http://www.dspace.cam.ac.uk:80/handle/1810/227544 Tue, 21 May 2013 17:59:11 GMT 2013-05-21T17:59:11Z http://www.dspace.cam.ac.uk:80/handle/1810/242000 Title: Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Authors: Renfree, Marilyn B; Papenfuss, Anthony T; Deakin, Janine E; Lindsay, James; Heider, Thomas; Belov, Katherine; Rens, Willem; Waters, Paul D; Pharo, Elizabeth A; Shaw, Geoff; Wong, Emily SW; Lefèvre, Christophe M; Nicholas, Kevin R; Kuroki, Yoko; Wakefield, Matthew J; Zenger, Kyall R; Wang, Chenwei; Ferguson-Smith, Malcolm; Nicholas, Frank W; Hickford, Danielle; Yu, Hongshi; Short, Kirsty R; Siddle, Hannah V; Frankenberg, Stephen R; Chew, Keng Y; Menzies, Brandon R; Stringer, Jessica M; Suzuki, Shunsuke; Hore, Timothy A; Delbridge, Margaret L; Patel, Hardip; Mohammadi, Amir; Schneider, Nanette Y; Hu, Yanqiu; O'Hara, William; Al Nadaf, Shafagh; Wu, Chen; Feng, Zhi-Ping; Cocks, Benjamin G; Wang, Jianghui; Flicek, Paul; Searle, Stephen MJ; Fairley, Susan; Beal, Kathryn; Herrero, Javier; Carone, Dawn M; Suzuki, Yutaka; Sugano, Sumio; Toyoda,Atsushi; Sakaki, Yoshiyuki; Kondo, Shinji; Nishida, Yuichiro; Tatsumoto, Shoji; Mandiou, Ion; Hsu, Arthur; McColl, Kaighin A; Lansdell, Benjamin; Weinstock, George; Kuczek, Elizabeth; McGrath, Annette; Wilson, Peter; Men, Artem; Hazar-Rethinam, Mehlika; Hall, Allison; Davis, John; Wood, David; Williams, Sarah; Sundaravadanam, Yogi; Muzny, Donna M; Jhangiani, Shalini N; Lewis, Lora R; Morgan, Margaret B; Okwuonu, Geoffrey O; Ruiz, San J; Santibanez, Jireh; Nazareth, Lynne; Cree, Andrew; Fowler, Gerald; Kovar, Christie L; Dinh, Huyen H; Joshi, Vandita; Jing, Chyn; Lara, Fremiet; Thornton, Rebecca; Chen, Lei; Deng, Jixin; Liu, Yue; Shen, Joshua Y; Song, Xing-Zhi; Edson, Janette; Troon, Carmen; Thomas, Daniel; Stephens, Amber; Yapa, Lankesha; Levchenko, Tanya; Gibbs, Richard A; Cooper, Desmond W; Speed, Terence P; Fujiyama, Asao; Graves, Jennifer A M; O'Neill, Rachel J; Pask, Andrew J; Forrest, Susan M; Worley, Kim C Abstract: Background. We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. Results. The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Conclusions. Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution. Fri, 30 Dec 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/242000 2011-12-30T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241599 Title: Evaluation of the role of location and distance in recruitment in respondent-driven sampling Authors: McCreesh, Nicky; Johnston, Lisa G; Copas, Andrew; Sonnenberg, Pam; Seeley, Janet; Hayes, Richard J; Frost, Simon DW; White, Richard G Abstract: Abstract Background Respondent-driven sampling(RDS) is an increasingly widely used variant of a link tracing design for recruiting hidden populations. The role of the spatial distribution of the target population has not been robustly examined for RDS. We examine patterns of recruitment by location, and how they may have biased an RDS study findings. Methods Total-population data were available on a range of characteristics on a population of 2402 male household-heads from an open cohort of 25 villages in rural Uganda. The locations of households were known a-priori. An RDS survey was carried out in this population, employing current RDS methods of sampling and statistical inference. Results There was little heterogeneity in the population by location. Data suggested more distant contacts were less likely to be reported, and therefore recruited, but if reported more distant contacts were as likely as closer contacts to be recruited. There was no evidence that closer proximity to a village meeting place was associated with probability of being recruited, however it was associated with a higher probability of recruiting a larger number of recruits. People living closer to an interview site were more likely to be recruited. Conclusions Household location affected the overall probability of recruitment, and the probability of recruitment by a specific recruiter. Patterns of recruitment do not appear to have greatly biased estimates in this study. The observed patterns could result in bias in more geographically heterogeneous populations. Care is required in RDS studies when choosing the network size question and interview site location(s). Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Mon, 17 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241599 2011-10-17T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241592 Title: A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map Authors: Wang, Chenwei; Deakin, Janine E; Rens, Willem; Zenger, Kyall R; Belov, Katherine; Marshall Graves, Jennifer A; Nicholas, Frank W Abstract: Abstract Background The limited (2X) coverage of the tammar wallaby (Macropus eugenii) genome sequence dataset currently presents a challenge for assembly and anchoring onto chromosomes. To provide a framework for this assembly, it would be a great advantage to have a dense map of the tammar wallaby genome. However, only limited mapping data are available for this non-model species, comprising a physical map and a linkage map. Results We combined all available tammar wallaby mapping data to create a tammar wallaby integrated map, using the Location DataBase (LDB) strategy. This first-generation integrated map combines all available information from the second-generation tammar wallaby linkage map with 148 loci, and extensive FISH mapping data for 492 loci, especially for genes likely to be located at the ends of wallaby chromosomes or at evolutionary breakpoints inferred from comparative information. For