1.1 981 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 The DNA sequences of T-DNA junctions suggest that complex T-DNA loci are formed by a recombination process resembling T-DNA integration Sylvie De Buck aut author ug_WE09 Anni Jacobs aut author ug_WE09 Marc Van Montagu aut author ug_WE09 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng After Agrobacterium-mediated plant transformation, multiple T-DNAs frequently integrate at the same position in the plant genome, resulting in the formation of inverted and direct repeats. Because these inverted repeats cannot be amplified and analyzed by PCR, Arabidopsis root cells were co-transformed with two different T-DNAs with distinct sequences adjacent to the T-DNA borders. Nine direct or inverted T-DNA border junctions were analyzed at the sequence level. Precise end-to-end fusions were found between two right border ends, whereas imprecise fusions and filler DNA were present in T-DNA linkages containing a left border end. The results suggest that end-to-end ligation of double-stranded T-DNAs occurs especially between right T-DNA ends and that illegitimate recombination on the basis of microhomology, deletions, repair activities and insertions of filler DNA is involved in the formation of left border T-DNA junctions. Therefore, a similar illegitimate recombination mechanism is proposed that is involved in the formation of complex T-DNA inserts as well as in the integration of the T-DNA in the plant genome. Biology and Life Sciences GENOME PROTEIN GENE STRANDED-DNA MEDIATED TRANSFORMATION ILLEGITIMATE RECOMBINATION PLANT-CELLS AGROBACTERIUM-TUMEFACIENS VIRD2 CONJUGATION ARABIDOPSIS http://hdl.handle.net/1854/LU-112589 10.1046/j.1365-313X.1999.00602.x 000084156700004 0960-7412 1999 PLANT JOURNAL Plant J. 0960-7412 1999 20 3 295 304 1999 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/112589/file/4161283 application/pdf restricted ug 112589 2004-01-14T13:35:00Z 2016-12-19T15:36:49Z A1 VABB-1 1 info:srw/schema/1/mods-v3.3xml conference C3 The genomic region encompassing the overlapping SOX11 and Lnc-SOX11-1:1 loci exhibits a complex DNA copy number and mRNA expression pattern Bieke Decaesteker aut author ug_GE02 0000-0003-2264-781X Sara De Brouwer aut author Robrecht Cannoodt aut author ug_GE02 0000-0003-3641-729X Dries Rombaut aut author ug_GE02 0000-0001-7526-7541 Wouter Van Loocke aut author ug_GE02 Annelies Fieuw aut author Fanny De Vloed aut author ug_GE02 Pieter-Jan Volders aut author ug_GE07 0000-0002-2685-2637 Björn Menten aut author ug_GE02 Rogier Versteeg aut author Patrick Reynolds aut author Michael Hogarty aut author Jan Koster aut author Franki Speleman aut author ug_GE02 0000-0002-6628-8559 Katleen De Preter aut author ug_GE02 0000-0002-7726-5096 4th OncoPoint research seminar eng Neuroblastoma (NB) is an aggressive lethal pediatric cancer of the developing sympatho-adrenergic nervous system and characterised by a very low mutation burden while exhibiting highly recurrent DNA copy number alterations. Chromosome 2p gain and more specifically MYCN amplification is observed in most of the high risk cases. Using high-resolution DNA copy number analysis, we identified three NB tumours and two NB cell lines with SOX11 focal amplification. SOX11 is located on 2p25 but independently amplified of MYCN, and a key gene involved in the development of the sympatho-adrenergic lineage and contributing to the NB phenotype as demonstrated by reduced colony formation capacity and induction of G1-S cell cycle arrest upon knock down in NB cells. The SOX11 gene consists of one exon and a very long 3’UTR, targeted by miRNA-204 and miRNA-542-3p, both lower expressed in NB tumours as compared to neuroblasts. Additionally, lnc-SOX11-1:1 is partially overlapping with this 3’UTR and transcribed in sense direction with SOX11. Recently high 3’UTR:CDS ratio’s for neuronal genes and specifically SOX11 were reported, indicating that 3’UTR:CDS ratio can play a role in the development of neuroblastoma. Interestingly, whole genome sequencing of the neuroblastoma CHP-126 cell line revealed a remarkable amplification consisting of the 3’UTR and 5’UTR of SOX11, but excluding the SOX11 exon. Nevertheless, SOX11 mRNA and protein levels were very high while multiple splicing events affecting the 3’UTR were noted. Further analyses are ongoing to explain these enigmatic observations. Biology and Life Sciences http://hdl.handle.net/1854/LU-7174333 2016 