text: DSpace Collection: http://hdl.handle.net/2381/95 2016-10-01T01:36:09Z 2016-10-01T01:36:09Z Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance Ali, N. Heslop-Harrison, John Seymour Ahmad, H. Graybosch, R. A. Hein, G. L. Schwarzacher, T. http://hdl.handle.net/2381/38017 2016-08-31T02:18:32Z 2016-08-30T15:21:37Z Title: Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance Authors: Ali, N.; Heslop-Harrison, John Seymour; Ahmad, H.; Graybosch, R. A.; Hein, G. L.; Schwarzacher, T. Abstract: Pyramiding of alien-derived Wheat streak mosaic virus (WSMV) resistance and resistance enhancing genes in wheat is a cost-effective and environmentally safe strategy for disease control. PCR-based markers and cytogenetic analysis with genomic in situ hybridisation were applied to identify alien chromatin in four genetically diverse populations of wheat (Triticum aestivum) lines incorporating chromosome segments from Thinopyrum intermedium and Secale cereale (rye). Out of 20 experimental lines, 10 carried Th. intermedium chromatin as T4DL*4Ai#2S translocations, while, unexpectedly, 7 lines were positive for alien chromatin (Th. intermedium or rye) on chromosome 1B. The newly described rye 1RS chromatin, transmitted from early in the pedigree, was associated with enhanced WSMV resistance. Under field conditions, the 1RS chromatin alone showed some resistance, while together with the Th. intermedium 4Ai#2S offered superior resistance to that demonstrated by the known resistant cultivar Mace. Most alien wheat lines carry whole chromosome arms, and it is notable that these lines showed intra-arm recombination within the 1BS arm. The translocation breakpoints between 1BS and alien chromatin fell in three categories: (i) at or near to the centromere, (ii) intercalary between markers UL-Thin5 and Xgwm1130 and (iii) towards the telomere between Xgwm0911 and Xbarc194. Labelled genomic Th. intermedium DNA hybridised to the rye 1RS chromatin under high stringency conditions, indicating the presence of shared tandem repeats among the cereals. The novel small alien fragments may explain the difficulty in developing well-adapted lines carrying Wsm1 despite improved tolerance to the virus. The results will facilitate directed chromosome engineering producing agronomically desirable WSMV-resistant germplasm. 2016-08-30T15:21:37Z Allele-specific recognition by LILRB3 and LILRA6 of a cytokeratin 8 - associated ligand on necrotic glandular epithelial cells Jones, Des C. Hewitt, Colin R. A. López-Álvarez, María R. Jahnke, Martin Russell, Alasdair I. Radjabova, Valeria Trowsdale, Alice R. Z. Trowsdale, John http://hdl.handle.net/2381/37877 2016-07-28T02:16:46Z 2016-07-27T14:37:41Z Title: Allele-specific recognition by LILRB3 and LILRA6 of a cytokeratin 8 - associated ligand on necrotic glandular epithelial cells Authors: Jones, Des C.; Hewitt, Colin R. A.; López-Álvarez, María R.; Jahnke, Martin; Russell, Alasdair I.; Radjabova, Valeria; Trowsdale, Alice R. Z.; Trowsdale, John Abstract: The LILRs are a family of receptors that regulate the activities of myelomonocytic cells. We found that specific allelic variants of two related members of the LILR family, LILRB3 and LILRA6, interact with a ligand exposed on necrotic glandular epithelial cells. The extracellular domains of LILRB3 and LILRA6 are very similar and their genes are highly polymorphic. A commonly occurring allele, LILRB3*12, displayed particularly strong binding of these necrotic cells and further screening of the products of LILRB3 alleles identified motifs that correlated with binding. Immunoprecipitation of the ligand from epithelial cell lysates using recombinant LILRB3*12, identified cytokeratins 8, 18 and 19. Purified proteins obtained from epithelial cell lysates, using anti-cytokeratin 8 antibodies, were able to activate LILRB3*12 reporter cells. Knock-down of cytokeratin 8 in epithelial cells abrogated expression of the LILRB3 ligand, while staining with recombinant LILRB3*12 showed co-localisation with cytokeratin 8 and 18 in permeabilised breast cancer cells. Necrosis is a common feature of tumours. The finding of a necrosis-associated ligand for these two receptors raises the possibility of a novel interaction that alters immune responses within the tumour microenvironment. Since LILRB3 and LILRA6 genes are highly polymorphic the interaction may influence an individual's immune response to tumours. 2016-07-27T14:37:41Z Analysis of gemini pollen 3 mutant suggests a broad function of AUGMIN in microtubule organization during sexual reproduction in Arabidopsis Oh, Sung - Aeong Jeon, Jien Park, Hyo - Jin Grini, Paul Eivind Twell, David Park, Soon - Ki http://hdl.handle.net/2381/37767 2016-06-16T02:16:29Z 2016-06-15T13:02:55Z Title: Analysis of gemini pollen 3 mutant suggests a broad function of AUGMIN in microtubule organization during sexual reproduction in Arabidopsis Authors: Oh, Sung - Aeong; Jeon, Jien; Park, Hyo - Jin; Grini, Paul Eivind; Twell, David; Park, Soon - Ki Abstract: In flowering plants, male gametes arise via meiosis of diploid pollen mother cells followed by two rounds of mitotic division. Haploid microspores undergo polar nuclear migration and asymmetric division at pollen mitosis I to segregate the male germline, followed by division of the germ cell to generate a pair of sperm cells. We previously reported two gemini pollen (gem) mutants that produced twin-celled pollen arising from polarity and cytokinesis defects at pollen mitosis I in Arabidopsis. Here, we report an independent mutant, gem3, with a similar division phenotype and severe genetic transmission defects through pollen. Cytological analyses revealed that gem3 disrupts cell division during male meiosis, at pollen mitosis I and during female gametophyte development. We show that gem3 is a hypomorphic allele (aug6-1) of AUGMIN subunit 6, encoding a conserved component in the augmin complex, which mediates microtubule (MT)-dependent MT nucleation in acentrosomal cells. We show that MT arrays are disturbed in gem3/aug6-1 during male meiosis and pollen mitosis I using fluorescent MT-markers. Our results demonstrate a broad role for the augmin complex in MT organization during sexual reproduction, and highlight gem3/aug6-1 mutants as a valuable tool for the investigation of augmin-dependent MT nucleation and dynamics in plant cells. 2016-06-15T13:02:55Z Mixtures with relatives: a pedigree perspective. Egeland, Thore Dørum, Guro Vigeland, Magnus Dehli Sheehan, Nuala A. http://hdl.handle.net/2381/37744 2016-06-15T02:16:42Z 2016-06-14T10:55:02Z Title: Mixtures with relatives: a pedigree perspective. Authors: Egeland, Thore; Dørum, Guro; Vigeland, Magnus Dehli; Sheehan, Nuala A. Abstract: DNA mixture evidence pertains to cases where several individuals may have contributed to a biological stain. Statistical methods and software for such problems are available and a large number of cases can be handled adequately. However, one class of mixture problems remains untreated in full generality in the literature, namely when the contributors may be related. Disregarding a plausible close relative of the perpetrator as an alternative contributor (identical twin is the most extreme case) may lead to overestimating the evidence against a suspect. Existing methods only accommodate pairwise relationships such as the case where the suspect and the victim are siblings, for example. In this paper we consider relationships in full generality, conveniently represented by pedigrees. In particular, these pedigrees may involve inbreeding, for instance when the parents of an individual of interest are first cousins. Furthermore our framework handles situations where the opposing parties in a court case (prosecution and defence) propose different family relationships. Consequently, our approach combines classical mixture and kinship problems. The basic idea of this paper is to formulate the problem in a way that allows for the exploitation of currently available methods and software designed originally for linkage applications. We have developed a freely available R package, euroMix based on another package, paramlink, and we illustrate the ideas and methods on real and simulated data. 2016-06-14T10:55:02Z Characterization and Diversity of Novel PIF/Harbinger DNA Transposons in Brassica Genomes Nouroz, Faisal Noreen, Shumaila Heslop-Harrison, J. S. (Pat) http://hdl.handle.net/2381/37674 2016-07-01T01:45:08Z 2016-05-31T15:36:10Z Title: Characterization and Diversity of Novel PIF/Harbinger DNA Transposons in Brassica Genomes Authors: Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J. S. (Pat) Abstract: Among DNA transposons, PIF/Harbinger is most recently identified superfamily characterized by 3 bp target site duplications (TSDs), flanked by 14-45 bp terminal inverted repeats (TIRs) and displaying DDD or DDE domain displaying transposase. Their autonomous elements contain two open reading frames, ORF1 and ORF2 encoding superfamily specific transposase and DNA-binding domain. Harbinger DNA transposons are recently identified in few plants. In present study, computational and molecular approaches were used for the identification of 8 Harbinger transposons, of which only 2 were complete with putative transposase, while rest 6 lack transposase and are considered as defective or non-autonomous elements. They ranged in size from 0.5-4 kb with 3 bp TSDs, 15-42 bp TIRs and internal AT rich regions. The PCR amplification of Brassica Harbinger transposase revealed diversity and ancient nature of these elements. The amplification polymorphism of some non-autonomous Harbingers showed species specific distribution. Phylogenetic analyses of transposase clustered them into two clades (monocot and dicot) and five sub-clades. The Brassica, Arabidopsis and Malus transposase clustered into genera specific sub-clades; although a lot of homology in transposase was observed. The multiple sequence alignment of Brassica and related transposase showed homology in five conserved blocks. The DD₃₅E triad and sequences showed similarity to already known Pong-like or Arabidopsis ATISI12 Harbinger transposase in contrast to other transposase having DD₄₇E or DD₄₈E motifs. The present study will be helpful in the characterization of Harbingers, their structural diversity in related genera and Harbinger based molecular markers for varietal/lines identifications. 2016-05-31T15:36:10Z Tryptophan-2,3-dioxygenase (TDO) inhibition ameliorates neurodegeneration by modulation of kynurenine pathway metabolites Breda, Carlo Sathyasaikumar, Korrapati V. Sograte Idrissi, Shama Notarangelo, Francesca M. Estranero, Jasper G. Moore, Gareth G. L. Green, Edward W. Kyriacou, Charalambos P. Schwarcz, Robert Giorgini, Flaviano http://hdl.handle.net/2381/37505 2016-05-12T02:11:26Z 2016-05-11T12:25:41Z Title: Tryptophan-2,3-dioxygenase (TDO) inhibition ameliorates neurodegeneration by modulation of kynurenine pathway metabolites Authors: Breda, Carlo; Sathyasaikumar, Korrapati V.; Sograte Idrissi, Shama; Notarangelo, Francesca M.; Estranero, Jasper G.; Moore, Gareth G. L.; Green, Edward W.; Kyriacou, Charalambos P.; Schwarcz, Robert; Giorgini, Flaviano Abstract: Metabolites of the kynurenine pathway (KP) of tryptophan (TRP) degradation have been closely linked to the pathogenesis of several neurodegenerative disorders. Recent work has highlighted the therapeutic potential of inhibiting two critical regulatory enzymes in this pathway-kynurenine-3-monooxygenase (KMO) and tryptophan-2,3-dioxygenase (TDO). Much evidence indicates that the efficacy of KMO inhibition arises from normalizing an imbalance between neurotoxic [3-hydroxykynurenine (3-HK); quinolinic acid (QUIN)] and neuroprotective [kynurenic acid (KYNA)] KP metabolites. However, it is not clear if TDO inhibition is protective via a similar mechanism or if this is instead due to increased levels of TRP-the substrate of TDO. Here, we find that increased levels of KYNA relative to 3-HK are likely central to the protection conferred by TDO inhibition in a fruit fly model of Huntington's disease and that TRP treatment strongly reduces neurodegeneration by shifting KP flux toward KYNA synthesis. In fly models of Alzheimer's and Parkinson's disease, we provide genetic evidence that inhibition of TDO or KMO improves locomotor performance and ameliorates shortened life span, as well as reducing neurodegeneration in Alzheimer's model flies. Critically, we find that treatment with a chemical TDO inhibitor is robustly protective in these models. Consequently, our work strongly supports targeting of the KP as a potential treatment strategy for several major neurodegenerative disorders and suggests that alterations in the levels of neuroactive KP metabolites could underlie several therapeutic benefits. 