loci whose positions are only approximately known, their location in the integrated map was refined on the basis of comparative information from opossum (Monodelphis domestica) and human. Interpolation of segments from the opossum and human assemblies into the integrated map enabled the subsequent construction of a tammar wallaby first-generation virtual genome map, which comprises 14336 markers, including 13783 genes recruited from opossum and human assemblies. Both maps are freely available at http://compldb.angis.org.au. Conclusions The first-generation integrated map and the first-generation virtual genome map provide a backbone for the chromosome assembly of the tammar wallaby genome sequence. For example, 78% of the 10257 gene-scaffolds in the Ensembl annotation of the tammar wallaby genome sequence (including 10522 protein-coding genes) can now be given a chromosome location in the tammar wallaby virtual genome map. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 18 Aug 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241592 2011-08-18T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238240 Title: The in vivoexpression of actin/salt-resistant hyperactive DNase I inhibits the development of anti-ssDNA and anti-histone autoantibodies in a murine model of systemic lupus erythematosus Authors: Manderson, Anthony P; Carlucci, Francesco; Lachmann, Peter J; Lazarus, Robert A; Festenstein, Richard J; Cook, Herbert T; Walport, Mark J; Botto, Marina Abstract: Abstract Systemic lupus erythematosus (SLE) is characterised by the production of autoantibodies against ubiquitous antigens, especially nuclear components. Evidence makes it clear that the development of these autoantibodies is an antigen-driven process and that immune complexes involving DNA-containing antigens play a key role in the disease process. In rodents, DNase I is the major endonuclease present in saliva, urine and plasma, where it catalyses the hydrolysis of DNA, and impaired DNase function has been implicated in the pathogenesis of SLE. In this study we have evaluated the effects of transgenic over-expression of murine DNase I endonucleases in vivo in a mouse model of lupus. We generated transgenic mice having T-cells that express either wild-type DNase I (wt.DNase I) or a mutant DNase I (ash.DNase I), engineered for three new properties – resistance to inhibition by G-actin, resistance to inhibition by physiological saline and hyperactivity compared to wild type. By crossing these transgenic mice with a murine strain that develops SLE we found that, compared to control non-transgenic littermates or wt.DNase I transgenic mice, the ash.DNase I mutant provided significant protection from the development of anti-single-stranded DNA and anti-histone antibodies, but not of renal disease. In summary, this is the first study in vivo to directly test the effects of long-term increased expression of DNase I on the development of SLE. Our results are in line with previous reports on the possible clinical benefits of recombinant DNase I treatment in SLE, and extend them further to the use of engineered DNase I variants with increased activity and resistance to physiological inhibitors. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Sun, 09 Apr 2006 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238240 2006-04-09T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238216 Title: The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z Authors: Rens, Willem; O'Brien, Patricia C M; Grutzner, Frank; Clarke, Oliver; Graphodatskaya, Daria; Tsend-Ayush, Enkhjargal; Trifonov, Vladimir A; Skelton, Helen; Wallis, Mary C; Johnston, Steve; Veyrunes, Frederic; Graves, Jennifer A M; Ferguson-Smith, Malcolm A Abstract: Abstract Background Sex-determining systems have evolved independently in vertebrates. Placental mammals and marsupials have an XY system, birds have a ZW system. Reptiles and amphibians have different systems, including temperature-dependent sex determination, and XY and ZW systems that differ in origin from birds and placental mammals. Monotremes diverged early in mammalian evolution, just after the mammalian clade diverged from the sauropsid clade. Our previous studies showed that male platypus has five X and five Y chromosomes, no SRY, and DMRT1 on an X chromosome. In order to investigate monotreme sex chromosome evolution, we performed a comparative study of platypus and echidna by chromosome painting and comparative gene mapping. Results Chromosome painting reveals a meiotic chain of nine sex chromosomes in the male echidna and establishes their order in the chain. Two of those differ from those in the platypus, three of the platypus sex chromosomes differ from those of the echidna and the order of several chromosomes is rearranged. Comparative gene mapping shows that, in addition to bird autosome regions, regions of bird Z chromosomes are homologous to regions in four platypus X chromosomes, that is, X1, X2, X3, X5, and in chromosome Y1. Conclusion Monotreme sex chromosomes are easiest to explain on the hypothesis that autosomes were added sequentially to the translocation chain, with the final additions after platypus and echidna divergence. Genome sequencing and contig anchoring show no homology yet between platypus and therian Xs; thus, monotremes have a unique XY sex chromosome system that shares some homology with the avian Z. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Fri, 16 Nov 2007 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238216 2007-11-16T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238045 Title: Ultrasonographic evaluation of the supraspinous ligament in a series of ridden and unridden horses and horses with unrelated back pathology Authors: Henson, Frances M D; Lamas, Luis; Knezevic, Sabina; Jeffcott, Leo B Abstract: Abstract Background Injury to the supraspinous ligament (SSL) is reported to cause back pain in the horse. The diagnosis is based on clinical examination and confirmed by ultrasonographic examination. The ultrasonographic appearance of the supraspinous ligament has been well described, but there are few studies that correlate ultrasonographic findings with clinical pain and/or pathology. This preliminary study aims to test the hypothesis that unridden horses (n = 13) have a significantly reduced frequency of occurrence of ultrasonographic changes of the SSL consistent with a diagnosis of desmitis when compared to ridden horses (n = 13) and those with clinical signs of back pain (n = 13). Results The supraspinous ligament of all horses was imaged between T(thoracic)6-T18 and ultrasonographic appearance. There was an average of 2.08 abnormal images per horse from the whole group. The average number of abnormalities in unridden horses was 4.92, in ridden horses 2.92 and in horses with clinical back pain 4.69. No lesions were found between T6 and T10 and 68% of lesions were found between T14 and T17. No significant difference (p < 0.05) was found between the three groups in the number or location of abnormal images. Conclusion The main conclusion was that every horse in this study (n = 39) had at least one site of SSL desmitis (range 2 to 11). It was clear that ultrasonographically diagnosed SSL desmitis cannot be considered as prima facie evidence of clinically significant disease and further evidence is required for a definitive diagnosis. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 01 Mar 2007 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238045 2007-03-01T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238010 Title: Development of a universal measure of quadrupedal forelimb-hindlimb coordination using digital motion capture and computerised analysis Authors: Hamilton, Lindsay; Franklin, Robin J M; Jeffery, Nick D Abstract: Abstract Background Clinical spinal cord injury in domestic dogs provides a model population in which to test the efficacy of putative therapeutic interventions for human spinal cord injury. To achieve this potential a robust method of functional analysis is required so that statistical comparison of numerical data derived from treated and control animals can be achieved. Results In this study we describe the use of digital motion capture equipment combined with mathematical analysis to derive a simple quantitative parameter – 'the mean diagonal coupling interval' – to describe coordination between forelimb and hindlimb movement. In normal dogs this parameter is independent of size, conformation, speed of walking or gait pattern. We show here that mean diagonal coupling interval is highly sensitive to alterations in forelimb-hindlimb coordination in dogs that have suffered spinal cord injury, and can be accurately quantified, but is unaffected by orthopaedic perturbations of gait. Conclusion Mean diagonal coupling interval is an easily derived, highly robust measurement that provides an ideal method to compare the functional effect of therapeutic interventions after spinal cord injury in quadrupeds. Mon, 17 Sep 2007 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238010 2007-09-17T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237998 Title: Chondrocyte outgrowth into a gelatin scaffold in a single impact load model of damage/repair - effect of BMP-2 Authors: Henson, Frances M D; Vincent, Thea A Abstract: Abstract Background Articular cartilage has little capacity for repair in vivo, however, a small number of studies have shown that, in vitro, a damage/repair response can be induced. Recent work by our group has shown that cartilage can respond to single impact load and culture by producing repair cells on the articular surface. The purpose of this study was to identify whether chondrocyte outgrowth into a 3D scaffold could be observed following single impact load and culture. The effect of bone morphogenic-2 (BMP-2) on this process was investigated. Methods Cartilage explants were single impact loaded, placed within a scaffold and cultured for up to 20 days +/- BMP-2. Cell numbers in the scaffold, on and extruding from the articular surface were quantified and the immunohistochemistry used to identify the cellular phenotype. Results Following single impact load and culture, chondrocytes were observed in a 3D gelatin scaffold under all culture conditions. Chondrocytes were also observed on the articular surface of the cartilage and extruding out of the parent cartilage and on to the cartilage surface. BMP-2 was demonstrated to quantitatively inhibit these events. Conclusion These studies demonstrate that articular chondrocytes can be stimulated to migrate out of parent cartilage following single impact load and culture. The addition of BMP-2 to the culture medium quantitatively reduced the repair response. It may be that the inhibitory effect of BMP-2 in this experimental model provides a clue to the apparent inability of articular cartilage to heal itself following damage in vivo. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 05 Dec 2007 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237998 2007-12-05T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237989 Title: Secreted factors from olfactory mucosa cells expanded as free-floating spheres increase neurogenesis in olfactory bulb neurosphere cultures Authors: Barraud, Perrine; He, Xiao-ling; Caldwell, Maeve; Franklin, Robin J M Abstract: Abstract Background The olfactory epithelium is a neurogenic tissue comprising a population of olfactory receptor neurons that are renewed throughout adulthood by a population of stem and progenitor cells. Because of their relative accessibility compared to intra-cranially located neural stem/progenitor cells, olfactory epithelium stem and progenitor cells make attractive candidates for autologous cell-based therapy. However, olfactory stem and progenitor cells expand very slowly when grown as free-floating spheres (olfactory-spheres) under growth factor stimulation in a neurosphere assay. Results In order to address whether olfactory mucosa cells extrinsically regulate proliferation and/or differentiation of immature neural cells, we cultured neural progenitor cells derived from mouse neonatal olfactory bulb or subventricular zone (SVZ) in the presence of medium conditioned by olfactory mucosa-derived spheres (olfactory-spheres). Our data demonstrated that olfactory mucosa cells produced soluble factors that affect bulbar neural progenitor cell differentiation but not their proliferation when compared to control media. In addition, olfactory mucosa derived soluble factors increased neurogenesis, especially favouring the generation of non-GABAergic neurons. Olfactory mucosa conditioned medium also contained several factors with neurotrophic/neuroprotective properties. Olfactory-sphere conditioned medium did not affect proliferation or differentiation of SVZ-derived neural progenitors. Conclusion These data suggest that the olfactory mucosa does not contain factors that are inhibitory to neural stem/progenitor cell proliferation but does contain factors that steer differentiation toward neuronal phenotypes. Moreover, they suggest that the poor expansion of olfactory-spheres may be in part due to intrinsic properties of the olfactory epithelial stem/progenitor cell population. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Mon, 18 Feb 2008 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237989 2008-02-18T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237981 Title: Construction of networks with intrinsic temporal structure from UK cattle movement data Authors: Heath, M Fred; Vernon, Matthew C; Webb, Cerian R Abstract: Abstract Background The implementation of national systems for recording the movements of cattle between agricultural holdings in the UK has enabled the development and parameterisation of network-based models for disease spread. These data can be used to form a network in which each cattle-holding location is represented by a single node and links between nodes are formed if there is a movement of cattle between them in the time period selected. However, this approach loses information on the time sequence of events thus reducing the accuracy of model predictions. In this paper, we propose an alternative way of structuring the data which retains information on the sequence of events but which still enables analysis of the structure of the network. The fundamental feature of this network is that nodes are not individual cattle-holding locations but are instead direct movements between pairs of locations. Links are made between nodes when the second node is a subsequent movement from the location that received the first movement. Results Two networks are constructed assuming (i) a 7-day and (ii) a 14-day infectious period using British Cattle Movement Service (BCMS) data from 2004 and 2005. During this time period there were 4,183,670 movements that could be derived from the database. In both networks over 98% of the connected nodes formed a single giant weak component. Degree distributions show scale-free behaviour over a limited range only, due to the heterogeneity of locations: farms, markets, shows, abattoirs. Simulation of the spread of disease across the networks demonstrates that this approach to restructuring the data enables efficient comparison of the impact of transmission rates on disease spread. Conclusion The redefinition of what constitutes a node has provided a means to simulate disease spread using all the information available in the BCMS database whilst providing a network that can be described analytically. This will enable the construction of generic networks with similar properties with which to assess the impact of small changes in network structure on disease dynamics. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 20 Mar 2008 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237981 2008-03-20T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237978 Title: Chromhome: A rich internet application for accessing comparative chromosome homology maps Authors: Nagarajan, Sridevi; Rens, Willem; Stalker, James; Cox, Tony; Ferguson-Smith, Malcolm A Abstract: Abstract Background Comparative genomics has become a significant research area in recent years, following the availability of a number of sequenced genomes. The comparison of genomes is of great importance in the analysis of functionally important genome regions. It can also be used to understand the phylogenetic relationships of species and the mechanisms leading to rearrangement of karyotypes during evolution. Many species have been studied at the cytogenetic level by cross species chromosome painting. With the large amount of such