DNA sequences in plants. Biology and Life Sciences technical advance ZINC-FINGER NUCLEASES Arabidopsis gene stacking CRE recombinase phi C31 integrase site-specific integration T-DNA FREE TRANSGENIC PLANTS DOUBLE-STRAND BREAKS AGROBACTERIUM-TUMEFACIENS HIGH-FREQUENCY FLORAL DIP ZYGOSACCHAROMYCES-ROUXII HOMOLOGOUS RECOMBINATION GENOME MODIFICATION EFFECTOR NUCLEASES http://hdl.handle.net/1854/LU-4110382 10.1111/tpj.12202 000320708300014 0960-7412 2013 PLANT JOURNAL Plant J. 0960-7412 2013 75 1 172 184 2013 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/4110382/file/4110389 application/pdf restricted ug 4110382 2013-08-07T13:49:46Z 2018-08-13T14:28:59Z A1 VABB-1 43 info:srw/schema/1/mods-v3.3xml journalArticle A1 Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during pronuclear development in equine zygotes produced by ICSI Sonia Heras Garcia aut author ug_UGent Katrien Smits aut author ug_DI08 0000-0002-8205-3725 Catharina De Schauwer aut author ug_DI04 0000-0002-4475-7094 Ann Van Soom aut author ug_DI08 0000-0001-5010-6311 eng Background: Global epigenetic reprogramming is considered to be essential during embryo development to establish totipotency. In the classic model first described in the mouse, the genome-wide DNA demethylation is asymmetric between the paternal and the maternal genome. The paternal genome undergoes ten-eleven translocation (TET)-mediated active DNA demethylation, which is completed before the end of the first cell cycle. Since TET enzymes oxidize 5-methylcytosine to 5-hydroxymethylcytosine, the latter is postulated to be an intermediate stage toward DNA demethylation. The maternal genome, on the other hand, is protected from active demethylation and undergoes replication-dependent DNA demethylation. However, several species do not show the asymmetric DNA demethylation process described in this classic model, since 5-methylcytosine and 5-hydroxymethylcytosine are present during the first cell cycle in both parental genomes. In this study, global changes in the levels of 5-methylcytosine and 5-hydroxymethylcytosine throughout pronuclear development in equine zygotes produced in vitro were assessed using immunofluorescent staining. Results: We were able to show that 5-methylcytosine and 5-hydroxymethylcytosine both were explicitly present throughout pronuclear development, with similar intensity levels in both parental genomes, in equine zygotes produced by ICSI. The localization patterns of 5-methylcytosine and 5-hydroxymethylcytosine, however, were different, with 5-hydroxymethylcytosine homogeneously distributed in the DNA, while 5-methylcytosine tended to be clustered in certain regions. Fluorescence quantification showed increased 5-methylcytosine levels in the maternal genome from PN1 to PN2, while no differences were found in PN3 and PN4. No differences were observed in the paternal genome. Normalized levels of 5-hydroxymethylcytosine were preserved throughout all pronuclear stages in both parental genomes. Conclusions: In conclusion, the horse does not seem to follow the classic model of asymmetric demethylation as no evidence of global DNA demethylation of the paternal pronucleus during the first cell cycle was demonstrated. Instead, both parental genomes displayed sustained and similar levels of methylation and hydroxymethylation throughout pronuclear development. Veterinary Sciences Biology and Life Sciences Horse Pronucleus Epigenetic reprogramming 5-Methylcytosine 5-Hydroxymethylcytosine DNA methylation DNA hydroxymethylation Active demethylation DNA METHYLATION PATTERNS EARLY MOUSE EMBRYO IN-VITRO PATERNAL GENOME BOVINE ZYGOTES MAMMALIAN DEVELOPMENT ACTIVE DEMETHYLATION FERTILIZATION OXIDATION VIVO http://hdl.handle.net/1854/LU-8517658 10.1186/s13072-017-0120-x 000397667300001 1756-8935 13 2017 EPIGENETICS & CHROMATIN Epigenetics Chromatin 1756-8935 2017 10 2017 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/8517658/file/8517660 application/pdf ug 8517658 2017-04-13T12:11:26Z 2018-11-13T14:55:46Z A1 VABB-1 44 info:srw/schema/1/mods-v3.3xml journalArticle A1 Diagnosis of Fanconi Anaemia by ionising radiation- or mitomycin C-induced micronuclei Flavia Zita Francies aut author Rosalind Wainwright aut author Janet Poole aut author Kim De Leeneer aut author ug_UZGent Ilse Coene aut author ug_UZGent Greet Wieme aut author ug_GE31 Hélène A Poirel aut author Bénédicte Brichard aut author Stephanie Vermeulen aut author ug_GE38 Anne Vral aut author ug_GE38 0000-0001-7879-6561 Jacobus Slabbert aut author Kathleen Claes aut author ug_GE31 ug_UZGent 0000-0003-0841-7372 Ans Baeyens aut author ug_GE38 eng Fanconi Anaemia (FA) is an autosomal recessive disorder characterised by defects in DNA repair, associated with chromosomal instability and cellular hypersensitivity to DNA cross-linking agents such as mitomycin C (MMC). The FA repair pathway involves complex DNA repair mechanisms crucial for genomic stability. Deficiencies in DNA repair genes give rise to chromosomal radiosensitivity. FA patients have shown increased clinical radio sensitivity by exhibiting adverse normal tissue side-effects. The study aimed to investigate chromosomal radiosensitivity of homozygous and heterozygous carriers of FA mutations using three micronucleus (MN) assays. The GO and S/G2 MN assays are cytogenetic assays to evaluate DNA damage induced by ionising radiation in different phases of the cell cycle. The MMC MN assay detects DNA damage induced by a crosslinking agent in the GO phase. Patients with a clinical diagnosis of FA and their parents were screened for the complete coding region of 20 FA genes. Blood samples of all FA patients and parents were exposed to ionising radiation of 2 and 4 Gy. Chromosomal radiosensitivity was evaluated in the GO and S/G2 phase. Most of our patients were homozygous for the founder mutation FANCG c.637_643delTACCGCC; p.(Tyr213Lysfs*6) while one patient was compound heterozygous for FANCG c.637_643delTACCGCC and FANCG c.1379G > A, p.(Gly460Asp), a novel missense mutation. Another patient was compound heterozygous for two deleterious FANCA mutations. In FA patients, the GO- and S/G2-MN assays show significantly increased chromosomal radiosensitivity and genomic instability. Moreover, chromosomal damage was significantly elevated in MMC treated FA cells. We also observed an increase in chromosomal radiosensitivity and genomic instability in the parents using 3 assays. The effect was significant using the MMC MN assay. The MMC MN assay is advantageous as it is less labour intense, time effective and has potential as a reliable alternative method for detecting FA patients from parents and controls. Medicine and Health Sciences Biology and Life Sciences Fanconi Anaemia DNA repair Chromosomal radiosensitivity Genomic instability Radiosensitivity BREAST-CANCER PATIENTS VITRO CHROMOSOMAL RADIOSENSITIVITY C.5101C-GREATER-THAN-T MUTATION DNA-REPAIR PATHWAY BRCA1 RISK GENE PROTECTION BREAKAGE http://hdl.handle.net/1854/LU-8537947 10.1016/j.dnarep.2017.11.001 000423895400002 1568-7864 2018 DNA REPAIR DNA Repair 1568-7864 2018 61 17 24 2018 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/8537947/file/8546035 application/pdf restricted ug 8537947 2017-11-18T10:38:05Z 2018-11-14T12:50:01Z A1 VABB-1 45 info:srw/schema/1/mods-v3.3xml journalArticle A1 Arabidopsis WEE1 kinase controls cell cycle arrest in response to activation of the DNA integrity checkpoint Kristof De Schutter aut author ug_LA21 0000-0003-2366-0557 Jérôme Joubès aut author ug_WE09 Toon Cools aut author ug_UGent Aurine Verkest aut author ug_UGent Florence Corellou aut author Elena Babiychuk aut author ug_WE09 Els Van Der Schueren aut author ug_UZGent Tom Beeckman aut author ug_WE09 0000-0001-8656-2060 Sergei Kushnir aut author ug_WE09 Dirk Inzé aut author ug_WE09 0000-0002-3217-8407 Lieven De Veylder aut author ug_WE09 eng Upon the incidence of DNA stress, the ataxia telangiectasia-mutated (ATM) and Rad3-related(ATR) signaling kinases activate a transient cell cycle arrest that allows cells to repair DNA before proceeding into mitosis. Although the ATM-ATRpathway is highly conserved over species, the mechanisms by which plant cells stop their cell cycle in response to the loss of genome integrity are unclear. We demonstrate that the cell cycle regulatory WEE1 kinase gene of Arabidopsis thaliana is transcriptionally activated upon the cessation of DNA replication or DNA damage in an ATR- or ATM-dependent manner, respectively. In accordance with a role for WEE1 in DNA stress signaling, WEE1-deficient plants showed no obvious cell division or endoreduplication phenotype when grown under nonstress conditions but were hypersensitive to agents that impair DNA replication. Induced WEE1 expression inhibited plant growth by arresting dividing cells in the G2-phase of the cell cycle. We conclude that the plant WEE1 gene is not rate-limiting for cycle progression under normal growth conditions but is a critical target of the ATR-ATM signaling cascades that inhibit the cell cycle upon activation of the DNA integrity checkpoints, coupling mitosis to DNA repair in cells that suffer DNA damage. Biology and Life Sciences CDC25 PHOSPHATASE TRANSCRIPTION FACTOR MEDIATED TRANSFORMATION SCHIZOSACCHAROMYCES-POMBE DAMAGE CHECKPOINT GENOME-WIDE ANALYSIS DEPENDENT KINASE PLANT DEVELOPMENT S PHASE GENOTOXIC STRESS http://hdl.handle.net/1854/LU-409102 10.1105/tpc.106.045047 000244757400019 1040-4651 2007 PLANT CELL Plant Cell 1040-4651 2007 19 1 211 225 2007 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/409102/file/3067597 application/pdf ug 409102 2008-05-15T15:03:00Z 2018-11-13T14:52:12Z A1 VABB-1 46 info:srw/schema/1/mods-v3.3xml journalArticle A1 Integrated and total HIV-1 DNA predict ex vivo viral outgrowth Maja Kiselinova aut author Ward De Spiegelaere aut author ug_DI03 0000-0003-2097-8439 Maria Jose Buzon aut author Eva Malatinková aut author ug_GE35 Mathias Lichterfeld aut author Linos Vandekerckhove aut author ug_GE32 ug_GE35 ug_UZGent eng The persistence of a reservoir of latently infected CD4 T cells remains one of the major obstacles to cure HIV. Numerous strategies are being explored to eliminate this reservoir. To translate these efforts into clinical trials, there is a strong need for validated biomarkers that can monitor the reservoir over time in vivo. A comprehensive study was designed to evaluate and compare potential HIV-1 reservoir biomarkers. A cohort of 25 patients, treated with suppressive antiretroviral therapy was sampled at three time points, with median of 2.5 years (IQR: 2.4-2.6) between time point 1 and 2; and median of 31 days (IQR: 28-36) between time point 2 and 3. Patients were median of 6 years (IQR: 3-12) on ART, and plasma viral load (<50 copies/ml) was suppressed for median of 4 years (IQR: 2-8). Total HIV-1 DNA, unspliced (us) and multiply spliced HIV-1 RNA, and 2LTR circles were quantified by digital PCR in peripheral blood, at 3 time points. At the second time point, a viral outgrowth assay (VOA) was performed, and integrated HIV-1 DNA and relative mRNA expression levels of HIV-1 restriction factors were quantified. No significant change was found for long-and short-term dynamics of all HIV-1 markers tested in peripheral blood. Integrated HIV-1 DNA was associated with total HIV-1 DNA (p<0.001, R-2=0.85), us HIV-1 RNA (p = 0.029, R-2=0.40), and VOA (p = 0.041, R-2=0.44). Replication-competent virus was detected in 80% of patients by the VOA and it correlated with total HIV-1 DNA (p = 0.039, R-2=0.54). The mean quantification difference between Alu-PCR and VOA was 2.88 log(10), and 2.23 log10 between total HIV-1 DNA and VOA. The levels of us HIV-1 RNA were inversely correlated with mRNA levels of several HIV-1 restriction factors (TRIM5 alpha, SAMHD1, MX2, SLFN11, pSIP1). Our study reveals important correlations between the viral outgrowth and total and integrated HIV-1 DNA measures, suggesting that the total pool of HIV-1 DNA may predict the size of the replication-competent virus in ART suppressed patients. Biology and Life Sciences HOST RESTRICTION FACTORS CD4(+) T-CELLS ANTIRETROVIRAL THERAPY LATENT RESERVOIR COMBINATION THERAPY PROVIRAL DNA PCR DATA INFECTION PERSISTENCE CURE http://hdl.handle.net/1854/LU-8501782 10.1371/journal.ppat.1005472 000378154800015 1553-7366 1553-7374 e1005472 2016 PLOS PATHOGENS PLoS Pathog. 1553-7366 1553-7374 2016 12 3 2016 I have retained and own the full copyright for this publication published https://biblio.ugent.be/publication/8501782/file/8501785 application/pdf https://biblio.ugent.be/publication/8501782/file/8502568 application/pdf ug 8501782 2017-01-12T15:26:12Z 2018-11-13T14:55:56Z A1 VABB-1 47 info:srw/schema/1/mods-v3.3xml journalArticle A1 Agrobacterium tumefaciens transformation and cotransformation frequencies of Arabidopsis thaliana root explants and tobacco protoplasts Sylvie De Buck aut author ug_WE09 Anni Jacobs aut author ug_WE09 Marc Van Montagu aut author ug_WE09 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng In view of the recent finding that different T-DNAs tend to ligate and integrate as repeats at single chromosomal positions, the frequency of transformation and cotransformation was determined during cocultivation of Arabidopsis thaliana root explants and Nicotiana tabacum protoplasts with two Agrobacterium strains. The transformation frequency of unselected A, thaliana shoots was lower than 1% whereas that of cocultivated tobacco protoplasts was approximately 18%, The cotransformation frequencies, defined as the frequencies with which cells transformed with a first T-DNA contained a second unselected T-DNA, were approximately 40% reproducible, irrespective of the selection, the transformation frequency, and the plant system used. Extrapolation of these results suggests that at least two independently transferred T-DNAs were present in 64% of the transformed plant cells, Molecular analysis of cocultivated N. tabacum shoots regenerated on nonselective medium showed that only a few transformants had a silenced (2/46) or truncated (1/46) T-DNA, Therefore, most integrated T-DNAs expressed their selectable or screenable markers in primary transgenic plants. Remarkably, 10 to 30% of the selected A. thaliana shoots or progenies lost the T-DNA marker they were selected on. As these regenerants contained the unselected T-DNA with a high frequency (17%), these selected plants might result from the expression of unstable, transiently expressed T-DNAs, In conclusion, a significant part of the T-DNAs is lost from the transformed cells. Biology and Life Sciences SEQUENCES VECTORS SELECTION COMPETENCE gene silencing T-DNA transfer transgene expression MEDIATED GENE-TRANSFER T-DNA PLANT-CELLS TRANSGENE EXPRESSION SINGLE-COPY INTEGRATION http://hdl.handle.net/1854/LU-178119 10.1094/MPMI.1998.11.6.449 000073691800002 0894-0282 1998 MOLECULAR PLANT-MICROBE INTERACTIONS Mol. Plant-Microbe Interact. 