2016-05-11T12:25:41Z shRNA-Based Screen Identifies Endocytic Recycling Pathway Components That Act as Genetic Modifiers of Alpha-Synuclein Aggregation, Secretion and Toxicity Gonçalves, Susana A. Macedo, Diana Raquel, Helena Simões, Pedro D. Giorgini, Flaviano Ramalho, José S. Barral, Duarte C. Ferreira Moita, Luís Outeiro, Tiago Fleming http://hdl.handle.net/2381/37497 2016-05-11T02:06:35Z 2016-05-10T11:24:43Z Title: shRNA-Based Screen Identifies Endocytic Recycling Pathway Components That Act as Genetic Modifiers of Alpha-Synuclein Aggregation, Secretion and Toxicity Authors: Gonçalves, Susana A.; Macedo, Diana; Raquel, Helena; Simões, Pedro D.; Giorgini, Flaviano; Ramalho, José S.; Barral, Duarte C.; Ferreira Moita, Luís; Outeiro, Tiago Fleming Abstract: Alpha-Synuclein (aSyn) misfolding and aggregation is common in several neurodegenerative diseases, including Parkinson's disease and dementia with Lewy bodies, which are known as synucleinopathies. Accumulating evidence suggests that secretion and cell-to-cell trafficking of pathological forms of aSyn may explain the typical patterns of disease progression. However, the molecular mechanisms controlling aSyn aggregation and spreading of pathology are still elusive. In order to obtain unbiased information about the molecular regulators of aSyn oligomerization, we performed a microscopy-based large-scale RNAi screen in living cells. Interestingly, we identified nine Rab GTPase and kinase genes that modulated aSyn aggregation, toxicity and levels. From those, Rab8b, Rab11a, Rab13 and Slp5 were able to promote the clearance of aSyn inclusions and rescue aSyn induced toxicity. Furthermore, we found that endocytic recycling and secretion of aSyn was enhanced upon Rab11a and Rab13 expression in cells accumulating aSyn inclusions. Overall, our study resulted in the identification of new molecular players involved in the aggregation, toxicity, and secretion of aSyn, opening novel avenues for our understanding of the molecular basis of synucleinopathies. 2016-05-10T11:24:43Z Multilocus analysis of introgression between two sand fly vectors of leishmaniasis Mazzoni, C. J. Araki, A. S. Ferreira, G. E. M. Azevedo, Renata V. D. M. Barbujani, G. Peixoto, A. A. http://hdl.handle.net/2381/37440 2016-04-26T02:06:41Z 2016-04-25T14:59:20Z Title: Multilocus analysis of introgression between two sand fly vectors of leishmaniasis Authors: Mazzoni, C. J.; Araki, A. S.; Ferreira, G. E. M.; Azevedo, Renata V. D. M.; Barbujani, G.; Peixoto, A. A. Abstract: Background The phlebotomine sand flies (Diptera:Psychodidae) Lutzomyia (Nyssomyia) intermedia Lutz & Neiva 1912 and Lutzomyia (Nyssomyia) whitmani Antunes & Coutinho 1932 are two very closely related species and important vectors of American cutaneous leishmaniasis. Two single-locus studies have revealed evidence for introgression between the two species in both mitochondrial and nuclear genomes. These findings have prompted the development of a multilocus approach to investigate in more detail the genetic exchanges between the two species. Results We analyzed ten nuclear loci using the "isolation with migration" model implemented in the IM program, finding evidence for introgression from L. intermedia towards L. whitmani in three loci. These results confirm that introgression is occurring between the two species and suggest variation in the effects of gene flow among the different regions of the genome. Conclusion The demonstration that these two vectors are not fully reproductively isolated might have important epidemiological consequences as these species could be exchanging genes controlling aspects of their vectorial capacity. Description: Additional file 1 Supplemental Table – Tests of neutrality. The table presents the results of neutrality tests Fu and Li's D* and F*, Fu's FS and Ramos-Onsins and Rozas' R2. [http://www.biomedcentral.com/content/supplementary/1471- 2148-8-141-S1.doc] Additional file 2 Genealogies of RpL17A and zetacop whole fragments. The figure shows trees of RpL17A and zetacop sequences (whole fragments) of L. intermedia (blue circles) and L. whitmani (red squares). The trees were estimated using the neighbor-joining method, Kimura-2-parameters distance and 1000 bootstrap replicates, and rooted using the middle-point between the two most distant sequences. [http://www.biomedcentral.com/content/supplementary/1471- 2148-8-141-S2.pdf] Additional file 3 Haplotype networks of RpL17A and zetacop whole fragments. The figure shows minimum spanning trees of RpL17A and zetacop sequences (whole fragments) of L. intermedia (blue) and L. whitmani (red). The circles are proportional to the haplotype frequencies and the black and grey lines connecting the haplotypes represent the number of mutational steps. [http://www.biomedcentral.com/content/supplementary/1471- 2148-8-141-S3.pdf] 2016-04-25T14:59:20Z Consent Codes: Upholding Standard Data Use Conditions Dyke, S. O. Philippakis, A. A. Rambla De Argila, J. Paltoo, D. N. Luetkemeier, E. S. Knoppers, B. M. Brookes, Anthony Joseph Spalding, J. D. Thompson, M. Roos, M. Boycott, K. M. Brudno, M. S. Hurles, M. Rehm, H. L. Matern, A. Fiume, M. Sherry, S. T. http://hdl.handle.net/2381/37401 2016-04-21T02:05:29Z 2016-04-20T10:24:00Z Title: Consent Codes: Upholding Standard Data Use Conditions Authors: Dyke, S. O.; Philippakis, A. A.; Rambla De Argila, J.; Paltoo, D. N.; Luetkemeier, E. S.; Knoppers, B. M.; Brookes, Anthony Joseph; Spalding, J. D.; Thompson, M.; Roos, M.; Boycott, K. M.; Brudno, M. S.; Hurles, M.; Rehm, H. L.; Matern, A.; Fiume, M.; Sherry, S. T. Abstract: A systematic way of recording data use conditions that are based on consent permissions as found in the datasets of the main public genome archives (NCBI dbGaP and EMBL-EBI/CRG EGA). 2016-04-20T10:24:00Z The Amino Acid Transporter JhI-21 Coevolves with Glutamate Receptors, Impacts NMJ Physiology, and Influences Locomotor Activity in Drosophila Larvae Ziegler, Anna B. Augustin, Hrvoje Clark, Nathan L. Berthelot-Grosjean, Martine M. Simonnet, Mégane Steinert, Joern R. Geillon, Flore Manière, Gérard Featherstone, David E. Grosjean, Yael http://hdl.handle.net/2381/37363 2016-04-20T02:04:31Z 2016-04-19T09:15:14Z Title: The Amino Acid Transporter JhI-21 Coevolves with Glutamate Receptors, Impacts NMJ Physiology, and Influences Locomotor Activity in Drosophila Larvae Authors: Ziegler, Anna B.; Augustin, Hrvoje; Clark, Nathan L.; Berthelot-Grosjean, Martine; M. Simonnet, Mégane; Steinert, Joern R.; Geillon, Flore; Manière, Gérard; Featherstone, David E.; Grosjean, Yael Abstract: Changes in synaptic physiology underlie neuronal network plasticity and behavioral phenomena, which are adjusted during development. The Drosophila larval glutamatergic neuromuscular junction (NMJ) represents a powerful synaptic model to investigate factors impacting these processes. Amino acids such as glutamate have been shown to regulate Drosophila NMJ physiology by modulating the clustering of postsynaptic glutamate receptors and thereby regulating the strength of signal transmission from the motor neuron to the muscle cell. To identify amino acid transporters impacting glutmatergic signal transmission, we used Evolutionary Rate Covariation (ERC), a recently developed bioinformatic tool. Our screen identified ten proteins co-evolving with NMJ glutamate receptors. We selected one candidate transporter, the SLC7 (Solute Carrier) transporter family member JhI-21 (Juvenile hormone Inducible-21), which is expressed in Drosophila larval motor neurons. We show that JhI-21 suppresses postsynaptic muscle glutamate receptor abundance, and that JhI-21 expression in motor neurons regulates larval crawling behavior in a developmental stage-specific manner. 2016-04-19T09:15:14Z Soft tissue sarcoma Eastley, Nicholas Charles Green, P. N. Ashford, R. U. http://hdl.handle.net/2381/37342 2016-04-19T02:04:30Z 2016-04-18T11:44:07Z Title: Soft tissue sarcoma Authors: Eastley, Nicholas Charles; Green, P. N.; Ashford, R. U. 2016-04-18T11:44:07Z Neural and non-neural contributions to sexual dimorphism of mid-day sleep in Drosophila melanogaster : a pilot study Khericha, Mobina Kolonchery, Jaison B. Tauber, Eran http://hdl.handle.net/2381/37334 2016-04-19T02:04:30Z 2016-04-18T10:36:44Z Title: Neural and non-neural contributions to sexual dimorphism of mid-day sleep in Drosophila melanogaster : a pilot study Authors: Khericha, Mobina; Kolonchery, Jaison B.; Tauber, Eran Abstract: Many of the characteristics associated with mammalian sleep are also observed in Drosophila melanogaster Meigen, making the fruit fly a powerful model organism for studying the genetics of this important process. Included among the similarities is the presence of sexual dimorphic sleep patterns, which, in flies, are manifested as increased mid-day sleep ('siesta') in males compared with females. In the present study, targeted mis-expression of the genes transformer (tra) and tra2 is used to either feminize or masculinize specific neural and non-neural tissues in the fly. Feminization of male D. melanogaster using three different GAL4 drivers that are expressed in the mushroom bodies induces a female-like reduced siesta, whereas the masculinization of females using these drivers triggers the male-like increased siesta. A similar reversal of sex-specific sleep is also observed by mis-expressing tra in the fat body, which is a key tissue in energy metabolism and hormone secretion. In addition, the daily expression levels of takeout, an important circadian clock output gene, are sexually dimorphic. Taken together, these experiments suggest that sleep sexual dimorphism in D. melanogaster is driven by multiple neural and non-neural circuits, within and outside the brain. 2016-04-18T10:36:44Z Corrections: Maternal caffeine intake during pregnancy and risk of fetal growth restriction: a large prospective observational study Konje, Justin Chi http://hdl.handle.net/2381/37329 2016-04-19T02:04:30Z 2016-04-18T10:23:58Z Title: Corrections: Maternal caffeine intake during pregnancy and risk of fetal growth restriction: a large prospective observational study Authors: Konje, Justin Chi Description: Correction to Maternal caffeine intake during pregnancy and risk of fetal growth restriction: a large prospective observational study, dx.doi.org/10.1136/bmj.a2332 available on the LRA at http://hdl.handle.net/2381/16058 2016-04-18T10:23:58Z Yeast DJ-1 superfamily members are required for diauxic-shift reprogramming and cell survival in stationary phase Miller-Fleming, L. Antas, P. Pais, T. F. Smalley, J. L. Giorgini, Flaviano Outeiro, T. F. http://hdl.handle.net/2381/37321 2016-04-16T03:01:49Z 2016-04-15T10:39:47Z Title: Yeast DJ-1 superfamily members are required for diauxic-shift reprogramming and cell survival in stationary phase Authors: Miller-Fleming, L.; Antas, P.; Pais, T. F.; Smalley, J. L.; Giorgini, Flaviano; Outeiro, T. F. Abstract: The yeast Hsp31 minifamily proteins (Hsp31, Hsp32, Hsp33, Hsp34) belong to the highly conserved DJ-1 superfamily. The human DJ-1 protein is associated with cancer and neurodegenerative disorders, such as Parkinson disease. However, the precise function of human and yeast DJ-1 proteins is unclear. Here we show that the yeast DJ-1 homologs have a role in diauxic-shift (DS), characterized by metabolic reprogramming because of glucose limitation. We find that the Hsp31 genes are strongly induced in DS and in stationary phase (SP), and that deletion of these genes reduces chronological lifespan, impairs transcriptional reprogramming at DS, and impairs the acquisition of several typical characteristics of SP, including autophagy induction. In addition, under carbon starvation, the HSP31 family gene-deletion strains display impaired autophagy, disrupted target of rapamycin complex 1 (TORC1) localization to P-bodies, and caused abnormal TORC1-mediated Atg13 phosphorylation. Repression of TORC1 by rapamycin in the gene-deletion strains completely reversed their sensitivity to heat shock. Taken together, our data indicate that Hsp31 minifamily is required for DS reprogramming and cell survival in SP, and plays a role upstream of TORC1. The enhanced understanding of the cellular function of these genes sheds light into the biological role of other members of the superfamily, including DJ-1, which is an attractive target for therapeutic intervention in cancer and in Parkinson disease. Description: The file associated with this record is under permanent embargo by the publisher. Please use the links above where the Published version is freely available. 