1.1 5431 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Henk Joos aut author Dirk Inzé aut author ug_WE09 0000-0002-3217-8407 Allan Caplan aut author ug_WE09 Monika Sormann aut author Marc Van Montagu aut author ug_WE09 Jeff Schell aut author eng Plant crown gall tumor cells result from the insertion and expression of a defined DNA sequence, called T-DNA, which is derived from the Ti plasmid, harbored by Agrobacterium tumefaciens strains. To study the function of the genes of the T-DNA of the nopaline Ti plasmid, pTiC58, a collection of mutants was isolated so that T-DNA genes are inactivated either separately or in various combinations. It was found that no single T-DNA gene or T-region border is absolutely essential for stable tumor formation. We have identified the gene responsible for synthesis in transformed cells of the phosphorylated sugar, agrocinopine, and at least three additional genes controlling the morphology of plant tumors. Two of these latter genes work together to inhibit shoot formation and ensure efficient tumorous growth. Inactivation of these genes can be suppressed by the addition of auxins. The third gene inhibits root formation and appears to play a role in the cytokinin-independent growth of transformed cells. Mutants missing all three genes do not induce tumors, nor shoot or root formation, although the mutant T-DNA sequence is transferred to plant cells. Biology and Life Sciences http://hdl.handle.net/1854/LU-6889730 10.1016/0092-8674(83)90290-8 A1983QN11800011 0092-8674 1983 0092-8674 1983 32 4 1057 1067 1983 No license (in copyright) published https://biblio.ugent.be/publication/6889730/file/6890562 application/pdf restricted ug 6889730 2015-07-29T17:22:33Z 2026-03-31T14:21:28Z A1 VABB-1 1 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Virginie Mortier aut author ug_GE32 0000-0002-9376-8910 Els Demecheleer aut author ug_GE32 Delfien Staelens aut author ug_GE32 Marlies Schauvliege aut author ug_GE32 Kenny Dauwe aut author ug_UGent Sylvie Dinakis aut author ug_GE32 Laura Hebberecht aut author Leen Vancoillie aut author ug_UGent Chris Verhofstede aut author ug_GE32 0000-0002-0645-1174 eng Background: Successfully treated HIV-1 infected patients have a sustained undetectable viral RNA load. In these cases the total HIV-1 DNA load may constitute a valuable tool to further follow the overall viral burden. The value of this marker outside of cure research has been rarely studied. Objectives: To develop a quantitative (q)PCR for total HIV-1 DNA quantification in buffy coat cells and to evaluate the value of this parameter in clinical follow-up. Study design: A qPCR using primers and a probe in the conserved HIV-1 LTR region was adapted for use on DNA extracted from buffy coat cells. Sensitivity, accuracy and reproducibility were evaluated using 8E5 cells and samples from naive and treatment experienced patients. The clinical value of DNA load analysis was assessed by testing 119 longitudinal samples from 9 patients before and after ART initiation and 249 cross sectional samples from therapy-experienced patients. Results: Inter- and intra-assay coefficients of variability were 5.56 and 5.94 (%CV). HIV-1 DNA was detected in 249 of the 263 (94.7%) patients on ART for at least 5 months (median: 53 months; IQR: 28-84 months). The HIV-1 DNA load varied between 0.60 and 3.37 copies/10(6) blood cells and showed significant correlation with the pre-ART CD4(+) T-cell count nadir and peak viral RNA load. ART initiation resulted in a slow and limited decline of the total HIV-1 DNA concentration. Conclusions: Quantification of total HIV-1 DNA from buffy coat cells is feasible, sensitive and reliable. Although determination of the on-therapy HIV-1 DNA load may be informative, regular testing has limited clinical value because of the very slow evolution. Medicine and Health Sciences Biology and Life Sciences HIV-1 DNA-load Provirus HIV-1 DNA quantification SUPPRESSIVE ANTIRETROVIRAL THERAPY REAL-TIME PCR STRUCTURED TREATMENT INTERRUPTIONS BLOOD MONONUCLEAR-CELLS CD4(+) T-CELLS DARUNAVIR/RITONAVIR MONOTHERAPY RESERVOIR IMPLICATIONS DISEASE PROGRESSION VIRAL REPLICATION IN-VIVO http://hdl.handle.net/1854/LU-8576068 10.1016/j.jcv.2018.07.008 000442361000014 1386-6532 2018 1386-6532 2018 106 58 63 2018 No license (in copyright) published https://biblio.ugent.be/publication/8576068/file/8615210 application/pdf ug 8576068 2018-10-04T09:02:35Z 2023-05-08T11:47:47Z A1 VABB-1 2 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Mieke Uyttendaele aut author ug_LA23 0000-0002-3134-8929 R Schukkink aut author B van Gemen aut author Johan Debevere aut author 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 0167-7012 1996 26 1-2 133 138 1996 published ug 189438 2004-01-14T13:41:00Z 2026-03-31T07:38:16Z A1 VABB-1 3 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 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 2026-03-31T13:12:45Z A1 VABB-1 4 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Marie-Alice Fraiture aut author ug_UGent Philippe Herman aut author Isabel Taverniers aut author Marc De Loose aut author ug_UGent Filip Van Nieuwerburgh aut author ug_FW01 0000-0001-8815-5485 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 0308-8146 2015 173 1259 1265 2015 No license (in copyright) published https://biblio.ugent.be/publication/5912308/file/6874110 application/pdf ug 5912308 2015-03-25T10:14:16Z 2026-03-31T14:17:20Z A1 VABB-1 5 info:srw/schema/1/mods-v3.3xml journalArticle Review A1 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_UGent 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 1750-1911 2014 6 6 603 622 2014 No license (in copyright) 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 2026-03-31T14:17:51Z A1 VABB-1 6 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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_UGent 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 21 p. 2010 1465-7392 2010 12 6 572 582 2010 No license (in copyright) published https://biblio.ugent.be/publication/998269/file/2937355 application/pdf restricted ug 998269 2010-06-30T14:12:16Z 2026-03-31T14:53:37Z A1 VABB-1 7 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Sandy Vanderauwera aut author ug_WE09 Nobuhiro Suzuki aut author Gad Miller aut author Brigitte Van De Cotte aut author ug_UGent 0000-0001-7236-9243 Stijn Morsa aut author ug_WE09 Jean-Luc Ravanat aut author Alicia Hegie aut author Christian Triantaphylides aut author Vladimir Shulaev aut author Marc Van Montagu aut author ug_WE09 Frank Van Breusegem aut author ug_WE09 0000-0002-3147-0860 Ron Mittler aut author eng Eukaryotic organisms evolved under aerobic conditions subjecting nuclear DNA to damage provoked by reactive oxygen species (ROS). Although ROS are thought to be a major cause of DNA damage, little is known about the molecular mechanisms protecting nuclear DNA from oxidative stress. Here we show that protection of nuclear DNA in plants requires a coordinated function of ROS-scavenging pathways residing in the cytosol and peroxisomes, demonstrating that nuclear ROS scavengers such as peroxiredoxin and glutathione are insufficient to safeguard DNA integrity. Both catalase (CAT2) and cytosolic ascorbate peroxidase (APX1) play a key role in protecting the plant genome against photorespiratory-dependent H2O2-induced DNA damage. In apx1/cat2 double-mutant plants, a DNA damage response is activated, suppressing growth via a WEE1 kinase-dependent cell-cycle checkpoint. This response is correlated with enhanced tolerance to oxidative stress, DNA stress-causing agents, and inhibited programmed cell death. Biology and Life Sciences hydrogen peroxide Arabidopsis stress tolerance http://hdl.handle.net/1854/LU-1188895 10.1073/pnas.1018359108 000286594800091 0027-8424 2011 0027-8424 2011 108 4 1711 1716 2011 No license (in copyright) published https://biblio.ugent.be/publication/1188895/file/3148713 application/pdf restricted ug 1188895 2011-03-15T14:25:12Z 2026-03-31T07:13:23Z A1 VABB-1 8 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 0000-0002-8427-4775 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 17 p.

2018 0261-4189 1460-2075 2018 37 8 2018 No license (in copyright) published https://biblio.ugent.be/publication/8561178/file/8561182 application/pdf restricted ug 8561178 2018-05-07T15:30:51Z 2023-05-08T11:47:12Z A1 VABB-1 9 info:srw/schema/1/mods-v3.3xml journalArticle Review A1 Liesbeth Everix aut author Shankari Nair aut author Cathryn H. S. Driver aut author Ingeborg Goethals aut author ug_GE32 0000-0001-7432-4452 Mike M. Sathekge aut author Thomas Ebenhan aut author Charlot Vandevoorde aut author Julie Bolcaen aut author eng Simple Summary The current routine treatment for glioblastoma (GB), the most lethal high-grade brain tumor in adults, aims to induce DNA damage in the tumor. However, the tumor cells might be able to repair that damage, which leads to therapy resistance. Fortunately, DNA repair defects are common in GB cells, and their survival is often based on a sole backup repair pathway. Hence, targeted drugs inhibiting essential proteins of the DNA damage response have gained momentum and are being introduced in the clinic. This review gives a perspective on the use of radiopharmaceuticals targeting DDR kinases for imaging in order to determine the DNA repair phenotype of GB, as well as for effective radionuclide therapy. Finally, four new promising radiopharmaceuticals are suggested with the potential to lead to a more personalized GB therapy. Despite numerous innovative treatment strategies, the treatment of glioblastoma (GB) remains challenging. With the current state-of-the-art therapy, most GB patients succumb after about a year. In the evolution of personalized medicine, targeted radionuclide therapy (TRT) is gaining momentum, for example, to stratify patients based on specific biomarkers. One of these biomarkers is deficiencies in DNA damage repair (DDR), which give rise to genomic instability and cancer initiation. However, these deficiencies also provide targets to specifically kill cancer cells following the synthetic lethality principle. This led to the increased interest in targeted drugs that inhibit essential DDR kinases (DDRi), of which multiple are undergoing clinical validation. In this review, the current status of DDRi for the treatment of GB is given for selected targets: ATM/ATR, CHK1/2, DNA-PK, and PARP. Furthermore, this review provides a perspective on the use of radiopharmaceuticals targeting these DDR kinases to (1) evaluate the DNA repair phenotype of GB before treatment decisions are made and (2) induce DNA damage via TRT. Finally, by applying in-house selection criteria and analyzing the structural characteristics of the DDRi, four drugs with the potential to become new therapeutic GB radiopharmaceuticals are suggested. Medicine and Health Sciences Biology and Life Sciences Cancer Research Oncology nuclear medicine radiopharmaceuticals targeted radionuclide therapy glioblastoma radiochemistry theranostics http://hdl.handle.net/1854/LU-01GS546VHYFRCPR631K1S16AEW 10.3390/cancers14071821 000782212000001 2072-6694 1821 32 p. 2022 2072-6694 MDPI AG 2022 14 7 2022 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/01GS546VHYFRCPR631K1S16AEW/file/01GS54BNXG8SNXQWCAE65H3EQA application/pdf ug 01GS546VHYFRCPR631K1S16AEW 2023-02-13T10:12:58Z 2026-03-31T08:19:06Z A1 VABB-1 10 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Leandro MO Lourenço aut author Bernardo A Iglesias aut author Patrícia MR Pereira aut author Henrique Girão aut author Rosa Fernandes aut author Maria GPMS Neves aut author José AS Cavaleiro aut author João Tomé aut author ug_UGent eng The new complexes tetra-platinum(II)-thiopyridylporphyrin 3 and tetra-platinum(II)-thiopyridylporphyrinato Zn(II) 4 were obtained by coordination of the peripheral thiopyridyl units of the free-base 5,10,15,20-tetrakis[2,3,5,6-tetrafluoro-4-(4-pyridylsulfanyl) phenyl] porphyrin 1 or their corresponding zinc complex 2, respectively, with four chloro(2,2'-bipyridine) platinum(II) [Pt(bpy)Cl](+) units. Both compounds were characterized by several spectroscopic techniques demonstrating a particular behaviour in the emission spectra due to the absence or presence of zinc. The tetra-platinum(II)-thiopyridylporphyrins exhibited an increase in the emission quantum yield when compared with the starting thiopyridylporphyrins 1 and 2. Spectroscopic studies of both platinum derivatives reveal their ability to interact unequivocally with DNA from calf thymus and DNA of low molecular weight from salmon sperms, and also with the most abundant protein in human blood plasma, human serum albumin (HSA). Herein, both tetra-platinum(II)-thiopyridylporphyrins 3 and 4 exhibit electrostatic surface binding with the negative phosphate groups of DNA. Similar to cationic-anionic binding with DNA, tetra-platinum(II)-thiopyridylporphyrinato zinc(II) demonstrates a particular binding intercalation mode with DNA. Photophysical studies demonstrated that both porphyrins are photostable and able to generate singlet oxygen (O-1(2)) after light irradiation. Exposure of pMT123 plasmid DNA to tetra-platinum(II)-thiopyridylporphyrins and irradiation with light lead to single-strand breakage as determined by the conversion of the supercoiled form of the plasmid (form I) into the nicked circular form (form II). The tetra-platinum(II)-thiopyridylporphyrinato Zn(II) demonstrates a particular intercalation binding mode with DNA and an ability to cleave DNA after photo-excitation. Chemistry DNA-BINDING PHOTODYNAMIC INACTIVATION TANDEM MASS-SPECTROMETRY PLATINUM COMPLEXES CATIONIC PORPHYRINS RESISTANT-BACTERIA CONJUGATES SYNTHESIS CANCER-CELLS AGENTS ZINC http://hdl.handle.net/1854/LU-7245195 10.1039/c4dt02697g 000346412500017 1477-9226 2015 1477-9226 2015 44 2 530 538 2015 No license (in copyright) published https://biblio.ugent.be/publication/7245195/file/7245211 application/pdf restricted ug 7245195 2016-06-07T10:06:10Z 2026-03-31T14:25:48Z A1 VABB-1 11 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Naoki Takahashi aut author ug_WE09 Tim Lammens aut author ug_GE35 0000-0001-8733-4027 Véronique Boudolf aut author ug_LA25 0000-0001-6771-142X Sara Maes aut author ug_WE09 Takeshi Yoshizumi aut author Geert De Jaeger aut author ug_WE09 0000-0001-6558-5669 Erwin Witters aut author Dirk Inzé aut author ug_WE09 0000-0002-3217-8407 Lieven De Veylder aut author ug_WE09 0000-0003-1150-4426 eng Complete and accurate chromosomal DNA replication is essential for the maintenance of the genetic integrity of all organisms. Errors in replication are buffered by the activation of DNA stress checkpoints; however, in plants, the relative importance of a coordinated induction of DNA repair and cell cycle-arresting genes in the survival of replication mutants is unknown. In a systematic screen for Arabidopsis thaliana E2F target genes, the E2F TARGET GENE 1 (ETG1) was identified as a novel evolutionarily conserved replisome factor. ETG1 was associated with the minichromosome maintenance complex and was crucial for efficient DNA replication. Plants lacking the ETG1 gene had serrated leaves due to cell cycle inhibition triggered by the DNA replication checkpoints, as shown by the transcriptional induction of DNA stress checkpoint genes. The importance of checkpoint activation was highlighted by double mutant analysis: whereas etg1 mutant plants developed relatively normally, a synthetically lethal interaction was observed between etg1 and the checkpoint mutants wee1 and atr, demonstrating that activation of a G2 cell cycle checkpoint accounts for survival of ETG1-deficient plants. Biology and Life Sciences DNA replication Arabidopsis DNA replication checkpoint ETG1 MCM proteins BIMOLECULAR FLUORESCENCE COMPLEMENTATION GENOME-WIDE IDENTIFICATION CYCLIN-DEPENDENT KINASES CELL-CYCLE ARABIDOPSIS-THALIANA TRANSCRIPTION FACTOR MCM PROTEINS GENE-EXPRESSION S-PHASE SACCHAROMYCES-CEREVISIAE http://hdl.handle.net/1854/LU-439482 10.1038/emboj.2008.107 000257497000005 0261-4189 2008 0261-4189 2008 27 13 1840 1851 2008 No license (in copyright) published https://biblio.ugent.be/publication/439482/file/3066248 application/pdf restricted ug 439482 2008-11-12T14:27:00Z 2026-03-31T14:04:52Z A1 VABB-1 12 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Danila Cabral aut author Mohamed Youssef Banora aut author José Dijair Antonino aut author Natalia Rodiuc aut author Paulo Vieira aut author Roberta R Coelho aut author Christian Chevalier aut author Thomas Eekhout aut author ug_WE09 0000-0002-2878-1553 Gilbert Engler aut author Lieven De Veylder aut author ug_WE09 0000-0003-1150-4426 Maria Fatima Grossi‐de‐Sa aut author Janice de Almeida Engler aut author eng Galls induced by plant‐parasitic nematodes involve a hyperactivation of the plant mitotic and endocycle machinery for their profit. Dedifferentiation of host root cells includes drastic cellular and molecular readjustments. In such background, potential DNA damage in the genome of gall cells is eminent. We questioned if DNA damage checkpoints activation followed by DNA repair occurred, or was eventually circumvented, in nematode‐induced galls. Galls display transcriptional activation of the DNA damage checkpoint kinase WEE1, correlated with its protein localization in the nuclei. The promoter of the stress marker gene SMR7 was evaluated under the WEE1‐knockout background. Drugs inducing DNA damage and a marker for DNA repair, PARP1 were used to understand mechanisms that might cope with