OncoPoint, 4th Research seminar, Abstracts 2016 10 10 2016 published ug 7174333 2016-04-04T19:19:08Z 2017-04-10T13:40:47Z C3 2 info:srw/schema/1/mods-v3.3xml bookChapter B2 Where are the Genii Loci? Marc Antrop aut author ug_WE12 eng Science General http://hdl.handle.net/1854/LU-125587 2000 Landscape - Our Home. Essays on the Culture of the European Landscape as a Task / Pedroli, B. (ed.). - Stuttgart : Freies Geistesleben, 2000. - Zeist : Indigo, 2000 29-34 p. 2000 29 34 2000 published ug 125587 2004-01-14T13:36:00Z 2016-12-19T15:40:02Z B2 VABB-4 3 info:srw/schema/1/mods-v3.3xml dissertation D1 Quantitative trait loci and beyond Veronique Storme aut author ug_WE02 ug_WE09 0000-0003-4762-6580 Wout Boerjan promoter ug_WE09 0000-0003-1495-510X eng Biology and Life Sciences http://hdl.handle.net/1854/LU-8137255 Ghent, Belgium Ghent University. Faculty of Sciences 2016 I have transferred the copyright for this publication to the publisher published Zwijnaarde : Technologiepark (FSVM-gebouw) https://biblio.ugent.be/publication/8137255/file/8137287 application/pdf restricted ug 8137255 2016-11-10T09:27:44Z 2017-01-16T10:52:40Z D1 4 info:srw/schema/1/mods-v3.3xml bookEditor B3 Loci sacri: understanding sacred places Thomas Coomans edt editor Herman De Dijn edt editor Jan De Maeyer edt editor Rajesh Heynickx edt editor Bart Verschaffel edt editor ug_TW01 eng This book collects 14 theoretical and historical articles on (the notion of) 'sacred place' and the reuse of sacred places. Philosophy and Religion Sacred Place sacrality http://hdl.handle.net/1854/LU-2015967 9789058678423 Leuven, Belgium Leuven University Press 2012 284 p. KADOC Studies on Religion, Culture and Society 9 95D1BFA2-45AA-11E5-88BC-1805A6EB1512 I have transferred the copyright for this publication to the publisher published https://biblio.ugent.be/publication/2015967/file/6765822 application/pdf restricted https://biblio.ugent.be/publication/2015967/file/6765823 application/pdf restricted ug 2015967 2012-02-02T12:14:50Z 2017-01-02T09:56:13Z B3 VABB-3 5 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 CHARACTERIZATION OF PORCINE POLYMORPHIC MICROSATELLITE LOCI. Wouter Coppieters aut author Alex Van De Weghe aut author Luc Peelman aut author ug_DI07 0000-0003-3853-5310 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 Alex Van Zeveren aut author ug_DI07 Yves Bouquet aut author eng Medicine and Health Sciences http://hdl.handle.net/1854/LU-202224 A1993LJ02100002 0268-9146 1993 ANIMAL GENETICS Anim. Genet. 0268-9146 1993 24 3 163 170 1993 published ug 202224 2004-01-14T13:42:00Z 2016-12-19T15:41:40Z A1 VABB-1 6 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Variant of TYR and Autoimmunity Susceptibility Loci in Generalized Vitiligo. Y Jin aut author SA Birlea aut author PR Fain aut author K Gowan aut author SL Riccardi aut author PJ Holland aut author CM Mailloux aut author AJD Sufit aut author SM Hutton aut author A Amadi-Myers aut author DC Bennett aut author MR Wallace aut author WT McCormack aut author EH Kemp aut author DJ Gawkrodger aut author AP Weetman aut author M Picardo aut author G Leone aut author A Taieb aut author T Jouary aut author K Ezzedine aut author Nanja van Geel aut author ug_GE15 0000-0002-3249-8195 Jo Lambert aut author ug_GE15 0000-0001-5303-9310 A Overbeck aut author RA Spritz aut author eng Abstract BACKGROUND: Generalized vitiligo is an autoimmune disease characterized by melanocyte loss, which results in patchy depigmentation of skin and hair, and is associated with an elevated risk of other autoimmune diseases. METHODS: To identify generalized vitiligo susceptibility loci, we conducted a genomewide association study. We genotyped 579,146 single-nucleotide polymorphisms (SNPs) in 1514 patients with generalized vitiligo who were of European-derived white (CEU) ancestry and compared the genotypes with publicly available control genotypes from 2813 CEU persons. We then tested 50 SNPs in two replication sets, one comprising 677 independent CEU patients and 1106 CEU controls and the other comprising 183 CEU simplex trios with generalized vitiligo and 332 CEU multiplex families. RESULTS: We detected significant associations between generalized vitiligo and SNPs at several loci previously associated with other autoimmune diseases. These included genes encoding major-histocompatibility-complex class I molecules (P=9.05x10(-23)) and class II molecules (P=4.50x10(-34)), PTPN22 (P=1.31x10(-7)), LPP (P=1.01x10(-11)), IL2RA (P=2.78x10(-9)), UBASH3A (P=1.26x10(-9)), and C1QTNF6 (P=2.21x10(-16)). We also detected associations between generalized vitiligo and SNPs in two additional immune-related loci, RERE (P=7.07x10(-15)) and GZMB (P=3.44x10(-8)), and in a locus containing TYR (P=1.60x10(-18)), encoding tyrosinase. CONCLUSIONS: We observed associations between generalized vitiligo and markers implicating multiple genes, some associated with other autoimmune diseases and one (TYR) that may mediate target-cell specificity and indicate a mutually exclusive relationship between susceptibility to vitiligo and susceptibility to melanoma. 