2016-04-15T10:39:47Z The small GTPase Rab11 co-localizes with α-synuclein in intracellular inclusions and modulates its aggregation, secretion and toxicity Chutna, O. Gonçalves, S. Villar-Piqué, A. Guerreiro, P. Marijanovic, Z. Mendes, T. Ramalho, J. Emmanouilidou, E. Ventura, S. Klucken, J. Barral, D. C. Giorgini, Flaviano Vekrellis, K. Outeiro, T. F. http://hdl.handle.net/2381/37314 2016-04-15T02:16:17Z 2016-04-14T11:45:22Z Title: The small GTPase Rab11 co-localizes with α-synuclein in intracellular inclusions and modulates its aggregation, secretion and toxicity Authors: Chutna, O.; Gonçalves, S.; Villar-Piqué, A.; Guerreiro, P.; Marijanovic, Z.; Mendes, T.; Ramalho, J.; Emmanouilidou, E.; Ventura, S.; Klucken, J.; Barral, D. C.; Giorgini, Flaviano; Vekrellis, K.; Outeiro, T. F. Abstract: Alpha-synuclein (aSyn) misfolding and aggregation are pathological features common to several neurodegenerative diseases, including Parkinson's disease (PD). Mounting evidence suggests that aSyn can be secreted and transferred from cell to cell, participating in the propagation and spreading of pathological events. Rab11, a small GTPase, is an important regulator in both endocytic and secretory pathways. Here, we show that Rab11 is involved in regulating aSyn secretion. Rab11 knockdown or overexpression of either Rab11a wild-type (Rab11a WT) or Rab11a GDP-bound mutant (Rab11a S25N) increased secretion of aSyn. Furthermore, we demonstrate that Rab11 interacts with aSyn and is present in intracellular inclusions together with aSyn. Moreover, Rab11 reduces aSyn aggregation and toxicity. Our results suggest that Rab11 is involved in modulating the processes of aSyn secretion and aggregation, both of which are important mechanisms in the progression of aSyn pathology in PD and other synucleinopathies. 2016-04-14T11:45:22Z Copy number variation of Fc gamma receptor genes in HIV-infected and HIV-tuberculosis co-infected individuals in sub-Saharan Africa Machado, L. R. Bowdrey, J. Ngaimisi, E. Habtewold, A. Minzi, O. Makonnen, E. Yimer, G. Amogne, W. Mugusi, S. Janabi, M. Aderaye, G. Mugusi, F. Viskaduraki, M. Aklillu, E. Hollox, Edward J. http://hdl.handle.net/2381/37270 2016-04-13T02:09:57Z 2016-04-12T12:07:02Z Title: Copy number variation of Fc gamma receptor genes in HIV-infected and HIV-tuberculosis co-infected individuals in sub-Saharan Africa Authors: Machado, L. R.; Bowdrey, J.; Ngaimisi, E.; Habtewold, A.; Minzi, O.; Makonnen, E.; Yimer, G.; Amogne, W.; Mugusi, S.; Janabi, M.; Aderaye, G.; Mugusi, F.; Viskaduraki, M.; Aklillu, E.; Hollox, Edward J. Abstract: AIDS, caused by the retrovirus HIV, remains the largest cause of morbidity in sub-Saharan Africa yet almost all genetic studies have focused on cohorts from Western countries. HIV shows high co-morbidity with tuberculosis (TB), as HIV stimulates the reactivation of latent tuberculosis (TB). Recent clinical trials suggest that an effective anti-HIV response correlates with non-neutralising antibodies. Given that Fcγ receptors are critical in mediating the non-neutralising effects of antibodies, analysis of the extensive variation at Fcγ receptor genes is important. Single nucleotide variation and copy number variation (CNV) of Fcγ receptor genes affects the expression profile, activatory/inhibitory balance, and IgG affinity of the Fcγ receptor repertoire of each individual. In this study we investigated whether CNV of FCGR2C, FCGR3A and FCGR3B as well as the HNA1 allotype of FCGR3B is associated with HIV load, response to highly-active antiretroviral therapy (HAART) and co-infection with TB. We confirmed an effect of TB-co-infection status on HIV load and response to HAART, but no conclusive effect of the genetic variants we tested. We observed a small effect, in Ethiopians, of FCGR3B copy number, where deletion was more frequent in HIV-TB co-infected patients than those infected with HIV alone. 2016-04-12T12:07:02Z GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies Beck, T. Hastings, R. K. Gollapudi, S. Free, R. C. Brookes, Anthony Joseph http://hdl.handle.net/2381/37268 2016-04-13T02:09:25Z 2016-04-12T12:00:07Z Title: GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies Authors: Beck, T.; Hastings, R. K.; Gollapudi, S.; Free, R. C.; Brookes, Anthony Joseph Abstract: To facilitate broad and convenient integrative visualization of and access to GWAS data, we have created the GWAS Central resource (http://www.gwascentral.org). This database seeks to provide a comprehensive collection of summary-level genetic association data, structured both for maximal utility and for safe open access (i.e., non-directional signals to fully preclude research subject identification). The resource emphasizes on advanced tools that allow comparison and discovery of relevant data sets from the perspective of genes, genome regions, phenotypes or traits. Tested markers and relevant genomic features can be visually interrogated across up to 16 multiple association data sets in a single view, starting at a chromosome-wide view and increasing in resolution down to individual bases. In addition, users can privately upload and view their own data as temporary files. Search and display utility is further enhanced by exploiting phenotype ontology annotations to allow genetic variants associated with phenotypes and traits of interest to be precisely identified, across all studies. Data submissions are accepted from individual researchers, groups and consortia, whereas we also actively gather data sets from various public sources. As a result, the resource now provides over 67 million P-values for over 1600 studies, making it the world's largest openly accessible online collection of summary-level GWAS association information. 2016-04-12T12:00:07Z Great-ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal Hallast, Pille Maisano Delser, P. Batini, Chiara Zadik, Daniel Rocchi, M. Schempp, W. Tyler-Smith, C. Jobling, Mark Alexander http://hdl.handle.net/2381/37258 2016-04-13T02:00:57Z 2016-04-12T09:14:58Z Title: Great-ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal Authors: Hallast, Pille; Maisano Delser, P.; Batini, Chiara; Zadik, Daniel; Rocchi, M.; Schempp, W.; Tyler-Smith, C.; Jobling, Mark Alexander Abstract: The distribution of genetic diversity in great-ape species is likely to have been affected by patterns of dispersal and mating. This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping in 19 great-ape males, combining the data with sequences extracted from the published whole genomes of 24 additional males to yield a total sample of 19 chimpanzees, four bonobos, 14 gorillas, and six orangutans, in which interpretable MSY sequence ranges from 2.61 to 3.80 Mb. This analysis reveals thousands of novel MSY variants and defines unbiased phylogenies. We compare these with mtDNA-based trees in the same individuals, estimating time-to-most-recent common ancestor (TMRCA) for key nodes in both cases. The two loci show high topological concordance and are consistent with accepted (sub)species definitions, but time depths differ enormously between loci and (sub)species, likely reflecting different dispersal and mating patterns. Gorillas and chimpanzees/bonobos present generally low and high MSY diversity, respectively, reflecting polygyny versus multimale-multifemale mating. However, particularly marked differences exist among chimpanzee subspecies: The western chimpanzee MSY phylogeny has a TMRCA of only 13.2 (10.8-15.8) thousand years, but that for central chimpanzees exceeds 1 million years. Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveals species-specific branch length variation that may reflect differences in long-term generation times. 2016-04-12T09:14:58Z Men B : lack of coverage or vaccine failure? Bayliss, Christopher D. Morrissey, Julie A. Borrow, R. http://hdl.handle.net/2381/37217 2016-08-10T01:45:09Z 2016-04-11T08:20:12Z Title: Men B : lack of coverage or vaccine failure? Authors: Bayliss, Christopher D.; Morrissey, Julie A.; Borrow, R. 2016-04-11T08:20:12Z Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of population structure during host colonisation Bayliss, Christopher David Bidmos, Fadil A. Anjum, Awais Manchev, Vladimir T. Richards, Rebecca L . Grossier, Jean-Philippe Wooldridge, K. G. Ketley, Julian M. Barrow, P. A. Jones, M. A. Tretyakov, Michael V. http://hdl.handle.net/2381/37211 2016-04-09T03:40:07Z 2016-04-08T11:05:48Z Title: Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of population structure during host colonisation Authors: Bayliss, Christopher David; Bidmos, Fadil A.; Anjum, Awais; Manchev, Vladimir T.; Richards, Rebecca L .; Grossier, Jean-Philippe; Wooldridge, K. G.; Ketley, Julian M.; Barrow, P. A.; Jones, M. A.; Tretyakov, Michael V. Abstract: Phase variation of surface structures occurs in diverse bacterial species due to stochastic, high frequency, reversible mutations. Multiple genes of Campylobacter jejuni are subject to phase variable gene expression due to mutations in polyC/G tracts. A modal length of nine repeats was detected for polyC/G tracts within C. jejuni genomes. Switching rates for these tracts were measured using chromosomally-located reporter constructs and high rates were observed for cj1139 (G8) and cj0031 (G9). Alteration of the cj1139 tract from G8 to G11 increased mutability 10-fold and changed the mutational pattern from predominantly insertions to mainly deletions. Using a multiplex PCR, major changes were detected in 'on/off' status for some phase variable genes during passage of C. jejuni in chickens. Utilization of observed switching rates in a stochastic, theoretical model of phase variation demonstrated links between mutability and genetic diversity but could not replicate observed population diversity. We propose that modal repeat numbers have evolved in C. jejuni genomes due to molecular drivers associated with the mutational patterns of these polyC/G repeats, rather than by selection for particular switching rates, and that factors other than mutational drift are responsible for generating genetic diversity during host colonization by this bacterial pathogen. 