DNA damage in galls. Our functional study revealed that gall cells lacking WEE1 conceivably entered mitosis prematurely disturbing the cell cycle despite the loss of genome integrity. The disrupted nuclei phenotype in giant cells hinted to the accumulation of mitotic defects. As well, WEE1‐knockout in Arabidopsis and downregulation in tomato repressed infection and reproduction of root‐knot nematodes. Together with data on DNA damaging drugs, we suggest a conserved function for WEE1 controlling a G1/S cell cycle arrest in response to replication defect in galls. Biology and Life Sciences Plant Science Physiology CELL-CYCLE PROGRESSION DNA-DAMAGE GIANT-CELLS POLY(ADP-RIBOSE) POLYMERASE ARABIDOPSIS GENES ENDOREDUPLICATION EXPRESSION MITOSIS MEIOSIS Arabidopsis thaliana cell cycle checkpoint control galls root-knot nematode Solanum lycopersicum WEE1 kinase http://hdl.handle.net/1854/LU-8630190 10.1111/nph.16185 000493172900001 0028-646X 1469-8137 2020 0028-646X 1469-8137 2020 225 1 430 447 2020 No license (in copyright) published https://biblio.ugent.be/publication/8630190/file/8630191 application/pdf https://biblio.ugent.be/publication/8630190/file/8637715 application/pdf restricted ug 8630190 2019-09-30T11:22:19Z 2023-05-08T11:50:09Z A1 VABB-1 13 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Veerke De Kock aut author Ronnie Willaert aut author Yannick Gansemans aut author ug_FW01 0000-0001-5018-044X Filip Van Nieuwerburgh aut author ug_FW01 0000-0001-8815-5485 Rani Baes aut author Eveline Peeters aut author eng Nucleoid organization in Crenarchaeota is mediated by a plethora of diverse families of small DNA-binding proteins. However, the role of the Lrs14 family, a prevalent family of small DNA-binding proteins within the Crenarchaeal order of the Sulfolobales, remained rather ambiguous. Previous studies have focused on gene regulatory functions of the Lrs14 family and have shown that the Lrs14-type protein AbfR1 is involved in the regulation of biofilm formation and motility in the model species Sulfolobus acidocaldarius. In this study, we set out to investigate the DNA-binding characteristics of the AbfR1 homolog in Metallosphaera sedula, a related mixotrophic species within Crenarchaeota. AbfR1(Ms) and AbfR1(Sa) share 50% amino acid sequence identity and are structurally very similar. We observed that heterologously purified AbfR1(Ms) forms dimers in solution and binds DNA in vitro in a non-sequence-specific manner with diverse DNA probes. Chromatin immunoprecipitation combined with high-throughput sequencing revealed an association of AbfR1(Ms) with numerous sites across the genome of M. sedula. This genome-wide association was found to correlate with adenine-thymine-rich regions and possibly with the global chromatin structure, rather than with specific DNA sequences. Notably, the most highly enriched AbfR1(Ms) binding sites were characterized by extended DNA regions spanning several thousand base pairs. Atomic force microscopy further demonstrated that AbfR1(Ms) promotes DNA condensation and aggregation, suggesting a role in chromatin architecture. These findings suggest that AbfR1(Ms), and possibly other related Lrs14 members, play a critical role in nucleoid organization, with properties resembling those of bacterial nucleoid-associated proteins. DNA-BINDING PROTEIN SULFOLOBUS-SOLFATARICUS METHANOTHERMUS-FERVIDUS GENOME SEQUENCE ARCHAEAL REGULATOR BIOFILM ARCHAEBACTERIUM CRENARCHAEON MOTILITY archaea atomic force microscopy chromatin nucleoid-associated proteins Sulfolobales winged helix-turn-helix http://hdl.handle.net/1854/LU-01KD5CZSBQ88N0PPQRJV5VPDY5 10.1002/mbo3.70059 001596311200001 2045-8827 e70059 29 p. 2025 2045-8827 2025 14 5 2025 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/01KD5CZSBQ88N0PPQRJV5VPDY5/file/01KD5D5J8ND0SDCRD1WC94PT06 application/pdf ug 01KD5CZSBQ88N0PPQRJV5VPDY5 2025-12-23T10:44:57Z 2026-03-31T15:19:28Z A1 VABB-1 14 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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_UGent 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 1438-2377 2001 213 2 107 112 2001 No license (in copyright) published https://biblio.ugent.be/publication/138834/file/4148399 application/pdf restricted ug 138834 2004-01-14T13:37:00Z 2026-03-31T07:25:56Z A1 VABB-1 15 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Daniël Broekaert aut author ug_UGent Roger Van Parijs aut author eng The characteristics of the newly synthesized main-band DNA in wounded and control pea seedlings were studied by analytical and preparative CsCl density gradient centrifugation in neutral and alkaline conditions, by Cs2SO4 gradient analysis in the absence or presence of Ag+ and Hg2+ in different concentrations, by examination of thermal denaturation, using the spectrophotometric technique or column chromatography on hydroxylapatite and by polyamino acid-kieselguhr column chromatography. The base composition calculated from the melting point is 43.2% GC and differs from the composition deduced from the density (35.7% GC). This discrepancy is caused by the presence of 4.9 to 5.3% 5-methylcytosine. All experiments show the similarity of the newly synthesized DNA (radioactivity profile) and the total DNA isolated from wounded and unwounded tissues (UV absorbancy) and point to the conclusion of a random base distribution in the pea genome. The presence of an AT or GC rich satellite DNA could not be demonstrated, even using selective Ag+ or Hg2+ complex formation and Cs2SO4 gradient centrifugation in conditions which reveal such DNA in other plant species. Biology and Life Sciences Chemistry http://hdl.handle.net/1854/LU-8710176 10.1016/S0044-328X(78)80161-5 A1978EJ94300005 0044-328X 1978 0044-328X 1978 86 1 41 53 1978 No license (in copyright) published https://biblio.ugent.be/publication/8710176/file/8710180 application/pdf restricted ug 8710176 2021-06-01T12:37:56Z 2023-05-08T11:52:58Z A1 VABB-1 16 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Sabine De Moor aut author ug_UGent Tom Vander Beken aut author ug_RE23 0000-0002-1596-5070 Stijn Van Daele aut author ug_UZGent eng DNA traces found at crime scenes and DNA records held in databases have already helped the police to solve numerous investigations into specific crimes. The police clearly benefit from the use of forensic science at an operational (i.e. case) level. This paper focuses on the use of forensic DNA at a strategic level: its use in the study of patterns of criminal behaviour. The usual sources of information for this type of research are recorded crime data, self-report studies and victimization surveys. However, as our review will show, these data sources cannot provide a complete picture of crime. We therefore propose an alternative approach to criminological research that takes into account DNA databases and has the potential to augment current methods and extend the existing knowledge beyond known offenders. The use of DNA databases has an important advantage for criminological research: it is possible to link offences committed by the same individual, whether the offender’s identity is known or not. By making a one-on-one comparison of police data with the corresponding DNA data, not only can co-offenders be studied, but a larger network of offenders connected to each other can also be analysed, even if their identity is unknown to the police. Social Sciences Co-offending Methodology Network analysis Serial offending Strategic research http://hdl.handle.net/1854/LU-8051899 10.1007/s10610-016-9327-9 000401472500004 1572-9869 2017 1572-9869 Dordrecht Springer 2017 23 2 175 192 2017 No license (in copyright) published https://biblio.ugent.be/publication/8051899/file/8051944 application/pdf restricted http://link.springer.com/article/10.1007/s10610-016-9327-9 ug 8051899 2016-08-19T15:23:14Z 2026-03-31T13:21:58Z A1 VABB-1 17 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Dieter Deforce aut author ug_FW01 0000-0002-0635-661X G Kokotos aut author EL Esmans aut author Andreas De Leenheer aut author ug_UGent Elfrida Van Den Eeckhout aut author eng Calf thymus DNA was incubated in vitro with a new aminocoumarin platinum(II) complex in order to study its interaction with DNA. The platinated DNA was hydrolyzed enzymatically to the 5'-mononucleotide level using DNAase I and nuclease P1. Analysis of the DNA hydrolysate with capillary zone electrophoresis (CZE), using sample stacking, revealed the presence of unhydrolyzed oligonucleotides in the platinated DNn. A homemade system, using only some plastic pipet tips, was constructed to collect the oligonucleotide fraction during CZE analysis. The platinum content of this fraction was determined using graphite furnace atomic absorption with Zeeman background correction. This system proved to be a useful tool to detect platinated DNA species (with a quantifiable detection limit for the detection of platinum of 0.78 ng). Subsequent gel filtration experiments confirmed the presence of high molecular weight oligonucleotides that were platinated. This was proven by reversal of the platination using thiourea and subsequent enzymatic hydrolysis to 5'-mononucleotides. Medicine and Health Sciences Chemistry DNA platinum preparative capillary zone electrophoresis atomic absorption http://hdl.handle.net/1854/LU-180500 10.1002/elps.1150191417 000076721400016 0173-0835 1998 0173-0835 1998 19 14 2454 2458 1998 No license (in copyright) published https://biblio.ugent.be/publication/180500/file/01HGFNM0T2Z4YFF858ZZJW2W1F application/pdf restricted ug 180500 2004-01-14T13:41:00Z 2026-03-31T13:19:29Z A1 VABB-1 18 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Kang Wang aut author ug_UGent Scott E Stachel aut author Benedikt Timmerman aut author Marc Van Montagu aut author ug_WE09 Patricia C Zambryski aut author eng The T-DNA transfer process of Agrobacterium tumefaciens is activated by the induction of the expression of the Ti plasmid virulence (vir) loci by plant signal molecules such as acetosyringone. The vir gene products act in trans to mobilize the T-DNA element from the bacterial Ti plasmid. The T-DNA is bounded by 25-base pair direct repeat sequences, which are the only sequences on the element essential for transfer. Thus, specific reactions must occur at the border sites to generate a transferable T-DNA copy. The T-DNA border sequences were shown in this study to be specifically nicked after vir gene activation. Border nicks were detected on the bottom strand just after the third or fourth base (+/- one or two nucleotides) of the 25-base pair transferpromoting sequence. Naturally occurring and base-substituted derivatives of the 25-base pair sequences are effective substrates for acetosyringone-induced border cleavage, whereas derivatives carrying only the first 15 or last 19 base pairs of the 25-base pair sequence are not. Site-specific border cleavages occur within 12 hours after acetosyringone induction and probably represent an early step in the T-DNA transfer process. Biology and Life Sciences http://hdl.handle.net/1854/LU-1903152 10.1126/science.235.4788.587 A1987F783400025 0036-8075 1987 0036-8075 1987 235 4788 587 591 1987 No license (in copyright) published https://biblio.ugent.be/publication/1903152/file/1903163 application/pdf restricted ug 1903152 2011-09-19T10:05:14Z 2026-03-31T07:38:52Z A1 VABB-1 19 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Ilse Theuns aut author Pieter Windels aut author Sylvie De Buck aut author ug_GE35 ug_UZGent 0000-0001-8048-0582 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 Erik Van Bockstaele aut author ug_UGent Marc De Loose aut author ug_UGent eng A T-DNA fingerprinting method is presented based on amplified fragment length polymorphism with an anchored polymerase chain reaction step. This method allows discrimination between different T-DNA inserts in stably transformed plants. The technique was evaluated by analyzing 51 transgenic Arabidopsis lines that had been characterized in detail by genomic blotting. Comparison of the obtained fingerprints with the available integration information demonstrated that fingerprints were correlated to the predicted patterns, except for the inverted repeat junctions and for those inserts with large deletions at the left or right border. Our experiments show that by using T-DNA fingerprinting multi-copy transgenic lines can be eliminated efficiently so that the technique can be used to enrich a population of transgenic plants for putative single-copy transformants. Biology and Life Sciences anchored PCR AFLP GMO detection T-DNA integration AGROBACTERIUM-TUMEFACIENS ILLEGITIMATE RECOMBINATION TRANSGENIC PLANTS BINARY VECTOR COPY NUMBER GENOMIC DNA INTEGRATION REPEATS SEQUENCES TOBACCO http://hdl.handle.net/1854/LU-156900 10.1023/A:1014415619527 000174573800009 0014-2336 2002 0014-2336 2002 123 1 75 84 2002 No license (in copyright) published https://biblio.ugent.be/publication/156900/file/6757702 application/pdf restricted ug 156900 2004-01-14T13:39:00Z 2026-03-31T07:31:15Z A1 VABB-1 20 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Marcella Holsters aut author ug_WE09 Raimundo Villarroel-Mandiola aut author ug_UGent Marc Van Montagu aut author ug_WE09 Jeff Schell aut author eng DNA of the crown gall tumor line W38T37::Tn7-1 was partially digested with Sau3A to an average molecular weight of 25 Md and ligated either directly or after size fractionation to BamHI cut cosmid pJC81 DNA. After in vitro packaging in phage λ particles and transduction to E. coli HB101, recombinants that expressed the Tn7 coded resistances to spectinomycin and trimethoprim were selected. The recombinant plasmids thus isolated contained part or the whole of Tn7 together with adjacent T-DNA. Four independent, large clones are described, three containing the left border of the T-DNA, one containing the right border and an intact copy of the Tn7 transposon. In this case all the Tn7 encoded genes were shown to have remained fully functional since the reisolated Tn7 was found to be capable of normal transposition in E. coli. The T-DNA in the W38T37::Tn7 tumor line is flanked both to the left and to the right by highly AT rich repetitive plant sequences. These results further demonstrate that foreign genes can be transferred, integrated and stably maintained in chromosomes of plant cells without undergoing any observable rearrangements. This method of cosmid cloning combined with direct selection for the desired recombinant colonies is of general application for the genomic cloning of transformed eukaryotic cells. Biology and Life Sciences http://hdl.handle.net/1854/LU-5918896 10.1007/BF00330799 A1982NN90000015 0026-8925 1982 0026-8925 1982 185 2 283 289 1982 No license (in copyright) published https://biblio.ugent.be/publication/5918896/file/5919661 application/pdf restricted ug 5918896 2015-03-31T15:18:37Z 2026-03-31T14:17:31Z A1 VABB-1 21 info:srw/schema/1/mods-v3.3xml bookChapter B2 Annelies De Paepe aut author ug_CA20 Sylvie De Buck aut author ug_GE35 ug_UZGent 0000-0001-8048-0582 Jonah Nolf aut author ug_WE09 0000-0002-4393-0852 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng Transgenic plants that harbor a single copy of the introduced transgene are preferable to those with multiple transgene copies because multiple T-DNA copies correlate with expression variability and susceptibility to silencing. Especially after the commonly used fl oral-dip Agrobacterium -mediated transformation method, the frequency of single-copy transformants is low. The CRE/ loxP recombinase-based strategy to resolve complex T-DNA loci has proven to be successful to effi ciently obtain single-copy T-DNA transformants by directly transforming loxP -containing T-DNA vectors in CRE -expressing Arabidopsis thaliana plants. This chapter describes in detail how to transform three available loxP -containing T-DNA vectors into CRE - producing Arabidopsis C24 plants and subsequently how to analyze the transgenic plants for the T-DNA locus structure. Biology and Life Sciences http://hdl.handle.net/1854/LU-2094448 10.1007/978-1-61779-558-9_26 9781617795572 9781617795589 2012 Jim M Dunwell edt editor Andy C Wetten edt editor 9781617795572 9781617795589 New York, NY, USA Springer 2012 317 333 2012 847 No license (in copyright) published https://biblio.ugent.be/publication/2094448/file/2094457 application/pdf restricted ug 2094448 2012-04-25T15:14:37Z 2026-03-31T09:16:14Z B2 VABB-4 22 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Lynda Beladjal aut author ug_UGent 0000-0002-5755-7235 Tom Gheysens aut author ug_UGent 0000-0002-8185-8986 James S Clegg aut author Mohamed Amar aut author Johan Mertens aut author ug_UGent eng We found that spores of Bacillus amyloliquefaciens rank amongst the most resistant to high temperatures with a maximum dry heat tolerance determined at 420 °C. We found that this extreme heat resistance was also maintained after several generations suggesting that the DNA was able to replicate after exposure to these temperatures. Nonetheless, amplifying the bacterial DNA using BOXA1R and (GTG)5 primers was unsuccessful immediately after extreme heating, but was successful after incubation of the heated then cooled spores. Moreover, enzymes such as amylases and proteases were active directly after heating and spore regeneration, indicating that DNA coding for these enzymes were not degraded at these temperatures. Our results suggest that extensive DNA damage may occur in spores of B. amyloliquefaciens directly after an extreme heat shock. However, the