0894-0282 1998 11 6 449 457 1998 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/178119/file/4170462 application/pdf restricted ug 178119 2004-01-14T13:41:00Z 2018-08-13T14:11:09Z A1 VABB-1 48 info:srw/schema/1/mods-v3.3xml journalArticle A1 The active microbial community more accurately reflects the anaerobic digestion process : 16S rRNA (gene) sequencing as a predictive tool Jo De Vrieze aut author ug_LA25 0000-0001-9365-8896 Ameet J Pinto aut author William T Sloan aut author Umer Zeeshan Ijaz aut author eng Background: Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing. Results: A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles. Conclusions: In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion. Biology and Life Sciences Biogas Illumina sequencing Methane Methanogenesis WATER TREATMENT PLANTS GRADIENT GEL-ELECTROPHORESIS METHANOGENIC PATHWAYS BIOGAS REACTORS BACTERIAL COMMUNITIES METHANE PRODUCTION PROCESS STABILITY CARBON ISOTOPES FOOD WASTE SCALE http://hdl.handle.net/1854/LU-8560387 10.1186/s40168-018-0449-9 000428911300001 2049-2618 63 2018 MICROBIOME Microbiome 2049-2618 2018 6 2018 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/8560387/file/8560389 application/pdf ug 8560387 2018-04-27T13:14:34Z 2018-11-13T14:51:28Z A1 VABB-1 49 info:srw/schema/1/mods-v3.3xml journalArticle A1 The plant-specific CDKB1-CYCB1 complex mediates homologous recombination repair in Arabidopsis Annika Weimer aut author ug_UGent Sascha Biedermann aut author Hirofumi Harashima aut author Farshad Roodbarkelari aut author Naoki Takahashi aut author Julia Foreman aut author Yonsheng Guan aut author Gaëtan Pochon aut author Maren Heese aut author Daniël Van Damme aut author ug_WE09 0000-0002-9385-4851 Keiko Sugimoto aut author Csaba Koncz aut author Peter Doerner aut author Masaaki Umeda aut author Arp Schnittger aut author eng Upon DNA damage, cyclin-dependent kinases (CDKs) are typically inhibited to block cell division. In many organisms, however, it has been found that CDK activity is required for DNA repair, especially for homology-dependent repair (HR), resulting in the conundrum how mitotic arrest and repair can be reconciled. Here, we show that Arabidopsis thaliana solves this dilemma by a division of labor strategy. We identify the plant-specific B1-type CDKs (CDKB1s) and the class of B1-type cyclins (CYCB1s) as major regulators of HR in plants. We find that RADIATION SENSITIVE 51 (RAD51), a core mediator of HR, is a substrate of CDKB1-CYCB1 complexes. Conversely, mutants in CDKB1 and CYCB1 fail to recruit RAD51 to damaged DNA. CYCB1; 1 is specifically activated after DNA damage and we show that this activation is directly controlled by SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a transcription factor that acts similarly to p53 in animals. Thus, while the major mitotic cell-cycle activity is blocked after DNA damage, CDKB1-CYCB1 complexes are specifically activated to mediate HR. Biology and Life Sciences GENOTOXIC STRESS RAD51 PARALOGS END RESECTION DEPENDENT-KINASES IONIZING-RADIATION CELL-CYCLE CONTROL DNA-DAMAGE RESPONSE DOUBLE-STRAND BREAKS homologous recombination DNA damage cyclin cell cycle CDK MESSENGER-RNA GAMMA-RAYS http://hdl.handle.net/1854/LU-8174727 10.15252/embj.201593083 000385707500004 0261-4189 2016 EMBO JOURNAL Embo J. 0261-4189 2016 35 19 2068 2086 2016 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/8174727/file/8174747 application/pdf ug 8174727 2016-11-28T13:27:54Z 2018-11-13T14:55:15Z A1 VABB-1 50 info:srw/schema/1/mods-v3.3xml journalArticle A1 Cloning and expression in Escherichia coli of the TL-DNA gene 4 of Agrobacterium tumefaciens under the control of the PR promoter of bacteriophage λ Cloning and expression in Escherichia coli of the TL-DNA gene 4 of Agrobacterium tumefaciens under the control of the PR promoter of bacteriophage lambda Lionel Sibold aut author Nicole Guiso aut author Marc De Beuckeleer aut author Marc Van Montagu aut author ug_WE09 eng A plasmid was constructed that directs expression of the TL-DNA gene 4 protein in E. coli. The different steps of the construction were as follows: i) a region of gene 4 encoding the amino-terminal portion of the protein was fused in frame to DNA encoding an enzymatically active carboxy-terminal fragment of beta-galactosidase. The hybrid gene was poorly expressed from the upstream lambda PL promoter carried by the vector. ii) in order to generate an efficient procaryotic ribosome binding site, a DNA fragment carrying the lambda PR promoter with the nearby Shine-Dalgarno (SD) sequence of gene cro was placed in front of the gene 4-lacZ fusion. A recombinant plasmid, termed pGV793, that expressed efficiently a fused protein 4-beta-galactosidase was identified among the Lac+ clones. DNA sequencing analysis showed that pGV793 carried a hybrid ribosome binding site composed of the cro SD sequence, a five bp sequence and the ATG codon of gene 4. Plasmid pGV793 directed the synthesis of three polypeptides of molecular weight 132 Kd, 126 Kd and 122 Kd that carried beta-galactosidase antigenic determinants. The largest polypeptide had the expected size for the hybrid protein. The fusion proteins which accounted for about 0.5% of the total cellular proteins were purified by immunoadsorption using anti-beta-galactosidase antiserum. iii) the complete gene 4 coding sequence was reconstituted, with the lambda PR promoter in place. The resulting pGV822 plasmid expressed a polypeptide whose molecular weight 27 Kd corresponded to the expected size for the gene 4 product. The pI was about 7. Biology and Life Sciences ribosome binding site TL-DNA gene 4 beta-galactosidase fusion proteins A. tumefaciens http://hdl.handle.net/1854/LU-6930706 10.1016/0300-9084(84)90149-4 A1984TX12800004 0300-9084 1984 BIOCHIMIE Biochimie 0300-9084 1984 66 7-8 547 556 1984 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/6930706/file/6932050 application/pdf restricted ug 6930706 2015-09-15T13:55:00Z 2016-12-19T15:47:24Z A1 VABB-1 51 info:srw/schema/1/mods-v3.3xml journalArticle A1 Assessment of primer/template mismatch effects on real-time PCR amplification of target taxa for GMO quantification Rim Ghedira aut author ug_UGent Nina Papazova aut author Marnik Vuylsteke aut author ug_GE31 Tom Ruttink aut author Isabel Taverniers aut author Marc De Loose aut author ug_WE09 eng GMO quantification, based on real-time PCR relies on the amplification of an event-specific transgene assay and a species-specific reference assay. The uniformity of the nucleotide sequences targeted by both assays across various transgenic varieties is an important prerequisite for correct quantification. Single nucleotide polymorphisms (SNPs) frequently occur in the maize genome and might lead to nucleotide variation in regions used to design primers and probes for reference assays. Further, they may affect the annealing of the primer to the template and reduce the efficiency of DNA amplification. We assessed the effect of a minor DNA template modification, such as a single base pair mismatch in the primer attachment site, on real-time PCR quantification. A model system was used based on the introduction of artificial mismatches between the forward primer and the DNA template in the reference assay targeting the maize starch synthase (SSIIb) gene. The results show that the presence of a mismatch between the primer and the DNA template causes partial to complete failure of the amplification of the initial DNA template depending on the type and location of the nucleotide mismatch. With this study, we show that the presence of a primer/template mismatch affects the estimated total DNA quantity to a varying degree. Biology and Life Sciences quantification GMO primer/template mismatch Genetically modified organism maize real-time PCR GENETICALLY-MODIFIED MAIZE POLYMERASE-CHAIN-REACTION TAQ DNA-POLYMERASE REFERENCE MOLECULES MODIFIED ORGANISMS MAYS L. QUANTITATION POLYMORPHISM DISCRIMINATION TECHNOLOGY http://hdl.handle.net/1854/LU-772476 10.1021/jf901976a 000270858200004 0021-8561 2009 JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY J. Agric. Food Chem. 0021-8561 2009 57 20 9370 9377 2009 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/772476/file/3065378 application/pdf restricted ug 772476 2009-11-05T11:43:38Z 2016-12-19T15:46:07Z A1 VABB-1 52 info:srw/schema/1/mods-v3.3xml journalArticle A1 The MCM-Binding Protein ETG1 Aids Sister Chromatid Cohesion Required for Postreplicative Homologous Recombination Repair Naoki Takahashi aut author ug_WE09 Mauricio Alberto Quimbaya Gomez aut author ug_UGent Veit Schubert aut author Tim Lammens aut author ug_GE35 0000-0001-8733-4027 Klaas Vandepoele aut author ug_WE09 0000-0003-4790-2725 Ingo Schubert aut author Minami Matsui aut author Dirk Inzé aut author ug_WE09 0000-0002-3217-8407 Geert Berx aut author ug_WE14 Lieven De Veylder aut author ug_WE09 eng The DNA replication process represents a source of DNA stress that causes potentially spontaneous genome damage. This effect might be strengthened by mutations in crucial replication factors, requiring the activation of DNA damage checkpoints to enable DNA repair before anaphase onset. Here, we demonstrate that depletion of the evolutionarily conserved minichromosome maintenance helicase-binding protein ETG1 of Arabidopsis thaliana resulted in a stringent late G2 cell cycle arrest. This arrest correlated with a partial loss of sister chromatid cohesion. The lack-of-cohesion phenotype was intensified in plants without functional CTF18, a replication fork factor needed for cohesion establishment. The synergistic effect of the etg1 and ctf18 mutants on sister chromatid cohesion strengthened the impact on plant growth of the replication stress caused by ETG1 deficiency because of inefficient DNA repair. We conclude that the ETG1 replication factor is required for efficient cohesion and that cohesion establishment is essential for proper development of plants suffering from endogenous DNA stress. Cohesion defects observed upon knockdown of its human counterpart suggest an equally important developmental role for the orthologous mammalian ETG1 protein. Biology and Life Sciences DNA-DAMAGE REPAIR SACCHAROMYCES-CEREVISIAE ARABIDOPSIS-THALIANA STRUCTURAL MAINTENANCE MEDIATED TRANSFORMATION IONIZING-RADIATION ATP HYDROLYSIS INTERPHASE NUCLEI SMC PROTEINS S-PHASE http://hdl.handle.net/1854/LU-878774 10.1371/journal.pgen.1000817 000274194300025 1553-7390 2010 PLOS GENETICS PLoS Genet. 1553-7390 SAN FRANCISCO PUBLIC LIBRARY SCIENCE 2010 6 1 2010 I don't know the status of the copyright for this publication published https://biblio.ugent.be/publication/878774/file/2937196 application/pdf ug 878774 2010-02-24T11:41:05Z 2017-01-02T09:56:38Z A1 VABB-1 53 info:srw/schema/1/mods-v3.3xml journalArticle A1 Live-cell analysis of DNA methylation during sexual reproduction in Arabidopsis reveals context and sex-specific dynamics controlled by noncanonical RdDM Mathieu Ingouff aut author Benjamin Selles aut author Caroline Michaud aut author Thiet M Vu aut author Frédéric Berger aut author Andrea J Schorn aut author Daphné Autran aut author Matthias Van Durme aut author ug_UGent Moritz Nowack aut author ug_WE09 Robert A Martienssen aut author Daniel Grimanelli aut author eng Cytosine methylation is a key epigenetic mark in many organisms, important for both transcriptional control and genome integrity. While relatively stable during somatic growth, DNA methylation is reprogrammed genome-wide during mammalian reproduction. Reprogramming is essential for zygotic totipotency and to prevent transgenerational inheritance of epimutations. However, the extent of DNA methylation reprogramming in plants remains unclear. Here, we developed sensors reporting with single-cell resolution CG and non-CG methylation in Arabidopsis. Live imaging during reproduction revealed distinct and sex-specific dynamics for both contexts. We found that CHH methylation in the egg cell depends on DOMAINS REARRANGED METHYLASE 2 (DRM2) and RNA polymerase V (Pol V), two main actors of RNA-directed DNA methylation, but does not depend on Pol IV. Our sensors provide insight into global DNA methylation dynamics at the single-cell level with high temporal resolution and offer a powerful tool to track CG and non-CG methylation both during development and in response to environmental cues in all organisms with methylated DNA, as we illustrate in mouse embryonic stem cells. Biology and Life Sciences EPIGENETIC INHERITANCE EARLY EMBRYOGENESIS SMALL RNA PLANT THALIANA GENOME CHROMATIN HETEROCHROMATIN DEMETHYLATION ENDOSPERM DNA methylation sensors reprogramming reproduction http://hdl.handle.net/1854/LU-8516864 10.1101/gad.289397.116 000393726000009 0890-9369 1549-5477 2017 GENES & DEVELOPMENT Genes Dev. 0890-9369 1549-5477 2017 31 1 72 83 2017 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/8516864/file/8516865 application/pdf ug 8516864 2017-04-04T12:26:33Z 2018-11-13T14:55:48Z A1 VABB-1 54 info:srw/schema/1/mods-v3.3xml