2016-04-08T11:05:48Z HGVS Recommendations for the Description of Sequence Variants: 2016 Update. den Dunnen, J. T. Dalgleish, Raymond Walter Miller Maglott, D. R. Hart, R. K. Greenblatt, M. S. McGowan-Jordan, J. Roux, A. F. Smith, T. Antonarakis, S. E. Taschner, P. E. Human Genome Variation Society (HGVS), the Human Variome Project (HVP) and the Human Genome Organisation (HUGO), http://hdl.handle.net/2381/37207 2016-04-09T03:39:43Z 2016-04-08T10:05:01Z Title: HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Authors: den Dunnen, J. T.; Dalgleish, Raymond Walter Miller; Maglott, D. R.; Hart, R. K.; Greenblatt, M. S.; McGowan-Jordan, J.; Roux, A. F.; Smith, T.; Antonarakis, S. E.; Taschner, P. E.; Human Genome Variation Society (HGVS), the Human Variome Project (HVP) and the Human Genome Organisation (HUGO), Abstract: The consistent and unambiguous description of sequence variants is essential to report and exchange information on the analysis of a genome. In particular, DNA diagnostics critically depends on accurate and standardized description and sharing of the variants detected. The sequence variant nomenclature system proposed in 2000 by the Human Genome Variation Society has been widely adopted and has developed into an internationally accepted standard. The recommendations are currently commissioned through a Sequence Variant Description Working Group (SVD-WG) operating under the auspices of three international organizations: the Human Genome Variation Society (HGVS), the Human Variome Project (HVP), and the Human Genome Organization (HUGO). Requests for modifications and extensions go through the SVD-WG following a standard procedure including a community consultation step. Version numbers are assigned to the nomenclature system to allow users to specify the version used in their variant descriptions. Here we present the current recommendations, HGVS version 15.11, and briefly summarize the changes that were made since the 2000 publication. Most focus has been on removing inconsistencies and tightening definitions allowing automatic data processing. An extensive version of the recommendations is available online, at http://www.HGVS.org/varnomen. This article is protected by copyright. All rights reserved. Description: The file associated with this record is under a 12-month embargo from publication in accordance with the publisher's self-archiving policy. The full text may be available through the publisher links provided above. 2016-04-08T10:05:01Z LSDBs and How they have Evolved. Dalgleish, Raymond Walter Miller http://hdl.handle.net/2381/37206 2016-04-09T03:39:40Z 2016-04-08T10:00:27Z Title: LSDBs and How they have Evolved. Authors: Dalgleish, Raymond Walter Miller Abstract: Locus specific databases (LSDBs) make a key contribution to our understanding of heritable and acquired human disorders, disease susceptibility, and adverse drug reactions. As data have accumulated in LSDBs, a greater reliance on their use has arisen in clinical practice. Even though LSDBs have existed in recognizable form for only a quarter of a century, their origin lies in the manual cataloging of data that began around 50 years ago. Analysis and recording of sequence variation in the globin genes, and the proteins which they encode, can confidently be said to be the foundation for what we now refer to as LSDBs. Their growth over the years has primarily been underpinned by software developments and the advent of the World Wide Web. However, it is also important to recognize the evolution of reporting standards and reference sequences, without which accurate and consistent reporting of sequence variants would be impossible. Nowadays, LSDBs exist for many human protein-coding genes and the focus of efforts has moved towards minor tidying up of the variant reporting nomenclature and processes for assuring the completeness, correctness and consistency of the data. The next twenty five years will doubtless witness further developments in the evolution of LSDBs. This article is protected by copyright. All rights reserved. Description: The file associated with this record is under a 12-month embargo from publication in accordance with the publisher's self-archiving policy. The full text may be available through the publisher links provided above. 2016-04-08T10:00:27Z EMQN best practice guidelines for the laboratory diagnosis of osteogenesis imperfecta van Dijk, F. S. Byers, P. H. Dalgleish, Raymond Walter Miller Malfait, F. Maugeri, A. Rohrbach, M. Symoens, S. Sistermans, E. A. Pals, G. http://hdl.handle.net/2381/37205 2016-04-09T03:40:13Z 2016-04-08T09:56:30Z Title: EMQN best practice guidelines for the laboratory diagnosis of osteogenesis imperfecta Authors: van Dijk, F. S.; Byers, P. H.; Dalgleish, Raymond Walter Miller; Malfait, F.; Maugeri, A.; Rohrbach, M.; Symoens, S.; Sistermans, E. A.; Pals, G. Abstract: Osteogenesis imperfecta (OI) comprises a group of inherited disorders characterized by bone fragility and increased susceptibility to fractures. Historically, the laboratory confirmation of the diagnosis OI rested on cultured dermal fibroblasts to identify decreased or abnormal production of abnormal type I (pro)collagen molecules, measured by gel electrophoresis. With the discovery of COL1A1 and COL1A2 gene variants as a cause of OI, sequence analysis of these genes was added to the diagnostic process. Nowadays, OI is known to be genetically heterogeneous. About 90% of individuals with OI are heterozygous for causative variants in the COL1A1 and COL1A2 genes. The majority of remaining affected individuals have recessively inherited forms of OI with the causative variants in the more recently discovered genes CRTAP, FKBP10, LEPRE1,PLOD2, PPIB, SERPINF1, SERPINH1 and SP7, or in other yet undiscovered genes. These advances in the molecular genetic diagnosis of OI prompted us to develop new guidelines for molecular testing and reporting of results in which we take into account that testing is also used to 'exclude' OI when there is suspicion of non-accidental injury. Diagnostic flow, methods and reporting scenarios were discussed during an international workshop with 17 clinicians and scientists from 11 countries and converged in these best practice guidelines for the laboratory diagnosis of OI. 2016-04-08T09:56:30Z HHV-8-unrelated primary effusion-like lymphoma associated with clonal loss of inherited chromosomally-integrated human herpesvirus-6A from the telomere of chromosome 19q Zhang, Enjie Cotton, Victoria E. Hidalgo-Bravo, Alberto Huang, Yan J Bell, A. F Jarrett, R. Wilkie, G. S. Davison, A. J. P Nacheva, E. Siebert, R. L. Majid, Aneela Kelpanides, Inga Jayne, Sandrine Dyer, Martin J. Royle, Nicola J. http://hdl.handle.net/2381/37199 2016-04-09T03:39:38Z 2016-04-08T08:57:24Z Title: HHV-8-unrelated primary effusion-like lymphoma associated with clonal loss of inherited chromosomally-integrated human herpesvirus-6A from the telomere of chromosome 19q Authors: Zhang, Enjie; Cotton, Victoria E.; Hidalgo-Bravo, Alberto; Huang, Yan; J Bell, A.; F Jarrett, R.; Wilkie, G. S.; Davison, A. J.; P Nacheva, E.; Siebert, R. L.; Majid, Aneela; Kelpanides, Inga; Jayne, Sandrine; Dyer, Martin J.; Royle, Nicola J. Abstract: Primary effusion lymphomas (PEL) are associated with human herpesvirus-8 (HHV-8) and usually occur in immunocompromised individuals. However, there are numerous reports of HHV-8-unrelated PEL-like lymphomas with unknown aetiology. Here we characterize an HHV-8-unrelated PEL-like lymphoma in an elderly woman who was negative for human immunodeficiency viruses 1 and 2, and hepatitis B and C. The woman was, however, a carrier of an inherited-chromosomally-integrated human herpesvirus-6A (iciHHV-6A) genome in one 19q telomere. The iciHHV-6A genome was complete in blood DNA, encoding a full set of protein-coding genes. Interestingly, the entire iciHHV-6A genome was absent from the HHV-8-unrelated-PEL-like lymphoma cells despite retention of both copies of chromosome 19. The somatic loss of the 19q-iciHHV-6A genome occurred very early during lymphoma development and we propose it occurred via telomere-loop formation and excision to release a circular viral genome that was subsequently lost. Whether release of the HHV-6A genome from the telomere contributed to lymphomagenesis, or was coincidental, remains unclear but this event may have deregulated the expression of HHV-6A or 19q genes or else disrupted telomere function. To establish the frequency and importance of iciHHV-6 loss from telomeres, the HHV-6 copy number should be assessed in tumours that arise in iciHHV-6 carriers. 2016-04-08T08:57:24Z Advanced-stage cervix cancer: rapid tumour growth rather than late diagnosis Symonds, Raymond Bolger, B. Hole, D. Mao, J. H. Cooke, T. http://hdl.handle.net/2381/37151 2016-04-07T02:25:09Z 2016-04-06T08:49:24Z Title: Advanced-stage cervix cancer: rapid tumour growth rather than late diagnosis Authors: Symonds, Raymond; Bolger, B.; Hole, D.; Mao, J. H.; Cooke, T. Abstract: Either diagnostic delay or tumour biology are possible factors governing the degree of spread at diagnosis of cervical cancer. To try to identify the most important parameter contributing to advanced stage, the duration of symptoms were recorded from patients scheduled for radiotherapy (n = 141) or radical hysterectomy (n = 36). In 146 cases tumour proliferation rates were evaluated following in vivo labelling with the DNA precursor BrdUrd. For symptomatic patients there was no association between duration of symptoms and stage at presentation. There was a significant trend for patients with increasing tumour stage to have more rapidly proliferating tumours with higher mean labelling index (LI) measurements (P = 0.001) and a shorter mean potential doubling time (Tpot) (P = 0.023). Socio economic deprivation may be associated with shorter Tpot values. The conclusion from this data is that stage at diagnosis is more dependent on the biological behaviour of the tumour, as expressed by proliferation rates, than delay in presentation. 2016-04-06T08:49:24Z Inter-Homolog Crossing-Over and Synapsis in Arabidopsis Meiosis Are Dependent on the Chromosome Axis Protein AtASY3 Ferdous, M. Higgins, James D. Osman, K. Lambing, C. Roitinger, E. Mechtler, K. Armstrong, S. J. Perry, R. Pradillo, M. Cuñado, N. Franklin, F. C. H. http://hdl.handle.net/2381/36972 2016-03-04T03:24:01Z 2016-03-03T13:00:31Z Title: Inter-Homolog Crossing-Over and Synapsis in Arabidopsis Meiosis Are Dependent on the Chromosome Axis Protein AtASY3 Authors: Ferdous, M.; Higgins, James D.; Osman, K.; Lambing, C.; Roitinger, E.; Mechtler, K.; Armstrong, S. J.; Perry, R.; Pradillo, M.; Cuñado, N.; Franklin, F. C. H. Editors: Hawley, R. S. Abstract: In this study we have analysed AtASY3, a coiled-coil domain protein that is required for normal meiosis in Arabidopsis. Analysis of an Atasy3-1 mutant reveals that loss of the protein compromises chromosome axis formation and results in reduced numbers of meiotic crossovers (COs). Although the frequency of DNA double-strand breaks (DSBs) appears moderately reduced in Atasy3-1, the main recombination defect is a reduction in the formation of COs. Immunolocalization studies in wild-type meiocytes indicate that the HORMA protein AtASY1, which is related to Hop1 in budding yeast, forms hyper-abundant domains along the chromosomes that are spatially associated with DSBs and early recombination pathway proteins. Loss of AtASY3 disrupts the axial organization of AtASY1. Furthermore we show that the AtASY3 and AtASY1 homologs BoASY3 and BoASY1, from the closely related species Brassica oleracea, are co-immunoprecipitated from meiocyte extracts and that AtASY3 interacts with AtASY1 via residues in its predicted coiled-coil domain. Together our results suggest that AtASY3 is a functional homolog of Red1. Since studies in budding yeast indicate that Red1 and Hop1 play a key role in establishing a bias to favor inter-homolog recombination (IHR), we propose that AtASY3 and AtASY1 may have a similar role in Arabidopsis. Loss of AtASY3 also disrupts synaptonemal complex (SC) formation. In Atasy3-1 the transverse filament protein AtZYP1 forms small patches rather than a continuous SC. The few AtMLH1 foci that remain in Atasy3-1 are found in association with the AtZYP1 patches. This is sufficient to prevent the ectopic recombination observed in the absence of AtZYP1, thus emphasizing that in addition to its structural role the protein is important for CO formation. 