successful germination of spores after inoculation and incubation indicates that these spores could have a very efective DNA repair mechanism, most likely protein-based, able to function after exposure to temperatures up to 420 °C. Therefore, we propose that B. amyloliquefaciens is one of the most heat resistant life forms known to science and can be used as a model organism for studying heat resistance and DNA repair. Furthermore, the extremely high temperature resistivity of these spores has exceptional consequences for general methodology, such as the use of dry heat sterilization and, therefore, virtually all studies in the broad area of high temperature biology. Biology and Life Sciences Earth and Environmental Sciences Heat resistance Bacillus spores Extremophiles DNA damage-repair BACILLUS-SUBTILIS SPORES DNA-REPAIR EXTREMELY RESISTANT SP-NOV HEAT IDENTIFICATION ENDOSPORES EXTRACTION PROTEINS DAMAGE http://hdl.handle.net/1854/LU-8567606 10.1007/s00792-018-1035-6 000442104000005 1431-0651 1433-4909 2018 1431-0651 1433-4909 2018 22 5 751 759 2018 No license (in copyright) published https://biblio.ugent.be/publication/8567606/file/8567644 application/pdf private https://biblio.ugent.be/publication/8567606/file/8614065 application/pdf restricted ug 8567606 2018-07-02T11:10:13Z 2023-05-08T11:47:26Z A1 VABB-1 23 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Musa Idris aut author Louis Coussement aut author ug_LA26 0000-0003-1736-4962 Maria M. M. Alves aut author Tim De Meyer aut author ug_LA26 0000-0003-2994-9693 Veerle Melotte aut author eng Background: DNA hypermethylation is an epigenetic feature that modulates gene expression, and its deregulation is observed in cancer. Previously, we identified a neural-related DNA hypermethylation fingerprint in colon cancer, where most of the top hypermethylated and downregulated genes have known functions in the nervous system. To evaluate the presence of this signature and its relevance to carcinogenesis in general, we considered 16 solid cancer types available in The Cancer Genome Atlas (TCGA). Results: All tested cancers showed significant enrichment for neural-related genes amongst hypermethylated genes. This signature was already present in two premalignant tissue types and could not be explained by potential confounders such as bivalency status or tumor purity. Further characterization of the neural-related DNA hypermethylation signature in colon cancer showed particular enrichment for genes that are overexpressed during neural differentiation. Lastly, an analysis of upstream regulators identified RE1-Silencing Transcription factor (REST) as a potential mediator of this DNA methylation signature. Conclusion: Our study confirms the presence of a neural-related DNA hypermethylation fingerprint in various cancers, of genes linked to neural differentiation, and points to REST as a possible regulator of this mechanism. We propose that this fingerprint indicates an involvement of DNA hypermethylation in the preservation of neural stemness in cancer cells. Biology and Life Sciences DNA hypermethylation Pan cancer Neural differentiation REST TRANSCRIPTIONAL REGULATION NEURONAL DIFFERENTIATION DNA METHYLATION HALLMARKS http://hdl.handle.net/1854/LU-01HCHEQ0JS9R2PV5CG1W5GF0QT 10.1186/s13072-023-00505-7 001040169700001 1756-8935 31 12 p. 2023 1756-8935 2023 16 1 2023 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/01HCHEQ0JS9R2PV5CG1W5GF0QT/file/01HCHETAAP6RR3JQW364K615CC application/pdf ug 01HCHEQ0JS9R2PV5CG1W5GF0QT 2023-10-12T08:05:41Z 2026-03-31T13:25:25Z A1 VABB-1 24 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Lucas Lang aut author Aladár Pettkó-Szandtner aut author Hasibe Tunçay Elbaşı aut author Hirotomo Takatsuka aut author Yuji Nomoto aut author Ahmad Zaki aut author Stefan Dorokhov aut author Geert De Jaeger aut author ug_WE09 0000-0001-6558-5669 Dominique Eeckhout aut author ug_UGent 0000-0001-5770-7670 Masaki Ito aut author Zoltán Magyar aut author László Bögre aut author Maren Heese aut author Arp Schnittger aut author eng The DNA of all organisms is constantly damaged by physiological processes and environmental conditions. Upon persistent damage, plant growth and cell proliferation are reduced. Based on previous findings that RBR1, the only Arabidopsis homolog of the mammalian tumor suppressor gene retinoblastoma, plays a key role in the DNA damage response in plants, we unravel here the network of RBR1 interactors under DNA stress conditions. This led to the identification of homologs of every DREAM component in Arabidopsis, including previously not recognized homologs of LIN52. Interestingly, we also discovered NAC044, a mediator of DNA damage response in plants and close homolog of the major DNA damage regulator SOG1, to directly interact with RBR1 and the DREAM component LIN37B. Consistently, not only mutants in NAC044 but also the double mutant of the two LIN37 homologs and mutants for the DREAM component E2FB showed reduced sensitivities to DNA-damaging conditions. Our work indicates the existence of multiple DREAM complexes that work in conjunction with NAC044 to mediate growth arrest after DNA damage. Biology and Life Sciences Health Toxicology and Mutagenesis Plant Science Biochemistry Genetics and Molecular Biology (miscellaneous) Ecology http://hdl.handle.net/1854/LU-8732094 10.26508/lsa.202101141 001087275900001 2575-1077 e202101141 20 p. 2021 2575-1077 2021 4 12 2021 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/8732094/file/8732096 application/pdf ug 8732094 2021-12-22T12:42:49Z 2026-03-31T13:32:08Z A1 VABB-1 25 info:srw/schema/1/mods-v3.3xml journalArticle A2 Francis E Nwilene aut author Keith M Harris aut author Olusegun Okhidievbie aut author Amos Onasanya aut author Yacouba Sere aut author Ivan Ingelbrecht aut author eng A morphological diversity study was conducted on African rice gall midge Orseolia oryzivora Harris & Gagné and two other African species, Orseolia bonzii Harris and Orseolia nwanzei Harris & Nwilene, sp. n. Morphological differences between adult and immature stages of the three species are slight and mainly evident in pupal characters. Due to limited differences in morphological characters, genomic DNA fingerprinting of these three insect species was carried out using random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) methods. Out of 90 operon primers, 15 showed polymorphism among the three species tested, generating 86 bands, 60 (70%) of which were polymorphic. Primer OPV6 produced three RAPD markers that distinguished the three Orseolia species. These markers were cloned and sequenced. Their sequence was then used to design six SCAR primer pairs. Each SCAR primer pair amplified and distinguished the three Orseolia species at genomic DNA level. Both SCAR and RAPD genomic DNA fingerprinting revealed that O. oryzivora and O. bonzii are most closely related and O. nwanzei is distinct. Each of the six SCAR primer pairs produced a specific DNA fragment size specific for O. nwanzei, O. oryzivora and O. bonzii. The DNA fingerprints will be useful for entomological survey, identification of new species and differentiating aggressive from non-aggressive species, aimed at the effective development of rice cultivars with durable resistance to African rice gall midge. Biology and Life Sciences SCAR Orseolia bonzii Orseolia oryzivora African rice gall midge Orseolia nwanzei fingerprinting DNA rice Eragrostis atrovirens http://hdl.handle.net/1854/LU-1989608 10.1017/S1742758406694058 1742-7584 2006 1742-7584 2006 26 4 256 265 2006 published ug 1989608 2012-01-17T13:12:56Z 2026-03-31T09:08:29Z A2 VABB-1 26 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Ivano Forgione aut author Magdalena Woloszynska aut author ug_UGent Marianna Pacenza aut author Adriana Chiappetta aut author Maria Greco aut author Fabrizio Araniti aut author Maria Rosa Abenavoli aut author Maria Van Lijsebettens aut author ug_UGent Maria Beatrice Bitonti aut author Leonardo Bruno aut author eng DNA methylation carried out by different methyltransferase classes is a relevant epigenetic modification of DNA which plays a relevant role in the development of eukaryotic organisms. Accordingly, in Arabidopsis thaliana loss of DNA methylation due to combined mutations in genes encoding for DNA methyltransferases causes several developmental abnormalities. The present study describes novel growth disorders in the drm1 drm2 cmt3 triple mutant of Arabidopsis thaliana, defective both in maintenance and de novo DNA methylation, and highlights the correlation between DNA methylation and the auxin hormone pathway. By using an auxin responsive reporter gene, we discovered that auxin accumulation and distribution were affected in the mutant compared to the wild type, from embryo to adult plant stage. In addition, we demonstrated that the defective methylation status also affected the expression of genes that regulate auxin hormone pathways from synthesis to transport and signalling and a direct relationship between differentially expressed auxin-related genes and altered auxin accumulation and distribution in embryo, leaf and root was observed. Finally, we provided evidence of the direct and organ-specific modulation of auxin-related genes through the DNA methylation process. Biology and Life Sciences Agronomy and Crop Science Plant Science Genetics General Medicine GENE BODY METHYLATION DNA METHYLATION CPG METHYLATION GENOME GROWTH DRM METHYLTRANSFERASE EVOLUTION BINDING ACTIVATION http://hdl.handle.net/1854/LU-8599208 10.1016/j.plantsci.2018.12.029 000461262100037 0168-9452 2019 0168-9452 2019 280 383 396 2019 No license (in copyright) published https://biblio.ugent.be/publication/8599208/file/8599210 application/pdf restricted ug 8599208 2019-02-05T13:58:42Z 2023-05-08T11:49:10Z A1 VABB-1 27 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Silvia Alvarez aut author Ana da Silva Almeida aut author Robert Albero aut author Mayukh Biswas aut author Angelica Barreto-Galvez aut author Thomas S. Gunning aut author Anam Shaikh aut author Tomas Aparicio aut author Agnieszka Anya Wendorff aut author Erich Piovan aut author Pieter Van Vlierberghe aut author ug_GE31 0000-0001-9063-7205 Steven Gygi aut author Jean Gautier aut author Advaitha Madireddy aut author Adolfo A Ferrando aut author eng The Plant Homeodomain 6 gene (PHF6) encodes a nucleolar and chromatin-associated leukemia tumor suppressor with proposed roles in transcription regulation. However, specific molecular mechanisms controlled by PHF6 remain rudimentarily understood. Here we show that PHF6 engages multiple nucleosome remodeling protein complexes including NuRD, SWI/SNF and ISWI factors, the replication machinery and DNA repair proteins. Moreover, following DNA damage, PHF6 localizes to sites of DNA injury and its loss impairs the resolution of DNA breaks with consequent accumulation of single- and double-stranded DNA lesions. Native chromatin immunoprecipitation sequencing analyses reveal that PHF6 specifically associates with difficult to replicate heterochromatin at satellite DNA regions enriched in Histone H3 lysine 9 trimethyl marks (H3K9me3) and single molecule locus-specific analyses identify PHF6 as an important regulator of genomic stability at fragile sites. These results extend our understanding of the molecular mechanisms controlling HSC homeostasis and leukemia transformation by placing PHF6 at the crossroads of chromatin remodeling, replicative fork dynamics and DNA repair. Medicine and Health Sciences Biology and Life Sciences Cell Biology Hematology Immunology Biochemistry KAP-1 PHOSPHORYLATION HEMATOPOIETIC STEM DAMAGE RESPONSE FANCONI-ANEMIA FRAGILE SITES MUTATIONS PROTEINS RECOMBINATION INSIGHTS FAILURE http://hdl.handle.net/1854/LU-8748165 10.1182/blood.2021014103 000813042600011 0006-4971 1528-0020 2022 0006-4971 1528-0020 2022 139 23 3418 3429 2022 No license (in copyright) published https://biblio.ugent.be/publication/8748165/file/8748166 application/pdf ug 8748165 2022-03-30T13:47:51Z 2026-03-31T07:22:21Z A1 VABB-1 28 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 G Lopes aut author Leen Vandaele aut author Tom Rijsselaere aut author ug_UGent Ann Van Soom aut author ug_DI08 0000-0001-5010-6311 A Rocha aut author eng In this work, we studied the incidence of DNA fragmentation, interpreted as apoptotic changes and assessed by the TUNEL assay, in cumulus cells and oocytes of immature Grade 1 cumulus-oocyte complexes (COCs) obtained from healthy bitches (n = 27) of three age groups: young (1-3 years; n = 13), adult (4-6 years; n = 8) and elderly (7-10 years; n = 6). Age affected (p < 0.05) Grade 1 COCs recovery rates, with young animals yielding more (p < 0.01) Grade 1 COCs than the other two age groups. Conversely, no differences were observed in the incidence of DNA fragmentation (TUNEL-positive) in cumulus cells or oocytes between the three age groups. Overall, more than 80% of Grade 1 COCs presented < 15% of TUNEL-positive cumulus cells and enclosed TUNEL-negative (intact DNA) oocytes. Despite a higher proportion of TUNEL-negative oocytes being found in the germinal vesicle stage, most of the oocytes with nuclear material compatible with meiosis resumption (MR) or with non-identifiable nuclear material (ND) did not present DNA fragmentation. No correlation was observed between DNA fragmentations in oocytes and in cumulus cells. We concluded that the morphological parameters used to classify canine Grade 1 COCs are reliable to select a homogeneous population of COCs with low incidence of DNA fragmentation. Furthermore, these results indicate that DNA fragmentation can only explain a minor proportion of the incidence of MR and degeneration in canine oocytes at collection. Veterinary Sciences IN-VITRO MATURATION MEIOTIC COMPETENCE DEVELOPMENTAL COMPETENCE NUCLEAR MATURATION OVARIAN FOLLICLE BOVINE OOCYTES CELL APOPTOSIS RECOVERY RATE BITCH ATRESIA http://hdl.handle.net/1854/LU-1167691 10.1111/j.1439-0531.2009.01557.x 000284429900007 0936-6768 2010 0936-6768 2010 45 6 e275 e281 2010 No license (in copyright) published https://biblio.ugent.be/publication/1167691/file/1167708 application/pdf restricted ug 1167691 2011-02-23T16:27:13Z 2026-03-31T07:09:48Z A1 VABB-1 29 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Roy HJ Erkens aut author Hugh Cross aut author Jan W Maas aut author Kim Hoenselaar aut author Lars Chatrou aut author ug_WE11 0000-0003-0131-0302 eng Age and the greenness of leaves have been frequently used as indicators for selecting herbarium specimens for molecular studies. Although plant DNA extraction and amplification have been common lab procedures for the past 20 years, no studies specifically investigated the success of these indicators. Here the predictive value of age and the greenness for extraction and amplification success is assessed, using a large number of herbarium specimens from different plant groups. The investigation of these indicators is important because herbarium material is a precious commodity, and is often the only remaining floral record of now extinct ecosystems. In cases where little leaf material is available, most researchers still attempt to extract DNA. This Study shows that age and greenness of leaves are unreliable indicators of extraction and amplification Success, although together they can have limited usefulness. Furthermore, we found that the amount of extracted DNA from herbarium specimens decreases with c. 1% per year in age of the specimens. Therefore, researchers sometimes should refrain from using old rare specimens because chances Of Success are unpredictable and precious herbarium material might be wasted. The uncritical use of indicators Such as age or leaf colour is therefore not recommendable. Furthermore, botanists should annotate how specimens were collected and dried because this information is essential for successful DNA extraction. Hopefully, similar studies will be reported in order to identify the best approaches to extract DNA from herbarium specimens. Biology and Life Sciences SENSITIVE DETECTION MITOCHONDRIAL-DNA PLANT SPECIMENS ANCIENT DNA NESTED-PCR PRESERVATION GENERA DEGRADATION ANNONACEAE best laboratory practice herbarium specimen collection and selection Guatteria Zehneria Rauwolf herbarium http://hdl.handle.net/1854/LU-8629482 10.3767/000651908X608052 000260759600014 0006-5196 2008 0006-5196 2008 53 2 407 428 2008 No license (in copyright) published https://biblio.ugent.be/publication/8629482/file/8629492 application/pdf restricted ug 8629482 2019-09-24T15:42:06Z 2023-05-08T11:50:08Z A1 VABB-1 30 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 15 p. 2016 1664-302X 2016 7 2016 No license (in copyright) published https://biblio.ugent.be/publication/7756487/file/7763475 application/pdf ug 7756487 2016-06-27T11:52:33Z 2026-03-31T14:26:29Z A1 VABB-1 31 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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_UGent 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 1525-0016 2016 24 9 1686 1696 2016 No license (in copyright) published https://biblio.ugent.be/publication/8132712/file/8132744 application/pdf restricted ug 8132712 2016-11-03T15:44:07Z 2026-03-31T14:28:00Z A1 VABB-1 32 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 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 0000-0003-1150-4426 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 1040-4651 2007 19 1 211 225 2007 No license (in copyright) published https://biblio.ugent.be/publication/409102/file/3067597 