journalArticle A1 Epigenetic switches of tobacco transgenes associate with transient redistribution of histone marks in callus culture Kateřina Křížová aut author Anna Depicker aut author ug_WE09 0000-0003-0105-7407 Aleš Kovařík aut author eng In plants, silencing is usually accompanied by DNA methylation and heterochromatic histone marks. We studied these epigenetic modifications in different epialleles of 35S promoter (P35S)-driven tobacco transgenes. In locus 1, the T-DNA was organized as an inverted repeat, and the residing neomycin phosphotransferase II reporter gene (P35S-nptII) was silenced at the posttranscriptional (PTGS) level. Transcriptionally silenced (TGS) epialleles were generated by trans-acting RNA signals in hybrids or in a callus culture. PTGS to TGS conversion in callus culture was accompanied by loss of the euchromatic H3K4me3 mark in the transcribed region of locus 1, but this change was not transmitted to the regenerated plants from these calli. In contrast, cytosine methylation that spread from the transcribed region into the promoter was maintained in regenerants. Also, the TGS epialleles generated by trans-acting siRNAs did not change their active histone modifications. Thus, both TGS and PTGS epialleles exhibit euchromatic (H3K4me3 and H3K9ac) histone modifications despite heavy DNA methylation in the promoter and transcribed region, respectively. However, in the TGS locus (271), abundant heterochromatic H3K9me2 marks and DNA methylation were present on P35S. Heterochromatic histone modifications are not automatically installed on transcriptionally silenced loci in tobacco, suggesting that repressive histone marks and cytosine methylation may be uncoupled. However, transient loss of euchromatic modifications may guide de novo DNA methylation leading to formation of stable repressed epialleles with recovered eukaryotic marks. Compilation of available data on epigenetic modification of inactivated P35S in different systems is provided. Biology and Life Sciences GENE-REGULATION PLANTS NICOTIANA-TABACUM DNA METHYLATION JMJC DOMAIN PROTEIN callus dedifferentiation tobacco DNA methylation transgene silencing histone modification TRANSCRIPTION PROMOTER CYTOSINE METHYLATION ARABIDOPSIS-THALIANA SOMACLONAL VARIATION http://hdl.handle.net/1854/LU-4224288 10.4161/epi.24613 000327623100011 1559-2294 2013 EPIGENETICS Epigenetics 1559-2294 2013 8 6 666 676 2013 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/4224288/file/4224298 application/pdf restricted ug 4224288 2014-01-08T10:13:22Z 2018-08-13T14:30:34Z A1 VABB-1 55 info:srw/schema/1/mods-v3.3xml journalArticle A1 Deficiency of the Arabidopsis helicase RTEL1 triggers a SOG1-dependent replication checkpoint in response to DNA cross-links Zhubing Hu aut author ug_UGent Toon Cools aut author ug_UGent Pooneh Kalhorzadeh aut author ug_UGent Jefri Heyman aut author ug_WE09 0000-0003-3266-4189 Lieven De Veylder aut author ug_WE09 eng To maintain genome integrity, DNA replication is executed and regulated by a complex molecular network of numerous proteins, including helicases and cell cycle checkpoint regulators. Through a systematic screening for putative replication mutants, we identified an Arabidopsis thaliana homolog of human Regulator of Telomere Length 1 (RTEL1), which functions in DNA replication, DNA repair, and recombination. RTEL1 deficiency retards plant growth, a phenotype including a prolonged S-phase duration and decreased cell proliferation. Genetic analysis revealed that rtel1 mutant plants show activated cell cycle checkpoints, specific sensitivity to DNA cross-linking agents, and increased homologous recombination, but a lack of progressive shortening of telomeres, indicating that RTEL1 functions have only been partially conserved between mammals and plants. Surprisingly, RTEL1 deficiency induces tolerance to the deoxynucleotide-depleting drug hydroxyurea, which could be mimicked by DNA cross-linking agents. This resistance does not rely on the essential replication checkpoint regulator WEE1 but could be blocked by a mutation in the SOG1 transcription factor. Taken together, our data indicate that RTEL1 is required for DNA replication and that its deficiency activates a SOG1-dependent replication checkpoint. Biology and Life Sciences KINASE GENE DAMAGE PLANTS REPAIR THALIANA GENOME INSTABILITY HOMOLOGOUS RECOMBINATION TELOMERE DYSFUNCTION INTEGRITY http://hdl.handle.net/1854/LU-5930802 10.1105/tpc.114.134312 000350764700016 1040-4651 2015 PLANT CELL Plant Cell 1040-4651 2015 27 1 149 161 2015 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/5930802/file/5930812 application/pdf restricted ug 5930802 2015-04-13T13:51:59Z 2016-12-19T15:45:55Z A1 VABB-1 56 info:srw/schema/1/mods-v3.3xml journalArticle A2 An improved semi-automated rapid method of extracting genomic DNA for molecular marker analysis in cocoa, Theobroma cacao L. Ranjana Bhattacharjee aut author Maria Kolesnikova-Allen aut author Peter Aikpokpodion aut author Sunday Taiwo aut author Ivan Ingelbrecht aut author ug_UGent eng DNA extraction is a time-consuming and expensive component of molecular marker analysis, constituting about 30–60% of the total time required for sample processing. Furthermore, the procedure for extracting high-quality DNA from tree species such as cocoa differs from extraction protocols suitable for other crop plants. This is accompanied by problems in collecting leaf tissues from field-grown cocoa trees, where storage facilities are not available and where transporting samples to laboratory for immediate refrigeration is usually impossible. We preserved cocoa leaf tissues in the field in an NaCl-CTAB-azide solution (as described in Rogstad, 1992), which did not require immediate refrigeration. This method also allowed preservation of leaf tissues for a few days during transportation and protected leaf tissues from bacterial and fungal attacks. Once transported to the laboratory, the samples were stored at 4°C for almost 1 y. To isolate good-quality DNA from stored leaf tissues, a rapid semiautomated and relatively high-throughput protocol was established. The procedure followed a modified CTAB/β-mercaptoethanol method of DNA extraction in a 96-well plate, and an automated system (i.e., GenoGrinder 2000) was used to grind the leaf tissues. The quality of DNA was not affected by long storage, and the quantity obtained per sample was adequate for about 1000 PCR reactions. Thus, this method allowed isolation of about 200 samples per day at a cost of $0.60 per sample and is a relatively high-throughput, low-cost extraction compared with conventional methods that use manual grinding and/or expensive kits. Biology and Life Sciences SSR high-throughput cocoa DNA extraction ball bearing http://hdl.handle.net/1854/LU-1991532 10.1007/BF02772686 0735-9640 2004 PLANT MOLECULAR BIOLOGY REPORTER Plant Mol Biol Rep. 0735-9640 2004 22 4 435 436 2004 published https://biblio.ugent.be/publication/1991532/file/1998245 application/pdf restricted ug 1991532 2012-01-17T16:04:00Z 2016-12-19T15:45:05Z A2 VABB-1 57 info:srw/schema/1/mods-v3.3xml conference C3 The active microbial community more accurately reflects the anaerobic digestion process : 16S rRNA (gene) sequencing as a predictive tool Jo De Vrieze aut author ug_LA25 0000-0001-9365-8896 3rd International conference on Biogas Microbiology (ICBM-3) eng Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterise amplicons, but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing. A significantly higher richness and overall diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea, yet, the difference was less pronounced for the bacteria. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet, the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles. The apparent strong difference between the total and active archaeal community, as determined on different community levels, indicates that the active archaeal community reflects a specialized and organized structure. In contrast, the total and active bacterial community showed a similar community structure, however, community composition also more strongly differed between the total and active community. In conclusion, the clear difference between RNA and DNA based community screening confirms the importance of this combined approach to obtain a broad general overview, not only on the total and active community, but also in terms of potential collaboration and competition and predicted functionality. These results can serve as a basis for further integrated process engineering of the anaerobic digestion process. Earth and Environmental Sciences Biology and Life Sciences http://hdl.handle.net/1854/LU-8529964 2017 Biogas Microbiology, 3rd International conference, Abstracts 2017 2017 I don't know the status of the copyright for this publication unpublished ug 8529964 2017-08-31T09:53:18Z 2018-11-13T14:54:48Z C3 58 info:srw/schema/1/mods-v3.3xml journalArticle A1 Evaluation of CRE-mediated excision approaches in Arabidopsis thaliana Gordana Marjanac aut author ug_WE09 Annelies De Paepe aut author ug_GE31 Ingrid Peck aut author ug_WE09 Anni Jacobs aut author ug_WE09 Sylvie De Buck aut author ug_WE09 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng The ability of the CRE recombinase to catalyze excision of a DNA fragment flanked by directly repeated lox sites has been exploited to modify gene expression and proved to function well in particular case studies. However, very often variability in CRE expression and differences in efficiency of CRE-mediated recombination are observed. Here, various approaches were investigated to reproducibly obtain optimal CRE activity. CRE recombination was analyzed either by transforming the CRE T-DNA into plants containing a lox-flanked fragment or by transforming a T-DNA harboring a lox-flanked fragment into plants producing the CRE recombinase. Although somatic CRE-mediated excision of a lox-flanked fragment was obtained in all transformants, a variable amount of germline-transmitted deletions was found among different independent transformants, irrespective of the orientation of transformation. Also, the efficiency of CRE-mediated excision correlated well with the CRE mRNA level. In addition, CRE-mediated fragment excision was compared after floral dip and after root tissue transformation when transforming in a CRE-expressing background. Importantly, less CRE activity was needed to excise the lox-flanked fragment from the transferred T-DNA after root tissue transformation than after floral dip transformation. We hypothesize that this is correlated with the lower T-DNA copy number inserted during root transformation as compared to floral dip transformation. Biology and Life Sciences TRANSFORMATION TRANSIENT EXPRESSION TOBACCO SYSTEM ROOT EXPLANTS TRANSGENIC PLANTS SELECTABLE MARKER GENE GLUCURONIDASE ACCUMULATION LEVELS T-DNA INTEGRATION SITE-SPECIFIC RECOMBINATION T-DNA root transformation floral dip Arabidopsis CRE/loxP recombination excision http://hdl.handle.net/1854/LU-409425 10.1007/s11248-007-9096-9 000254353900008 0962-8819 2008 TRANSGENIC RESEARCH Transgenic Res. 0962-8819 2008 17 2 239 250 2008 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/409425/file/3065498 application/pdf restricted ug 409425 2008-05-15T18:03:00Z 2018-08-13T14:28:43Z A1 VABB-1 59 info:srw/schema/1/mods-v3.3xml journalArticle A1 Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli Pieter Meysman aut author Hai Dang Thanh aut author Kris Laukens aut author Riet De Smet aut author ug_UGent Yan Wu aut author Kathleen Marchal aut author ug_TW05 ug_WE09 0000-0002-2169-4588 Kristof Engelen aut author eng Recognition of genomic binding sites by transcription factors can occur through base-specific recognition, or by recognition of variations within the structure of the DNA macromolecule. In this article, we investigate what information can be retrieved from local DNA structural properties that is relevant to transcription factor binding and that cannot be captured by the nucleotide sequence alone. More specifically, we explore the benefit of employing the structural characteristics of DNA to create binding-site models that encompass indirect recognition for the Escherichia coli model organism. We developed a novel methodology [Conditional Random fields of Smoothed Structural Data (CRoSSeD)], based on structural scales and conditional random fields to model and predict regulator binding sites. The value of relying on local structural-DNA properties is demonstrated by improved classifier performance on a large number of biological datasets, and by the detection of novel binding sites which could be validated by independent data sources, and which could not be identified using sequence data alone. We further show that the CRoSSeD-binding-site models can be related to the actual molecular mechanisms of the transcription factor DNA binding, and thus cannot only be used for prediction of novel sites, but might also give valuable insights into unknown binding mechanisms of transcription factors. Biology and Life Sciences SEQUENCE GENE B-DNA CORE PROMOTER MOLECULAR-DYNAMICS SIMULATIONS PROTEIN IDENTIFICATION RECOGNITION PARAMETERS STABILITY http://hdl.handle.net/1854/LU-3186410 10.1093/nar/gkq1071 000286675300001 0305-1048 e6 2011 NUCLEIC ACIDS RESEARCH Nucleic Acids Res. 0305-1048 2011 39 2 2011 I have retained and own the full copyright for this publication published https://biblio.ugent.be/publication/3186410/file/3186439 application/pdf ug 3186410 2013-04-08T15:27:50Z 2018-08-16T07:45:18Z A1 VABB-1 60 info:srw/schema/1/mods-v3.3xml bookChapter B2 Agrobacterium and Ti plasmids Marc Van Montagu aut author ug_WE09 P Zambryski aut author eng Agrobacteria are motile, aerobic, rod-shaped phytopathogenic bacteria that induce crown gall or hairy roots growths due to the transfer of a particular segment of their Ti or Ri plasmid, called the transferred (T)-DNA, from the