information, it has become vital to computerize the data and make them accessible worldwide. Chromhome http://www.chromhome.org is a comprehensive web application that is designed to provide cytogenetic comparisons among species and to fulfil this need. Results The Chromhome application architecture is multi-tiered with an interactive client layer, business logic and database layers. Enterprise java platform with open source framework OpenLaszlo is used to implement the Rich Internet Chromhome Application. Cross species comparative mapping raw data are collected and the processed information is stored into MySQL Chromhome database. Chromhome Release 1.0 contains 109 homology maps from 51 species. The data cover species from 14 orders and 30 families. The homology map displays all the chromosomes of the compared species as one image, making comparisons among species easier. Inferred data also provides maps of homologous regions that could serve as a guideline for researchers involved in phylogenetic or evolution based studies. Conclusion Chromhome provides a useful resource for comparative genomics, holding graphical homology maps of a wide range of species. It brings together cytogenetic data of many genomes under one roof. Inferred painting can often determine the chromosomal homologous regions between two species, if each has been compared with a common third species. Inferred painting greatly reduces the need to map entire genomes and helps focus only on relevant regions of the chromosomes of the species under study. Future releases of Chromhome will accommodate more species and their respective gene and BAC maps, in addition to chromosome painting data. Chromhome application provides a single-page interface (SPI) with desktop style layout, delivering a better and richer user experience. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 26 Mar 2008 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237978 2008-03-26T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237970 Title: Flying lemurs - the "flying tree shrews"? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade Authors: Nie, Wenhui; Fu, Beiyuan; O'Brien, Patricia C M; Wang, Jinhuan; Su, Weiting; Tanomtong, Alongklod; Volobouev, Vitaly; Ferguson-Smith, Malcolm A; Yang, Fengtang Abstract: Abstract Background Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous. Results To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome. Conclusion Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 30 Apr 2008 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237970 2008-04-30T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237915 Title: Expression of genes associated with immunity in the endometrium of cattle with disparate postpartum uterine disease and fertility Authors: Herath, Shan; Lilly, Sonia T; Santos, Natalia R; Gilbert, Robert O; Goetze, Leopold; Bryant, Clare; White, John O; Cronin, James; Sheldon, I Martin Abstract: Abstract Background Contamination of the uterine lumen with bacteria is ubiquitous in cattle after parturition. Some animals develop endometritis and have reduced fertility but others have no uterine disease and readily conceive. The present study tested the hypothesis that postpartum cattle that develop persistent endometritis and infertility are unable to limit the inflammatory response to uterine bacterial infection. Methods Endometrial biopsies were collected several times during the postpartum period from animals that were subsequently infertile with persistent endometritis (n = 4) or had no clinical disease and conceived to first insemination (n = 4). Quantitative PCR was used to determine the expression of candidate genes in the endometrial biopsies, including the Toll-like receptor (TLR 1 to 10) family of innate immune receptors, inflammatory mediators and their cognate receptors. Selected proteins were examined by immunohistochemistry. Results The expression of genes encoding pro-inflammatory mediators such as interleukins (IL1A, IL1B and IL6), and nitric oxide synthase 2 (NOS2) were higher during the first week post partum than subsequently. During the first week post partum, there was higher gene expression in infertile than fertile animals of TLR4, the receptor for bacterial lipopolysaccharide, and the pro-inflammatory cytokines IL1A and IL1B, and their receptor IL1R2. The expression of genes encoding other Toll-like receptors, transforming growth factor beta receptor 1 (TGFBR1) or prostaglandin E2 receptors (PTGER2 and PTGER4) did not differ significantly between the animal groups. Gene expression did not differ significantly between infertile and fertile animals after the first week postpartum. However, there were higher ratios of IL1A or IL1B mRNA to the anti-inflammatory cytokine IL10, during the first week post partum in the infertile than fertile animals, and the protein products of these genes were mainly localised to the epithelium of the endometrium. Conclusion Cattle may maintain fertility by limiting the inflammatory response to postpartum bacterial infection in the endometrium during the first week after parturition. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 28 May 2009 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237915 2009-05-28T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237850 Title: Evidence for a lineage of virulent bacteriophages that target Campylobacter Authors: Timms, Andrew R; Cambray-Young, Joanna; Scott, Andrew E; Petty, Nicola K; Connerton, Phillippa L; Clarke, Louise; Seeger, Kathy; Quail, Michael A; Cummings, Nicola; Maskell, Duncan; Thomson, Nicholas R; Connerton, Ian F Abstract: Abstract Background Our understanding of the dynamics of genome stability versus gene flux within bacteriophage lineages is limited. Recently, there has been a renewed interest in the use of bacteriophages as 'therapeutic' agents; a prerequisite for their use in such therapies is a thorough understanding of their genetic complement, genome stability and their ecology to avoid the dissemination or mobilisation of phage or bacterial virulence and toxin genes. Campylobacter, a food-borne pathogen, is one of the organisms for which the use of bacteriophage is being considered to reduce human exposure to this organism. Results Sequencing and genome analysis was performed for two Campylobacter bacteriophages. The genomes were extremely similar at the nucleotide level (≥ 96%) with most differences accounted for by novel insertion sequences, DNA methylases and an approximately 10 kb contiguous region of metabolic genes that were dissimilar at the sequence level but similar in gene function between the two phages. Both bacteriophages contained a large number of radical S-adenosylmethionine (SAM) genes, presumably involved in boosting host metabolism during infection, as well as evidence that many genes had been acquired from a wide range of bacterial species. Further bacteriophages, from the UK Campylobacter typing set, were screened for the presence of bacteriophage structural genes, DNA methylases, mobile genetic elements and regulatory genes identified from the genome sequences. The results indicate that many of these bacteriophages are related, with 10 out of 15 showing some relationship to the sequenced genomes. Conclusions Two large virulent Campylobacter bacteriophages were found to show very high levels of sequence conservation despite separation in time and place of isolation. The bacteriophages show adaptations to their host and possess genes that may enhance Campylobacter metabolism, potentially advantaging both the bacteriophage and its host. Genetic conservation has been shown to extend to other Campylobacter bacteriophages, forming a highly conserved lineage of bacteriophages that predate upon campylobacters and indicating that highly adapted bacteriophage genomes can be stable over prolonged periods of time. Mon, 29 Mar 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237850 2010-03-29T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237843 Title: The effect of oxygen tension on calcium homeostasis in bovine articular chondrocytes Authors: White, Rachel; Gibson, John S Abstract: Abstract Background Articular chondrocytes normally experience a lower O2 tension compared to that seen by many other tissues. This level may fall further in joint disease. Ionic homeostasis is essential for chondrocyte function but, at least in the case of H+ ions, it is sensitive to changes in O2 levels. Ca2+ homeostasis is also critical but the effect of changes in O2 tension has not been investigated on this parameter. Here we define the effect of hypoxia on Ca2+ homeostasis in bovine articular chondrocytes. Methods Chondrocytes from articular cartilage slices were isolated enzymatically using collagenase. Cytoplasmic Ca2+ levels ([Ca2+]i) were followed fluorimetrically using Fura-2 to determine the effect of changes in O2 tension. The effects of ion substitution (replacing extracellular Na+ with NMDG+ and chelating Ca2+ with EGTA) were tested. Levels of reactive oxygen species (ROS) and the mitochondrial membrane potential were measured and correlated with [Ca2+]i. Results A reduction in O2 tension from 20% to 1% for 16-18 h caused [Ca2+]i to approximately double, reaching 105 ± 23 nM (p < 0.001). Ion substitutions indicated that Na+/Ca2+ exchange activity was not inhibited at low O2 levels. At 1% O2, ROS levels fell and mitochondria depolarised. Restoring ROS levels (with an oxidant H2O2, a non-specific ROS generator Co2+ or the mitochondrial complex II inhibitor antimycin A) concomitantly reduced [Ca2+]i. Conclusions O2 tension exerts a significant effect on [Ca2+]i. The proposed mechanism involves ROS from mitochondria. Findings emphasise the importance of using realistic O2 tensions when studying the physiology and pathology of articular cartilage and the potential interactions between O2, ROS and Ca2+. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Sun, 25 Apr 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237843 2010-04-25T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237842 Title: Multiple rearrangements in cryptic species of electric knifefish, Gymnotus carapo (Gymnotidae, Gymnotiformes) revealed by chromosome painting Authors: Nagamachi, Cleusa Y; Pieczarka, Julio C; Milhomem, Susana S R; O'Brien, Patricia C M; de Souza, Augusto C P; Ferguson-Smith, Malcolm A Abstract: Abstract Background Gymnotus (Gymnotidae, Gymnotiformes) is the Neotropical electric fish genus with the largest geographic distribution and the largest number of species, 33 of which have been validated. The diploid number varies from 2n = 39-40 to 2n = 54. Recently we studied the karyotype of morphologically indistinguishable samples from five populations of G. carapo sensu stricto from the Eastern Amazon of Brazil. We found two cytotypes, 2n = 42 (30 M/SM + 12 ST/A) and 2n = 40 (34 M/SM + 6 ST/A) and we concluded that the differences between the two cryptic species are due to pericentric inversions and one tandem fusion. Results In this study we use for the first time, whole chromosome probes prepared by FACS of the Gymnotus carapo