application/pdf ug 409102 2008-05-15T15:03:00Z 2026-03-31T10:24:18Z A1 VABB-1 33 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 13 p. 2017 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 2026-03-31T14:30:38Z A1 VABB-1 34 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Ian Vandenbussche aut author 0000-0001-8792-190X Andrea Sass aut author ug_UGent 0000-0001-9396-7648 Marta Pinto-Carbó aut author Olga Mannweiler aut author Leo Eberl aut author Tom Coenye aut author ug_FW02 0000-0002-6407-0601 eng Respiratory tract infections by the opportunistic pathogen Burkholderia cenocepacia often lead to severe lung damage in cystic fibrosis (CF) patients. New insights in how to tackle these infections might emerge from the field of epigenetics, as DNA methylation is an important regulator of gene expression. The present study focused on two DNA methyltransferases (MTases) in B. cenocepacia strains J2315 and K56-2 and their role in regulating gene expression. In silico predicted DNA MTase genes BCAL3494 and BCAM0992 were deleted in both strains, and the phenotypes of the resulting deletion mutants were studied: deletion mutant Delta BCAL3494 showed changes in biofilm structure and cell aggregation, while Delta BCAM0992 was less motile. B. cenocepacia wild-type cultures treated with sinefungin, a known DNA MTase inhibitor, exhibited the same phenotype as DNA MTase deletion mutants. Single-molecule real-time sequencing was used to characterize the methylome of B. cenocepacia, including methylation at the origin of replication, and motifs CACAG and GTWWAC were identified as targets of BCAL3494 and BCAM0992, respectively. All genes with methylated motifs in their putative promoter region were identified, and qPCR experiments showed an upregulation of several genes, including biofilmand motility-related genes, in MTase deletion mutants with unmethylated motifs, explaining the observed phenotypes in these mutants. In summary, our data confirm that DNA methylation plays an important role in regulating the expression of B. cenocepacia genes involved in biofilm formation, cell aggregation, and motility. IMPORTANCE: CF patients diagnosed with Burkholderia cenocepacia infections often experience rapid deterioration of lung function, known as cepacia syndrome. B. cenocepacia has a large multireplicon genome, and much remains to be learned about regulation of gene expression in this organism. From studies in other (model) organisms, it is known that epigenetic changes through DNA methylation play an important role in this regulation. The identification of B. cenocepacia genes of which the expression is regulated by DNA methylation and identification of the regulatory systems involved in this methylation are likely to advance the biological understanding of B. cenocepacia cell adaptation via epigenetic regulation. In time, this might lead to novel approaches to tackle B. cenocepacia infections in CF patients. Medicine and Health Sciences Burkholderia DNA methylation epigenetics CEPACIA COMPLEX ESCHERICHIA-COLI SINGLE-MOLECULE METHYLTRANSFERASES RECOMBINATION EPIDEMIOLOGY RESTRICTION BACTERIA SEQUENCE INSIGHTS http://hdl.handle.net/1854/LU-8672957 10.1128/msphere.00455-20 000568742700021 2379-5042 e00455-20 17 p. 2020 2379-5042 2020 5 4 2020 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/8672957/file/8672961 application/pdf ug 8672957 2020-08-31T12:49:55Z 2023-05-08T11:51:43Z A1 VABB-1 35 info:srw/schema/1/mods-v3.3xml dissertation D1 Anneleen Decock aut author ug_GE31 0000-0002-1091-0927 Jo Vandesompele promoter ug_GE31 0000-0001-6274-0184 Franki Speleman promoter ug_GE31 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 XVII, 182 p. Ghent, Belgium Ghent University. Faculty of Medicine and Health Sciences 2016 No license (in copyright) published Gent : Aula Universiteit https://biblio.ugent.be/publication/8109145/file/8109215 application/pdf ug 8109145 2016-10-11T09:28:10Z 2026-03-31T14:27:46Z D1 36 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Zdena Koukoliková-Nicola aut author Raymond D Shillito aut author Barbara Hohn aut author Kan Wang aut author Marc Van Montagu aut author ug_WE09 Patricia Zambryski aut author ug_WE09 eng Co-cultivation of Agrobacterium tumefaciens with plant cells leads to the induction of circular copies of the T-DNA segment of the large tumour-inducing (Ti) plasmid in the bacterial cells. These circular molecules are presumably intermediates in DNA transfer from the A. tumefaciens genome to the plant cells. In support of this suggestion, the junction of the T-DNA circles occurs precisely in the 25-base pair terminal sequence involved in T-DNA transfer. Biology and Life Sciences http://hdl.handle.net/1854/LU-6974895 10.1038/313191a0 A1985AAB1100039 0028-0836 1985 0028-0836 1985 313 5999 191 196 1985 No license (in copyright) published https://biblio.ugent.be/publication/6974895/file/6975880 application/pdf restricted ug 6974895 2015-11-04T15:46:39Z 2026-03-31T14:23:23Z A1 VABB-1 37 info:srw/schema/1/mods-v3.3xml dissertation D1 Dieter Buyst aut author ug_WE07 0000-0002-5897-4823 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 XVIII, 210 + annexes p. Ghent, Belgium Ghent University. Faculty of Sciences 2015 No license (in copyright) published Gent : Aula Universiteit https://biblio.ugent.be/publication/7010798/file/7011244 application/pdf restricted ug 7010798 2015-12-15T11:44:53Z 2026-03-31T14:23:49Z D1 38 info:srw/schema/1/mods-v3.3xml journalArticle Review A1 José Antonio Pedroza-Garcia aut author ug_UGent Yanli Xiang aut author ug_UGent 0000-0002-0954-857X Lieven De Veylder aut author ug_WE09 0000-0003-1150-4426 eng Being sessile organisms, plants are ubiquitously exposed to stresses that can affect the DNA replication process or cause DNA damage. To cope with these problems, plants utilize DNA damage response (DDR) pathways, consisting of both highly conserved and plant-specific elements. As a part of this DDR, cell cycle checkpoint control mechanisms either pause the cell cycle, to allow DNA repair, or lead cells into differentiation or programmed cell death, to prevent the transmission of DNA errors in the organism through mitosis or to its offspring via meiosis. The two major DDR cell cycle checkpoints control either the replication process or the G2/M transition. The latter is largely overseen by the plant-specific SOG1 transcription factor, which drives the activity of cyclin-dependent kinase inhibitors and MYB3R proteins, which are rate limiting for the G2/M transition. By contrast, the replication checkpoint is controlled by different players, including the conserved kinase WEE1 and likely the transcriptional repressor RBR1. These checkpoint mechanisms are called upon during developmental processes, in retrograde signaling pathways, and in response to biotic and abiotic stresses, including metal toxicity, cold, salinity, and phosphate deficiency. Additionally, the recent expansion of research from Arabidopsis to other model plants has revealed species-specific aspects of the DDR. Overall, it is becoming evidently clear that the DNA damage checkpoint mechanisms represent an important aspect of the adaptation of plants to a changing environment, hence gaining more knowledge about this topic might be helpful to increase the resilience of plants to climate change. Biology and Life Sciences DNA damage cell cycle progression checkpoint control environmental stress HOMOLOGOUS RECOMBINATION REPAIR SYSTEMIC ACQUIRED-RESISTANCE ROOT-GROWTH INHIBITION DOUBLE-STRAND BREAKS PROTEIN-KINASE CK2 UV-B STRESS RIBONUCLEOTIDE REDUCTASE REPLICATION CHECKPOINT GENE-TRANSCRIPTION GENOME STABILITY http://hdl.handle.net/1854/LU-8732032 10.1111/tpj.15567 000720917100001 0960-7412 1365-313X 2022 0960-7412 1365-313X 2022 109 3 490 507 2022 No license (in copyright) published https://biblio.ugent.be/publication/8732032/file/8738784 application/pdf restricted ug 8732032 2021-12-22T07:44:30Z 2023-05-08T11:53:46Z A1 VABB-1 39 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Pablo Vangeenderhuysen aut author ug_DI04 0000-0002-5492-6904 Matthijs Vynck aut author ug_DI04 0000-0001-9875-385X Liesa Engelen aut author Adrian Covaci aut author Tim Nawrot aut author Trancizeo Lipenga aut author ug_FW03 Roger Peró Gascón aut author ug_FW03 0000-0001-5019-1405 Sarah De Saeger aut author ug_FW03 ug_FW58 0000-0002-2160-7253 Marthe De Boevre aut author ug_CA05 ug_FW03 0000-0002-6151-5126 Valerie Mccormack aut author Lynn Vanhaecke aut author ug_DI04 0000-0003-0400-2188 Lieselot Hemeryck aut author ug_DI04 0000-0002-2451-3375 eng DNA adductomics is the study of the whole of DNA adducts in a biological sample and is a valuable asset to exposomics research. To date, a clear view on how to analyze larger sample series is lacking in DNA adductomics, and the preprocessing of untargeted DNA adductomics data is seldom applied. This work aimed to optimize a DNA adductomics data preprocessing workflow (in true untargeted mode). Building upon the xcms R package, we optimized parameters for peak detection, retention time alignment, and peak grouping to reliably detect and integrate putative DNA adduct LC-MS peaks. Next, to ensure reliable downstream data analysis, six sample- and feature-based normalization methods were tested and quantitatively evaluated in two data sets (placental tissue, n = 375, and blood samples, n = 51). As a result, a successful and reproducible procedure for optimization of xcms parameters for DNA adductomics is proposed. Furthermore, evaluation of normalization methods demonstrated the importance and limitations of objective (RSD* and D-ratio) and subjective, i.e., visual (PCA score plot) evaluation. This work supports reproducible and transparent untargeted DNA adductomics data preprocessing to be implemented in large-scale exposomics studies. Chemistry MASS-SPECTROMETRY EXPOSURE IDENTIFICATION ALIGNMENT HEALTH RISK http://hdl.handle.net/1854/LU-01KN45M60AVNEPZ9T3A2SY7656 10.1021/acs.analchem.5c06549 001715675700001 0003-2700 1520-6882 2026 0003-2700 1520-6882 2026 98 12 8947 8955 2026 No license (in copyright) published https://biblio.ugent.be/publication/01KN45M60AVNEPZ9T3A2SY7656/file/01KN46BBDCGMSNV50FADNDNMCF application/pdf restricted ug 01KN45M60AVNEPZ9T3A2SY7656 2026-04-01T09:22:37Z 2026-04-02T10:37:41Z A1 VABB-1 40 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 11 p. 2011 0305-1048 2011 39 2 2011 No license (in copyright) published https://biblio.ugent.be/publication/3186410/file/3186439 application/pdf ug 3186410 2013-04-08T15:27:50Z 2026-03-31T13:04:04Z A1 VABB-1 41 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Sophie Janssens aut author ug_GE35 0000-0003-1702-1636 Antoine Tinel aut author Saskia Lippens aut author ug_WE14 0000-0002-8261-3462 Jürg Tschopp aut author eng Abstract: Activation of NF-kappa B following genotoxic stress allows time for DNA-damage repair and ensures cell survival accounting for acquired chemoresistance, an impediment to effective cancer therapy. Despite this clinical relevance, little is known about pathways that enable genotoxic-stress-induced NF-kappa B induction. Previously, we reported a role for the p53-inducible death-domain-containing protein, PIDD, in caspase-2 activation and apoptosis in response to DNA damage. We now demonstrate that PIDD plays a critical role in DNA-damage-induced NF-kappa B activation. Upon genotoxic stress, a complex between PIDD, the kinase RIP1, and a component of the NF-kappa B-activating kinase complex, NEMO, is formed. PIDD expression enhances genotoxic-stress-induced NF-kappa B activation through augmented sumoylation and ubiquitination of NEMO. Depletion of PIDD and RIP1, but not caspase-2, abrogates DNA-damage-induced NEMO modification and NF-kappa B activation. We propose that PIDD acts as a molecular switch, controlling the balance between life and death upon DNA damage. Biology and Life Sciences DOMAIN-CONTAINING PROTEIN NECROSIS-FACTOR-ALPHA TOPOISOMERASE-II SUMO-1 MODIFICATION GENOTOXIC STRESS NEMO/IKK-GAMMA KINASE RIP NUCLEAR COMPLEX SIGNAL http://hdl.handle.net/1854/LU-1202491 10.1016/j.cell.2005.09.036 000234177200016 0092-8674 2005 0092-8674 2005 123 6 1079 1092 2005 No license (in copyright) published https://biblio.ugent.be/publication/1202491/file/1202903 application/pdf restricted ug 1202491 2011-04-05T13:15:28Z 2026-03-31T07:14:38Z A1 VABB-1 42 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 1559-2294 2013 8 6 666 676 2013 No license (in copyright) published https://biblio.ugent.be/publication/4224288/file/4224298 application/pdf restricted ug 4224288 2014-01-08T10:13:22Z 2026-03-31T13:42:04Z A1 VABB-1 43 info:srw/schema/1/mods-v3.3xml bookChapter B2 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 Stanley Maloy edt editor Kelly Hughes edt editor 9780080961569 Amsterdam, The Netherlands Elsevier Science 2013 55 57 2013 No license (in copyright) published https://biblio.ugent.be/publication/5842554/file/5842563 application/pdf restricted ug 5842554 2015-02-09T14:33:01Z 2026-03-31T14:15:26Z B2 VABB-4 44 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Esther MN Dohmann aut author Mitchell P Levesque aut author Lieven De Veylder aut author ug_WE09 0000-0003-1150-4426 Ilka Reichardt aut author Gerd Jürgens aut author Markus Schmid aut author Claus Schwechheimer aut author eng The COP9 signalosome (CSN) is required for the full activity of cullin-RING E3 ubiquitin ligases (CRLs) in eukaryotes. CSN exerts its function on CRLs by removing the ubiquitin-related NEDD8 conjugate from the cullin subunit of CRLs. CSN seems, thereby, to control CRL disassembly or CRL subunit stability. In Arabidopsis thaliana, loss of CSN function leads to constitutive photomorphogenic (cop) seedling development and a post-germination growth arrest. The underlying molecular cause of this growth arrest is currently unknown. Here, we show that Arabidopsis csn mutants are delayed in G2 phase progression. This cell cycle arrest correlates with the induction of the DNA damage response pathway and is suggestive of the activation of a DNA damage checkpoint. In support of this hypothesis, we detected gene conversion events in csn mutants that are indicative of DNA double-strand breaks. DNA damage is also apparent in mutants of the NEDD8 conjugation pathway and in mutants of the E3 ligase subunits CULLIN4, COP1 and DET1, which share phenotypes with csn mutants. In summary, our data suggest that Arabidopsis csn mutants undergo DNA damage, which might be the cause of the delay in G2 cell cycle progression. Biology and Life Sciences cell cycle COP9 signalosome DNA damage DOUBLE-STRAND BREAKS MEDIATING LIGHT CONTROL DNA-DAMAGE RESPONSE E3 UBIQUITIN LIGASE CELL-PROLIFERATION S-PHASE COP9/SIGNALOSOME SUBUNITS ASPERGILLUS-NIDULANS IONIZING-RADIATION AUXIN RESPONSE http://hdl.handle.net/1854/LU-439485 10.1242/dev.020743 000255747700012 0950-1991 2008 0950-1991 2008 135 11 2013 2022 2008 No license (in copyright) published https://biblio.ugent.be/publication/439485/file/3066252 application/pdf restricted ug 439485 2008-11-12T14:28:00Z 2026-03-31T14:04:52Z A1 VABB-1 45 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Kyle Mc Kibbin aut author ug_UGent Mahsa Shabani aut author ug_GE39 ug_RE23 0000-0001-7128-0474 Maarten Larmeseau aut author eng Biological samples containing DNA that is attributed to deceased relatives, can now undergo genetic testing at a reasonable cost due to revolutionary improvements in sampling, sequencing, and analytical techniques. This artifact DNA testing, or ‘artDNA’, includes genetic analysis of hair locks, stamps, envelopes with saliva traces or teeth. ArtDNA can reveal valuable information about a deceased relative or one’s genetic background, but it also presents novel ethical dilemmas and legal uncertainties for genetic researchers and commercial testing services. In this paper, we provide an analysis of some of the unique ethical and legal risks of such testing and provide needed recommendations for practitioners of private family artDNA testing. ArtDNA testing generates ethical and legal risks regarding the privacy and autonomy of deceased individuals, the rights of living relatives over their ancestor’s genetic information, and the rights of living persons to control their own genetic information. To mitigate these risks, practitioners can conduct certain preliminary testing to ascertain the identity of a DNA donor and estimate the time that has elapsed postmortem. Generally, the ethical and legal concerns will be higher when a shorter period has passed between the death of the DNA donor and the time of artifact DNA testing. Regardless, all artDNA testing present some risks, and practitioners should exercise professional judgement as necessary. Law and Political Science Medicine and Health Sciences Philosophy and Religion Bioethics Forensic genetics Artifact DNA Direct-to-consumer testing Genetic genealogy Genetic privacy http://hdl.handle.net/1854/LU-01GK7MCXNTPSYRJX8QAVFXV6TQ 10.1007/s00439-022-02508-y 000912626100001 0340-6717 1432-1203 2023 0340-6717 1432-1203 2023 142 3 331 341 2023 No license (in copyright) published https://biblio.ugent.be/publication/01GK7MCXNTPSYRJX8QAVFXV6TQ/file/01GK7MFNPC91YJDTF57Q0M11N5 application/pdf restricted https://biblio.ugent.be/publication/01GK7MCXNTPSYRJX8QAVFXV6TQ/file/01KGPBFXAVGXMMZQKCTPGQCD1H application/vnd.openxmlformats-officedocument.wordprocessingml.document ug 01GK7MCXNTPSYRJX8QAVFXV6TQ 2022-12-01T20:00:12Z 2026-03-31T15:25:53Z A1 VABB-1 46 info:srw/schema/1/mods-v3.3xml dissertation D1 