bacterium into the plant cell. Once stably integrated in the plant genome, the T-DNA element encodes plant hormones and opines in order to create a biological niche where the agrobacteria can grow and proliferate. Two genetic regions on the Ti/Ri plasmid are essential for Agrobacterium to transfer DNA to plant cells, the T-DNA mentioned above, and the virulence (vir) region. Vir genes encode protein products to generate a transferable single-stranded copy of the T-DNA region, and a membrane-spanning channel to export the T strand and virulence proteins from the bacterium to the plant cell. This natural genetic engineering system has been genetically manipulated to become a vector for plant genetic engineering. Agrobacterium-derived gene vectors have become a fundamental tool to the molecular dissection of all aspects of plant biology and to introduce genes that confer new desirable traits for agriculture as well. By 2009, some 13 million hectares of these so-called genetically modified (GM) crops (representing over 9% of the total area under agricultural production) were grown, mostly in North and South America and China, with the global market value of GM crops being over $9 billion. Biology and Life Sciences Crown gall Agrobacterium GM plants GMO Opines Hairy roots Plant genetic engineering Plant genetic modification vir genes Ti plasmid T-DNA binary vector T-DNA http://hdl.handle.net/1854/LU-5842554 10.1016/B978-0-12-374984-0.01542-4 9780080961569 2013 Brenner's encyclopedia of genetics, vol. 1 Stanley Maloy edt editor Kelly Hughes edt editor 9780080961569 Amsterdam, The Netherlands Elsevier Science 2013 55 57 2013 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/5842554/file/5842563 application/pdf restricted ug 5842554 2015-02-09T14:33:01Z 2017-01-02T09:55:43Z B2 VABB-4 61 info:srw/schema/1/mods-v3.3xml journalArticle A1 Nuclear and polysomal transcripts of T-DNA in octopine crown gall suspension and callus cultures Lothar Willmitzer aut author Leon Otten aut author Gisela Simons aut author Wolfgang Schmalenbach aut author Joachim Schröder aut author Gudrun Schröder aut author Marc Van Montagu aut author ug_WE09 Guido De Vos aut author Jeff Schell aut author eng To establish a detailed map of the transcribed parts of the T-DNA in two octopine crown gall lines grown in suspension culture, T-DNA-derived steady-state nuclear and polysomal RNA as well as RNA synthesized in isolated nuclei purified from the crown gall tissues, was analyzed by Southern blot hybridization to specific fragments of the T-region of the octopine plasmid pTi ACH5. In addition total RNA isolated from the same lines grown as callus tissue on solid agar, was analyzed for T-DNA specific transcripts. The results show that all of the T-DNA is trancribed although different segments are transcribed to significantly different extents. Roughly the same hybridization patterns was found for nuclear and polysomal poly-A+ and poly-A− RNA. The transcription pattern was found to be different for cells in the stationary phase of growth compared with actively growing cells. Biology and Life Sciences http://hdl.handle.net/1854/LU-5673011 10.1007/BF00269667 A1981MA66300012 0026-8925 1981 MOLECULAR & GENERAL GENETICS Mol. Gen. Genet. 0026-8925 1981 182 2 255 262 1981 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/5673011/file/5673098 application/pdf restricted ug 5673011 2014-08-13T17:38:03Z 2018-08-13T14:34:49Z A1 VABB-1 62 info:srw/schema/1/mods-v3.3xml journalArticle A1 High-throughput CRISPR vector construction and characterization of DNA modifications by generation of tomato hairy roots Thomas Jacobs aut author ug_WE09 Gregory B Martin aut author eng Targeted DNA mutations generated by vectors with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology have proven useful for functional genomics studies. While most cloning strategies are simple to perform, they generally use multiple steps and can require several days to generate the ultimate constructs. The method presented here is based on DNA assembly and can produce fully functional CRISPR vectors in a single cloning reaction. Vector construction can also be pooled, further increasing the efficiency and utility of the process. A modification of the method is used to create CRISPR vectors with multiple gene targets. CRISPR vectors are then transformed into tomato hairy roots to generate transgenic materials with targeted DNA modifications. Hairy roots are a useful system for testing vector functionality as they are technically simple to generate and amenable to large-scale production. The methods presented here will have wide application as they can be used to generate a variety of CRISPR vectors and be used in a wide range of plant species. Biology and Life Sciences GENOME SYSTEM GUIDE RNA GENE-EXPRESSION HUMAN-CELLS TRANSFORMATION PLANTS AGROBACTERIUM-RHIZOGENES plant transformation plant biotechnology genome editing DNA assembly genetic engineering CRISPR/Cas9 Agrobacterium rhizogenes Issue 110 Molecular Biology MULTIPLEX BIOLOGY http://hdl.handle.net/1854/LU-8201140 10.3791/53843 000380256000052 1940-087X e53843 2016 JOVE-JOURNAL OF VISUALIZED EXPERIMENTS J. Vis. Exp. 1940-087X 2016 110 2016 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/8201140/file/8201144 application/pdf restricted ug 8201140 2016-12-02T06:55:08Z 2016-12-21T15:43:00Z A1 VABB-1 63 info:srw/schema/1/mods-v3.3xml journalArticle A1 DNA stress checkpoint control and plant development Toon Cools aut author ug_UGent Lieven De Veylder aut author ug_WE09 Charles Gasser edt editor Caroline Dean edt editor eng Plants are sedentary, and so have unavoidably close contact with agents that target their genome integrity. To sense and react to these threats, plants have evolved DNA stress checkpoint mechanisms that arrest the cell cycle and activate the DNA repair machinery to preserve the genome content. Although the pathways that maintain DNA integrity are largely conserved among eukaryotic organisms, plants put different accents on cell cycle control under DNA stress and might have their own way to cope with it. Biology and Life Sciences GENOTOXIC STRESS GENOME INSTABILITY ARABIDOPSIS-THALIANA TOPOISOMERASE-VI COMPLEX CELL-CYCLE CHECKPOINT EARLY EMBRYONIC LETHALITY GENE-EXPRESSION CAF-1 MUTANTS KINASE DAMAGE http://hdl.handle.net/1854/LU-528543 10.1016/j.pbi.2008.09.012 000262974900005 1369-5266 2009 Current Opinion in Plant Biology Curr. Opin. Plant Biol. 1369-5266 2009 12 1 23 28 2009 I don't know the status of the copyright for this publication published https://biblio.ugent.be/publication/528543/file/536603 application/pdf restricted ug 528543 2009-03-23T16:48:16Z 2018-08-13T14:34:22Z A1 VABB-1 64 info:srw/schema/1/mods-v3.3xml journalArticle A1 Attenuation of cGAS-STING signaling is mediated by a p62/SQSTM1-dependent autophagy pathway activated by TBK1 Thaneas Prabakaran aut author Chiranjeevi Bodda aut author Christian Krapp aut author Bao-cun Zhang aut author Maria H Christensen aut author Chenglong Sun aut author Line Reinert aut author Yujia Cai aut author Soren B Jensen aut author Morten K Skouboe aut author Jens R Nyengaard aut author Craig B Thompson aut author Robert Jan Lebbink aut author Ganes C Sen aut author Geert van Loo aut author ug_WE14 0000-0003-1304-7732 Rikke Nielsen aut author Masaaki Komatsu aut author Lene N Nejsum aut author Martin R Jakobsen aut author Mads Gyrd-Hansen aut author Soren R Paludan aut author eng Negative regulation of immune pathways is essential to achieve resolution of immune responses and to avoid excess inflammation. DNA stimulates type I IFN expression through the DNA sensor cGAS, the second messenger cGAMP, and the adaptor molecule STING. Here, we report that STING degradation following activation of the pathway occurs through autophagy and is mediated by p62/SQSTM1, which is phosphorylated by TBK1 to direct ubiquitinated STING to autophagosomes. Degradation of STING was impaired in p62-deficient cells, which responded with elevated IFN production to foreign DNA and DNA pathogens. In the absence of p62, STING failed to traffic to autophagy-associated vesicles. Thus, DNA sensing induces the cGAS-STING pathway to activate TBK1, which phosphorylates IRF3 to induce IFN expression, but also phosphorylates p62 to stimulate STING degradation and attenuation of the response. Biology and Life Sciences Medicine and Health Sciences E3 UBIQUITIN LIGASE GMP-AMP SYNTHASE IMMUNE-RESPONSES DNA SENSOR LISTERIA-MONOCYTOGENES SELECTIVE AUTOPHAGY ANTIVIRAL RESPONSE IMMUNOGENIC TUMORS INTRACELLULAR DNA TUBERCULOSIS DNA autophagy DNA sensing innate immunity p62/SQSTM1 STING http://hdl.handle.net/1854/LU-8561178 10.15252/embj.201797858 000430061000004 0261-4189 1460-2075 e97858 2018 EMBO JOURNAL Embo J. 0261-4189 1460-2075 2018 37 8 2018 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/8561178/file/8561182 application/pdf restricted ug 8561178 2018-05-07T15:30:51Z 2018-11-13T14:53:04Z A1 VABB-1 65 info:srw/schema/1/mods-v3.3xml conference C3 Droplet digital PCR, the new tool in HIV reservoir quantification? Ward De Spiegelaere aut author ug_DI03 0000-0003-2097-8439 Maja Kiselinova aut author Eva Malatinková aut author ug_GE35 Alexander Pasternak aut author Ben Berkhout aut author Linos Vandekerckhove aut author ug_GE32 ug_GE35 ug_UZGent 6th International workshop on HIV Persistence, Reservoirs and Eradication Strategies eng Background: Digital PCR is a relatively old concept for absolute quantification of DNA using PCR, but recent technological developments allowed its wide use. The current state of art technique for performing digital PCR is based on microdroplet technology. Direct absolute quantification relieves the necessity of standard curves and increases assay accuracy. In addition, the end point PCR set-up allows higher assay flexibility and decreases quantitative bias due to variations in PCR efficiency. In the present work, these theoretical advantages were assessed on the QX100 droplet digital PCR (Bio-rad) on various virological markers to assess the possible use of ddPCR in HIV research. Methods: First, ddPCR was compared to a highly sensitive method of real-time PCR based quantification of cellular associated spliced and unspliced HIV RNA. Second, different methods of DNA extractions in combination with ddPCR were compared for quantification of total and episomal HIV DNA. Hereby, the maximal amount of restriction digested DNA was assessed in the ddPCR. Third, a touchdown procedure was optimized for an HIV specific primer probe set with a low melting temperature using touchdown ddPCR. Results: The comparsion of the nested real-time quantitative PCR to ddPCR indicated that ddPCR is at least equally sensitive to qPCR but also that false positive negative control samples may interfere with quantification at the level of single copies. Episomal 2LTR quantification was compared on ddPCR between total DNA extracted DNA and plasmid purified DNA, revealing a higher accuracy of 2LTR measurements in the total DNA extracts. Assessment of total DNA load in digital PCR reactions revealed a higher tolerance for inhibition compared to qPCR, but a strong influence of the concentration of restriction digestion mix on ddPCR efficiency. Finally, a touchdown procedure revealed that digital PCR can combine a higher flexibility in assay design while retaining accurate quantitative power compared to qPCR Conclusions: We transferred 4 assays used in HIV reservoir research to the ddPCR platform. Although ddPCR has some major advantages for low level quantification in HIV reservoir research, some technical hurdles, including the occurrence of false negative control samples need still be addressed to ameliorate the current technology. Biology and Life Sciences HIV latency quantification ddPCR reservoir HIV digital PCR http://hdl.handle.net/1854/LU-5704829 2013 HIV Persistence, Reservoirs and Eradication Strategies, 6th International workshop 2013 2013 I have retained and own the full copyright for this publication published https://biblio.ugent.be/publication/5704829/file/5704830 application/pdf ug 5704829 2014-09-18T14:35:51Z 2018-08-13T14:35:01Z C3 66 info:srw/schema/1/mods-v3.3xml journalArticle A1 Ethics of modifying the mitochondrial genome A L Bredenoord aut author W Dondorp aut author Guido Pennings aut author ug_LW01 0000-0003-0754-8055 G de Wert aut author eng Recent preclinical studies have shown the feasibility of specific variants of nuclear transfer to prevent mitochondrial DNA disorders. Nuclear transfer could be a valuable reproductive option for carriers of mitochondrial mutations. A clinical application of nuclear transfer, however, would entail germ-line modification, more specifically a germ-line modification of the mitochondrial genome. One of the most prominent objections against germ-line modification is the fear that it would become possible to alter 'essential characteristics' of a future person, thereby possibly violating the child's right to an open future. As only the nuclear DNA would contain the ingredients for individual characteristics, modification of the mtDNA is often considered less controversial than modification of the nuclear DNA. This paper discusses the tenability of this dichotomy. After having clarified the concept of germ-line modification, it argues that modification of the mtDNA is not substantively different from modification of the nuclear DNA in terms of its effects on the identity of the future person. Subsequently the paper assesses how this conclusion affects the moral evaluation of nuclear transfer to prevent mtDNA disorders. It concludes that the moral acceptability of germ-line modification does not depend on whether it alters the identity of the future child-all germ-line modifications do-but on whether it safeguards the child's right to an open future. If nuclear transfer to prevent mtDNA disorders becomes safe and effective, then dismissing it because it involves germ-line