2016-03-03T13:00:31Z DNA methylation changes induced by long and short photoperiods in Nasonia Pegoraro, Mirko Bafna, Akanksha Davies, Nathaniel J. Shuker, D. M. Tauber, Eran http://hdl.handle.net/2381/36883 2016-02-26T03:28:14Z 2016-02-25T13:02:46Z Title: DNA methylation changes induced by long and short photoperiods in Nasonia Authors: Pegoraro, Mirko; Bafna, Akanksha; Davies, Nathaniel J.; Shuker, D. M.; Tauber, Eran Abstract: Many organisms monitor the annual change in day length and use this information for the timing of their seasonal response. However, the molecular mechanisms underlying photoperiodic timing are largely unknown. The wasp Nasonia vitripennis is an emerging model organism that exhibits a strong photoperiodic response: Short autumnal days experienced by females lead to the induction of developmental arrest (diapause) in their progeny, allowing winter survival of the larvae. How female Nasonia control the developmental trajectory of their offspring is unclear. Here, we took advantage of the recent discovery that DNA methylation is pervasive in Nasonia and tested its role in photoperiodism. We used reduced representation bisulfite sequencing (RRBS) to profile DNA methylation in adult female wasps subjected to different photoperiods and identified substantial differential methylation at the single base level. We also show that knocking down DNA methyltransferase 1a (Dnmt1a), Dnmt3, or blocking DNA methylation pharmacologically, largely disrupts the photoperiodic diapause response of the wasps. To our knowledge, this is the first example for a role of DNA methylation in insect photoperiodic timing. 2016-02-25T13:02:46Z Trouble at the races Jobling, Mark Alexander http://hdl.handle.net/2381/36877 2016-02-26T03:26:37Z 2016-02-25T09:57:02Z Title: Trouble at the races Authors: Jobling, Mark Alexander 2016-02-25T09:57:02Z The music of the genes Jobling, Mark Alexander http://hdl.handle.net/2381/36876 2016-02-26T03:26:34Z 2016-02-25T09:52:13Z Title: The music of the genes Authors: Jobling, Mark Alexander 2016-02-25T09:52:13Z The sperm's tale Jobling, Mark Alexander http://hdl.handle.net/2381/36875 2016-02-26T03:26:09Z 2016-02-25T09:48:43Z Title: The sperm's tale Authors: Jobling, Mark Alexander 2016-02-25T09:48:43Z Nucleotide sequence of conjugative prophage Φ1207.3 (formerly Tn1207.3) carrying the mef(A)/msr(D) genes for efflux resistance to macrolides in Streptococcus pyogenes Iannelli, F. Santagati, M. Santoro, F. Oggioni, Marco Rinaldo Stefani, S. Pozzi, G. http://hdl.handle.net/2381/36860 2016-02-25T03:26:57Z 2016-02-24T11:10:20Z Title: Nucleotide sequence of conjugative prophage Φ1207.3 (formerly Tn1207.3) carrying the mef(A)/msr(D) genes for efflux resistance to macrolides in Streptococcus pyogenes Authors: Iannelli, F.; Santagati, M.; Santoro, F.; Oggioni, Marco Rinaldo; Stefani, S.; Pozzi, G. Abstract: Genetic element Φ1207.3 (formerly Tn1207.3) is a prophage of Streptococcus pyogenes which carries the macrolide efflux resistance genes mef(A)/msr(D) and is capable of conjugal transfer among streptococci. Complete nucleotide sequence showed that Φ1207.3 is 52,491 bp in length and contained 58 open reading frames (ORFs). A manual homology-based annotation with functional prediction of the hypothetical gene product was possible only for 34 out of 58 ORFs. Φ1207.3 codes for two different C-methylation systems, several phage structural genes, a lysis cassette (composed by a holin and a peptidoglycan hydrolase), and three site-specific resolvases of the serine recombinase family. 2016-02-24T11:10:20Z Toward male individualization with rapidly mutating y-chromosomal short tandem repeats. Ballantyne, K. N. Ralf, A. Aboukhalid, R. Achakzai, N. M. Anjos, M. J. Ayub, Q. Balažic, J. Ballantyne, J. Ballard, D. J. Berger, B. Bobillo, C. Bouabdellah, M. Burri, H. Capal, T. Caratti, S. Cárdenas, J. Cartault, F. Carvalho, E. F. Carvalho, M. Cheng, B. Coble, M. D. Comas, D. Corach, D. D'Amato, M. E. Davison, S. de Knijff, P. De Ungria, M. C. Decorte, R. Dobosz, T. Dupuy, B. M. Elmrghni, S. Gliwiński, M. Gomes, S. C. Grol, L. Haas, C. Hanson, E. Henke, J. Henke, L. Herrera-Rodríguez, F. Hill, C. R. Holmlund, G. Honda, K. Immel, U. D. Inokuchi, S. Jobling, Mark A. Kaddura, M. Kim, J. S. Kim, S. H. Kim, W. King, Turi Emma Klausriegler, E. Kling, D. Kovačević, L. Kovatsi, L. Krajewski, P. Kravchenko, S. Larmuseau, M. H. Lee, E. Y. Lessig, R. Livshits, L. A. Marjanović, D. Minarik, M. Mizuno, N. Moreira, H. Morling, N. Mukherjee, M. Munier, P. Nagaraju, J. Neuhuber, F. Nie, S. Nilasitsataporn, P. Nishi, T. Oh, H. H. Olofsson, J. Onofri, V. Palo, J. U. Pamjav, H. Parson, W. Petlach, M. Phillips, C. Ploski, R. Prasad, S. P. Primorac, D. Purnomo, G. A. Purps, J. Rangel-Villalobos, H. Rębała, K. Rerkamnuaychoke, B. Gonzalez, D. R. Robino, C. Roewer, L. Rosa, A. Sajantila, A. Sala, A. Salvador, J. M. Sanz, P. Schmitt, C. Sharma, A. K. Silva, D. A. Shin, K. J. Sijen, T. Sirker, M. Siváková, D. Skaro, V. Solano-Matamoros, C. Souto, L. Stenzl, V. Sudoyo, H. Syndercombe-Court, D. Tagliabracci, A. Taylor, D. Tillmar, A. Tsybovsky, I. S. Tyler-Smith, C. van der Gaag, K. J. Vanek, D. Völgyi, A. Ward, D. Willemse, P. Yap, E. P. Yong, R. Y. Pajnič, I. Z. Kayser, M. http://hdl.handle.net/2381/36856 2016-02-25T03:27:02Z 2016-02-24T10:53:20Z Title: Toward male individualization with rapidly mutating y-chromosomal short tandem repeats. Authors: Ballantyne, K. N.; Ralf, A.; Aboukhalid, R.; Achakzai, N. M.; Anjos, M. J.; Ayub, Q.; Balažic, J.; Ballantyne, J.; Ballard, D. J.; Berger, B.; Bobillo, C.; Bouabdellah, M.; Burri, H.; Capal, T.; Caratti, S.; Cárdenas, J.; Cartault, F.; Carvalho, E. F.; Carvalho, M.; Cheng, B.; Coble, M. D.; Comas, D.; Corach, D.; D'Amato, M. E.; Davison, S.; de Knijff, P.; De Ungria, M. C.; Decorte, R.; Dobosz, T.; Dupuy, B. M.; Elmrghni, S.; Gliwiński, M.; Gomes, S. C.; Grol, L.; Haas, C.; Hanson, E.; Henke, J.; Henke, L.; Herrera-Rodríguez, F.; Hill, C. R.; Holmlund, G.; Honda, K.; Immel, U. D.; Inokuchi, S.; Jobling, Mark A.; Kaddura, M.; Kim, J. S.; Kim, S. H.; Kim, W.; King, Turi Emma; Klausriegler, E.; Kling, D.; Kovačević, L.; Kovatsi, L.; Krajewski, P.; Kravchenko, S.; Larmuseau, M. H.; Lee, E. Y.; Lessig, R.; Livshits, L. A.; Marjanović, D.; Minarik, M.; Mizuno, N.; Moreira, H.; Morling, N.; Mukherjee, M.; Munier, P.; Nagaraju, J.; Neuhuber, F.; Nie, S.; Nilasitsataporn, P.; Nishi, T.; Oh, H. H.; Olofsson, J.; Onofri, V.; Palo, J. U.; Pamjav, H.; Parson, W.; Petlach, M.; Phillips, C.; Ploski, R.; Prasad, S. P.; Primorac, D.; Purnomo, G. A.; Purps, J.; Rangel-Villalobos, H.; Rębała, K.; Rerkamnuaychoke, B.; Gonzalez, D. R.; Robino, C.; Roewer, L.; Rosa, A.; Sajantila, A.; Sala, A.; Salvador, J. M.; Sanz, P.; Schmitt, C.; Sharma, A. K.; Silva, D. A.; Shin, K. J.; Sijen, T.; Sirker, M.; Siváková, D.; Skaro, V.; Solano-Matamoros, C.; Souto, L.; Stenzl, V.; Sudoyo, H.; Syndercombe-Court, D.; Tagliabracci, A.; Taylor, D.; Tillmar, A.; Tsybovsky, I. S.; Tyler-Smith, C.; van der Gaag, K. J.; Vanek, D.; Völgyi, A.; Ward, D.; Willemse, P.; Yap, E. P.; Yong, R. Y.; Pajnič, I. Z.; Kayser, M. Abstract: Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database. 2016-02-24T10:53:20Z Monoclonal antibodies against all known variants of EspA: development of a simple diagnostic test for enteropathogenic Escherichia coli based on a key virulence factor Praekelt, Uta Reissbrodt, R. Kresse, A. Pavankumar, A. Sankaran, K. James, Roger Jesudason, M. Anandan, S. Prakasam, A. Balaji, V. Dutta, S. Dutta, S. Ramamurthy, T. Fischer, R. Sander, P. Schaumann, R. Navarro, A. Williams, Peter H. http://hdl.handle.net/2381/36851 2016-02-25T03:26:44Z 2016-02-24T10:05:16Z Title: Monoclonal antibodies against all known variants of EspA: development of a simple diagnostic test for enteropathogenic Escherichia coli based on a key virulence factor Authors: Praekelt, Uta; Reissbrodt, R.; Kresse, A.; Pavankumar, A.; Sankaran, K.; James, Roger; Jesudason, M.; Anandan, S.; Prakasam, A.; Balaji, V.; Dutta, S.; Dutta, S.; Ramamurthy, T.; Fischer, R.; Sander, P.; Schaumann, R.; Navarro, A.; Williams, Peter H. Abstract: Enteropathogenic Escherichia coli (EPEC) are a major cause of infant diarrhoea in developing countries and a significant public health issue in industrialized countries. Currently there are no simple tests available for the diagnosis of EPEC. Serology of O-antigens is widely used routinely in many laboratories throughout the world, even though it has been known for many years to be an unreliable indicator of EPEC virulence. We have developed a simple, low-cost immunodiagnostic test based on the EspA filament, an essential virulence factor of EPEC and the related enterohaemorrhagic E. coli (EHEC). Using recombinant proteins of the five major variants of EspA as immunogens, we raised a panel of three monoclonal antibodies in mice that detects all variants of the native target in bacterial cultures. The antibodies proved suitable for application in sandwich-type assays, including ELISA and lateral flow immunoassays (LFI). Prototypes for both assays were specific for EPEC and EHEC strains when tested against a panel of control micro-organisms. We have also developed a simple, affordable culture medium, A/E medium, which optimizes expression of EspA allowing improved sensitivity of detection compared with standard Dulbecco's modified Eagle's medium. Together these reagents form the basis of robust, informative tests for EPEC for use especially in developing countries but also for routine screening in any clinical laboratory. 2016-02-24T10:05:16Z A global analysis of Y-chromosomal haplotype diversity for 23 STR loci Purps, J. Siegert, S. Willuweit, S. Nagy, M. Alves, C. Salazar, R. Angustia, S. M. Santos, L. H. Anslinger, K. Bayer, B. Ayub, Q. Corach, D. Caputo, M. D'Amato, M. E. Davison, S. Decorte, R. Larmuseau, M. H. Ottoni, C. Rickards, O. Lu, D. Jiang, C. Núñez, C. Dobosz, T. Jonkisz, A. Frank, W. E. Furac, I. Gehrig, C. Castella, V. Grskovic, B. Haas, C. Wobst, J. Hadzic, G. Pancorbo, M. M. Drobnic, K Honda, K. Hou, Y. Zhou, D. Li, Y. Hu, S. Chen, S. Immel, U. D. Lessig, R. Jakovski, Z. Olofsson, J. K. Ilievska, T. Klann, A. E. García, C. C. de Knijff, P. Kraaijenbrink, T. Kondili, A. Miniati, P. Vouropoulou, M. Kovacevic, L. Marjanovic, D. Morling, N. Lindner, I. Mansour, I. Al-Azem, M. Andari, A. E. Marino, M. Furfuro, S. Locarno, L. Martín, P. Luque, G. M. Alonso, A. Onofri, V. Miranda, L. S. Moreira, H. Mizuno, N. Iwashima, Y. Neto, R. S. Nogueira, T. L. Silva, R. Nastainczyk-Wulf, M. Edelmann, J. Kohl, M. Tagliabracci, A. Nie, S. Wang, X. Cheng, B. Pamjav, H. Volgyi, A. Barany, G. Pawlowski, R. Wei, W. Maciejewska, A. Pelotti, S. Pepinski, W. Abreu-Glowacka, M. Phillips, C. Cárdenas, J. Rey-Gonzalez, D. Salas, A. Brisighelli, F. Capelli, C. Xue, Y. Toscanini, U. Piccinini, A. Piglionica, M. Baldassarra, S. L. Ploski, R. Konarzewska, M. Jastrzebska, E. Robino, C. Sajantila, A. Palo, J. U. Tyler-Smith, C. Guevara, E. Salvador, J. Ungria, M. C. Rodriguez, J. J. Schmidt, U. Schlauderer, N. Saukko, P. Schneider, P. M. Sirker, M. Shin, K. J. Bafalluy, M. B. Oh, Y. N. Skitsa, I. Ampati, A. Smith, T. G. Calvit, L. S. Stenzl, V. Capal, T. Tillmar, A. Nilsson, H. Turrina, S. Martínez-Jarreta, B. De Leo, D. Verzeletti, A. Cortellini, V. Wetton, J. H. Gwynne, G. M. Jobling, M. A. Whittle, M. R. Sumita, D. R. Wolańska-Nowak, P. Yong, R. Y. Egyed, B. Krawczak, M. Nothnagel, M. Roewer, L. Balitzki, B. Tschumi, S. Ballard, D. Court, D. S. Barrantes, X. Bäßler, G. Wiest, T. Berger, B. Niederstätter, H. Parson, W. Davis, C. Budowle, B. Burri, H. Borer, U. Koller, C. Carvalho, E. F. Domingues, P. M. Chamoun, W. T. Coble, M. D. Hill, C. R. http://hdl.handle.net/2381/36838 2016-02-24T03:24:38Z 2016-02-23T14:43:29Z Title: A global analysis of Y-chromosomal haplotype diversity for 23 STR loci Authors: Purps, J.; Siegert, S.; Willuweit, S.; Nagy, M.; Alves, C.; Salazar, R.; Angustia, S. M.; Santos, L. H.; Anslinger, K.; Bayer, B.; Ayub, Q.; Corach, D.; Caputo, M.; D'Amato, M. E.; Davison, S.; Decorte, R.; Larmuseau, M. H.; Ottoni, C.; Rickards, O.; Lu, D.; Jiang, C.; Núñez, C.; Dobosz, T.; Jonkisz, A.; Frank, W. E.; Furac, I.; Gehrig, C.; Castella, V.; Grskovic, B.; Haas, C.; Wobst, J.; Hadzic, G.; Pancorbo, M. M.; Drobnic, K; Honda, K.; Hou, Y.; Zhou, D.; Li, Y.; Hu, S.; Chen, S.; Immel, U. D.; Lessig, R.; Jakovski, Z.; Olofsson, J. K.; Ilievska, T.; Klann, A. E.; García, C. C.; de Knijff, P.; Kraaijenbrink, T.; Kondili, A.; Miniati, P.; Vouropoulou, M.; Kovacevic, L.; Marjanovic, D.; Morling, N.; Lindner, I.; Mansour, I.; Al-Azem, M.; Andari, A. E.; Marino, M.; Furfuro, S.; Locarno, L.; Martín, P.; Luque, G. M.; Alonso, A.; Onofri, V.; Miranda, L. S.; Moreira, H.; Mizuno, N.; Iwashima, Y.; Neto, R. S.; Nogueira, T. L.; Silva, R.; Nastainczyk-Wulf, M.; Edelmann, J.; Kohl, M.; Tagliabracci, A.; Nie, S.; Wang, X.; Cheng, B.; Pamjav, H.; Volgyi, A.; Barany, G.; Pawlowski, R.; Wei, W.; Maciejewska, A.; Pelotti, S.; Pepinski, W.; Abreu-Glowacka, M.; Phillips, C.; Cárdenas, J.; Rey-Gonzalez, D.; Salas, A.; Brisighelli, F.; Capelli, C.; Xue, Y.; Toscanini, U.; Piccinini, A.; Piglionica, M.; Baldassarra, S. L.; Ploski, R.; Konarzewska, M.; Jastrzebska, E.; Robino, C.; Sajantila, A.; Palo, J. U.; Tyler-Smith, C.; Guevara, E.; Salvador, J.; Ungria, M. C.; Rodriguez, J. J.; Schmidt, U.; Schlauderer, N.; Saukko, P.; Schneider, P. M.; Sirker, M.; Shin, K. J.; Bafalluy, M. B.; Oh, Y. N.; Skitsa, I.; Ampati, A.; Smith, T. G.; Calvit, L. S.; Stenzl, V.; Capal, T.; Tillmar, A.; Nilsson, H.; Turrina, S.; Martínez-Jarreta, B.; De Leo, D.; Verzeletti, A.; Cortellini, V.; Wetton, J. H.; Gwynne, G. M.; Jobling, M. A.; Whittle, M. R.; Sumita, D. R.; Wolańska-Nowak, P.; Yong, R. Y.; Egyed, B.; Krawczak, M.; Nothnagel, M.; Roewer, L.; Balitzki, B.; Tschumi, S.; Ballard, D.; Court, D. S.; Barrantes, X.; Bäßler, G.; Wiest, T.; Berger, B.; Niederstätter, H.; Parson, W.; Davis, C.; Budowle, B.; Burri, H.; Borer, U.; Koller, C.; Carvalho, E. F.; Domingues, P. M.; Chamoun, W. T.; Coble, M. D.; Hill, C. R. Abstract: In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent. 2016-02-23T14:43:29Z Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum. Hunt, H. V. Badakshi, F. Romanova, O. Howe, C. J. Jones, M. K. Heslop-Harrison, John Seymour http://hdl.handle.net/2381/36836 2016-02-24T03:24:10Z 2016-02-23T14:32:59Z Title: Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum. Authors: Hunt, H. V.; Badakshi, F.; Romanova, O.; Howe, C. J.; Jones, M. K.; Heslop-Harrison, John Seymour Abstract: Panicum miliaceum (broomcorn millet) is a tetraploid cereal, which was among the first domesticated crops, but is now a minor crop despite its high water use efficiency. The ancestors of this species have not been determined; we aimed to identify likely candidates within the genus, where phylogenies are poorly resolved. Nuclear and chloroplast DNA sequences from P. miliaceum and a range of diploid and tetraploid relatives were used to develop phylogenies of the diploid and tetraploid species. Chromosomal in situ hybridization with genomic DNA as a probe was used to characterize the genomes in the tetraploid P. miliaceum and a tetraploid accession of P. repens. In situ hybridization showed that half the chromosomes of P. miliaceum hybridized more strongly with labelled genomic DNA from P. capillare, and half with labelled DNA from P. repens. Genomic DNA probes differentiated two sets of 18 chromosomes in the tetraploid P. repens. Our phylogenetic data support the allotetraploid origin of P. miliaceum, with the maternal ancestor being P. capillare (or a close relative) and the other genome being shared with P. repens. Our P. repens accession was also an allotetraploid with two dissimilar but closely related genomes, the maternal genome being similar to P. sumatrense. Further collection of Panicum species, particularly from the Old World, is required. It is important to identify why the water-efficient P. miliaceum is now of minimal importance in agriculture, and it may be valuable to exploit the diversity in this species and its ancestors. 2016-02-23T14:32:59Z Comparative analysis of the conserved functions of Arabidopsis DRL1 and yeast KTI12. Jun, S. E. Cho, K. H. Hwang, J. Y. Abdel-Fattah, W. Hammermeister, A. G. Schaffrath, Raffael Bowman, J. L. Kim, G. T. http://hdl.handle.net/2381/36820 2016-02-24T03:23:52Z 2016-02-23T11:41:04Z Title: Comparative analysis of the conserved functions of Arabidopsis DRL1 and yeast KTI12. Authors: Jun, S. E.; Cho, K. H.; Hwang, J. Y.; Abdel-Fattah, W.; Hammermeister, A. G.; Schaffrath, Raffael; Bowman, J. L.; Kim, G. T. Abstract: Patterning of the polar axis during the early leaf developmental stage is established by cell-to-cell communication between the shoot apical meristem (SAM) and the leaf primordia. In a previous study, we showed that the DRL1 gene, which encodes a homolog of the Elongator-associated protein KTI12 of yeast, acts as a positive regulator of adaxial leaf patterning and shoot meristem activity. To determine the evolutionally conserved functions of DRL1, we performed a comparison of the deduced amino acid sequence of DRL1 and its yeast homolog, KTI12, and found that while overall homology was low, well-conserved domains were presented. DRL1 contained two conserved plant-specific domains. Expression of the DRL1 gene in a yeast KTI12-deficient yeast mutant suppressed the growth retardation phenotype, but did not rescue the caffeine sensitivity, indicating that the role of Arabidopsis Elongator-associated protein is partially conserved with yeast KTI12, but may have changed between yeast and plants in response to caffeine during the course of evolution. In addition, elevated expression of DRL1 gene triggered zymocin sensitivity, while overexpression of KTI12 maintained zymocin resistance, indicating that the function of Arabidopsis DRL1 may not overlap with yeast KTI12 with regards to toxin sensitivity. In this study, expression analysis showed that class-I KNOX genes were downregulated in the shoot apex, and that YAB and KAN were upregulated in leaves of the Arabidopsis drl1-101 mutant. Our results provide insight into the communication network between the SAM and leaf primordia required for the establishment of leaf polarity by mediating histone acetylation or through other mechanisms. 2016-02-23T11:41:04Z What hinders minority ethnic access to cancer genetics services and what may help? Allford, A. Qureshi, N. Barwell, Julian Lewis, C. Kai, J. http://hdl.handle.net/2381/36817 2016-02-24T03:25:16Z 2016-02-23T10:12:19Z Title: What hinders minority ethnic access to cancer genetics services and what may help? Authors: Allford, A.; Qureshi, N.; Barwell, Julian; Lewis, C.; Kai, J. Abstract: Ethnic disparities in use of cancer genetics services raise concerns about equitable opportunity to benefit from familial cancer risk assessment, improved survival and quality of life. This paper considers available research to explore what may hinder or facilitate minority ethnic access to cancer genetics services. We sought to inform service development for people of South Asian, African or Irish origin at risk of familial breast, ovarian, colorectal and prostate cancers in the UK. Relevant studies from the UK, North America and Australasia were identified from six electronic research databases. Current evidence is limited but suggests low awareness and understanding of familial cancer risk among minority ethnic communities studied. Socio-cultural variations in beliefs, notably stigma about cancer or inherited risk of cancer, are identified. These factors may affect seeking of advice from providers and disparities in referral. Achieving effective cross-cultural communication in the complex contexts of both cancer and genetics counselling, whether between individuals and providers, when mediated by third party interpreters, or within families, pose further challenges. Some promising experience of facilitating minority ethnic access has been gained by introduction of culturally sensitive provider and counselling initiatives, and by enabling patient self-referral. However, further research to inform and assess these interventions, and others that address the range of challenges identified for cancer genetics services are needed. This should be based on a more comprehensive understanding of what happens at differing points of access and interaction at community, cancer care and genetic service levels. 2016-02-23T10:12:19Z Aggregation-prone proteins modulate huntingtin inclusion body formation in yeast Kantcheva, Ralitsa B. Mason, Robert Giorgini, Flaviano http://hdl.handle.net/2381/36808 2016-02-23T03:26:59Z 2016-02-22T11:54:53Z Title: Aggregation-prone proteins modulate huntingtin inclusion body formation in yeast Authors: Kantcheva, Ralitsa B.; Mason, Robert; Giorgini, Flaviano Abstract: Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a polyglutamine expansion in the huntingtin (HTT) protein. The expression of mutant HTT in the baker's yeast Saccharomyces cerevisiae recapitulates many of the cellular phenotypes observed in mammalian HD models. Mutant HTT aggregation and toxicity in yeast is influenced by the presence of the Rnq1p and Sup35p prions, as well as other glutamine/asparagine-rich aggregation-prone proteins. Here we investigated the ability of a subset of these proteins to modulate mutant HTT aggregation and to substitute for the prion form of Rnq1p. We find that overexpression of either the putative prion Ybr016wp or the Sup35p prion restores aggregation of mutant HTT in yeast cells lacking the Rnq1p prion. These results indicate that an interchangeable suite of aggregation-prone proteins regulates mutant HTT aggregation dynamics in yeast, which may have implications for mutant HTT aggregation in human cells. 2016-02-22T11:54:53Z Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library Lowe, N. Rees, J. S. Roote, J. Ryder, E. Armean, I. M. Johnson, G. Drummond, E. Spriggs, H. Drummond, J. Magbanua, J. P. Naylor, H. Sanson, B. Bastock, R. Huelsmann, S. Trovisco, V. Landgraf, M. Knowles-Barley, S. Armstrong, J. D. White-Cooper, H. Hansen, Celia Phillips, R. G. Lilley, K. S. Russell, S. St Johnston, D. http://hdl.handle.net/2381/36806 2016-02-23T03:27:52Z 2016-02-22T11:39:24Z Title: Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library Authors: Lowe, N.; Rees, J. S.; Roote, J.; Ryder, E.; Armean, I. M.; Johnson, G.; Drummond, E.; Spriggs, H.; Drummond, J.; Magbanua, J. P.; Naylor, H.; Sanson, B.; Bastock, R.; Huelsmann, S.; Trovisco, V.; Landgraf, M.; Knowles-Barley, S.; Armstrong, J. D.; White-Cooper, H.; Hansen, Celia; Phillips, R. G.; Lilley, K. S.; Russell, S.; St Johnston, D. Abstract: Although we now have a wealth of information on the transcription patterns of all the genes in the Drosophila genome, much less is known about the properties of the encoded proteins. To provide information on the expression patterns and subcellular localisations of many proteins in parallel, we have performed a large-scale protein trap screen using a hybrid piggyBac vector carrying an artificial exon encoding yellow fluorescent protein (YFP) and protein affinity tags. From screening 41 million embryos, we recovered 616 verified independent YFP-positive lines representing protein traps in 374 genes, two-thirds of which had not been tagged in previous P element protein trap screens. Over 20 different research groups then characterized the expression patterns of the tagged proteins in a variety of tissues and at several developmental stages. In parallel, we purified many of the tagged proteins from embryos using the affinity tags and identified co-purifying proteins by mass spectrometry. The fly stocks are publicly available through the Kyoto Drosophila Genetics Resource Center. All our data are available via an open access database (Flannotator), which provides comprehensive information on the expression