Toon Cools aut author ug_UGent Lieven De Veylder promoter ug_WE09 0000-0003-1150-4426 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 VI, 190 p. Ghent, Belgium Ghent University. Faculty of Sciences 2011 No license (in copyright) published Zwijnaarde : Technologiepark (FSVM building) https://biblio.ugent.be/publication/1216535/file/4335544 application/pdf https://biblio.ugent.be/publication/1216535/file/8770220 application/pdf private ug 1216535 2011-05-03T17:26:36Z 2026-03-31T07:15:56Z D1 47 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Jonathan Maelfait aut author ug_WE14 0000-0002-1476-0583 Elena Seiradake aut author Jan Rehwinkel aut author eng HIV-1 infects dendritic cells (DCs) without triggering an effective innate antiviral immune response. As a consequence, the induction of adaptive immune responses controlling virus spread is limited. In a recent issue of Immunity, Lahaye and colleagues show that intricate interactions of HIV capsid with the cellular cofactor cyclophilin A (CypA) control infection and innate immune activation in DCs. Manipulation of HIV-1 capsid to increase its affinity for CypA results in reduced virus infectivity and facilitates access of the cytosolic DNA sensor cGAS to reverse transcribed DNA. This in turn induces a strong host response. Here, we discuss these findings in the context of recent developments in innate immunity and consider the implications for disease control and vaccine design. Biology and Life Sciences cGAS CypA cytosolic DNA sensor dendritic cells HIV-1 HIV-1 capsid innate antiviral immunity IMMUNODEFICIENCY-VIRUS TYPE-1 CYCLIC GMP-AMP RESTRICTION FACTOR SAMHD1 DOUBLE-STRANDED DNA HUMAN CYCLOPHILIN-A DENDRITIC CELLS I INTERFERON INTRACELLULAR DNA EARLY STEPS NONDIVIDING CELLS http://hdl.handle.net/1854/LU-8591844 10.1002/bies.201400019 000337682800006 0265-9247 2014 0265-9247 2014 36 7 649 657 2014 published ug 8591844 2019-01-28T12:18:51Z 2023-05-08T11:48:42Z A1 VABB-1 48 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Lieselot Carrette aut author ug_UGent 0000-0002-5217-2774 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 1439-4227 2014 15 1 103 107 2014 No license (in copyright) published https://biblio.ugent.be/publication/4293585/file/4293601 application/pdf restricted ug 4293585 2014-02-17T13:52:56Z 2026-03-31T13:52:36Z A1 VABB-1 49 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 0022-2615 2004 53 9 927 933 2004 published ug 7187256 2016-04-18T12:50:28Z 2026-03-31T14:25:20Z A1 VABB-1 50 info:srw/schema/1/mods-v3.3xml conference C1 Henri Vander Eecken aut author Julien Fautrez aut author Frank Roels aut author ug_UGent 8th International congress of Neurology eng The extinction by Feulgen-stained DNA was measured by microscopical histophotometry (Lison), in individual nuclei of neurons of the lateral genicalute bodies and granular layer of the visual cortex, after unilateral ocular enucleation. Mean DNA content of neurons increased significantly with 25-30%, in both regions bilaterally, but not in the temporal cortex unrelated to the optic system. The nucleolus-associated chromatin, although very prominent in neurons, cannot alone be responsible for this increase because it represents approx. only 9% of total nuclear DNA. Compared to other organs showing increased DNA when function is modified (Fautrez et al), our results suggest that neurons in the visual centres possess an autonomous activity which is in part suppressed by the nervous impulses from the retina. Medicine and Health Sciences DNA Feulgen stain histophotometry L Lison neurons nucleolus associated chromatin http://hdl.handle.net/1854/LU-8545315 1965 1965 115 117 1965 published ug 8545315 2018-01-17T16:29:11Z 2026-03-31T13:13:21Z C1 VABB-5 51 info:srw/schema/1/mods-v3.3xml conference C3 Maja Kiselinova aut author ug_UZGent Ward De Spiegelaere aut author ug_DI11 0000-0003-2097-8439 Maria Jose Buzon aut author Eva Malatinková aut author ug_UGent Mathias Lichterfeld aut author Linos Vandekerckhove aut author ug_GE35 ug_UZGent 0000-0002-8600-1631 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 2015 2015 published ug 6858912 2015-07-01T23:55:20Z 2026-03-31T14:21:13Z C3 52 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Maja Kiselinova aut author ug_UZGent Ward De Spiegelaere aut author ug_DI11 0000-0003-2097-8439 Maria Jose Buzon aut author Eva Malatinková aut author ug_UGent Mathias Lichterfeld aut author Linos Vandekerckhove aut author ug_GE35 ug_UZGent 0000-0002-8600-1631 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 17 p. 2016 1553-7366 1553-7374 2016 12 3 2016 No license (in copyright) 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 2026-03-31T14:29:19Z A1 VABB-1 53 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 0022-1007 1998 188 5 985 990 1998 No license (in copyright) 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 2026-03-31T13:23:14Z A1 VABB-1 54 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Dorthe S. Pedersen aut author Frederik Coppens aut author ug_WE09 0000-0001-6565-5145 Lu Ma aut author Martin Antosch aut author Barbara Marktl aut author Thomas Merkle aut author Gerrit Beemster aut author ug_WE09 Andreas Houben aut author Klaus D. Grasser aut author eng The high mobility group (HMG)-box represents a DNA-binding domain that is found in various eukaryotic DNA-interacting proteins. Proteins that contain three copies of the HMG-box domain, termed 3 x HMG-box proteins, appear to be specific to plants. The Arabidopsis genome encodes two 3 x HMG-box proteins that were studied here. DNA interactions were examined using electrophoretic mobility shift assays, whereas expression, subcellular localization and chromosome association were mainly analysed by different types of fluorescence microscopy. The 3 x HMG-box proteins bind structure specifically to DNA, display DNA bending activity and, in addition to the three HMG-box domains, the basic N-terminal domain contributes to DNA binding. The expression of the two Arabidopsis genes encoding 3 x HMG-box proteins is linked to cell proliferation. In synchronized cells, expression is cell cycle dependent and peaks in cells undergoing mitosis. 3 x HMG-box proteins are excluded from the nuclei of interphase cells and localize to the cytosol, but, during mitosis, they associate with condensed chromosomes. The 3 x HMG-box2 protein generally associates with mitotic chromosomes, while 3 x HMG-box1 is detected specifically at 45S rDNA loci. In addition to mitotic chromosomes the 3 x HMG-box proteins associate with meiotic chromosomes, suggesting that they are involved in a general process of chromosome function related to cell division, such as chromosome condensation and/or segregation. Biology and Life Sciences MOBILITY GROUP PROTEINS mitotic chromosome rDNA HMGB DNA interaction chromatin Arabidopsis HMG-box domain MAIZE HMGA CHROMATIN GENE GENOME ASSOCIATION ARABIDOPSIS-THALIANA HISTONE H3 CELL-CYCLE NUCLEOLAR DOMINANCE http://hdl.handle.net/1854/LU-1986438 10.1111/j.1469-8137.2011.03828.x 000296850800006 0028-646X 2011 0028-646X 2011 192 3 577 589 2011 No license (in copyright) published https://biblio.ugent.be/publication/1986438/file/1986452 application/pdf restricted ug 1986438 2012-01-13T16:00:57Z 2026-03-31T09:08:25Z A1 VABB-1 55 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 1350-9047 2013 20 3 490 502 2013 No license (in copyright) published https://biblio.ugent.be/publication/3211010/file/3211028 application/pdf restricted ug 3211010 2013-05-13T09:15:42Z 2026-03-31T13:04:49Z A1 VABB-1 56 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Marie-Alice Fraiture aut author ug_UGent Philippe Herman aut author Loic Lefèvre aut author Isabel Taverniers aut author Marc De Loose aut author ug_UGent Dieter Deforce aut author ug_FW01 0000-0002-0635-661X Nancy H Roosens aut author eng Background: In order to provide a system fully integrated with qPCR screening, usually used in GMO routine analysis, as well as being able to detect, characterize and identify a broad spectrum of GMOs in food/feed matrices, two bidirectional DNA walking methods targeting p35S or tNOS, the most common transgenic elements found in GM crops, were developed. These newly developed DNA walking methods are completing the previously implemented DNA walking method targeting the t35S pCAMBIA element. Results: First, the newly developed DNA walking methods, anchored on the sequences used for the p35S or tNOS qPCR screening, were tested on Bt rice that contains these two transgenic elements. Second, the methods were assessed on a maize sample containing a low amount of the GM MON863 event, representing a more complex matrix in terms of genome size and sensitivity. Finally, to illustrate its applicability in GMO routine analysis by enforcement laboratories, the entire workflow of the integrated strategy, including qPCR screening to detect the potential presence of GMOs and the subsequent DNA walking methods to characterize and identify the detected GMOs, was applied on a GeMMA Scheme Proficiency Test matrix. Via the characterization of the transgene flanking region between the transgenic cassette and the plant genome as well as of a part of the transgenic cassette, the presence of GMOs was properly confirmed or infirmed in all tested samples. Conclusion: Due to their simple procedure and their short time-frame to get results, the developed DNA walking methods proposed here can be easily implemented in GMO routine analysis by the enforcement laboratories. In providing crucial information about the transgene flanking regions and/or the transgenic cassettes, this DNA walking strategy is a key molecular tool to prove the presence of GMOs in any given food/feed matrix. Agriculture and Food Sciences REAL-TIME PCR FLANKING SEQUENCE DETERMINATION UNAUTHORIZED GMOS PRODUCTS GENES FOOD http://hdl.handle.net/1854/LU-6842118 10.1186/s12896-015-0191-3 000359686500001 1472-6750 76 11 p. 2015 1472-6750 2015 15 2015 No license (in copyright) published https://biblio.ugent.be/publication/6842118/file/6901533 application/pdf ug 6842118 2015-06-23T08:49:03Z 2026-03-31T14:21:02Z A1 VABB-1 57 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Mohammad Atighi Quchan Atigh aut author Bruno Verstraeten aut author ug_WE14 0000-0003-3573-1463 Tim De Meyer aut author ug_LA26 0000-0003-2994-9693 Tina Kyndt aut author ug_LA25 0000-0002-5267-5013 eng A role for DNA hypomethylation has recently been suggested in the interaction between bacteria and plants; it is unclear whether this phenomenon reflects a conserved response. Treatment of plants of monocot rice and dicot tomato with nematode-associated molecular patterns from different nematode species or bacterial pathogen-associated molecular pattern flg22 revealed global DNA hypomethylation. A similar hypomethylation response was observed during early gall induction by Meloidogyne graminicola in rice. Evidence for the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon treatment with DNA methylation inhibitor 5-azacytidine. Whole-genome bisulphite sequencing of young galls revealed massive hypomethylation in the CHH context, while not for CG or CHG nucleotide contexts. Further, CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point but, rather, was correlated with a delayed transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway and DECREASED DNA METHYLATION 1. We demonstrated that DNA hypomethylation is associated with reduced susceptibility in rice towards root-parasitic nematodes and is likely to be part of the basal pattern-triggered immunity response in plants. Biology and Life Sciences Plant Science Physiology basal defence DNA hypomethylation Meloidogyne graminicola nematodes Oryza sativa pattern‐triggered immunity RdDM rice TRANSPOSABLE ELEMENTS ROOT-KNOT MELOIDOGYNE-GRAMINICOLA EPIGENETIC REGULATION FUNCTIONAL-ROLE SMALL RNAS METHYLATION ARABIDOPSIS DEMETHYLATION RESISTANCE http://hdl.handle.net/1854/LU-8655744 10.1111/nph.16532 000527868600001 0028-646X 1469-8137 2020 0028-646X 1469-8137 2020 227 2 545 558 2020 Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Public License (CC BY-NC-ND 4.0) published https://biblio.ugent.be/publication/8655744/file/8670083 application/pdf ug 8655744 2020-04-01T06:23:52Z 2026-03-31T14:19:19Z A1 VABB-1 58 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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_GE35 ug_UZGent 0000-0002-8600-1631 Ward De Spiegelaere aut author ug_DI11 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 9 p. 2015 2045-2322 2015 5 2015 No license (in copyright) published https://biblio.ugent.be/publication/6929096/file/6929098 application/pdf ug 6929096 2015-09-14T09:12:40Z 2026-03-31T14:22:55Z A1 VABB-1 59 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Zulma Beatriz Quirolo aut author M Alejandra Sequeira aut author José Martins aut author ug_WE07 0000-0001-7350-2253 Veronica I Dodero aut author eng Transcription factors are proteins lying at the endpoint of signaling pathways that control the complex process of DNA transcription. Typically, they are structurally disordered in the inactive state, but in response to an external stimulus, like a suitable ligand, they change their conformation, thereby activating DNA transcription in a spatiotemporal fashion. The observed disorder or fuzziness is functionally beneficial because it can add adaptability, versatility, and reversibility to the interaction. In this context, mimetics of the basic region of the GCN4 transcription factor (Tf) and their interaction with dsDNA sequences would be suitable models to explore the concept of conformational fuzziness experimentally. Herein, we present the first example of a system that mimics the DNA sequence-specific recognition by the GCN4 Tf through the formation of a non- covalent tetra-component complex: peptide-azo beta-CyD(dimer)-peptide-DNA. The non-covalent complex is constructed on the one hand by a 30 amino acid peptide corresponding to the basic region of GCN4 and functionalized with an adamantane moiety, and on the other hand an allosteric receptor, the azoCyDdimer, that has an azobenzene linker connecting two beta-cyclodextrin units. The azoCyDdimer responds to light stimulus, existing as two photo-states: the first thermodynamically stable with an E:Z isomer ratio of 95:5 and the second obtained after irradiation with ultraviolet light, resulting in a photostationary state with a 60:40 E:Z ratio. Through electrophoretic shift assays and circular dichroism spectroscopy, we demonstrate that the E isomer is responsible for dimerization and recognition. The formation of the non-covalent tetra component complex occurs in the presence of the GCN4 cognate dsDNA sequence (' 5-..ATGA cg TCAT..-3 ') but not with (' 5-..ATGA c TCAT..-3 ') that differs in only one spacing nucleotide. Thus, we demonstrated that the tetra-component complex is formed in a specific manner that depends on the geometry of the ligand, the peptide length, and the ds DNA sequence. We hypothesized that the mechanism of interaction is sequential, and it can be described by the polymorphism model of static fuzziness. We argue that chemically modified peptides of the GCN4 Tf are suitable minimalist experimental models to investigate conformational fuzziness in protein-DNA interactions. Chemistry FUZZY COMPLEXES PROTEINS GCN4 mimetic peptides-DNA E:Z photoisomerization conformational fuzziness http://hdl.handle.net/1854/LU-8638827 10.3390/molecules24132508 000476700300162 1420-3049 2508 20 p. 2019 1420-3049 2019 24 13 2019 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/8638827/file/8638828 application/pdf ug 8638827 2019-12-13T12:09:55Z 2023-05-08T11:50:25Z A1 VABB-1 60 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 EB Vangeel aut author S Kempke aut author J Bakusic aut author L Godderis aut author P Luyten aut author L Van Heddegem aut author Veerle Compernolle aut author ug_GE32 ug_UZGent 0000-0001-5477-9804 P Persoons aut author D Lambrechts aut author B Izzi aut author K Freson aut author S Claes aut author eng Objective: Although the precise mechanisms are not yet understood, previous studies have suggested that chronic fatigue syndrome (CFS) is associated with hypothalamic-pituitary-adrenal (HPA) axis dysregulation and trauma in early childhood. Consistent with findings suggesting that early life stress-induced DNA methylation changes may underlie dysregulation of the HPA axis, we previously found evidence for the involvement of glucocorticoid receptor (GR) gene (NR3C1) methylation in whole blood of CFS patients. Methods: In the current study, we assessed NR3C1-1F region DNA methylation status in peripheral blood from a new and independent sample of 80 female CFS patients and 91 female controls. In CFS patients, history of childhood trauma subtypes was evaluated using the Childhood Trauma Questionnaire short form (CTQ-SF). Results: Although absolute methylation differences were small, the present study confirms our previous findings of NR3C1-1F DNA hypomethylation at several CpG sites in CFS patients as compared to controls. Following multiple testing correction, only CpG_8 remained significant (DNA methylation difference: 1.3% versus 1.5%, p < 0.001). In addition, we found associations between DNA methylation and severity of fatigue as well as with childhood emotional abuse in CFS patients, although these findings were not significant after correction for multiple testing. Conclusions: In conclusion, we replicated findings of NR3C1-1F DNA hypomethylation in CFS patients versus