modification is unjustified. Social Sciences GERM-LINE-THERAPY OVUM-NUCLEAR-TRANSPLANTATION DNA DISORDERS DISEASE MICE TRANSMISSION ENHANCEMENT PROTOCOL MTDNA http://hdl.handle.net/1854/LU-1229019 10.1136/jme.2010.037481 000286456100008 0306-6800 2010 JOURNAL OF MEDICAL ETHICS J. Med. Ethics 0306-6800 2010 37 2 97 100 2010 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1229019/file/6752194 application/pdf ug 1229019 2011-05-22T19:50:37Z 2018-08-13T14:07:47Z A1 VABB-1 67 info:srw/schema/1/mods-v3.3xml journalArticle A1 Isolation of tobacco DNA segments with plant promoter activity Lieve MF Herman aut author Marc Van Montagu aut author ug_WE09 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng We constructed a promoter probe vector, pGVL120, to isolate plant DNA segments with promoter activity in tobacco. Plant nuclear DNA Sau3A fragments were inserted in front of the npt-II sequence, and a mixture of recombinant plasmids was mobilized to Agrobacterium sp. and used to transform tobacco protoplasts. By kanamycin selection, transformed plant cell lines containing NPT-II T-DNAs were isolated. Eight of these cell lines were regenerated and analyzed for the levels of NPT-II activity in stem, root, midrib, and leaf. These levels demonstrated novel regulation patterns in each isolate. One cell line, T20, was analyzed in detail and found to contain four different T-DNAs. One of the recloned T-DNAs, T20-2, contains an insert of 401 base pairs in front of the NPT-II sequence, and by reintroducing this T-DNA into plant cells we could demonstrate that this insert provides a promoter sequence. The NPT-II enzyme activity under the control of the P20 promoter is especially high in stem and root, but low in leaf and callus, both in the originally isolated T20 plant and in independently isolated transformants with the T20-2 T-DNA. Biology and Life Sciences http://hdl.handle.net/1854/LU-323041 A1986E956800041 0270-7306 1986 MOLECULAR AND CELLULAR BIOLOGY Mol. Cell. Biol. 0270-7306 1986 6 12 4486 4492 1986 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/323041/file/560177 application/pdf restricted http://mcb.asm.org/cgi/content/abstract/6/12/4486 ug 323041 2005-11-21T16:41:00Z 2018-08-13T14:23:30Z A1 VABB-1 68 info:srw/schema/1/mods-v3.3xml journalArticle A1 Corresponding mitochondrial DNA and niche divergence for crested newt candidate species Ben Wielstra aut author Wouter Beukema aut author ug_DI05 Jan W Arntzen aut author Andrew K Skidmore aut author Albertus G Toxopeus aut author Niels Raes aut author eng Genetic divergence of mitochondrial DNA does not necessarily correspond to reproductive isolation. However, if mitochondrial DNA lineages occupy separate segments of environmental space, this supports the notion of their evolutionary independence. We explore niche differentiation among three candidate species of crested newt (characterized by distinct mitochondrial DNA lineages) and interpret the results in the light of differences observed for recognized crested newt species. We quantify niche differences among all crested newt (candidate) species and test hypotheses regarding niche evolution, employing two ordination techniques (PCA-env and ENFA). Niche equivalency is rejected: all (candidate) species are found to occupy significantly different segments of environmental space. Furthermore, niche overlap values for the three candidate species are not significantly higher than those for the recognized species. As the three candidate crested newt species are, not only in terms of mitochondrial DNA genetic divergence, but also ecologically speaking, as diverged as the recognized crested newt species, our findings are in line with the hypothesis that they represent cryptic species. We address potential pitfalls of our methodology. Biology and Life Sciences ABSENCE DATA MODELS PHYLOGEOGRAPHY DELIMITATION SPECIATION ECOLOGY AREAS http://hdl.handle.net/1854/LU-8522037 10.1371/journal.pone.0046671 000309973900198 1932-6203 e46671 2012 PLOS ONE PLoS One 1932-6203 2012 7 9 2012 I have retained and own the full copyright for this publication published https://biblio.ugent.be/publication/8522037/file/8522040 application/pdf ug 8522037 2017-06-01T14:21:57Z 2018-08-16T07:59:52Z A1 VABB-1 69 info:srw/schema/1/mods-v3.3xml journalArticle A1 Uptake, integration, expression and genetic transmission of a selectable chimaeris gene by plant protoplasts Rüdiger Hain aut author Priska Stabel aut author Armin P Czernilofsky aut author Hans-Henning Steinbiß aut author Luis Herrera-Estrella aut author Jeff Schell aut author eng Genetic transformation of Nicotiana tabacum protoplasts was achieved by incubation of protoplasts with a plasmid DNA-calcium phosphate coprecipitate, followed by fusion of the protoplasts in the presence of polyvinyl alcohol and subsequent exposure to high pH. A derivative of the plasmid pBR322 containing a chimaeric gene, consisting of the nopaline synthase promoter, the coding region of the aminoglycoside phosphotransferase gene of Tn5 and the polyadenylation signal region of the octopine synthase gene, was used for these transformation experiments. This chimaeric gene confers resistance of transformed plant cells to kanamycin. This novel transformation procedure reproducibly yielded transformants at frequencies of approximately 0.01%. Aminoglycoside phosphotransferase II activity was detected in both transformed calli and in regenerated plants. DNA from some of the transformed clones was analyzed by Southern blot hybridization. The input DNA appears to be integrated into high molecular weight cellular DNA. Genetic analysis of one of the kanamycin resistant plants shows that the chimaeric gene is transmitted to the progeny as a single dominant trait in a Mendelian fashion. As a comparison the input DNA was also introduced into tobacco protoplasts using Agrobacterium tumefaciens and Ti-plasmid derived gene vectors. Biology and Life Sciences http://hdl.handle.net/1854/LU-6974879 10.1007/BF00330254 A1985AJE6900001 0026-8925 1985 MOLECULAR & GENERAL GENETICS Mol. Gen. Genet. 0026-8925 1985 199 2 161 168 1985 published ug 6974879 2015-11-04T15:46:23Z 2018-11-13T14:52:07Z A1 VABB-1 70 info:srw/schema/1/mods-v3.3xml journalArticle A1 Protective Th1 immune responses against chronic toxoplasmosis induced by a protein-protein vaccine combination but not by its DNA-protein counterpart E Jongert aut author Delfien Verhelst aut author ug_UGent M. Abady aut author E Petersen aut author N Gargano aut author eng Vaccine-induced protection against toxoplasmosis is correlated with cellular immune responses to Taxoplasma gondii, both in animals and man. The goal of the current study was to evaluate whether the combination of a recombinant protein and a plasmid DNA vaccine could offer an advantage over the protein mixture, and protect outbred mice against infection with T gondii. To this purpose, the chimeric protein rEC2, encoding antigenic fragments of surface-associated proteins MIC2, MIC3 and SAG1, was combined with pGRA7 plasmid DNA or rGRA7 protein. High levels of antibodies were elicited by both vaccine formulations. The protein-DNA vaccine elicited a polarized Th1/Th2 immune response, characterized by IFN-gamma and IL-10, and afforded low protection (24%) against brain cyst formation. In contrast, the protein-protein vaccine elicited a Th1-focused immune response, characterized by IFN-gamma and IL-2 production, conferring a strong protection (79%) against brain cyst formation in chronic toxoplasmosis. We show here that GERBU adjuvanted protein vaccines confer better protection against toxoplasmosis than the protein-DNA heterologous vaccine. Crown Copyright (C) 2008 Published by Elsevier Ltd. All rights reserved. Veterinary Sciences CONGENITAL TOXOPLASMOSIS SURFACE PROTEIN MYCOBACTERIUM-TUBERCULOSIS HOST-CELLS GONDII INFECTION Th1/Th2 Toxoplasma gondii Heterologous vaccine MICE ANTIGENS SAG1 COMPLEX IMMUNIZATION http://hdl.handle.net/1854/LU-536018 10.1016/j.vaccine.2008.07.032 000260148900010 0264-410X 2008 VACCINE Vaccine 0264-410X Oxford ; UNITED KINGDOM ELSEVIER SCI LTD 2008 26 41 5289 5295 2008 I don't know the status of the copyright for this publication published https://biblio.ugent.be/publication/536018/file/536028 application/pdf restricted ug 536018 2009-04-01T11:09:43Z 2018-08-13T14:34:31Z A1 VABB-1 71 info:srw/schema/1/mods-v3.3xml journalArticle A2 Management and Object Behavior of Statecharts through Statechart DNA Benjamin De Leeuw aut author Albert Hoogewijs aut author ug_WE01 eng We propose composed strings called ”statechart DNA” as essential building blocks for a new statechart (sc) abstraction method. We define the simplified statechart (ssc) and show that our definition covers the UML 2.0 sc model, by matching it to all model elements of the StateMachine package of the UML 2.0 metamodel and to the OCL constraints on these model elements. A Model Driven Architecture (MDA) is defined, inspired by a PIM-to- PIM model transformation procedure between UML sc models and ssc models. We discuss the rationale behind action abstraction in ssc models. This framework is used to isolate sc DNA, first in ssc models, then in UML sc models. We show how sc DNA, a compaction of sc construction primitives, can be used to define behavior model metrics and more generally, to manage and maintain evolving object behavior. State machine versioning is an important application of statechart DNA to manage industrial model repositories. Technology and Engineering Model checking Statecharts UML State machine versioning http://hdl.handle.net/1854/LU-697226 1790-0832 2009 WSEAS TRANSACTIONS on INFORMATION SCIENCE and APPLICATIONS WSEAS trans. inf. sci. appl. 1790-0832 WSEAS 2009 6 5 859 871 2009 published https://biblio.ugent.be/publication/697226/file/1139597 application/pdf ug 697226 2009-06-14T16:51:35Z 2016-12-19T15:46:46Z A2 VABB-1 72 info:srw/schema/1/mods-v3.3xml conference C1 Gene vectors for higher plants Jeff Schell aut author Marc Van Montagu aut author ug_WE09 Jean-Pierre Hernalsteens aut author Henri De Greve aut author Jan Leemans aut author Csaba Koncz aut author Lothar Willmitzer aut author Leon Otten aut author Joachim Schröder aut author Gudrun Schröder aut author Lowell D Owens edt editor Beltsville symposium in Agricultural Research eng Tumor-inducing (Ti) plasmids, carried by Agrobacterium tumefaciens have been shown to be responsible for crown gall formation in plants. Ti plasmids are natural gene vectors with which Agrobacteria achieve the transfer and stable maintenance of a defined DNA segment (called T­region) into the nucleus of transformed plant cells. Using site-specific mutagenesis, it was possible to introduce mutations in different parts of the T-region. The transcription of the T-DNA in wild-type and mutant crown galls was compared, and it was found that the induction of specific developmental patterns could be correlated with the absence of specific T-DNA transcripts. Double mutants were obtained in which the expres­sion of all the "onc" genes was abolished. Tobacco, potato, and petunia plant cells harboring such inactivated T-DNAs were shown to regenerate normal, fertile plants that transmit the T-DNA segment as a single Mendelian locus. Structural genes, coding for opine synthase enzymes, were shown to be fully active. Several T-DNA genes were sequenced, and transcription promoter and termination signals were identified. Biology and Life Sciences http://hdl.handle.net/1854/LU-6918474 9780865981126 9780246119476 1983 Beltsville Symposia in Agricultural Research 9780865981126 9780246119476 Totowa, NJ, USA Rowman & Allanheld 1983 7 197 213 1983 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/6918474/file/6918510 application/pdf restricted ug 6918474 2015-08-31T16:08:48Z 2017-01-02T09:53:26Z C1 VABB-5 73 info:srw/schema/1/mods-v3.3xml journalArticle A1 VirD proteins of Agrobacterium tumefaciens are required for the formation of a covalent DNA-protein complex at the 5' terminus of T-strand molecules Alfredo Herrera-Estrella aut author Zhong-mei Chen aut author Marc Van Montagu aut author ug_WE09 Kan Wang aut author eng The T-DNA transfer process of Agrobacterium tumefaciens is activated by the induction of the Ti plasmid virulence (vir) loci by plant signal molecules such as acetosyringone. Upon initiation of the T-DNA transfer process, site-specific nicks occur at the 25-bp border sequences. This cleavage leads to the generation of a free, linear ssT-DNA molecule which is bound by sequence non-specific VirE proteins. Here we present evidence for the involvement of other acetosyringone-induced proteins in the formation of a covalent complex between the T-strand and protein, designated the T-complex. Alkaline gel-electrophoretic analysis showed that proteins specifically bind to the 5' termini of nicked T-DNA molecules. The T-complex can be formed in Escherichia coli when the VirD1 and VirD2 proteins are expressed. Biology and Life Sciences http://hdl.handle.net/1854/LU-1918729 A1988R465900005 0261-4189 1988 EMBO JOURNAL Embo J. 0261-4189 1988 7 13 4055 4062 1988 I don't know the status of the copyright for this publication published https://biblio.ugent.be/publication/1918729/file/1918734 application/pdf restricted http://www.ncbi.nlm.nih.gov/pmc/articles/PMC455113/?tool=pubmed ug 1918729 2011-09-29T15:43:41Z 2018-11-13T14:51:29Z A1 VABB-1 74 info:srw/schema/1/mods-v3.3xml journalArticle A1 Specific dsDNA recognition by a mimic of the DNA binding domain of the c-Myc/Max transcription factor Yara Ruiz Garcia aut author ug_UGent Y Vladimir Pabon-Martinez aut author CI Edvard Smith aut author Annemieke Madder aut author ug_WE07 0000-0003-0179-7608 eng We here report on the synthesis of the first mimic of the DNA binding domain of the c-Myc/Max-bHLH-ZIP transcription factor able to selectively recognize its cognate E-box sequence 50'-CACGTG-3' through the major groove of the double-stranded DNA. The designed peptidosteroid conjugate was shown to be effective as DNA binder in the presence of excess competitor DNA. Chemistry Biology and Life Sciences PEPTIDE DIMERS MYC-MAX CANCER LIGHT GENE PROTEIN TARGET NANOPARTICLES ONCOPROTEIN THERAPY http://hdl.handle.net/1854/LU-8541271 10.1039/c7cc01705g 000403572100027 1359-7345 1364-548X 2017 CHEMICAL COMMUNICATIONS Chem. Commun. 