sensu strictu species, cytotype with 2n = 42. Using two color hybridizations we were able to distinguish pairs 1, 2, 3, 7, 9, 14, 16, 18, 19, 20 and 21. It was not possible to separate by FACS and distinguish each of the following chromosome pairs even with dual color FISH: {4,8}; {10,11}; {5,6,17}; {12,13,15}. The FISH probes were then used in chromosome painting experiments on metaphases of the 2n = 40 cytotype. While some chromosomes show conserved synteny, others are rearranged in different chromosomes. Eight syntenic associations were found. Conclusions These results show that the karyotype differences between these cryptic species are greater than assumed by classical cytogenetics. These data reinforce the previous supposition that these two cytotypes are different species, despite the absence of morphological differences. Additionally, the homology of repetitive DNA between the two provides evidence of recent speciation. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Mon, 26 Apr 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237842 2010-04-26T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237827 Title: Assessing the role of contact tracing in a suspected H7N2 influenza A outbreak in humans in Wales Authors: Eames, Ken T D; Webb, Cerian; Thomas, Kathrin; Smith, Josie; Salmon, Roland; Temple, J Mark F Abstract: Abstract Background The detailed analysis of an outbreak database has been undertaken to examine the role of contact tracing in controlling an outbreak of possible avian influenza in humans. The outbreak, initiating from the purchase of infected domestic poultry, occurred in North Wales during May and June 2007. During this outbreak, extensive contact tracing was carried out. Following contact tracing, cases and contacts believed to be at risk of infection were given treatment/prophylaxis. Methods We analyse the database of cases and their contacts identified for the purposes of contact tracing in relation to both the contact tracing burden and effectiveness. We investigate the distribution of numbers of contacts identified, and use network structure to explore the speed with which treatment/prophylaxis was made available and to estimate the risk of transmission in different settings. Results Fourteen cases of suspected H7N2 influenza A in humans were associated with a confirmed outbreak among poultry in May-June 2007. The contact tracing dataset consisted of 254 individuals (cases and contacts, of both poultry and humans) who were linked through a network of social contacts. Of these, 102 individuals were given treatment or prophylaxis. Considerable differences between individuals' contact patterns were observed. Home and workplace encounters were more likely to result in transmission than encounters in other settings. After an initial delay, while the outbreak proceeded undetected, contact tracing rapidly caught up with the cases and was effective in reducing the time between onset of symptoms and treatment/prophylaxis. Conclusions Contact tracing was used to link together the individuals involved in this outbreak in a social network, allowing the identification of the most likely paths of transmission and the risks of different types of interactions to be assessed. The outbreak highlights the substantial time and cost involved in contact tracing, even for an outbreak affecting few individuals. However, when sufficient resources are available, contact tracing enables cases to be identified before they result in further transmission and thus possibly assists in preventing an outbreak of a novel virus. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 27 May 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237827 2010-05-27T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237811 Title: In Helicobacter pylori auto-inducer-2, but not LuxS/MccAB catalysed reverse transsulphuration, regulates motility through modulation of flagellar gene transcription Authors: Shen, Feifei; Hobley, Laura; Doherty, Neil; Loh, John T; Cover, Timothy L; Sockett, R Elizabeth; Hardie, Kim R; Atherton, John C Abstract: Abstract Background LuxS may function as a metabolic enzyme or as the synthase of a quorum sensing signalling molecule, auto-inducer-2 (AI-2); hence, the mechanism underlying phenotypic changes upon luxS inactivation is not always clear. In Helicobacter pylori, we have recently shown that, rather than functioning in recycling methionine as in most bacteria, LuxS (along with newly-characterised MccA and MccB), synthesises cysteine via reverse transsulphuration. In this study, we investigated whether and how LuxS controls motility of H. pylori, specifically if it has its effects via luxS-required cysteine metabolism or via AI-2 synthesis only. Results We report that disruption of luxS renders H. pylori non-motile in soft agar and by microscopy, whereas disruption of mccA Hp or mccB Hp (other genes in the cysteine provision pathway) does not, implying that the lost phenotype is not due to disrupted cysteine provision. The motility defect of the ΔluxS Hp mutant was complemented genetically by luxS Hp and also by addition of in vitro synthesised AI-2 or 4, 5-dihydroxy-2, 3-pentanedione (DPD, the precursor of AI-2). In contrast, exogenously added cysteine could not restore motility to the ΔluxS Hp mutant, confirming that AI-2 synthesis, but not the metabolic effect of LuxS was important. Microscopy showed reduced number and length of flagella in the ΔluxS Hp mutant. Immunoblotting identified decreased levels of FlaA and FlgE but not FlaB in the ΔluxS Hp mutant, and