controls. Our results support the hypothesis of HPA axis dysregulation and enhanced GR sensitivity in CFS. Medicine and Health Sciences NR3C1 HPA axis Glucocorticoid receptor DNA methylation Chronic fatigue syndrome Childhood trauma http://hdl.handle.net/1854/LU-01GWPACVFADMK512H48MTXW225 10.1016/j.jpsychores.2017.11.011 000423010300009 0022-3999 1879-1360 2018 0022-3999 1879-1360 2018 104 55 60 2018 published ug 01GWPACVFADMK512H48MTXW225 2023-03-29T09:15:17Z 2026-03-31T14:56:12Z A1 VABB-1 61 info:srw/schema/1/mods-v3.3xml journalArticle A2 Ranjana Bhattacharjee aut author Maria Kolesnikova-Allen aut author Peter Aikpokpodion aut author Sunday Taiwo aut author Ivan Ingelbrecht aut author 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 0735-9640 2004 22 4 435 436 2004 No license (in copyright) published https://biblio.ugent.be/publication/1991532/file/1998245 application/pdf restricted ug 1991532 2012-01-17T16:04:00Z 2026-03-31T09:08:53Z A2 VABB-1 62 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Christine Helsen aut author Vanessa Dubois aut author ug_GE33 0000-0001-8894-2980 Annelien Verfaillie aut author Jacques Young aut author Mieke Trekels aut author Renee Vancraenenbroeck aut author Marc De Maeyer aut author Frank Claessens aut author eng DNA binding as well as ligand binding by nuclear receptors has been studied extensively. Both binding functions are attributed to isolated domains of which the structure is known. The crystal structure of a complete receptor in complex with its ligand and DNA-response element, however, has been solved only for the peroxisome proliferator-activated receptor gamma (PPAR gamma)-retinoid X receptor alpha (RXR alpha) heterodimer. This structure provided the first indication of direct interactions between the DNA-binding domain (DBD) and ligand-binding domain (LBD). In this study, we investigated whether there is a similar interface between the DNA- and ligand-binding domains for the androgen receptor (AR). Despite the structural differences between the AR- and PPAR gamma-LBD, a combination of in silico modeling and docking pointed out a putative interface between AR-DBD and AR-LBD. The surfaces were subjected to a point mutation analysis, which was inspired by known AR mutations described in androgen insensitivity syndromes and prostate cancer. Surprisingly, AR-LBD mutations D695N, R710A, F754S, and P766A induced a decrease in DNA binding but left ligand binding unaffected, while the DBD-residing mutations K590A, K592A, and E621A lowered the ligand-binding but not the DNA-binding affinity. We therefore propose that these residues are involved in allosteric communications between the AR-DBD and AR-LBD. Medicine and Health Sciences Biology and Life Sciences GENE-MUTATIONS GLUCOCORTICOID-RECEPTOR STRUCTURAL BASIS INSENSITIVITY SYNDROME CRYSTAL-STRUCTURE RECOGNITION ESTROGEN PROTEIN FXXLF IDENTIFICATION http://hdl.handle.net/1854/LU-8737880 10.1128/MCB.00151-12 000306764100006 0270-7306 1098-5549 2012 0270-7306 1098-5549 2012 32 15 3033 3043 2012 published ug 8737880 2022-01-31T10:42:16Z 2023-05-08T11:53:57Z A1 VABB-1 63 info:srw/schema/1/mods-v3.3xml conference C3 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 2017 2017 unpublished ug 8529964 2017-08-31T09:53:18Z 2026-03-31T14:35:22Z C3 64 info:srw/schema/1/mods-v3.3xml journalArticle Article; Proceedings Paper A1 Peter Dubruel aut author ug_WE07 0000-0002-5928-7726 Joost De Strycker aut author Philippe Westbroek aut author ug_TW11 Ken Bracke aut author ug_GE35 0000-0001-5906-4605 Eduard Temmerman aut author ug_UGent J Vandervoort aut author A Ludwig aut author Etienne Schacht aut author ug_UGent Conference on Polymers in the 3rd Millennium eng We report the synthesis and physicochemical evaluation of a series of cationic polymethacrylates as vectors for gene delivery. Two different types of polymer have been synthesized: The first is a series of polymers containing tertiary amine, pyridine, imidazole and acid groups; the second is a series of polyamines containing poly(ethylene oxide) (PEO) blocks or grafts. The ability of the different polymers to condense DNA has been studied by agarose gel electrophoresis; all polymers are able to condense DNA, their ability to do so being dependent on their chemical composition and molecular weight. The particle size of the different polymer-DNA complexes formed has been measured by dynamic light scattering: complexes have a particle size of around 50 nm. A clear effect of the chemical composition of the polymers on the zeta potential of their complexes with DNA is evident. (C) 2002 Society of Chemical Industry. Chemistry Medicine and Health Sciences gene therapy polymethacrylates DNA condensation agarose gel electrophoresis polymer-DNA complexes zeta potential IN-VITRO DNA TRANSFECTION ADENOVIRUS COMPLEXES BLOCK EFFICIENCY POLYMERS CARRIERS http://hdl.handle.net/1854/LU-162451 10.1002/pi.866 000179103200018 0959-8103 1097-0126 2002 0959-8103 1097-0126 2002 51 10 948 957 2002 No license (in copyright) published https://biblio.ugent.be/publication/162451/file/01KJWMHG7N2KYA9VATK834EGGJ application/pdf restricted ug 162451 2004-01-14T13:39:00Z 2026-03-31T05:29:17Z A1 VABB-1 65 info:srw/schema/1/mods-v3.3xml journalArticle Review A1 Jonathan Maelfait aut author ug_WE14 0000-0002-1476-0583 Jan Rehwinkel aut author eng ZBP1 is an innate immune sensor for double-stranded nucleic acids adopting the Z conformation. Z-RNA/DNA is generated during viral infections and in autoinflammation and cancer. By inducing regulated cell death and proinflammatory signaling, ZBP1 plays multifaceted roles in disease pathology. Nucleic acid sensing is a central process in the immune system, with far-reaching roles in antiviral defense, autoinflammation, and cancer. Z-DNA binding protein 1 (ZBP1) is a sensor for double-stranded DNA and RNA helices in the unusual left-handed Z conformation termed Z-DNA and Z-RNA. Recent research established ZBP1 as a key upstream regulator of cell death and proinflammatory signaling. Recognition of Z-DNA/RNA by ZBP1 promotes host resistance to viral infection but can also drive detrimental autoinflammation. Additionally, ZBP1 has interesting roles in cancer and other disease settings and is emerging as an attractive target for therapy. Biology and Life Sciences Medicine and Health Sciences DNA-DEPENDENT ACTIVATOR INNATE IMMUNE-RESPONSES IFN-REGULATORY FACTORS DOUBLE-STRANDED-RNA BINDING DOMAIN DAI DLM-1/ZBP1 PROTEIN NECROPTOSIS CYTOMEGALOVIRUS INHIBITION http://hdl.handle.net/1854/LU-01HJ3N5ANRA583MECH3DJ97VVG 10.1084/jem.20221156 001028868600001 0022-1007 1540-9538 e20221156 12 p. 2023 0022-1007 1540-9538 2023 220 8 2023 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/01HJ3N5ANRA583MECH3DJ97VVG/file/01HJ3NF6RRDJWW7B91WBNJ21C7 application/pdf ug 01HJ3N5ANRA583MECH3DJ97VVG 2023-12-20T13:03:11Z 2026-03-31T13:26:37Z A1 VABB-1 66 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Facundo Ramos aut author Laura Durán aut author Mar Sánchez aut author Adrián Campos aut author David Hernandez Villamor aut author ug_LA25 0000-0002-9055-4431 Francisco Antequera aut author Andrés Clemente-Blanco aut author eng Homologous recombination is essential to maintain genome stability in response to DNA damage. Here, we have used genome-wide sequencing to quantitatively analyze at nucleotide resolution the dynamics of DNA end resection, re-synthesis, and gene conversion at a double-strand break. Resection initiates asymmetrically in an MRX-independent manner before proceeding steadily in both directions. Sgs1, Exo1, Rad51, and Srs2 differently regulate the rate and symmetry of early and late resection. Exo1 also ensures the coexistence of resection and re-synthesis, while Srs2 guarantees a constant and symmetrical DNA re -polymerization. Gene conversion is MMR independent, spans only a minor fraction of the resected region, and its unidirectionality depends on Srs2. Finally, these repair factors prevent the development of alterations remote from the DNA lesion, such as subtelomeric instability, duplication of genomic regions, and over-replication of Ty elements. Altogether, this approach allows a quantitative analysis and a direct genome-wide visualization of DNA repair by homologous recombination. Biology and Life Sciences DOUBLE-STRAND BREAKS MOLECULAR-STRUCTURES DAMAGE RESPONSE REPAIR REPLICATION HELICASE RESECTION COMPLEX PROTEINS SAE2 http://hdl.handle.net/1854/LU-01HHKYRXTNXHN7XVCX7FR5VVHN 10.1016/j.celrep.2021.110201 000747197600006 2211-1247 110201 22 p. 2022 2211-1247 2022 38 2 2022 Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Public License (CC BY-NC-ND 4.0) published https://biblio.ugent.be/publication/01HHKYRXTNXHN7XVCX7FR5VVHN/file/01HHKYSPB1A2V0JXF2AJ1075YC application/pdf ug 01HHKYRXTNXHN7XVCX7FR5VVHN 2023-12-14T10:43:19Z 2026-03-31T13:19:47Z A1 VABB-1 67 info:srw/schema/1/mods-v3.3xml conference C3 Ward De Spiegelaere aut author ug_DI11 0000-0003-2097-8439 Maja Kiselinova aut author ug_UZGent Eva Malatinková aut author ug_UGent Alexander Pasternak aut author Ben Berkhout aut author Linos Vandekerckhove aut author ug_GE35 ug_UZGent 0000-0002-8600-1631 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 2013 2013 No license (in copyright) published https://biblio.ugent.be/publication/5704829/file/5704830 application/pdf ug 5704829 2014-09-18T14:35:51Z 2026-03-31T14:11:17Z C3 68 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Theresa Obermueller aut author Joris Hautekiet aut author Maria Paula Busto aut author Dries Reynders aut author ug_WE02 0000-0001-6875-048X Liliana Belgioia aut author Annemieke Cats aut author Duncan C. Gilbert aut author Stefan A. Koerber aut author Sabine Mai aut author Didier Meulendijks aut author Franz Roedel aut author Ho-Young Yhim aut author Svetlana Hetjens aut author Christel Weiss aut author Christina L. Rasmussen aut author Aivara Urbute aut author Freija Verdoodt aut author Susanne K. Kjaer aut author Miriam Reuschenbach aut author Els Goetghebeur aut author ug_WE02 0000-0002-8896-0721 Magnus von Knebel Doeberitz aut author Marc Arbyn aut author ug_UGent Elena-Sophie Prigge aut author eng Background: High-risk human papillomavirus (hrHPV) types represent the aetiological agents in a major proportion of anal squamous cell carcinomas (ASCC). Several studies have suggested a prognostic relevance of HPV-related markers, particularly hrHPV DNA and p16(INK4a) (p16) protein expression, in patients with ASCC. However, broader evaluation of these prognostic marker candidates has been hampered by small cohort sizes and heterogeneous survival data among the individual studies. We conducted an individual patient data (IPD) meta-analysis to determine the prognostic value of hrHPV DNA and p16 in patients with ASCC while controlling for major clinical and tumour covariates. Patients and methods: A systematic literature search was conducted to identify all published studies analysing p16 alone or in combination with hrHPV DNA and reporting survival data in patients with ASCC. Clinical and tumour-related IPD were requested from authors of potentially eligible studies. Survival analyses were performed with a proportional hazard Cox model stratified by study and adjusted for relevant covariates. The study-specific hazard ratios (HRs) for the exposures were pooled using a random-effects model. Kaplan-Meier curves from different studies were pooled per exposure group and weighted by the study's total sample size. Results: Seven studies providing IPD from 693 patients with ASCC could be included in the meta-analysis. Seventy-six percent of patients were p16+/hrHPV DNA+, whereas 11% were negative for both markers. A discordant marker status was observed in 13% of cases. Patients with p16+/hrHPV DNA+ ASCC showed significantly superior overall survival (OS) compared with patients with p16-/hrHPV DNA- tumours (pooled adjusted HR = 0.26 [95% confidence interval {CI}, 0.14-0.50]) with pooled three-year OS rates of 86% (95% CI, 82-90%) versus 39% (95% CI, 24-54%). Patients with discordant p16 and hrHPV DNA status showed intermediate three-year OS rates (75% [95% CI, 56-86%] for p16+/ hrHPV DNA- and 55% [95% CI, 35-71%] for p16-/hrHPV DNA+ ASCC). Conclusion: This first IPD meta-analysis controlling for confounding variables shows that patients with p16+/hrHPV DNA+ ASCC have a significantly better survival than patients with p16-/hrHPV DNA- tumours. (C) 2021 Elsevier Ltd. All rights reserved. Medicine and Health Sciences Mathematics and Statistics SQUAMOUS-CELL-CARCINOMA HPV-POSITIVE HEAD P16 OVEREXPRESSION EXPRESSION INFECTION ANUS LINES SENSITIVITY PREVENTION WORLDWIDE ASCC Anal squamous cell carcinoma HPV p16 Meta-analysis IPD http://hdl.handle.net/1854/LU-8759667 10.1016/j.ejca.2021.07.041 000701900000019 0959-8049 1879-0852 2021 0959-8049 1879-0852 2021 157 165 178 2021 No license (in copyright) published https://biblio.ugent.be/publication/8759667/file/8759680 application/pdf restricted ug 8759667 2022-06-29T21:52:25Z 2026-03-31T14:01:14Z A1 VABB-1 69 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 0261-4189 1988 7 13 4055 4062 1988 Information pending 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 2026-03-31T13:22:14Z A1 VABB-1 70 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 1359-7345 1364-548X 2017 53 49 6653 6656 2017 No license (in copyright) published https://biblio.ugent.be/publication/8541271/file/8541272 application/pdf restricted ug 8541271 2017-12-11T18:38:54Z 2026-03-31T13:12:58Z A1 VABB-1 71 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Jan Gielen aut author ug_UGent 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 0022-0957 1999 50 337 1421 1422 1999 No license (in copyright) published https://biblio.ugent.be/publication/112647/file/4167609 application/pdf restricted ug 112647 2004-01-14T13:35:00Z 2026-03-31T06:57:38Z A1 VABB-1 72 info:srw/schema/1/mods-v3.3xml journalArticle A2 Benjamin De Leeuw aut author Albert Hoogewijs aut author ug_WE02 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 1790-0832 WSEAS 2009 6 5 859 871 2009 No license (in copyright) published https://biblio.ugent.be/publication/697226/file/1139597 application/pdf ug 697226 2009-06-14T16:51:35Z 2026-03-31T14:23:22Z A2 VABB-1 73 info:srw/schema/1/mods-v3.3xml journalArticle Review A1 Toon Cools aut author ug_UGent Lieven De Veylder aut author ug_WE09 0000-0003-1150-4426 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 1369-5266 2009 12 1 23 28 2009 Information pending published https://biblio.ugent.be/publication/528543/file/536603 application/pdf restricted ug 528543 2009-03-23T16:48:16Z 2026-03-31T14:09:27Z A1 VABB-1 74 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Jilke De Wilde aut author ug_GE31 0000-0003-0392-7162 Ruben Van Paemel aut author ug_UZGent 0000-0001-7324-3570 Andries De Koker aut author ug_UGent 0000-0003-3939-7650 Sofie Roelandt aut author ug_GE31 0009-0005-7741-9023 Sofie Van de Velde aut author ug_GE31 Nico Callewaert aut author ug_GE31 ug_WE10 0000-0003-2069-6917 Jo Van Dorpe aut author ug_GE32 ug_UZGent 0000-0001-8175-2930 David Creytens aut author ug_GE32 ug_UZGent 0000-0002-6064-1673 Bram De Wilde aut author ug_GE35 ug_UZGent 0000-0003-0213-1322 Katleen De Preter aut author ug_GE31 0000-0002-7726-5096 eng Currently, we cannot provide a conclusive diagnosis for 3 to 5% of people who are confronted with cancer. These patients have Cancer of Unknown Primary (CUP), i.e. a metastasized cancer for which the tissue-of-origin cannot be determined. Studies have shown that the DNA methylation profile is a unique ‘fingerprint’ that can be used to classify tumors. Here we use cfRRBS (cell-free reduced representation bisulfite sequencing), a technique that allows us to identify the methylation profile starting from minimal amounts of highly fragmented DNA, for CUP diagnosis on FFPE tissue and liquid biopsies. We collected 80 primary tumor FFPE samples covering 16 tumor entities together with 15 healthy plasma samples to use as custom cfRRBS reference dataset. Entity specific methylation regions (ESRs) are defined for each entity to build a classifier based on non-negative least squares (NNLS) deconvolution. This classification framework was tested on 30 FFPE, 19 plasma and 40 pleural and peritoneal effusion samples of both known metastatic tumors and clinical CUPs for which pathological investigation finally resulted in a cancer diagnosis. Using this framework, 27/30 FFPE (all CUPs) and 16/19 plasma samples (10/13 CUPs) obtained an accurate diagnosis, with a minimal DNA input of 400 pg. Of the 40 pleural and peritoneal effusion samples, diagnosis is possible in 9/27 samples with negative/inconclusive cytology (6/13 CUPs), showing that cfDNA methylation profiling could complement routine cytological analysis. However, a low “cfDNA – high molecular weight DNA ratio” has a considerable impact on the prediction accuracy. Moreover, the accuracy improves significantly if the predicted tumor percentage is higher than 7%. This proof-of-concept study shows the feasibility of using DNA methylation profiling on FFPE and liquid biopsy samples such as blood, ascites and pleural effusions in a fast and affordable way. Our novel RRBS-based technique requires minimal DNA input, can be performed in less than one week and is highly adaptable to specific diagnostic problems as we only use 5 FFPE references per tumor entity. We believe that cfRRBS methylation profiling could be a valuable addition to the pathologist’s toolbox in the diagnosis of CUPs. Medicine and Health Sciences