2010 Massachusetts Medical Society Medicine and Health Sciences http://hdl.handle.net/1854/LU-967848 000277311200006 0028-4793 2010 NEW ENGLAND JOURNAL OF MEDICINE N Engl J Med. 0028-4793 2010 362 18 1686 1697 2010 published ug 967848 2010-06-02T11:25:09Z 2016-12-19T15:46:30Z A1 VABB-1 7 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Simultaneous mapping of multiple gene loci with pooled segregants Jürgen Claesen aut author Lieven Clement aut author ug_WE02 Ziv Shkedy aut author Maria R Foulquié-Moreno aut author Tomasz Burzykowski aut author eng The analysis of polygenic, phenotypic characteristics such as quantitative traits or inheritable diseases remains an important challenge. It requires reliable scoring of many genetic markers covering the entire genome. The advent of high-throughput sequencing technologies provides a new way to evaluate large numbers of single nucleotide polymorphisms (SNPs) as genetic markers. Combining the technologies with pooling of segregants, as performed in bulked segregant analysis (BSA), should, in principle, allow the simultaneous mapping of multiple genetic loci present throughout the genome. The gene mapping process, applied here, consists of three steps: First, a controlled crossing of parents with and without a trait. Second, selection based on phenotypic screening of the offspring, followed by the mapping of short offspring sequences against the parental reference. The final step aims at detecting genetic markers such as SNPs, insertions and deletions with next generation sequencing (NGS). Markers in close proximity of genomic loci that are associated to the trait have a higher probability to be inherited together. Hence, these markers are very useful for discovering the loci and the genetic mechanism underlying the characteristic of interest. Within this context, NGS produces binomial counts along the genome, i.e., the number of sequenced reads that matches with the SNP of the parental reference strain, which is a proxy for the number of individuals in the offspring that share the SNP with the parent. Genomic loci associated with the trait can thus be discovered by analyzing trends in the counts along the genome. We exploit the link between smoothing splines and generalized mixed models for estimating the underlying structure present in the SNP scatterplots. Biology and Life Sciences IDENTIFICATION SEQUENCING DATA TRAIT http://hdl.handle.net/1854/LU-3195690 10.1371/journal.pone.0055133 000315159200007 1932-6203 e55133 2013 PLOS ONE PLoS One 1932-6203 2013 8 2 2013 I have retained and own the full copyright for this publication published https://biblio.ugent.be/publication/3195690/file/4236477 application/pdf ug 3195690 2013-04-17T14:53:57Z 2016-12-21T15:42:34Z A1 VABB-1 8 info:srw/schema/1/mods-v3.3xml journalArticle Note A1 Dinucleotide repeat polymorphism at the bovine MM12E6 and MM8D3 loci. Guy Mommens aut author Wouter Coppieters aut author Alex Van De Weghe aut author Alex Van Zeveren aut author ug_DI07 Yves Bouquet aut author eng Medicine and Health Sciences http://hdl.handle.net/1854/LU-200067 A1994PR31900020 0268-9146 1994 ANIMAL GENETICS Anim. Genet. 0268-9146 1994 25 5 368 368 1994 published ug 200067 2004-01-14T13:42:00Z 2016-12-19T15:45:48Z A1 VABB-1 9 info:srw/schema/1/mods-v3.3xml bookEditor B3 Binominal syntagms as loci of synchronic variation and diachronic change Lieselotte Brems edt editor Bernard De Clerck edt editor ug_LW22 Katrien Verveckken edt editor eng http://hdl.handle.net/1854/LU-8512796 2016 207 p. Language Sciences 53 published https://biblio.ugent.be/publication/8512796/file/8529041 application/vnd.openxmlformats-officedocument.wordprocessingml.document restricted ug 8512796 2017-03-06T16:15:28Z 2017-08-22T07:03:52Z B3 VABB-3 10 1.1title any "dna loci"titleanydna loci