RT-PCR showed that the expression of flaA, flgE, motA, motB, flhA and fliI but not flaB was reduced. Addition of DPD but not cysteine to the ΔluxS Hp mutant restored flagellar gene transcription, and the number and length of flagella. Conclusions Our data show that as well as being a metabolic enzyme, H. pylori LuxS has an alternative role in regulation of motility by modulating flagellar transcripts and flagellar biosynthesis through production of the signalling molecule AI-2. Thu, 05 Aug 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237811 2010-08-05T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237723 Title: Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis Authors: Ward, Philip N; Holden, Matthew T G; Leigh, James A; Lennard, Nicola; Bignell, Alexandra; Barron, Andy; Clark, Louise; Quail, Michael A; Woodward, John; Barrell, Bart G; Egan, Sharon A; Field, Terence R; Maskell, Duncan; Kehoe, Michael; Dowson, Christopher G; Chanter, Neil; Whatmore, Adrian M; Bentley, Stephen D; Parkhill, Julian Abstract: Abstract Background Streptococcus uberis, a Gram positive bacterial pathogen responsible for a significant proportion of bovine mastitis in commercial dairy herds, colonises multiple body sites of the cow including the gut, genital tract and mammary gland. Comparative analysis of the complete genome sequence of S. uberis strain 0140J was undertaken to help elucidate the biology of this effective bovine pathogen. Results The genome revealed 1,825 predicted coding sequences (CDSs) of which 62 were identified as pseudogenes or gene fragments. Comparisons with related pyogenic streptococci identified a conserved core (40%) of orthologous CDSs. Intriguingly, S. uberis 0140J displayed a lower number of mobile genetic elements when compared with other pyogenic streptococci, however bacteriophage-derived islands and a putative genomic island were identified. Comparative genomics analysis revealed most similarity to the genomes of Streptococcus agalactiae and Streptococcus equi subsp. zooepidemicus. In contrast, streptococcal orthologs were not identified for 11% of the CDSs, indicating either unique retention of ancestral sequence, or acquisition of sequence from alternative sources. Functions including transport, catabolism, regulation and CDSs encoding cell envelope proteins were over-represented in this unique gene set; a limited array of putative virulence CDSs were identified. Conclusion S. uberis utilises nutritional flexibility derived from a diversity of metabolic options to successfully occupy a discrete ecological niche. The features observed in S. uberis are strongly suggestive of an opportunistic pathogen adapted to challenging and changing environmental parameters. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 28 Jan 2009 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237723 2009-01-28T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237718 Title: Disruption of chromosome 11 in canine fibrosarcomas highlights an unusual variability of CDKN2B in dogs. Authors: Aguirre-Hernandez, Jesus; Milne, Bruce S; Queen, Chris; O'Brien, Patricia C M; Hoather, Tess; Haugland, Sean; Ferguson-Smith, Malcolm A; Dobson, Jane M; Sargan, David R Abstract: Abstract Background In dogs in the western world neoplasia constitutes the most frequently diagnosed cause of death. Although there appear to be similarities between canine and human cancers, rather little is known about the cytogenetic and molecular alterations in canine tumours. Different dog breeds are susceptible to different types of cancer, but the genetic basis of the great majority of these predispositions has yet to be discovered. In some retriever breeds there is a high incidence of soft tissue sarcomas and we have previously reported alterations of chromosomes 11 and 30 in two poorly differentiated fibrosarcomas. Here we extend our observations and present a case report on detail rearrangements on chromosome 11 as well as genetic variations in a tumour suppressor gene in normal dogs. Results BAC hybridisations on metaphases of two fibrosarcomas showed complex rearrangements on chromosome 11, and loss of parts of this chromosome. Microsatellite markers on a paired tumour and blood DNA pointed to loss of heterozygosity on chromosome 11 in the CDKN2B-CDKN2A tumour suppressor gene cluster region. PCR and sequencing revealed the homozygous loss of coding sequences for these genes, except for exon 1β of CDKN2A, which codes for the N-terminus of p14ARF. For CDKN2B exon 1, two alleles were observed in DNA from blood; one of them identical to the sequence in the dog reference genome and containing 4 copies of a 12 bp repeat found only in the canine gene amongst all species so far sequenced; the other allele was shorter due to a missing copy of the repeat. Sequencing of this exon in 141 dogs from 18 different breeds revealed a polymorphic region involving a GGC triplet repeat and a GGGGACGGCGGC repeat. Seven alleles were recorded and sixteen of the eighteen breeds showed heterozygosity. Conclusion Complex chromosome rearrangements were observed on chromosome 11 in two Labrador retriever fibrosarcomas. The chromosome alterations were reflected in the loss of sequences corresponding to two tumour suppressor genes involved in cell-cycle progression. Sequencing of CDKN2B across many different breeds revealed a widespread polymorphism within the first exon of the gene, immediately before the ankyrin coding sequences. Thu, 30 Jul 2009 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237718 2009-07-30T23:00:00Z