cancer of unknown primary circulating cell-free DNA DNA methylation computational deconvolution formalin-fixed paraffin embedded tissue liquid biopsies CELL-FREE DNA PROGNOSTIC-FACTORS MALIGNANT ASCITES LIQUID BIOPSY TUMOR-TISSUE CLASSIFICATION MULTICENTER IMMUNOHISTOCHEMISTRY IDENTIFICATION VALIDATION http://hdl.handle.net/1854/LU-01HZH190Y2S4RYSCC3HEY20KWA 10.1016/j.labinv.2024.102091 001334216100001 0023-6837 1530-0307 102091 16 p. 2024 0023-6837 1530-0307 2024 104 8 2024 Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Public License (CC BY-NC-ND 4.0) published https://biblio.ugent.be/publication/01HZH190Y2S4RYSCC3HEY20KWA/file/01HZH407AWTP1JZ1N3XRTK9MKH application/pdf private https://biblio.ugent.be/publication/01HZH190Y2S4RYSCC3HEY20KWA/file/01JE6B7DDSR53DE5Z6KD1T3MGM application/pdf restricted ug 01HZH190Y2S4RYSCC3HEY20KWA 2024-06-04T07:09:06Z 2026-03-31T14:23:45Z A1 VABB-1 75 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Flavia Zita Francies aut author Rosalind Wainwright aut author Janet Poole aut author Kim De Leeneer aut author ug_GE31 ug_UZGent 0000-0002-9319-411X Ilse Coene aut author ug_UZGent Greet Wieme aut author ug_GE55 ug_UZGent 0000-0003-2718-5300 Hélène A Poirel aut author Bénédicte Brichard aut author Stephanie Vermeulen aut author ug_UGent 0000-0002-9655-2293 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 0000-0002-2578-7917 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 1568-7864 2018 61 17 24 2018 No license (in copyright) published https://biblio.ugent.be/publication/8537947/file/8546035 application/pdf restricted ug 8537947 2017-11-18T10:38:05Z 2026-03-31T14:59:16Z A1 VABB-1 76 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Sylvie De Buck aut author ug_GE35 ug_UZGent 0000-0001-8048-0582 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 0894-0282 1998 11 6 449 457 1998 No license (in copyright) published https://biblio.ugent.be/publication/178119/file/4170462 application/pdf restricted ug 178119 2004-01-14T13:41:00Z 2026-03-31T07:35:32Z A1 VABB-1 77 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Rim Ghedira aut author ug_UGent Nina Papazova aut author Marnik Vuylsteke aut author ug_GE31 ug_WE10 Tom Ruttink aut author ug_WE09 0000-0002-1012-9399 Isabel Taverniers aut author Marc De Loose aut author ug_UGent 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 0021-8561 2009 57 20 9370 9377 2009 No license (in copyright) published https://biblio.ugent.be/publication/772476/file/3065378 application/pdf restricted ug 772476 2009-11-05T11:43:38Z 2026-03-31T13:25:59Z A1 VABB-1 78 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Magy Sallam aut author Mohamed Mysara aut author Mohammed Abderrafi Benotmane aut author Anne P. G. Crijns aut author Daan Spoor aut author Filip Van Nieuwerburgh aut author ug_FW01 0000-0001-8815-5485 Dieter Deforce aut author ug_FW01 0000-0002-0635-661X Sarah Baatout aut author ug_WE05 Pieter-Jan Guns aut author An Aerts aut author Raghda Ramadan aut author eng Radiation-Induced CardioVascular Disease (RICVD) is an important concern in thoracic radiotherapy with complex underlying pathophysiology. Recently, we proposed DNA methylation as a possible mechanism contributing to RICVD. The current study investigates DNA methylation in heart-irradiated rats and radiotherapy-treated breast cancer (BC) patients. Rats received fractionated whole heart X-irradiation (0, 0.92, 6.9 and 27.6 Gy total doses) and blood was collected after 1.5, 3, 7 and 12 months. Global and gene-specific methylation of the samples were evaluated; and gene expression of selected differentially methylated regions (DMRs) was validated in rat and BC patient blood. In rats receiving an absorbed dose of 27.6 Gy, DNA methylation alterations were detected up to 7 months with differential expression of cardiac-relevant DMRs. Of those, SLMAP showed increased expression at 1.5 months, which correlated with hypomethylation. Furthermore, E2F6 inversely correlated with a decreased global longitudinal strain. In BC patients, E2F6 and SLMAP exhibited differential expression directly and 6 months after radiotherapy, respectively. This study describes a systemic radiation fingerprint at the DNA methylation level, elucidating a possible association of DNA methylation to RICVD pathophysiology, to be validated in future mechanistic studies. Biology and Life Sciences Chemistry DNA methylation gene expression cardiovascular disease ionizing radiation breast cancer patient http://hdl.handle.net/1854/LU-01GNF2KK98NW71RAC3YHC9W4H8 10.3390/ijms232416214 000902457500001 1422-0067 16214 21 p. 2022 1422-0067 2022 23 24 2022 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/01GNF2KK98NW71RAC3YHC9W4H8/file/01GNF2N59Y872XXD83ASFSB6CJ application/pdf ug 01GNF2KK98NW71RAC3YHC9W4H8 2022-12-29T13:54:35Z 2026-03-31T13:19:37Z A1 VABB-1 79 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Maartje Massen aut author Kim Lommen aut author Kim A. D. Wouters aut author Johan Vandersmissen aut author Wim Van Criekinge aut author ug_LA26 0000-0003-2971-5539 James G. Herman aut author Veerle Melotte aut author Leo J. Schouten aut author Manon van Engeland aut author Kim M. Smits aut author eng Background DNA methylation biomarkers for early detection, risk stratification and treatment response in cancer have been of great interest over the past decades. Nevertheless, clinical implementation of these biomarkers is limited, as only < 1% of the identified biomarkers is translated into a clinical or commercial setting. Technical factors such as a suboptimal genomic location of the assay and inefficient primer or probe design have been emphasized as important pitfalls in biomarker research. Here, we use eleven diagnostic DNA methylation biomarkers for colorectal cancer (ALX4, APC, CDKN2A, MGMT, MLH1, NDRG4, SDC2, SFRP1, SFRP2, TFPI1 and VIM), previously described in a systematic literature search, to evaluate these pitfalls. Results To assess the genomic assay location, the optimal genomic locations according to TCGA data were extracted and compared to the genomic locations used in the published assays for all eleven biomarkers. In addition, all primers and probes were technically evaluated according to several criteria, based on literature and expert opinion. Both assay location and assay design quality varied widely among studies. Conclusions Large variation in both assay location and design hinders the development of future DNA methylation biomarkers as well as inter-study comparability. Medicine and Health Sciences Biology and Life Sciences CELL-FREE DNA CPG ISLAND HYPERMETHYLATION COLORECTAL-CANCER FECAL DNA POTENTIAL MARKER PROMOTER HYPERMETHYLATION GENE METHYLATION STOOL SAMPLES SERUM SFRP2 Epigenetics DNA methylation Diagnosis Biomarkers Assay design Genomic location Cancer biomarkers http://hdl.handle.net/1854/LU-01GWXYRNM91PKF1A28FRSZZW9E 10.1186/s13148-022-01273-z 000788319500003 1868-7075 1868-7083 56 12 p. 2022 1868-7075 1868-7083 2022 14 1 2022 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/01GWXYRNM91PKF1A28FRSZZW9E/file/01GX695C7DRT0YZD4XPB6JD4EF application/pdf ug 01GWXYRNM91PKF1A28FRSZZW9E 2023-04-01T08:25:57Z 2026-03-31T05:49:14Z A1 VABB-1 80 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 0000-0003-1150-4426 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 1040-4651 2015 27 1 149 161 2015 No license (in copyright) published https://biblio.ugent.be/publication/5930802/file/5930812 application/pdf restricted ug 5930802 2015-04-13T13:51:59Z 2026-03-31T14:17:43Z A1 VABB-1 81 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Joana Sabino-Pinto aut author E. Tobias Krause aut author Molly C. Bletz aut author An Martel aut author ug_DI05 0000-0001-7609-5649 Frank Pasmans aut author ug_DI05 0000-0003-3160-503X Sebastian Steinfartz aut author Miguel Vences aut author eng Epidemiology relies on understanding the distribution of pathogens which often can be detected through DNA-based techniques, such as quantitative Polymerase Chain Reaction (qPCR). Typically, the DNA of each individual sample is separately extracted and undergoes qPCR analysis. However, when performing field surveys and long-term monitoring, a large fraction of the samples is generally expected to be negative, especially in geographical areas still considered free of the pathogen. If pathogen detection within a population - rather than determining its individual prevalence - is the focus, work load and monetary costs can be reduced by pooling samples for DNA extraction. We test and refine a user-friendly technique where skin swabs can be pooled during DNA extraction to detect the amphibian chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans (Bsal). We extracted pools with different numbers of samples (from one to four swabs), without increasing reaction volumes, and each pool had one sample inoculated with a predetermined zoospore amount. Pool size did not reduce the ability to detect the two fungi, except if inoculated with extremely low zoospore amounts (one zoospore). We confirm that pooled DNA extraction of cutaneous swabs can substantially reduce processing time and costs without minimizing detection sensitivity. This is of relevance especially for the new emerging pathogen Bsal, for which pooled DNA extraction had so far not been tested and massive monitoring efforts in putatively unaffected regions are underway. Veterinary Sciences BATRACHOCHYTRIUM-DENDROBATIDIS SP-NOV PCR CHYTRIDIOMYCOSIS DISEASE SALAMANDRIVORANS PROTOCOL SAMPLES SPREAD ASSAYS Batrachochytrium dendrobatidis B. salamandrivorans chytridiomycosis epidemiology pathogen survey Prepman Qiagen http://hdl.handle.net/1854/LU-8625947 10.1163/15685381-20181011 000455990000003 0173-5373 1568-5381 2019 0173-5373 1568-5381 2019 40 1 29 39 2019 No license (in copyright) published https://biblio.ugent.be/publication/8625947/file/8625948 application/pdf restricted ug 8625947 2019-08-27T07:37:14Z 2023-05-08T11:50:00Z A1 VABB-1 82 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Sunee Kertbundit aut author Henri De Greve aut author Francine Deboeck aut author Marc Van Montagu aut author ug_WE09 Jean-Pierre Hernalsteens aut author eng Vectors were constructed for the isolation of random transcriptional and translational β-glucuronidase gene fusions in plants. This system is based on the random integration of the transferred DNA (T-DNA) into the plant nuclear genome. The <i>Escherichia coli</i> β-glucuronidase coding sequence without promoter, and also devoid of its ATG initiation site in the translational gene fusion vector, was inserted in the T-DNA with its 5' end at a distance of 4 base pairs from the right T-DNA border sequence. Transgenic plants can be selected by using a chimeric (P35S-nptII-3' ocs) kanamycin-resistance gene present in the same T-DNA. Subsequent screening of these for β-glucuronidase expression allows the identification of clones harboring a fusion of the β-glucuronidase coding sequence with plant 5' regulatory sequences. After transformation of <i>Arabidopsis thaliana</i> C24 root explants, β-glucuronidase expression was detected in 54% and 1.6% of the plants transformed with the transcriptional and translational fusion vectors, respectively. Several different patterns of tissue-specific β-glucuronidase expression were identified. The plant upstream sequence of a β-glucuronidase fusion that is specifically expressed in the phloem of all organs was cloned and sequenced. After introduction in <i>A. thaliana</i> C24 and <i>Nicotiana tabacum</i> SR1, this sequence mediates the same highly phloem-specific β-glucuronidase expression pattern as in the original transgenic plant from which it was isolated. These data demonstrate that this system facilitates the isolation and analysis of plant DNA sequences mediating regulated gene expression. Biology and Life Sciences AGROBACTERIUM-TUMEFACIENS MEDIATED TRANSFORMATION PLANT-CELLS DNA EXPRESSION SEQUENCES CLONING VECTORS IDENTIFICATION EXPLANTS PLANT GENE EXPRESSION INSERTIONAL MUTAGENESIS PROMOTER CLONING TRANSGENIC PLANTS PHLOEM-SPECIFIC GENE EXPRESSION http://hdl.handle.net/1854/LU-8628561 10.1073/pnas.88.12.5212 A1991FR44800031 0027-8424 1991 0027-8424 1991 88 12 5212 5216 1991 No license (in copyright) published https://biblio.ugent.be/publication/8628561/file/8628587 application/pdf restricted ug 8628561 2019-09-17T13:06:39Z 2023-05-08T11:50:06Z A1 VABB-1 83 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 0300-9084 1984 66 7-8 547 556 1984 No license (in copyright) published https://biblio.ugent.be/publication/6930706/file/6932050 application/pdf restricted ug 6930706 2015-09-15T13:55:00Z 2026-03-31T14:22:57Z A1 VABB-1 84 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 0009-0003-3597-5254 Moritz Nowack aut author ug_WE09 0000-0001-8918-7577 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 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 2026-03-31T14:30:33Z A1 VABB-1 85 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 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 2026-03-31T14:28:37Z A1 VABB-1 86 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Geert Huys aut author ug_UGent Margo Cnockaert aut author ug_WE10 0000-0001-7319-7463 Sharon L Abbott aut author J Michael Janda aut author Peter Vandamme aut author ug_WE10 0000-0002-5581-7937 eng It has been shown previously, based largely on DNA-DNA hybridizations and partial 16S rRNA gene sequencing, that Hafnia alvei is genotypically heterogeneous and consists of at least two DNA hybridization groups (HGs). In the present study, the taxonomic status of H. alvei HGs 1 and 2 was reassessed. A panel of 24 reference strains and isolates previously assigned to one of the two HGs in H. alvei was subjected to (GTG)(5)-PCR fingerprinting; this resulted in the delineation of two (GTG)(5)-PCR clusters in perfect accordance with the respective HG designations. Based on full 16S rRNA gene sequencing of a selection of reference strains, H. alvei HGs 1 and 2 showed internal sequence similarities of 99.8 and 99.5%, respectively. Between the two groups, sequence similarities ranged from 98.8 to 99.1%. Mean DNA-DNA hybridization values of 74.7-99.9% were obtained within each of the two HGs, whereas cross-hybridizations between members of H. alvei HG 1 (including ATCC 133371) and HG 2 revealed only 32.7-48.7% DNA-DNA hybridization. Previously published and new phenotypic data revealed that a combination of malonate assimilation and beta-glucosidase activity enabled correct assignment of Hafnia isolates to one of the two HGs. Collectively, taxonomic data from this study confirm that H. alvei comprises at least two taxa at the species level, of which HG 1 corresponds to H. alvei sensu stricto because it includes the type strain ATCC 13337(T). Strains formerly classified as members of H. alvei HG 2 represent a novel species, for which the name Hafnia paralvei sp. nov. is proposed; ATCC 29927(T) (=CDC 4510-73(T) =LMG 24706(T)), the former reference strain of H. alvei HG 2, is designated the type strain. Biology and Life Sciences DEOXYRIBONUCLEIC-ACID IDENTIFICATION GENUS HAFNIA DNA http://hdl.handle.net/1854/LU-1203775 10.1099/ijs.0.018606-0 000281175700004 1466-5026 2010 1466-5026 2010 60 8 1725 1728 2010 No license (in copyright) published https://biblio.ugent.be/publication/1203775/file/1203869 application/pdf restricted ug 1203775 2011-04-06T16:49:44Z 2026-03-31T07:14:45Z A1 VABB-1 87 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Masja Schmidt aut author Amber Werbrouck aut author 0000-0003-3854-7717 Nick Verhaeghe aut author ug_GE39 0000-0001-9956-4970 Elke De Wachter aut author Steven Simoens aut author Lieven Annemans aut author ug_GE39 0000-0001-8305-7210 Koen Putman aut author eng Objectives: The most cost-effective newborn screening strategy for cystic fibrosis (CF) for Flanders, Belgium, is unknown. The aim of this study was to assess the cost-effectiveness of four existing newborn screening strategies for CF: IRT-DNA (immunoreactive trypsinogen, cystic fibrosis transmembrane conductance regulator (CFTR) gene mutation analysis), IRT-PAP (pancreatitis-associated protein), IRT-PAP-DNA, and IRT-PAP-DNA-EGA (extended CFTR gene analysis). Methods: Using data from published literature, the cost-effectiveness of the screening strategies was calculated for a hypothetical cohort of 65,606 newborns in Flanders, Belgium. A healthcare payer perspective was used, and the direct medical costs associated with screening were taken into account. The robustness of the model outcomes was assessed in sensitivity analyses. Results: The IRT-PAP strategy was the most cost-effective strategy in terms of costs per CF case detected (euro9314 per CF case detected). The IRT-DNA strategy was more costly (euro13,966 per CF case detected), but with an expected sensitivity of 93.4% also the most effective strategy, and was expected to detect 2.2 more cases of CF than the IRT-PAP strategy. The incremental cost-effectiveness ratio of IRT-DNA vs. IRT-PAP was euro54,180/extra CF case detected. The IRT-PAP-DNA strategy and the IRT-PAP-DNA-EGA strategy were both strongly dominated by the IRT-PAP strategy. Conclusion: The IRT-PAP strategy was the most cost-effective strategy in terms of costs per CF case detected. However, the strategy did not fulfil the European Cystic Fibrosis Society guidelines for sensitivity and positive predictive value. Therefore, the more costly and more effective IRT-DNA strategy may be the most appropriate newborn screening strategy for Flanders. Medicine and