1359-7345 1364-548X 2017 53 49 6653 6656 2017 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/8541271/file/8541272 application/pdf restricted ug 8541271 2017-12-11T18:38:54Z 2018-11-13T14:56:33Z A1 VABB-1 75 info:srw/schema/1/mods-v3.3xml journalArticle A1 The transcription factor IRF1 and guanylate-binding proteins target activation of the AIM2 inflammasome by Francisella infection Si Ming Man aut author Rajendra Karki aut author RK Subbarao Malireddi aut author Geoffrey Neale aut author Peter Vogel aut author Masahiro Yamamoto aut author Mohamed Lamkanfi aut author ug_GE35 Thirumala-Devi Kanneganti aut author eng Inflammasomes are critical for mounting host defense against pathogens. The molecular mechanisms that control activation of the AIM2 inflammasome in response to different cytosolic pathogens remain unclear. Here we found that the transcription factor IRF1 was required for activation of the AIM2 inflammasome during infection with the Francisella tularensis subspecies novicida (F. novicida), whereas engagement of the AIM2 inflammasome by mouse cytomegalovirus (MCMV) or transfected double-stranded DNA did not require IRF1. Infection of F. novicida detected by the DNA sensor cGAS and its adaptor STING induced type I interferon-dependent expression of IRF1, which drove the expression of guanylate-binding proteins (GBPs); this led to intracellular killing of bacteria and DNA release. Our results reveal a specific requirement for IRF1 and GBPs in the liberation of DNA for sensing by AIM2 depending on the pathogen encountered by the cell. Medicine and Health Sciences HOST-DEFENSE GENE REGULATORY ELEMENTS INNATE IMMUNITY INTRACELLULAR LPS CYTOPLASMIC DNA TULARENSIS CASPASE-11 RECEPTOR INDUCTION RESPONSES http://hdl.handle.net/1854/LU-6895985 10.1038/ni.3118 000353305200009 1529-2908 2015 NATURE IMMUNOLOGY Nat. Immunol. 1529-2908 2015 16 5 467 475 2015 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/6895985/file/6898359 application/pdf restricted ug 6895985 2015-08-05T15:23:06Z 2016-12-19T15:47:04Z A1 VABB-1 76 info:srw/schema/1/mods-v3.3xml journalArticle A1 Library construction for next-generation sequencing: overviews and challenges Steven R Head aut author H Kiyomi Komori aut author Sarah A LaMere aut author Thomas Whisenant aut author Filip Van Nieuwerburgh aut author ug_FW01 Daniel R Salomon aut author Phillip Ordoukhanian aut author eng High-throughput sequencing, also known as next-generation sequencing (NGS), has revolutionized genomic research. In recent years, NGS technology has steadily improved, with costs dropping and the number and range of sequencing applications increasing exponentially. Here, we examine the critical role of sequencing library quality and consider important challenges when preparing NGS libraries from DNA and RNA sources. Factors such as the quantity and physical characteristics of the RNA or DNA source material as well as the desired application (i.e., genome sequencing, targeted sequencing, RNA-seq, ChIP-seq, RIP-seq, and methylation) are addressed in the context of preparing high quality sequencing libraries. In addition, the current methods for preparing NGS libraries from single cells are also discussed. Biology and Life Sciences CHIP-SEQ IN-VIVO GENE-EXPRESSION WIDE IDENTIFICATION ANALYSIS REVEALS EMBRYONIC STEM-CELLS SINGLE-BASE RESOLUTION RNA-BINDING PROTEINS DNA METHYLATION ANALYSIS ChIP-seq RIP-seq RNA-seq DNA-seq deep sequencing DNA RNA library preparation next-generation sequencing NONCODING RNAS http://hdl.handle.net/1854/LU-4416337 10.2144/000114133 000331491800004 0736-6205 2014 BIOTECHNIQUES Biotechniques 0736-6205 2014 56 2 61 77 2014 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/4416337/file/5652224 application/pdf restricted ug 4416337 2014-06-13T15:41:58Z 2018-08-13T14:33:09Z A1 VABB-1 77 info:srw/schema/1/mods-v3.3xml journalArticle A1 Distribution of the rDNA and three classes of highly repetitive DNA in the chromatin of interphase nuclei of Arabidopsis thaliana Distribution of the rDNA and 3 classes of highly repetitive DNA in the chromatin of interphase nuclei of Arabidopsis thaliana Serge Bauwens aut author ug_WE09 Patric Van Oostveldt aut author ug_LA25 Gilbert Engler aut author ug_WE09 Marc Van Montagu aut author ug_WE09 eng The distribution of the ribosomal RNA (rRNA) genes and three classes of highly repetitive DNA in the chromatin of interphase nuclei of Arabidopsis thaliana was studied for the first time through non-isotopic in situ hybridization and luminescence digital imaging microscopy. Each of the three classes of highly repetitive DNA exhibited a characteristic hybridization pattern, and one class was seen to be primarily localized on two chromocentres, which would allow it to distinguish a particular chromosome. The rDNA was consistently localized on the two largest chromocentres and on one or two smaller chromocentres. A limited number of nuclei exhibited more than four labelled chromocentres, indicative of either polypoidy or differential amplification of the rDNA. In nuclei where the nucleolus could be clearly observed, the nucleolar associated chromocentres (NACs) were seen to be labelled by the ribosomal DNA (rDNA) probe. Biology and Life Sciences DROSOPHILA-MELANOGASTER OPTICAL MICROSCOPY SPATIAL-ORGANIZATION FLUORESCENCE INSITU HYBRIDIZATION 3-DIMENSIONAL ORGANIZATION CHROMOSOME DOMAINS SEQUENCE POSITION SITES http://hdl.handle.net/1854/LU-221460 10.1007/BF00360685 A1991GD67600006 0009-5915 1991 CHROMOSOMA Chromosoma 0009-5915 1991 101 1 41 48 1991 published ug 221460 2004-05-24T13:24:00Z 2018-08-23T08:02:26Z A1 VABB-1 78 info:srw/schema/1/mods-v3.3xml journalArticle A1 Complete nucleotide sequence of the T-DNA region of the plant tumour-inducing Agrobacterium tumefaciens Ti plasmid pTiC58 Jan Gielen aut author ug_WE09 Nancy Terryn aut author ug_CA20 Raimundo Villarroel-Mandiola aut author ug_UGent Marc Van Montagu aut author ug_WE09 eng The complete nucleotide sequence has been determined of the T-DNA region from the plant tumour-inducing Agrobacterium tumefaciens nopaline Ti plasmid pTiC58. The T-DNA itself consists of 24 782 bp flanked by two direct 25 bp repeats, the border sequences. In addition, 3622 bp located at the left and 1070 bp at the right of the T-DNA borders were sequenced. Twenty-two open reading frames that code for proteins larger than 125 amino acids have been identified. Biology and Life Sciences sequence T-DNA Agrobacterium tumefaciens http://hdl.handle.net/1854/LU-112647 10.1093/jexbot/50.337.1421 000081942600017 0022-0957 1999 JOURNAL OF EXPERIMENTAL BOTANY J. Exp. Bot. 0022-0957 1999 50 337 1421 1422 1999 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/112647/file/4167609 application/pdf restricted ug 112647 2004-01-14T13:35:00Z 2018-08-13T14:06:11Z A1 VABB-1 79 info:srw/schema/1/mods-v3.3xml journalArticle A1 Laser capture microdissection in forensic research: a review Mado Vandewoestyne aut author ug_FW01 Dieter Deforce aut author ug_FW01 0000-0002-0635-661X eng In forensic sciences, short tandem repeat (STR) analysis has become the prime tool for DNA-based identification of the donor(s) of biological stains and/or traces. Many traces, however, contain cells and, hence, DNA, from more than a single individual, giving rise to mixed genotypes and the subsequent difficulties in interpreting the results. An even more challenging situation occurs when cells of a victim are much more abundant than the cells of the perpetrator. Therefore, the forensic community seeks to improve cell-separation methods in order to generate single-donor cell populations from a mixed trace in order to facilitate DNA typing and identification. Laser capture microdissection (LCM) offers a valuable tool for precise separation of specific cells. This review summarises all possible forensic applications of LCM, gives an overview of the staining and detection options, including automated detection and retrieval of cells of interest, and reviews the DNA extraction protocols compatible with LCM of cells from forensic samples. Science General Sexual assault Forensics Laser capture microdissection Cell separation techniques POLYMERASE-CHAIN-REACTION SEXUAL ASSAULT EVIDENCE IN-SITU HYBRIDIZATION EPITHELIAL-CELLS CHORIONIC VILLI DNA SPERM SPERMATOZOA STAINS SEPARATION http://hdl.handle.net/1854/LU-1019377 10.1007/s00414-010-0499-4 000282826800001 0937-9827 2010 INTERNATIONAL JOURNAL OF LEGAL MEDICINE Int. J. Legal Med. 0937-9827 2010 124 6 513 521 2010 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1019377/file/1862786 application/pdf restricted https://biblio.ugent.be/publication/1019377/file/1019385 application/pdf private ug 1019377 2010-08-09T11:41:34Z 2018-11-13T14:49:24Z A1 VABB-1 80 info:srw/schema/1/mods-v3.3xml journalArticle A1 Synthesis and improved cross-linking properties of C5-modified furan bearing PNAs Joke Elskens aut author ug_WE07 Alex Manicardi aut author ug_WE07 Valentina Costi aut author Annemieke Madder aut author ug_WE07 0000-0003-0179-7608 Roberto Corradini aut author eng Over the past decades, peptide nucleic acid/DNA (PNA:DNA) duplex stability has been improved via backbone modification, often achieved via introducing an amino acid side chain at the - or -position in the PNA sequence. It was previously shown that interstrand cross-linking can further enhance the binding event. In this work, we combined both strategies to fine-tune PNA crosslinking towards single stranded DNA sequences using a furan oxidation-based crosslinking method; for this purpose, -l-lysine and -l-arginine furan-PNA monomers were synthesized and incorporated in PNA sequences via solid phase synthesis. It was shown that the l-lysine -modification had a beneficial effect on crosslink efficiency due to pre-organization of the PNA helix and a favorable electrostatic interaction between the positively-charged lysine and the negatively-charged DNA backbone. Moreover, the crosslink yield could be optimized by carefully choosing the type of furan PNA monomer. This work is the first to describe a selective and biocompatible furan crosslinking strategy for crosslinking of -modified PNA sequences towards single-stranded DNA. Chemistry PNA backbone modification furan crosslinking chiral monomers PEPTIDE NUCLEIC-ACIDS DNA-BINDING IN-VIVO OLIGONUCLEOTIDE RECOGNITION EXPRESSION CELLS RNA CONJUGATION SELECTIVITY http://hdl.handle.net/1854/LU-8541285 10.3390/molecules22112010 000416528400206 1420-3049 2010 2017 MOLECULES Molecules 1420-3049 2017 22 11 2017 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/8541285/file/8541286 application/msword ug 8541285 2017-12-11T20:56:00Z 2018-11-13T14:56:00Z A1 VABB-1 81 info:srw/schema/1/mods-v3.3xml journalArticle A1 Elution behavior of short dsDNA strands in silicon micropillar array columns in ion pair reversed-phase chromatography mode Lei Zhang aut author Bivragh Majeed aut author Frederic Lynen aut author ug_WE07 0000-0002-4690-7690 Chris Van Hoof aut author Wim De Malsche aut author eng In the present paper, dsDNA separation has been studied in a silicon micro-pillar array column using ion-pair reversed-phase HPLC (IP-RP-HPLC). The deep-etched (32.0μm) silicon micro-pillar array was fabricated by advanced deep-UV lithography and by a dedicated Bosch etch process and then sealed by anodic bonding to a Pyrex glass. The pillar surface was subsequently conditioned hydrophobic. Working in isocratic mode under non-retained conditions, van Deemter curves of dsDNA and coumarin were established to assess the performance of the micro-pillar array column, resulting in plate heights of only a few μm. Working in gradient mode, separations of dsDNA fragments were evaluated. The relevant gradient operation parameters were studied to understand their influence on dsDNA separations. The correlation between DNA length and retention was measured and theoretically described in a length range of 50-500bp, promising for the determination of DNA of an unknown length. Finally, a separation example demonstrated the excellent separation power of on-chip IP-RP chromatography by achieving a large operation range of DNA length (10-300bp) with a 5bp difference among 11 dsDNA fragments. Biology and Life Sciences Lab on a chip silicon micro-pillar array column DNA chromatography Ion-pair RP-HPLC PERFORMANCE LIQUID-CHROMATOGRAPHY CAPILLARY-ELECTROPHORESIS MICROFLUIDIC CHIP GRADIENT-ELUTION DNA FRAGMENTS SEPARATION FABRICATION MICROCHIP http://hdl.handle.net/1854/LU-2967148 10.1002/elps.201200226 000310476600012 0173-0835 2012 ELECTROPHORESIS Electrophoresis 0173-0835 2012 33 21 3205 3212 2012 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/2967148/file/2970247 application/pdf restricted https://biblio.ugent.be/publication/2967148/file/2967149 application/msword private ug 2967148 2012-08-02T16:46:13Z 2018-08-13T14:19:54Z A1 VABB-1 82 info:srw/schema/1/mods-v3.3xml journalArticle A1 Construction and characterization of a plasmid containing a nearly full-size DNA copy of bacteriophage MS2 RNA Studies on the bacteriophage MS2, 37 : construction and characterization of a plasmid containing a nearly full-size DNA copy of bacteriophage MS2 RNA Studies on the bacteriophage MS2, XXXVII : construction and characterization of a plasmid containing a nearly full-size DNA copy of bacteriophage MS2 RNA René Devos aut author John Van Emmelo aut author Roland Contreras aut author ug_WE14 Walter Fiers aut author ug_UGent eng Biology and Life Sciences http://hdl.handle.net/1854/LU-1926876 10.1016/0022-2836(79)90295-X A1979GN50700008 0022-2836 1979 JOURNAL OF MOLECULAR BIOLOGY J. Mol. Biol. 0022-2836 1979 