patterns, subcellular localisations and in vivo interaction partners of the trapped proteins. Our resource substantially increases the number of available protein traps in Drosophila and identifies new markers for cellular organelles and structures. Description: Supplementary material available online at http://dev.biologists.org/lookup/suppl/doi:10.1242/dev.111054/-/DC1 2016-02-22T11:39:24Z Approaches for identifying germ cell mutagens: Report of the 2013 IWGT workshop on germ cell assays(☆) Yauk, C. L. Aardema, M. J. Benthem, J. V. Bishop, J. B. Dearfield, K. L. DeMarini, D. M. Dubrova, Yuri Eugenjevitch Honma, M. Lupski, J. R. Marchetti, F. Meistrich, M. L. Pacchierotti, F. Stewart, J. Waters, M. D. Douglas, G. R. http://hdl.handle.net/2381/36786 2016-02-19T03:24:27Z 2016-02-18T12:05:05Z Title: Approaches for identifying germ cell mutagens: Report of the 2013 IWGT workshop on germ cell assays(☆) Authors: Yauk, C. L.; Aardema, M. J.; Benthem, J. V.; Bishop, J. B.; Dearfield, K. L.; DeMarini, D. M.; Dubrova, Yuri Eugenjevitch; Honma, M.; Lupski, J. R.; Marchetti, F.; Meistrich, M. L.; Pacchierotti, F.; Stewart, J.; Waters, M. D.; Douglas, G. R. Abstract: This workshop reviewed the current science to inform and recommend the best evidence-based approaches on the use of germ cell genotoxicity tests. The workshop questions and key outcomes were as follows. (1) Do genotoxicity and mutagenicity assays in somatic cells predict germ cell effects? Limited data suggest that somatic cell tests detect most germ cell mutagens, but there are strong concerns that dictate caution in drawing conclusions. (2) Should germ cell tests be done, and when? If there is evidence that a chemical or its metabolite(s) will not reach target germ cells or gonadal tissue, it is not necessary to conduct germ cell tests, notwithstanding somatic outcomes. However, it was recommended that negative somatic cell mutagens with clear evidence for gonadal exposure and evidence of toxicity in germ cells could be considered for germ cell mutagenicity testing. For somatic mutagens that are known to reach the gonadal compartments and expose germ cells, the chemical could be assumed to be a germ cell mutagen without further testing. Nevertheless, germ cell mutagenicity testing would be needed for quantitative risk assessment. (3) What new assays should be implemented and how? There is an immediate need for research on the application of whole genome sequencing in heritable mutation analysis in humans and animals, and integration of germ cell assays with somatic cell genotoxicity tests. Focus should be on environmental exposures that can cause de novo mutations, particularly newly recognized types of genomic changes. Mutational events, which may occur by exposure of germ cells during embryonic development, should also be investigated. Finally, where there are indications of germ cell toxicity in repeat dose or reproductive toxicology tests, consideration should be given to leveraging those studies to inform of possible germ cell genotoxicity. 2016-02-18T12:05:05Z Metabolic molecular markers of the tidal clock in the marine crustacean Eurydice pulchra O'Neill, J. S. Lee, Kate D. Zhang, Lin Feeney, K. Webster, S. G. Blades, Matthew James Kyriacou, Charalambos P. Hastings, M. H. Wilcockson, D. C. http://hdl.handle.net/2381/36779 2016-02-19T03:24:22Z 2016-02-18T11:10:21Z Title: Metabolic molecular markers of the tidal clock in the marine crustacean Eurydice pulchra Authors: O'Neill, J. S.; Lee, Kate D.; Zhang, Lin; Feeney, K.; Webster, S. G.; Blades, Matthew James; Kyriacou, Charalambos P.; Hastings, M. H.; Wilcockson, D. C. Abstract: In contrast to the well mapped molecular orchestration of circadian timekeeping in terrestrial organisms, the mechanisms that direct tidal and lunar rhythms in marine species are entirely unknown. Using a combination of biochemical and molecular approaches we have identified a series of metabolic markers of the tidal clock of the intertidal isopod Eurydice pulchra. Specifically, we show that the overoxidation of peroxiredoxin (PRX), a conserved marker of circadian timekeeping in terrestrial eukaryotes [1], follows a circatidal (approximately 12.4 hours) pattern in E. pulchra, in register with the tidal pattern of swimming. In parallel, we show that mitochondrially encoded genes are expressed with a circatidal rhythm. Together, these findings demonstrate that PRX overoxidation rhythms are not intrinsically circadian; rather they appear to resonate with the dominant metabolic cycle of an organism, regardless of its frequency. Moreover, they provide the first molecular leads for dissecting the tidal clockwork. 2016-02-18T11:10:21Z Disrupted seasonal biology impacts health, food security and ecosystems Stevenson, T. J. Visser, M. E. Arnold, W. Barrett, P. Biello, S. Dawson, A. Denlinger, D. L. Dominoni, D. Ebling, F. J. Elton, S. Evans, N. Ferguson, H. M. Foster, R. G. Hau, M. Haydon, D. T. Hazlerigg, D. G. Heideman, P. Hopcraft, J. G. Jonsson, N. N. Kronfeld-Schor, N. Kumar, V. Lincoln, G. A. MacLeod, R. Martin, S. A. Martinez-Bakker, M. Nelson, R. J. Reed, T. Robinson, J. E. Rock, D. Schwartz, W. J. Steffan-Dewenter, I. Tauber, Eran Thackeray, S. J. Umstatter, C. Yoshimura, T. Helm, B. http://hdl.handle.net/2381/36777 2016-02-19T03:24:11Z 2016-02-18T10:58:21Z Title: Disrupted seasonal biology impacts health, food security and ecosystems Authors: Stevenson, T. J.; Visser, M. E.; Arnold, W.; Barrett, P.; Biello, S.; Dawson, A.; Denlinger, D. L.; Dominoni, D.; Ebling, F. J.; Elton, S.; Evans, N.; Ferguson, H. M.; Foster, R. G.; Hau, M.; Haydon, D. T.; Hazlerigg, D. G.; Heideman, P.; Hopcraft, J. G.; Jonsson, N. N.; Kronfeld-Schor, N.; Kumar, V.; Lincoln, G. A.; MacLeod, R.; Martin, S. A.; Martinez-Bakker, M.; Nelson, R. J.; Reed, T.; Robinson, J. E.; Rock, D.; Schwartz, W. J.; Steffan-Dewenter, I.; Tauber, Eran; Thackeray, S. J.; Umstatter, C.; Yoshimura, T.; Helm, B. Abstract: The rhythm of life on earth is shaped by seasonal changes in the environment. Plants and animals show profound annual cycles in physiology, health, morphology, behaviour and demography in response to environmental cues. Seasonal biology impacts ecosystems and agriculture, with consequences for humans and biodiversity. Human populations show robust annual rhythms in health and well-being, and the birth month can have lasting effects that persist throughout life. This review emphasizes the need for a better understanding of seasonal biology against the backdrop of its rapidly progressing disruption through climate change, human lifestyles and other anthropogenic impact. Climate change is modifying annual rhythms to which numerous organisms have adapted, with potential consequences for industries relating to health, ecosystems and food security. Disconcertingly, human lifestyles under artificial conditions of eternal summer provide the most extreme example for disconnect from natural seasons, making humans vulnerable to increased morbidity and mortality. In this review, we introduce scenarios of seasonal disruption, highlight key aspects of seasonal biology and summarize from biomedical, anthropological, veterinary, agricultural and environmental perspectives the recent evidence for seasonal desynchronization between environmental factors and internal rhythms. Because annual rhythms are pervasive across biological systems, they provide a common framework for trans-disciplinary research. 2016-02-18T10:58:21Z Integration of genetic and physical maps of the Primula vulgarisS locus and localization by chromosome in situ hybridization Heslop-Harrison, Pat Li, J. Webster, M. A. Wright, J. Cocker, J. M. Smith, M. C. Badakshi, Farah Gilmartin, P. M. http://hdl.handle.net/2381/36746 2016-02-18T03:18:32Z 2016-02-17T10:41:16Z Title: Integration of genetic and physical maps of the Primula vulgarisS locus and localization by chromosome in situ hybridization Authors: Heslop-Harrison, Pat; Li, J.; Webster, M. A.; Wright, J.; Cocker, J. M.; Smith, M. C.; Badakshi, Farah; Gilmartin, P. M. Abstract: Heteromorphic flower development in Primula is controlled by the S locus. The S locus genes, which control anther position, pistil length and pollen size in pin and thrum flowers, have not yet been characterized. We have integrated S-linked genes, marker sequences and mutant phenotypes to create a map of the P. vulgaris S locus region that will facilitate the identification of key S locus genes. We have generated, sequenced and annotated BAC sequences spanning the S locus, and identified its chromosomal location. We have employed a combination of classical genetics and three-point crosses with molecular genetic analysis of recombinants to generate the map. We have characterized this region by Illumina sequencing and bioinformatic analysis, together with chromosome in situ hybridization. We present an integrated genetic and physical map across the P. vulgaris S locus flanked by phenotypic and DNA sequence markers. BAC contigs encompass a 1.5-Mb genomic region with 1 Mb of sequence containing 82 S-linked genes anchored to overlapping BACs. The S locus is located close to the centromere of the largest metacentric chromosome pair. These data will facilitate the identification of the genes that orchestrate heterostyly in Primula and enable evolutionary analyses of the S locus. 2016-02-17T10:41:16Z Persistent Staphylococcus aureus isolates from two independent cases of bacteremia display increased bacterial fitness and novel immune evasion phenotypes. Richards, R. L. Haigh, Richard David Pascoe, B. Sheppard, S. K. Price, F. Jenkins, D. Rajakumar, Kumar Morrissey, Julie Ann http://hdl.handle.net/2381/36711 2016-02-16T03:27:08Z 2016-02-15T10:32:14Z Title: Persistent Staphylococcus aureus isolates from two independent cases of bacteremia display increased bacterial fitness and novel immune evasion phenotypes. Authors: Richards, R. L.; Haigh, Richard David; Pascoe, B.; Sheppard, S. K.; Price, F.; Jenkins, D.; Rajakumar, Kumar; Morrissey, Julie Ann Abstract: Staphylococcus aureus bacteremia cases are complicated by bacterial persistence and treatment failure despite the confirmed in vitro susceptibility of the infecting strain to administered antibiotics. A high incidence of methicillin-resistant S. aureus (MRSA) bacteremia cases are classified as persistent and are associated with poorer patient outcomes. It is still unclear how S. aureus evades the host immune system and resists antibiotic treatment for the prolonged duration of a persistent infection. In this study, the genetic changes and associated phenotypic traits specific to S. aureus persistent bacteremia were identified by comparing temporally dispersed isolates from persistent infections (persistent isolates) originating from two independent persistent S. aureus bacteremia cases with the initial infection isolates and with three resolved S. aureus bacteremia isolates from the same genetic background. Several novel traits were associated specifically with both independent sets of persistent S. aureus isolates compared to both the initial isolates and the isolates from resolved infections (resolved isolates). These traits included (i) increased growth under nutrient-poor conditions; (ii) increased tolerance of iron toxicity; (iii) higher expression of cell surface proteins involved in immune evasion and stress responses; and (iv) attenuated virulence in a Galleria mellonella larva infection model that was not associated with small-colony variation or metabolic dormancy such as had been seen previously. Whole-genome sequence analysis identified different single nucleotide mutations within the mprF genes of all the isolates with the adaptive persistence traits from both independent cases. Overall, our data indicate a novel role for MprF function during development of S. aureus persistence by increasing bacterial fitness and immune evasion. 