Health Sciences Newborn screening cystic fibrosis health economic evaluation cost-effectiveness analysis decision analytic modelling COST-EFFECTIVENESS DIAGNOSIS TRYPSINOGEN MANAGEMENT INFANTS ASSAYS http://hdl.handle.net/1854/LU-8624473 10.1080/17843286.2019.1604472 000469687900001 1784-3286 2295-3337 2020 1784-3286 2295-3337 2020 75 3 212 220 2020 No license (in copyright) published https://biblio.ugent.be/publication/8624473/file/8624474 application/pdf restricted ug 8624473 2019-08-07T09:44:02Z 2023-05-08T11:49:57Z A1 VABB-1 88 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Thomas Condijts aut author ug_UZGent Liesl Bourdeaud'huy aut author Kelly Tilleman aut author ug_UZGent Sylvie Lierman aut author ug_UZGent Chantal Dewinter aut author ug_UZGent Elizaveta Padalko aut author ug_GE32 ug_UZGent 0000-0002-8101-6957 eng Hepatitis B virus (HBV) incorporates into spermatozoa which raises safety concerns about paternofetal transmission performing intracytoplasmatic sperm injection (ICSI) in men with chronic hepatitis B (cHB). HBV reduces sperm cell motility, assuming spermatozoa with highest motility are least HBV-incorporated. This study investigates an ICSI preparation technique (swim-up) to isolate most motile spermatozoa in order to select HBV-free spermatozoa. Semen and blood samples were collected from four patients with cHB. Spermatozoa were incubated in trajectories of gamete medium to create non-motile, motile/non-progressive and motile/progressive fractions. After DNA-extraction, HBV DNA loads were determined in every fraction. Participants (mean age 31) were HBsAg+(4/4), anti-HBc+(4/4) and HBV DNA+(2/4). They were treated (3/4) with entecavir(1/4) or tenofovir (2/4) and had no adverse sperm parameters(3/4). CRP-gene was detected in 95/96 sample fractions, proving successful DNA-extraction. HBV DNA was detected in none of the sample fractions, except for the motile, non-progressive fraction of one patient (HBeAg+, HBV DNA+). Since no HBV DNA was detected in progressive fractions, this study suggests swim-up a successful strategy to select HBV-free spermatozoa. Since all but one fraction was HBV DNA-negative, this study also suggests that patients with well-controlled disease have no HBV-contaminated sample fractions. This study encourages evaluation of guidelines restricting reproductive possibilities in men with cHB. Medicine and Health Sciences MALE-INFERTILITY SEMEN QUALITY VIRUS TRANSMISSION EXPRESSION INFECTION TENOFOVIR OOCYTES EMBRYOS IMPACT HBV infertility spermatozoa swim-up http://hdl.handle.net/1854/LU-8715538 10.1111/and.13732 000582484400029 0303-4569 1439-0272 e13732 8 p. 2020 0303-4569 1439-0272 2020 52 10 2020 No license (in copyright) published https://biblio.ugent.be/publication/8715538/file/8715539 application/pdf restricted ug 8715538 2021-07-09T13:57:38Z 2023-05-08T11:53:11Z A1 VABB-1 89 info:srw/schema/1/mods-v3.3xml journalArticle Review A1 Maísa Renata Ferro Dos Santos aut author ug_UGent 0000-0002-1336-5434 Edoardo Giuili aut author ug_GE31 0000-0003-2763-3767 Andries De Koker aut author ug_UGent 0000-0003-3939-7650 Celine Everaert aut author ug_GE31 0000-0001-7772-4259 Katleen De Preter aut author ug_GE31 0000-0002-7726-5096 eng In this review, we provide a comprehensive overview of the different computational tools that have been published for the deconvolution of bulk DNA methylation (DNAm) data. Here, deconvolution refers to the estimation of cell-type proportions that constitute a mixed sample. The paper reviews and compares 25 deconvolution methods (supervised, unsupervised or hybrid) developed between 2012 and 2023 and compares the strengths and limitations of each approach. Moreover, in this study, we describe the impact of the platform used for the generation of methylation data (including microarrays and sequencing), the applied data pre-processing steps and the used reference dataset on the deconvolution performance. Next to reference-based methods, we also examine methods that require only partial reference datasets or require no reference set at all. In this review, we provide guidelines for the use of specific methods dependent on the DNA methylation data type and data availability. Medicine and Health Sciences Biology and Life Sciences DNA methylation profiling computational deconvolution tool comparison EPIGENOME-WIDE ASSOCIATION CELL-TYPE DECONVOLUTION CLASSIFICATION HETEROGENEITY EXPRESSION CAPTURE http://hdl.handle.net/1854/LU-01HZH0ZMSH54R7P6HP6N6SREE6 10.1093/bib/bbae234 001273453500002 1467-5463 1477-4054 bbae234 12 p. 2024 1467-5463 1477-4054 2024 25 3 2024 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/01HZH0ZMSH54R7P6HP6N6SREE6/file/01HZH13X8VAMBQKNM0YHBNEKCC application/pdf ug 01HZH0ZMSH54R7P6HP6N6SREE6 2024-06-04T07:03:59Z 2026-04-24T06:55:17Z A1 VABB-1 90 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 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 0026-8925 1981 182 2 255 262 1981 No license (in copyright) published https://biblio.ugent.be/publication/5673011/file/5673098 application/pdf restricted ug 5673011 2014-08-13T17:38:03Z 2026-03-31T14:10:36Z A1 VABB-1 91 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Alex Manicardi aut author ug_UGent 0000-0003-0083-1392 Andrea Rozzi aut author Saša Korom aut author Roberto Corradini aut author eng Peptide nucleic acids (PNAs) are polyamide analogues of nucleic acids, very effective in terms of affinity and selectivity in DNA/RNA recognition. As other supramolecular entities, the PNA structure has been an interesting scaffold for the development of new molecules, aimed to DNA and RNA recognition, with improved or completely new properties. This review describes recent work, with the aim of describing how the design of these molecules has evolved in recent years, using increasingly effective tools, from simple crystal structure analysis to molecular dynamics and metadynamics. Modified PNA with additional modules appended, either on the backbone or on the nucleobase, are described. Polyfunctional molecules with both backbone and nucleobase modification are then considered. Finally, recent examples of architectures obtained by conjugation of PNAs to inorganic nanostructures as cargo systems for diagnostics and nano-biotechnology are presented. Biology and Life Sciences Technology and Engineering PNA chirality DNA recognition microRNA nanomedicine MESOPOROUS SILICA NANOPARTICLES HELICAL B-DNA MOLECULAR-DYNAMICS GAMMA-PNA CRYSTAL-STRUCTURE IN-VIVO CHEMICAL BIOLOGY MIXED-SEQUENCE TRIPLE-HELIX GENOMIC DNA http://hdl.handle.net/1854/LU-8646363 10.1080/10610278.2017.1371720 000415626000003 1061-0278 1029-0478 2017 1061-0278 1029-0478 2017 29 11 784 795 2017 No license (in copyright) published https://biblio.ugent.be/publication/8646363/file/01JKT9JEAMGHMR966WXGBTYT9Y application/pdf restricted ug 8646363 2020-02-06T11:24:24Z 2026-03-31T14:16:45Z A1 VABB-1 92 info:srw/schema/1/mods-v3.3xml dissertation D1 Pieter Windels aut author Anna Depicker promoter ug_WE09 0000-0003-0105-7407 Marc De Loose promoter ug_UGent Erik Van Bockstaele promoter ug_UGent eng Biology and Life Sciences http://hdl.handle.net/1854/LU-3161746 251 p. Ghent, Belgium Ghent University. Faculty of Sciences 2004 published ug 3161746 2013-03-11T11:03:09Z 2026-03-31T14:38:23Z D1 93 info:srw/schema/1/mods-v3.3xml conference C1 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 4 p. 2017 2017 2017 No license (in copyright) published https://biblio.ugent.be/publication/8542587/file/8542588 application/pdf ug 8542587 2017-12-19T15:20:50Z 2026-03-31T13:13:06Z C1 VABB-5 94 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Daisy Vanrompay aut author ug_LA22 0000-0002-1713-0421 Eric Cox aut author ug_DI04 0000-0003-4281-2990 P KAISER aut author S LAWSON aut author M VAN LOOCK aut author G VOLCKAERT aut author BM GODDDEERIS aut author eng Plasmid DNA (pcDNA1::MOMP A) expressing the major outer membrane protein of an avian Chlamydophila psittaci serovar A strain was tested for its ability to induce protective immunity against challenge with the same C. psittaci serovar. A combined parenteral (intramuscular injection) and mucosal route (DNA drops administered to the nares) of DNA inoculation was compared to three other, different routes of administration (intramuscular inoculation, DNA drops administered to the nares and aerosol immunization). In addition, the effect of turkey interferon gamma (tIFN-gamma) on intramuscular immunization was evaluated by co-expressing pCIneo::tIFN-gamma. A significant level of protection was observed in turkeys immunized via the combined parenteral/mucosal route, the intramuscular route or by aerosol. Severe clinical signs and lesions were observed in the nonvaccinated control groups, in 80% of turkeys inoculated with a mixture of pcDNA1::MOMP A and pCIneo::tIFN-gamma and in 60% of turkeys vaccinated with DNA drops administered to the nares. The use of MOMP-based DNA Vaccination as a means of preventing severe clinical signs and lesions in a turkey model of C. psittaci infection was demonstrated, as was down-regulation of the immune response by co-expression of tIFN-gamma. Medicine and Health Sciences Veterinary Sciences http://hdl.handle.net/1854/LU-145967 10.1046/j.1365-2567.2001.01215.x 000168980400013 0019-2805 1365-2567 2001 0019-2805 1365-2567 2001 103 1 106 112 2001 No license (in copyright) published https://biblio.ugent.be/publication/145967/file/01HK9TSGW72PX6A2CABGQ17X8K application/pdf restricted ug 145967 2004-01-14T13:38:00Z 2026-03-31T13:19:48Z A1 VABB-1 95 info:srw/schema/1/mods-v3.3xml journalArticle Review A1 Claudina Perez Novo aut author ug_UGent Claus Bachert aut author ug_UGent 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 1528-4050 2015 15 1 27 32 2015 No license (in copyright) published https://biblio.ugent.be/publication/6862684/file/6862751 application/pdf restricted ug 6862684 2015-07-03T15:14:06Z 2026-03-31T14:21:15Z A1 VABB-1 96 info:srw/schema/1/mods-v3.3xml dissertation D1 Jacopo Di Sora aut author ug_UGent 0000-0002-9783-5666 Alain Goossens promoter ug_WE09 0000-0002-1599-551X eng Tomaten geteeld in hydrocultuur worden steeds vaker getroffen door de harige wortelziekte (HRD), veroorzaakt door rhizogene agrobacteriën. Deze ziekte leidt tot overmatige wortelgroei, een lagere fruitopbrengst en aanzienlijke economische verliezen. HRD ontstaat wanneer het T-DNA van het pRi-plasmide van deze bacteriën wordt overgedragen naar plantencellen, waar het integreert in het gastheergenoom en ziektegerelateerde processen activeert. Hoewel het T-DNA codeert voor meerdere eiwitten die HRD bevorderen, zijn hun moleculaire functies grotendeels onbekend. Dit proefschrift had als doel de moleculaire functies van deze T-DNA-eiwitten te ontrafelen. We identificeerden vier eiwitten geschikt voor interactieonderzoek en gebruikten Y2H-seq om hun interactienetwerken in tomaat te analyseren. Eén van de vier eiwitten werd gevalideerd met binaire methoden als interactiepartner van een chromatine-remodelleringsfactor en in planta-experimenten werden gebruikt voor functionele analyse van deze interactie. Daarnaast werd de enzymatische activiteit van twee T-DNA-eiwitten onderzocht, waarvan er één betrokken bleek bij de synthese van metabolieten die plantengroei en stressreacties reguleren. Deze bevindingen bieden nieuw inzicht in de moleculaire mechanismen van de T-DNA eiwitten van HRD. Biology and Life Sciences Chemistry Technology and Engineering http://hdl.handle.net/1854/LU-01JWZM2EBAMX6N9BSRGWTHD60E 233 p. Ghent, Belgium Ghent University. Faculty of Bioscience Engineering 2025 No license (in copyright) published Gent : Campus Zwijnaarde, FSVM-gebouw https://biblio.ugent.be/publication/01JWZM2EBAMX6N9BSRGWTHD60E/file/01JWW3TRV0PHY42SWHP4FGG3YY application/pdf private(changes to open on 2040-12-31) ug 01JWZM2EBAMX6N9BSRGWTHD60E 2025-06-05T08:42:08Z 2026-03-31T14:49:24Z D1 97 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Gordana Marjanac aut author ug_WE09 Annelies De Paepe aut author ug_CA20 Ingrid Peck aut author ug_WE09 Anni Jacobs aut author ug_WE09 Sylvie De Buck aut author ug_GE35 ug_UZGent 0000-0001-8048-0582 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 0962-8819 2008 17 2 239 250 2008 No license (in copyright) published https://biblio.ugent.be/publication/409425/file/3065498 application/pdf restricted ug 409425 2008-05-15T18:03:00Z 2026-03-31T13:26:32Z A1 VABB-1 98 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Andrea Pagano aut author Carolina Gomes aut author Evy Timmerman aut author ug_GE31 0000-0002-6662-1884 Paweł Sulima aut author Jerzy Andrzej Przyborowski aut author Dariusz Kruszka aut author Francis Impens aut author ug_GE31 0000-0003-2886-9616 Jorge Almiro Pinto Paiva aut author eng Introduction: DNA methylation plays major roles in the epigenetic regulation of gene expression, transposon and transcriptional silencing, and DNA repair, with implications in developmental processes and phenotypic plasticity. Relevantly for woody species, DNA methylation constitutes a regulative layer in cell wall dynamics associated with xylogenesis. The use of methyltransferase and/or demethylase inhibitors has been proven informative to shed light on the methylome dynamics behind the regulation of these processes. Methods: The present work employs the cytidine analog zebularine to inhibit DNA methyltransferases and induce DNA hypomethylation in Salix purpurea plantlets grown in vitro and in soil. An integrative approach was adopted to highlight the effects of zebularine on proteomic dynamics, revealing age-specific (3 weeks of in vitro culture and 1 month of growth in soil) and tissue-specific (stem and root) effects. Results and discussion: After 3 weeks of recovery from zebularine treatment, a decrease of 5-mC levels was observed in different genomic contexts in the roots of explants that were exposed to zebularine, whereas a functionally heterogeneous subset of protein entries was differentially accumulated in stem samples, including entries related to cell wall biosynthesis, tissue morphogenesis, and hormonal regulation. Significant proteomic remodeling was revealed in the development from in vitro to in-soil culture, but no significant changes in 5-mC levels were observed. The identification of tissue-specific proteomic hallmarks in combination with hypomethylating agents provides new insights into the role of DNA methylation and proteome in early plant development in willow species. Proteomic data are available via ProteomeXchange with identifier PXD045653. WGBS data are available under BioProject accession PRJNA889596. Biology and Life Sciences proteomic plant development DNA methylation cytidine analogue purple willow http://hdl.handle.net/1854/LU-01HQEC95WE9HST760P3DY6NRJX 10.3389/fpls.2023.1304327 001154007400001 1664-462X 1304327 14 p. 2024 1664-462X 2024 14 2024 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/01HQEC95WE9HST760P3DY6NRJX/file/01HQECA6W657BV2YANB0PASDXG application/pdf ug 01HQEC95WE9HST760P3DY6NRJX 2024-02-24T20:18:07Z 2026-03-31T13:26:45Z A1 VABB-1 99 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Marina De Filette aut author Silke Soehle aut author Sebastian Ulbert aut author Justin Richner aut author Michael S Diamond aut author Alessandro Sinigaglia aut author Luisa Barzon aut author Stefan Roels aut author Julianna Lisziewicz aut author Orsolya Lorincz aut author Niek Sanders aut author ug_DI07 0000-0003-4585-0343 eng West Nile virus (WNV) is a mosquito-borne flavivirus that is endemic in Africa, the Middle East, Europe and the United States. There is currently no antiviral treatment or human vaccine available to treat or prevent WNV infection. DNA plasmid-based vaccines represent a new approach for controlling infectious diseases. In rodents, DNA vaccines have been shown to induce B cell and cytotoxic T cell responses and protect against a wide range of infections. In this study, we formulated a plasmid DNA vector expressing the ectodomain of the E-protein of WNV into nanoparticles by using linear polyethyleneimine (lPEI) covalently bound to mannose and examined the potential of this vaccine to protect against lethal WNV infection in mice. Mice were immunized twice (prime - boost regime) with the WNV DNA vaccine formulated with lPEI-mannose using different administration routes (intramuscular, intradermal and topical). In parallel a heterologous boost with purified recombinant WNV envelope (E) protein was evaluated. While no significant E-protein specific humoral response was generated after DNA immunization, protein boosting of DNA-primed mice resulted in a marked increase in total neutralizing antibody titer. In addition, E-specific IL-4 T-cell immune responses were detected by ELISPOT after protein boost and CD8(+) specific IFN-gamma expression was observed by flow cytometry. Challenge experiments using the heterologous immunization regime revealed protective immunity to homologous and virulent WNV infection. Biology and Life Sciences DOMAIN-III RESPONSES UNITED-STATES CLINICAL-TRIALS ENVELOPE PROTEIN NEUTRALIZING ANTIBODIES T-CELL IN-VITRO GENE DELIVERY DENDRITIC CELLS http://hdl.handle.net/1854/LU-6839374 10.1371/journal.pone.0087837 000336971300003 1932-6203 e87837 10 p. 2014 1932-6203 2014 9 2 2014 No license (in copyright) published https://biblio.ugent.be/publication/6839374/file/6839425 application/pdf https://biblio.ugent.be/publication/6839374/file/6864601 application/pdf ug 6839374 2015-06-22T15:36:17Z 2026-03-31T14:21:01Z A1 VABB-1 100 1.1dna101100srw.ServerChoicescrdna