128 4 595 619 1979 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1926876/file/1928932 application/pdf; charset=binary restricted ug 1926876 2011-10-13T11:16:04Z 2018-08-13T14:12:13Z A1 VABB-1 83 info:srw/schema/1/mods-v3.3xml journalArticle A1 Genetic and physical map of the pLAFR1 vector E Vanbleu aut author Kathleen Marchal aut author ug_TW05 ug_WE09 0000-0002-2169-4588 J Vanderleyden aut author eng This paper presents the complete sequencing and annotation of the pLAFR1 vector. pLAFR is a tetracycline-resistant "cosmid" cloning vector, which is derived from the 20 kb plasmid pRK290, a RK2-derivative. Due to its broad host range, the pLAFR1 vector has been widely used in the genetic analysis of a broad number of gram-negative bacterial species. The availability of the complete pLAFR1 sequence will most definitely help in the construction and analysis of clone libraries based on pRK290 or pLAFR vectors. Biology and Life Sciences cosmid cloning vector RK2 broad host range RANGE PLASMID RK2 DNA-BINDING-PROTEIN TRANSCRIPTIONAL REPRESSOR ACTIVITY GRAM-NEGATIVE BACTERIA CONJUGATIVE TRANSFER NUCLEOTIDE-SEQUENCE TRANSFER ORIGIN VEGETATIVE REPLICATION ESCHERICHIA-COLI INCP PLASMIDS http://hdl.handle.net/1854/LU-3187224 10.1080/10425170410001723949 000222752000012 1042-5179 2004 DNA SEQUENCE DNA Seq. 1042-5179 2004 15 3 225 227 2004 published ug 3187224 2013-04-08T16:30:10Z 2018-09-25T14:23:54Z A1 VABB-1 84 info:srw/schema/1/mods-v3.3xml journalArticle A1 Mutation of POLG is associated with progressive external ophthalmoplegia characterized by mtDNA deletions Gert Van Goethem aut author Bart Dermaut aut author ug_GE31 ug_UZGent 0000-0003-4090-5181 Ann Löfgren aut author Jean-Jacques Martin aut author Christine Van Broeckhoven aut author eng Progressive external ophthalmoplegias (PEO) characterized by accumulation of large-scale mitochondrial DNA (mtDNA) deletions are rare human diseases. We mapped a new locus for dominant PEO at 15q22-q26 in a Belgian pedigree and identified a heterozygous mutation (Y955C) in the polymerase motif B of the mtDNA polymerase gamma (POLG). We identified three additional POLG missense mutations compatible with recessive PEO In two nuclear families. POLG is the only DNA polymerase responsible for mtDNA replication. Biology and Life Sciences MULTIPLE DELETIONS MITOCHONDRIAL-DNA POLYMERASE REPLICATION DISORDER GAMMA GENE http://hdl.handle.net/1854/LU-3201079 10.1038/90034 000169656400008 1061-4036 2001 NATURE GENETICS Nature Genet. 1061-4036 2001 28 3 211 212 2001 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/3201079/file/3205687 application/pdf restricted ug 3201079 2013-04-24T15:08:59Z 2018-08-13T14:23:04Z A1 VABB-1 85 info:srw/schema/1/mods-v3.3xml journalArticle A1 New platinum(II)-bipyridyl corrole complexes: synthesis, characterization and binding studies with DNA and HSA Bernardo A Iglesias aut author Joana FB Barata aut author Patrícia MR Pereira aut author Henrique Girão aut author Rosa Fernandes aut author João Tomé aut author ug_WE07 Maria GPMS Neves aut author José AS Cavaleiro aut author eng Chemistry Platinum(II) complexes Human serum albumin (HSA) trans-A(2)B corroles Corroles Deoxyribonucleic acid (DNA) Plasmid DNA (pDNA) HUMAN SERUM-ALBUMIN FREE-BASE CORROLES MESOSUBSTITUTED CORROLES MANGANESE(III) CORROLE PLATINUM COMPLEXES FLUORESCENCE BEHAVIOR NUCLEASE ACTIVITY COUPLING REACTION CHARGED CORROLES IN-VITRO http://hdl.handle.net/1854/LU-7140044 10.1016/j.jinorgbio.2015.08.016 000367563200004 0162-0134 2015 JOURNAL OF INORGANIC BIOCHEMISTRY J. Inorg. Biochem. 0162-0134 2015 153 32 41 2015 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/7140044/file/7140055 application/pdf restricted ug 7140044 2016-03-09T13:18:35Z 2016-12-19T15:42:39Z A1 VABB-1 86 info:srw/schema/1/mods-v3.3xml journalArticle A1 Expression of human and murine interleukin-5 in eukaryotic systems Jan Tavernier aut author ug_GE31 0000-0002-7609-6462 René Devos aut author José Van der Heyden aut author Guido Hauquier aut author Rita Bauden aut author Ina Faché aut author Eric Kawashima aut author Joël Vandekerckhove aut author ug_UGent Roland Contreras aut author ug_WE14 Walter Fiers aut author ug_UGent eng Biology and Life Sciences http://hdl.handle.net/1854/LU-1925642 10.1089/dna.1.1989.8.491 A1989AN97200004 0198-0238 1989 DNA-A JOURNAL OF MOLECULAR & CELLULAR BIOLOGY DNA 0198-0238 1989 8 7 491 501 1989 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1925642/file/7775134 application/pdf restricted https://biblio.ugent.be/publication/1925642/file/1927832 application/pdf; charset=binary private ug 1925642 2011-10-13T11:16:04Z 2018-08-13T14:12:11Z A1 VABB-1 87 info:srw/schema/1/mods-v3.3xml journalArticle A1 An Agrobacterium-transformed cell culture from the monocot Asparagus officinalis Jean-Pierre Hernalsteens aut author Lin Thia-Toong aut author Jeff Schell aut author Marc Van Montagu aut author ug_WE09 eng Cultured stem fragments from the monocotyledonous plant Asparagus officinalis infected by the oncogenic bacterium Agrobacterium tumefaciens developed tumorous proliferations. This tissue was propagated in vitro on hormone-free culture medium. The T-DNA-encoded markers nopaline and agrocinopine were unambiguously detected in these tissues. The data demonstrate that stable T-DNA transfer as well as expression of T-DNA genes is possible in at least some monocotyledonous plants. This opens new possibilities for plant genetic engineering using the Ti plasmid as a gene vector. Biology and Life Sciences nopaline agrocinopine opines transformation monocotyledons Asparagus officinalis asparagus Agrobacterium tumefaciens http://hdl.handle.net/1854/LU-6930721 A1984TX37100001 0261-4189 1984 EMBO JOURNAL EMBO J. 0261-4189 1984 3 13 3039 3041 1984 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/6930721/file/6930816 application/pdf restricted http://www.ncbi.nlm.nih.gov/pmc/articles/PMC557813/ ug 6930721 2015-09-15T13:55:15Z 2016-12-19T15:38:54Z A1 VABB-1 88 info:srw/schema/1/mods-v3.3xml dissertation D1 Exploring the neuroblastoma DNA methylome: from biology to biomarker Anneleen Decock aut author ug_GE31 0000-0002-1091-0927 Jo Vandesompele promoter ug_GE31 0000-0001-6274-0184 Franki Speleman promoter ug_GE31 ug_UZGent 0000-0002-6628-8559 Maté Ongenaert promoter ug_GE02 eng Neuroblastoma (NB), a childhood tumor arising from immature sympathetic nervous system cells, is a heterogeneous disease with prognosis ranging from excellent long-term survival to high-risk with fatal outcome. In order to determine the most appropriate treatment modality, patients are stratified into risk groups at the time of diagnosis, based on combinations of clinical and biological parameters, namely age of the patient, tumor stage, histology, grade of differentiation, MYCN oncogene amplification, chromosome 11q aberration and DNA ploidy. However, use of this risk classification system has shown that accurate assessment of NB prognosis remains difficult and that additional prognostic markers are warranted. Therefore, we aimed to identify prognostic tumor DNA methylation biomarkers for NB. To find new biomarkers, we profiled the primary tumor DNA methylome using methyl-CpG-binding domain (MBD) sequencing, i.e. massively parallel sequencing of methylation-enriched DNA fractions, captured using the high affinity of MBD to bind methylated cytosines. As proof of principle, we applied this technology to 8 NB cell lines, and in combination with mRNA expression studies, this led to a first selection of 43 candidate biomarkers. Next, methylation-specific PCR (MSP) assays were designed, to allow candidate-specific methylation analysis in a primary tumor cohort of 89 samples. As such, we identified new prognostic DNA methylation biomarkers, and delineated the technological aspects and data analysis pipeline to set up a more extended biomarker study. In this follow-up study, the DNA methylome of 102 primary tumors, selected for risk classification and survival, was characterized by MBD sequencing. Differential methylation analyses between the prognostic patient groups put forward 78 top-ranking biomarker candidates, which were subsequently tested on two independent cohorts of 132 and 177 samples, adopting the high-throughput MSP pipeline of our pilot study. Multiple individual MSP assays were prognostically validated and through the implementation of a newly developed statistical framework, a robust 58-marker methylation signature predicting overall and event-free survival was established. This study represents the largest DNA methylation (biomarker) study in NB so far. The MBD sequencing data were shared with the research community through the format of a data descriptor. As such, these data are fully available to others, ensuring its reusability for other research purposes. To illustrate how these data can be applied to gain new insights into the NB pathology, we characterized the DNA methylome of stage 4S NB, a special type of NB found in infants with widespread metastases at diagnosis that paradoxically is associated with an excellent outcome due to its remarkable capacity to undergo spontaneous regression. More specifically, we compared promoter methylation levels between stage 4S, stage 1/2 (localized disease with favorable prognosis) and stage 4 (metastatic disease with dismal prognosis) tumors, and showed that specific chromosomal locations are enriched in stage 4S differentially methylated promoters and that specific subtelomeric promoters are hypermethylated in stage 4S. Furthermore, genes involved in important oncogenic pathways, in neural crest development and differentiation, and in epigenetic processes are differentially methylated and expressed in stage 4S. In conclusion, by exploring the DNA methylome of NB, we have not only demonstrated that DNA methylation patterns are intimately related to NB biology, but also found additional clinically relevant prognostic biomarkers. Medicine and Health Sciences DNA methylation neuroblastoma prognostic biomarker http://hdl.handle.net/1854/LU-8109145 Ghent, Belgium Ghent University. Faculty of Medicine and Health Sciences 2016 I have transferred the copyright for this publication to the publisher published Gent : Aula Universiteit https://biblio.ugent.be/publication/8109145/file/8109215 application/pdf restricted(changes to open on 2019-11-08) ug 8109145 2016-10-11T09:28:10Z 2017-01-16T10:52:29Z D1 89 info:srw/schema/1/mods-v3.3xml journalArticle A1 Impact of allelic dropout on evidential value of forensic DNA profiles Filip Van Nieuwerburgh aut author ug_FW01 Els Goetghebeur aut author ug_CA05 ug_WE02 ug_WE56 Mado Vandewoestyne aut author ug_FW01 Dieter Deforce aut author ug_FW01 0000-0002-0635-661X eng Motivation: Two methods are commonly used to report on evidence carried by forensic DNA profiles: the 'Random Man Not Excluded' (RMNE) approach and the likelihood ratio (LR) approach. It is often claimed a major advantage of the LR method that dropout can be assessed probabilistically. Results: In this article, a new RMNE measure is proposed that likewise accounts for allelic dropout in an observed forensic DNA pro. le. We discuss the necessary calculations, underline their simplicity and provide a tool for performing the calculations. mixtures http://hdl.handle.net/1854/LU-515180 10.1093/bioinformatics/btn608 000262518300011 1367-4803 2009 BIOINFORMATICS 1367-4803 2009 25 2 225 229 2009 published https://biblio.ugent.be/publication/515180/file/515192 application/pdf ug 515180 2009-03-06T12:12:11Z 2018-08-13T14:34:09Z A1 VABB-1 90 info:srw/schema/1/mods-v3.3xml journalArticle A1 DNA replication in plants: characterization of a cdc6 homologue from Arabidopsis thaliana GBA Ramos aut author Janice de Almeida Engler aut author ug_WE09 PCG Ferreira aut author Adriana S Hemerly aut author ug_WE09 eng Cdc6 is a key regulator of DNA replication in eukaryotes. In this work, the expression pattern of an Arabidopsis cdc6 homologue is characterized by RT-PCR and in situ hybridization. The data suggest that cdc6At expression is cell cycle regulated. During development, high cdc6At mRNA levels are found in regular cycling cells. In addition, cdc6At expression is also observed in cells that are probably undergoing endoreduplication, suggesting a possible role of Cdc6At in this process in plants. Biology and Life Sciences PROTEIN INITIATION GROWTH S-PHASE FISSION YEAST SACCHAROMYCES-CEREVISIAE BUDDING YEAST prereplication complex DNA replication Arabidopsis thaliana CDC6 http://hdl.handle.net/1854/LU-169934 10.1093/jexbot/52.364.2239 000171847400020 0022-0957 2001 JOURNAL OF EXPERIMENTAL BOTANY J. Exp. Bot. 0022-0957 2001 52 364 2239 2240 2001 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/169934/file/4148128 application/pdf restricted ug 169934 2004-01-14T13:40:00Z 2018-08-13T14:10:51Z A1 VABB-1 91 info:srw/schema/1/mods-v3.3xml journalArticle A1 Synthesis and incorporation of a furan-modified adenosine building block for DNA interstrand crosslinking Anup M Jawalekar aut author Marieke Op de Beeck aut author ug_UGent Floris L van Delft aut author Annemieke Madder aut author ug_WE07 0000-0003-0179-7608 eng 2'-O-(3-(Furan-2-yl)propyl)adenosine was synthesized and evaluated for interstrand crosslink (ICL) formation in DNA duplexes. In situ oxidation of the furan moiety with NIS showed rapid crosslink formation to dA and dC, while dT and dG were inactive. Chemistry RIBOSOME OXIDATION BASE DUPLEXES MODIFIED OLIGONUCLEOTIDES LINKED DNA RNA DERIVATIVES http://hdl.handle.net/1854/LU-1854819 10.1039/c0cc04667a 000287530700007 1359-7345 2011 CHEMICAL COMMUNICATIONS Chem. Commun. 