2016-02-15T10:32:14Z An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli Nehring, R. B. Gu, F. Lin, H. Y. Gibson, J. L. Blythe, M. J. Wilson, R. Bravo Núñez, M. A. Hastings, P. J. Louis, Edward John Frisch, R. L. Hu, J. C. Rosenberg, S. M. http://hdl.handle.net/2381/36645 2016-04-07T12:09:13Z 2016-02-10T09:44:44Z Title: An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli Authors: Nehring, R. B.; Gu, F.; Lin, H. Y.; Gibson, J. L.; Blythe, M. J.; Wilson, R.; Bravo Núñez, M. A.; Hastings, P. J.; Louis, Edward John; Frisch, R. L.; Hu, J. C.; Rosenberg, S. M. Abstract: With the wide availability of whole-genome sequencing (WGS), genetic mapping has become the rate-limiting step, inhibiting unbiased forward genetics in even the most tractable model organisms. We introduce a rapid deconvolution resource and method for untagged causative mutations after mutagenesis, screens, and WGS in Escherichia coli. We created Deconvoluter-ordered libraries with selectable insertions every 50 kb in the E. coli genome. The Deconvoluter method uses these for replacement of untagged mutations in the genome using a phage-P1-based gene-replacement strategy. We validate the Deconvoluter resource by deconvolution of 17 of 17 phenotype-altering mutations from a screen of N-ethyl-N-nitrosourea-induced mutants. The Deconvoluter resource permits rapid unbiased screens and gene/function identification and will enable exploration of functions of essential genes and undiscovered genes/sites/alleles not represented in existing deletion collections. This resource for unbiased forward-genetic screens with mapping-by-sequencing ('forward genomics') demonstrates a strategy that could similarly enable rapid screens in many other microbes. 2016-02-10T09:44:44Z Inhibition of matrix metalloproteinases attenuates brain damage in experimental meningococcal meningitis Ricci, S. Grandgirard, D. Wenzel, M. Braccini, T. Salvatore, P. Oggioni, Marco Rinaldo Leib, S. L. Koedel, U. http://hdl.handle.net/2381/36565 2016-02-05T03:27:05Z 2016-02-04T11:07:50Z Title: Inhibition of matrix metalloproteinases attenuates brain damage in experimental meningococcal meningitis Authors: Ricci, S.; Grandgirard, D.; Wenzel, M.; Braccini, T.; Salvatore, P.; Oggioni, Marco Rinaldo; Leib, S. L.; Koedel, U. Abstract: Background: Approximately 7% of survivors from meningococcal meningitis (MM) suffer from neurological sequelae due to brain damage in the course of meningitis. The present study focuses on the role of matrix metalloproteinases (MMPs) in a novel mouse model of MM-induced brain damage. Methods: The model is based on intracisternal infection of BALB/c mice with a serogroup C Neisseria meningitidis strain. Mice were infected with meningococci and randomised for treatment with the MMP inhibitor batimastat (BB-94) or vehicle. Animal survival, brain injury and host-response biomarkers were assessed 48 h after meningococcal challenge. Results: Mice that received BB-94 presented significantly diminished MMP-9 levels (p < 0.01), intracerebral bleeding (p < 0.01), and blood-brain barrier (BBB) breakdown (p < 0.05) in comparison with untreated animals. In mice suffering from MM, the amount of MMP-9 measured by zymography significantly correlated with both intracerebral haemorrhage (p < 0.01) and BBB disruption (p < 0.05). Conclusions: MMPs significantly contribute to brain damage associated with experimental MM. Inhibition of MMPs reduces intracranial complications in mice suffering from MM, representing a potential adjuvant strategy in MM post-infection sequelae. 2016-02-04T11:07:50Z Genomic Analysis of Serogroup Y Neisseria meningitidis Isolates Reveals Extensive Similarities Between Carriage and Disease-Associated Organisms Oldfield, N. J. Harrison, O. B. Bayliss, Christopher David Maiden, M. C. Ala'Aldeen, D. A. Turner, D. P. http://hdl.handle.net/2381/36560 2016-02-05T03:27:12Z 2016-02-04T10:51:00Z Title: Genomic Analysis of Serogroup Y Neisseria meningitidis Isolates Reveals Extensive Similarities Between Carriage and Disease-Associated Organisms Authors: Oldfield, N. J.; Harrison, O. B.; Bayliss, Christopher David; Maiden, M. C.; Ala'Aldeen, D. A.; Turner, D. P. Abstract: BACKGROUND: Neisseria meningitidis is a frequent colonizer of the human nasopharynx with asymptomatic carriage providing the reservoir for invasive, disease-causing strains. Serogroup Y (MenY) strains are a major cause of meningococcal disease. High resolution genetic analyses of carriage and disease isolates can establish epidemiological relationships and identify potential virulence factors. METHODS: Whole genome sequence data were obtained from UK MenY carriage isolates from 1997-2010 (n=99). Sequences were compared to those from MenY invasive isolates from 2010 and 2011 (n=73) using a gene-by-gene approach. RESULTS: Comparisons across 1,605 core genes resolved 91% of isolates into one of eight clusters containing closely related disease and carriage isolates. Six clusters contained carried meningococci isolated in 1997-2001 suggesting temporal stability. One cluster of isolates, predominately sharing the designation Y: P1.5-1,10-1: F4-1: ST-1655 (cc23), was resolved into a sub-cluster with 86% carriage isolates and a second with 90% invasive isolates. These sub-clusters were defined by specific allelic differences in five core genes encoding glycerate kinase (glxK), valine-pyruvate transaminase (avtA), superoxide dismutase (sodB) and two hypothetical proteins. CONCLUSIONS: High resolution genetic analyses detected long-term temporal stability and temporally-overlapping carriage and disease populations for MenY clones but also evidence of a disease-associated clone. Description: The file associated with this record is under a 12-month embargo from publication in accordance with the publisher's self-archiving policy. The full text may be available through the publisher links provided above. 2016-02-04T10:51:00Z Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168 Anjum, Awais Brathwaite, K. J. Aidley, Jack Connerton, P. L. Cummings, N. J. Parkhill, J. Connerton, I. Bayliss, Christopher D. http://hdl.handle.net/2381/36559 2016-04-14T14:45:48Z 2016-02-04T10:43:07Z Title: Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168 Authors: Anjum, Awais; Brathwaite, K. J.; Aidley, Jack; Connerton, P. L.; Cummings, N. J.; Parkhill, J.; Connerton, I.; Bayliss, Christopher D. Abstract: Phase-variable restriction-modification systems are a feature of a diverse range of bacterial species. Stochastic, reversible switches in expression of the methyltransferase produces variation in methylation of specific sequences. Phase-variable methylation by both Type I and Type III methyltransferases is associated with altered gene expression and phenotypic variation. One phase-variable gene of Campylobacter jejuni encodes a homologue of an unusual Type IIG restriction-modification system in which the endonuclease and methyltransferase are encoded by a single gene. Using both inhibition of restriction and PacBio-derived methylome analyses of mutants and phase-variants, the cj0031c allele in C. jejuni strain NCTC11168 was demonstrated to specifically methylate adenine in 5'CCCGA and 5'CCTGA sequences. Alterations in the levels of specific transcripts were detected using RNA-Seq in phase-variants and mutants of cj0031c but these changes did not correlate with observed differences in phenotypic behaviour. Alterations in restriction of phage growth were also associated with phase variation (PV) of cj0031c and correlated with presence of sites in the genomes of these phages. We conclude that PV of a Type IIG restriction-modification system causes changes in site-specific methylation patterns and gene expression patterns that may indirectly change adaptive traits. 2016-02-04T10:43:07Z Large-scale structure of brown rat (Rattus norvegicus) populations in England: effects on rodenticide resistance Haniza, M. Z. Adams, S. Jones, E. P. MacNicoll, A. M. Mallon, Eamonn Bernard Smith, R. H. Lambert, M. S. http://hdl.handle.net/2381/36535 2016-02-03T03:17:06Z 2016-02-02T15:49:29Z Title: Large-scale structure of brown rat (Rattus norvegicus) populations in England: effects on rodenticide resistance Authors: Haniza, M. Z.; Adams, S.; Jones, E. P.; MacNicoll, A. M.; Mallon, Eamonn Bernard; Smith, R. H.; Lambert, M. S. Abstract: The brown rat (Rattus norvegicus) is a relatively recent (<300 years) addition to the British fauna, but by association with negative impacts on public health, animal health and agriculture, it is regarded as one of the most important vertebrate pest species. Anticoagulant rodenticides were introduced for brown rat control in the 1950s and are widely used for rat control in the UK, but long-standing resistance has been linked to control failures in some regions. One thus far ignored aspect of resistance biology is the population structure of the brown rat. This paper investigates the role population structure has on the development of anticoagulant resistance. Using mitochondrial and microsatellite DNA, we examined 186 individuals (from 15 counties in England and one location in Wales near the Wales-England border) to investigate the population structure of rural brown rat populations. We also examined individual rats for variations of the VKORC1 gene previously associated with resistance to anticoagulant rodenticides. We show that the populations were structured to some degree, but that this was only apparent in the microsatellite data and not the mtDNA data. We discuss various reasons why this is the case. We show that the population as a whole appears not to be at equilibrium. The relative lack of diversity in the mtDNA sequences examined can be explained by founder effects and a subsequent spatial expansion of a species introduced to the UK relatively recently. We found there was a geographical distribution of resistance mutations, and relatively low rate of gene flow between populations, which has implications for the development and management of anticoagulant resistance. 2016-02-02T15:49:29Z Copy number variation of scavenger-receptor cysteine rich domains within DMBT1 and Crohn's disease Polley, S. Prescott, N. Nimmo, E. Veal, C. Vind, I. Munkholm, P. Fode, P. Mansfield, J. Andersen, P. S. Satsangi, J. Mathew, C. G. Hollox, Edward http://hdl.handle.net/2381/36492 2016-02-02T03:14:52Z 2016-02-01T11:37:59Z Title: Copy number variation of scavenger-receptor cysteine rich domains within DMBT1 and Crohn's disease Authors: Polley, S.; Prescott, N.; Nimmo, E.; Veal, C.; Vind, I.; Munkholm, P.; Fode, P.; Mansfield, J.; Andersen, P. S.; Satsangi, J.; Mathew, C. G.; Hollox, Edward Abstract: Previous work has shown that the gene DMBT1, which encodes a large secreted epithelial glycoprotein known as salivary agglutinin, gp340, hensin or muclin, is an innate immune defence protein that binds bacteria. A deletion variant of DMBT1 has been previously associated with Crohn's disease, and a DMBT1−/− knockout mouse has increased levels of colitis induced by dextran sulphate. DMBT1 has a complex copy number variable structure, with two, independent, rapidly mutating copy number variable regions, called CNV1 and CNV2. Because the copy number variable regions are predicted to affect the number of bacteria-binding domains, different alleles may alter host–microbe interactions in the gut. Our aim was to investigate the role of this complex variation in susceptibility to Crohn's disease by assessing the previously reported association. We analysed the association of both copy number variable regions with presence of Crohn's disease, and its severity, on three case–control cohorts. We also reanalysed array comparative genomic hybridisation data (aCGH) from a large case–control cohort study for both copy number variable regions. We found no association with a linear increase in copy number, nor when the CNV1 is regarded as presence or absence of a deletion allele. Taken together, we show that the DMBT1 CNV does not affect susceptibility to Crohn's disease, at least in Northern Europeans. 2016-02-01T11:37:59Z