1359-7345 2011 47 10 2796 2798 2011 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/1854819/file/1895681 application/pdf ug 1854819 2011-07-08T03:21:11Z 2018-08-13T14:11:32Z A1 VABB-1 92 info:srw/schema/1/mods-v3.3xml journalArticle A2 New method for electrochemical detection of proteins and nucleic acids Stanislav Trashin aut author ug_LA07 Mikhail Yu Vagin aut author Galina P Karpacheva aut author SZ Ozkan aut author Arkady A Karyakin aut author rus A new approach to detection of proteins and DNA based on the use of electrodes shielded by thin liquid organic film is proposed. The possibility of electrochemical registration of proteins, due to their extraction into organic medium is demonstrated. The effect is useful for protein analytical determination. Using shielded electrodes, a new method of label-free electrochemical DNA registering was elaborated. High sensitivity sufficient to distinguish a single point mutation in an oligonucleotide is the feature of the new approach. Technology and Engineering biosensors biochemistry electrochemical electrodes electrochemical sensors liquid films molecular biophysics proteins thin film sensors electrochemical detection protein extraction nucleic acid electrode shielding thin liquid organic film label-free electrochemical DNA single-point mutation oligonucleotide http://hdl.handle.net/1854/LU-871287 1813-8586 2008 JOURNAL OF NANO AND MICROSYSTEM TECHNIQUE J. Nano Microsyst. Tech. 1813-8586 2008 8 49 54 2008 published ug 871287 2010-02-19T16:36:27Z 2018-06-26T11:32:13Z A2 VABB-1 93 info:srw/schema/1/mods-v3.3xml journalArticle A1 Modular cloning in plant cells Mansour Karimi aut author ug_WE09 0000-0002-0246-9318 Björn De Meyer aut author ug_WE09 Pierre Hilson aut author ug_WE09 eng New plant genes are being discovered at a rapid pace. Yet, in most cases, their precise function remains elusive. The recent advent of recombinational cloning techniques has significantly improved our ability to investigate gene functions systematically. For example, proteins fused with diverse fluorescent tags can be expressed at will using versatile cloning cassettes. In addition, novel binary T-DNA vectors are now available to assemble multiple DNA fragments simultaneously, which greatly facilitate plant cell and protein engineering. Biology and Life Sciences SITE-SPECIFIC RECOMBINATION ARABIDOPSIS FUNCTIONAL GENOMICS TRANSCRIPTION FACTOR ORFEOME CLONING DNA CLONING PROTEINS SYSTEM GENES http://hdl.handle.net/1854/LU-331318 10.1016/j.tplants.2005.01.008 000227934900001 1360-1385 2005 TRENDS IN PLANT SCIENCE Trends Plant Sci. 1360-1385 2005 10 3 103 105 2005 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/331318/file/3075895 application/pdf restricted ug 331318 2006-04-14T13:32:00Z 2018-08-13T14:24:10Z A1 VABB-1 94 info:srw/schema/1/mods-v3.3xml conference P1 Statechart DNA Benjamin De Leeuw aut author Albert Hoogewijs aut author ug_WE01 Nikos Mastorakis edt editor 10th WSEAS International Conference on Automation & Information (ICAI'09) eng We introduce and explore a new statechart (sc) abstraction method and define a simplified statechart (ssc) model. We study the basic building blocks (so the term `DNA') of UML sc models. Within this formal approach, we untangle the object-oriented concepts characterizing the UML. We treat triggers, guards and effects as related to each other, but make no reference to any explicit value (type) in the computation. This abstract approach allows us to introduce mathematical manipulations of UML sc, in line with the theory of regular automata. Statechart DNA has been applied in defining complexity metrics for UML sc models, the automatic generation of model test cases and behavior manipulations in CASE tool environments. Technology and Engineering State machine versioning UML Statecharts Model checking http://hdl.handle.net/1854/LU-610262 000265594700046 1790-5117 2009 Recent advances in Electrical Engineering 1790-5117 WSEAS 2009 293 299 2009 I have transferred the copyright for this publication to the publisher published ug 610262 2009-05-08T09:26:28Z 2016-12-19T15:35:08Z P1 VABB-5 95 info:srw/schema/1/mods-v3.3xml conference C3 Comprehensive longitudinal characterization of HIV-1 reservoir markers in patients on stable antiretroviral treatment Maja Kiselinova aut author Ward De Spiegelaere aut author ug_DI03 0000-0003-2097-8439 Maria Jose Buzon aut author Eva Malatinková aut author ug_GE35 Mathias Lichterfeld aut author Linos Vandekerckhove aut author ug_GE32 ug_GE35 ug_UZGent 13th European meeting on HIV & Hepatitis: Treatment strategies and antiviral drug resistance eng Background: There is an increasing interest in characterisation of the viral reservoir in patients on long-term antiretroviral therapy in the context of HIV cure studies. The main question remains which assay is most relevant to accurately predict the size of the replication competent viral reservoir. Although both PCR and viral outgrowth assays have been proposed, mainly PCR based assays have been validated in clinical trials. Conflicting data exists about the correlation of viral outgrowth assays and PCR based assays. In addition, within individual patients, the long term variability of PCR reservoir markers of total HIV DNA, 2LTR circles and full length cell-associated (CA) RNA is poorly addressed. Materials and Methods: We set-up a study with a well-defined patient cohort (N=25) to characterize the longitudinal kinetics of the viral reservoir by PCR based methods and to assess the correlation of the viral reservoir markers with the viral outgrowth assay. Blood samples were drawn at three time points with median (IQR) of 2.5 years (IQR 2.4-2.6) between time point 1 and 2; and median of 31 days (28-36) between time point 2 and 3. Total HIV-1 DNA, unspliced (us-) and multiply spliced (ms-) HIV-1 RNA, and 2LTR circles were quantified in peripheral blood mononuclear cells (PBMCs) using droplet digital PCR. Parameters of HIV-1 persistence were quantified at 3 time points. Alu-PCR was used to quantify integrated HIV-1 DNA. Viral outgrowth assay and integrated HIV-1 DNA were performed at one time point (2nd time point). Results: No significant change was found for long- and short-term dynamics of all markers (total HIV-1 DNA, unspliced and multiply spliced HIV-1 RNA, and 2LTR circles) of HIV-1 persistence in peripheral blood. Integrated HIV-1 DNA was detected in all patients with median (IQR) of 3.04 (2.65-3.37) log10 copies/10⁶ PBMCs; and it correlated well with total HIV-1 DNA (p=0.002, R²=0.54); unspliced HIV-1 RNA (p=0.001, R²=0.40); and viral outgrowth assay (p=0.014, R²=0.20). Replication competent virus was detected in 80% (20/25) of patients and it correlated well with total HIV-1 DNA (p=0.017, R²=0.54). The mean difference (bias) between the HIV copy numbers generated with Alu-PCR and viral outgrowth assay, assessed with Bland-Altman test, was 2.38 ± 0.83 log10 (95% Limits of Agreement). And a corresponding bias between total HIV-1 DNA and VOA was 0.8 ± 0.72 log10 (95% Limits of Agreement). Conclusion: This study supports the finding that viral reservoir size and long- and short-term dynamics remain stable over time in patients receiving stable cART. Our study shows the presence of a very stable reservoir in terms of viral dynamics (2LTR circles and CA RNA) in patient under ART. Interestingly, we found a correlation between integrated HIV DNA and the viral outgrowth assay, indicating that a stable fraction of integrated HIV is replication competent. Medicine and Health Sciences HIV-1 integrated HIV-1 DNA viral outgrowth assay total HIV-1 DNA http://hdl.handle.net/1854/LU-6858912 2015 HIV & Hepatitis, 13th European meeting, Abstracts 2015 2015 published ug 6858912 2015-07-01T23:55:20Z 2016-12-19T15:36:58Z C3 96 info:srw/schema/1/mods-v3.3xml conference C3 Quantification of integrated HIV DNA by repetitive sampling Alu-HIV PCR and Poisson statistics Ward De Spiegelaere aut author ug_DI03 0000-0003-2097-8439 Eva Malatinková aut author ug_GE35 Filip Van Nieuwerburgh aut author ug_FW01 Una O'Doherty aut author Linos Vandekerckhove aut author ug_GE32 ug_GE35 ug_UZGent 6th International workshop on HIV Persistence, Reservoirs and Eradication Strategies eng Medicine and Health Sciences Alu digital PCR HIV Poisson statistics Proviral DNA integrated HIV DNA http://hdl.handle.net/1854/LU-5704817 2013 HIV Persistence, Reservoirs and Eradication Strategies, 6th International workshop 2013 2013 I have retained and own the full copyright for this publication published https://biblio.ugent.be/publication/5704817/file/5704821 application/pdf ug 5704817 2014-09-18T14:29:41Z 2018-08-13T14:35:01Z C3 97 info:srw/schema/1/mods-v3.3xml conference C3 Transfer and expression of foreign genes in plants Jeff Schell aut author Marc Van Montagu aut author ug_WE09 Jean-Pierre Hernalsteens aut author Lothar Willmitzer aut author Jan Leemans aut author Henk Joos aut author Leon Otten aut author Henri De Greve aut author Marcella Holsters aut author ug_WE09 Patricia Zambryski aut author ug_WE09 Luis Herrera-Estrella aut author Anna Depicker aut author ug_WE09 0000-0003-0105-7407 3rd Annual congress for Recombinant DNA Research eng Biology and Life Sciences http://hdl.handle.net/1854/LU-6889715 10.1089/dna.1983.2.165 A1983QT91200010 0198-0238 1983 DNA - A JOURNAL OF MOLECULAR & CELLULAR BIOLOGY DNA J. Mol. Cellul. Biol. 0198-0238 1983 2 2 165 165 1983 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/6889715/file/6918584 application/pdf restricted ug 6889715 2015-07-29T17:22:20Z 2016-12-19T15:36:58Z C3 98 info:srw/schema/1/mods-v3.3xml journalArticle A1 Hairy root production in Arabidopsis thaliana: cotransformation with a promoter-trap vector results in complex T-DNA integration patterns Mansour Karimi aut author ug_WE09 0000-0002-0246-9318 Marc Van Montagu aut author ug_WE09 Godelieve Gheysen aut author ug_LA25 0000-0003-1929-5059 eng In comparison with the production of transgenic plants, the generation of hairy roots has the advantage that more independent transgenic lines can be produced in a shorter period of time. Therefore, we wanted to combine this approach with the promoter-trapping strategy to identify nematode-induced plant promoters. For the efficient production and culture of transgenic hairy root lines of Arabidopsis thaliana, the standard Agrobacterium rhizogenes transformation procedure was modified to avoid rapid callusing of the hairy roots. An average of 0.72 independent kanamycin-resistant (Km(R)) roots were obtained per leaf piece. However, a much lower frequency of reporter gene activation was obtained than expected from experiments with the same vectors in Agrobacterium tumefaciens: of more than 700 independent Km(R) hairy roots tested, only 8 were beta-glucuronidase (GUS) positive. DNA hybridization was done on ten hairy root lines, of which one had a single truncated T-DNA and the others multiple copies of T-DNA that led to complex hybridization patterns. In a parallel analysis of A. thaliana plants transformed with the same vectors using A. tumefaciens, relatively simple T-DNA integration patterns were obtained. The low occurrence of GUS-positive hairy root lines in our experiments could be explained by the multiple T-DNA copies, especially in inverted array, that result in high frequencies of gene inactivation. Biology and Life Sciences Arabidopsis thaliana Agrobacterium rhizogenes hairy root promoter trapping AGROBACTERIUM-RHIZOGENES TRANSGENE EXPRESSION BETA-GLUCURONIDASE CHALCONE SYNTHASE PHYSICAL MAP SINGLE-COPY MARKER GENE PLANTS TUMEFACIENS SEQUENCES http://hdl.handle.net/1854/LU-170285 10.1007/s002990050723 000084314200006 0721-7714 1999 PLANT CELL REPORTS Plant Cell Reports 0721-7714 1999 19 2 133 142 1999 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/170285/file/4169109 application/pdf restricted ug 170285 2004-01-14T13:40:00Z 2018-08-13T14:10:51Z A1 VABB-1 99 info:srw/schema/1/mods-v3.3xml journalArticle A1 Turkeys are protected from infection with Chlamydia psittaci by plasmid DNA vaccination against the major outer membrane protein Daisy Vanrompay aut author ug_LA22 Eric Cox aut author ug_DI04 0000-0003-4281-2990 Guido Volckaert aut author Bruno Goddeeris aut author ug_UGent eng Plasmid DNA expressing the major outer membrane protein (MOMP) of an avian Chlamydia psittaci serovar A strain has been tested for its ability to raise an immune response and induce protection against challenge with the same serovar. A combined parenteral (intramuscular injection) and mucosal route (DNA drops administered to the nares) of DNA inoculation was compared with gene gun-based immunization. The gene gun delivery of pcDNA1/MOMP as well as the intramuscular-intranasal DNA delivery primed both T-helper and B cell memory, although rMOMP-expressing cells did not induce high antibody responses. Evidence for the priming of the memory was provided by the fact that the pcDNA1/MOMP inoculations raised antibodies belonging to the IgG and not IgM isotype. However, in response to challenge only five out of 15 vaccinated turkeys showed four-fold increases in serum IgG after challenge. By contrast, evidence for the priming of T cell memory in response to challenge was found in all vaccinated turkeys, as shown by the significantly heightened proliferative responses of peripheral blood lymphocytes following vaccination. Both immunization methods produced similar serological and lymphocyte proliferative responses. Notwithstanding the immunization method, a significant level of protection was observed in all pcDNA1/MOMP-immunized turkeys. The efficacy of MOMP-based DNA vaccination as a means of preventing severe clinical signs, lesions and chlamydia excretion in a turkey model of C. psittaci infection was demonstrated. Biology and Life Sciences MURINE MODEL MONOCLONAL-ANTIBODIES TRACHOMATIS IMMUNITY CELLS IMMUNIZATION EFFICACY VACCINES GENE KNOCKOUT MICE GENITAL-TRACT INFECTION turkeys vaccination chlamydia http://hdl.handle.net/1854/LU-118906 000083180000008 0009-9104 1999 CLINICAL AND EXPERIMENTAL IMMUNOLOGY Clin. Exp. Immunol. 0009-9104 1999 118 1 49 55 1999 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/118906/file/4269017 application/pdf restricted ug 118906 2004-01-14T13:35:00Z 2018-08-13T14:07:13Z A1 VABB-1 100 1.1dna101100srw.ServerChoicescrdna