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278 results on '"Rutherford, Kim"'

51. ACT: the Artemis comparison tool

Author

Carver, Tim J., Rutherford, Kim M., Berriman, Matthew, Rajandream, Marie-Adele, Barrell, Barclay G., and Parkhill, Julian

Published
2005

52. GeneDB: a resource for prokaryotic and eukaryotic organisms

Author

Hertz-Fowler, Christiane, Peacock, Chris S., Wood, Valerie, Aslett, Martin, Kerhornou, Arnaud, Mooney, Paul, Tivey, Adrian, Berriman, Matthew, Hall, Neil, Rutherford, Kim, Parkhill, Julian, Ivens, Alasdair C., Rajandream, Marie-Adele, and Barrell, Bart

Published
2004

53. The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism

Author

Hall, Neil, Berriman, Matthew, Lennard, Nicola J., Harris, Barbara R., Hertz-Fowler, Christiane, Bart-Delabesse, Emmanuelle N., Gerrard, Caroline S., Atkin, Rebecca J., Barron, Andrew J., Bowman, Sharen, Bray-Allen, Sarah P., Bringaud, Frédéric, Clark, Louise N., Corton, Craig H., Cronin, Ann, Davies, Robert, Doggett, Jonathon, Fraser, Audrey, Grüter, Eric, Hall, Sarah, Harper, A. David, Kay, Mike P., Leech, Vanessa, Mayes, Rebecca, Price, Claire, Quail, Michael A., Rabbinowitsch, Ester, Reitter, Christopher, Rutherford, Kim, Sasse, Jürgen, Sharp, Sarah, Shownkeen, Ratna, MacLeod, Annette, Taylor, Sonya, Tweedie, Alison, Turner, C. Michael R., Tait, Andrew, Gull, Keith, Barrell, Bart, and Melville, Sara E.

Published
2003

54. PHI-base: the pathogen–host interactions database

Author

Urban, Martin, primary, Cuzick, Alayne, additional, Seager, James, additional, Wood, Valerie, additional, Rutherford, Kim, additional, Venkatesh, Shilpa Yagwakote, additional, De Silva, Nishadi, additional, Martinez, Manuel Carbajo, additional, Pedro, Helder, additional, Yates, Andy D, additional, Hassani-Pak, Keywan, additional, and Hammond-Kosack, Kim E, additional

Published
2019
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55. Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change

Author

Todd, Erica V., primary, Ortega-Recalde, Oscar, additional, Liu, Hui, additional, Lamm, Melissa S., additional, Rutherford, Kim M., additional, Cross, Hugh, additional, Black, Michael A., additional, Kardailsky, Olga, additional, Marshall Graves, Jennifer A., additional, Hore, Timothy A., additional, Godwin, John R., additional, and Gemmell, Neil J., additional

Published
2019
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58. Stress, novel sex genes and epigenetic reprogramming orchestrate socially-controlled sex change

Author

Todd, Erica V, primary, Ortega-Recalde, Oscar, additional, Liu, Hui, additional, Lamm, Melissa S, additional, Rutherford, Kim M, additional, Cross, Hugh, additional, Black, Michael A, additional, Kardailsky, Olga, additional, Marshall Graves, Jennifer A, additional, Hore, Timothy A, additional, Godwin, John R, additional, and Gemmell, Neil J, additional

Published
2018
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60. Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species

Author

Dussex, Nicolas, Taylor, Helen, Stovall, William, Rutherford, Kim, Dodds, Ken, Clarke, Shannon, Gemmel, Neil, Dussex, Nicolas, Taylor, Helen, Stovall, William, Rutherford, Kim, Dodds, Ken, Clarke, Shannon, and Gemmel, Neil

Abstract

Next‐generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS method Genotyping‐By‐Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily exploited by the 19th century commercial sealing industry and has since rapidly recolonized most of its former range from a few isolated colonies. Using 26,026 neutral single nucleotide polymorphisms (SNPs), we assessed genetic variation within and between NZFS colonies. We identified low levels of population differentiation across the species range (<1% of variation explained by regional differences) suggesting a state of near panmixia. Nonetheless, we observed subtle population substructure between West Coast and Southern East Coast colonies and a weak, but significant (p = 0.01), isolation‐by‐distance pattern among the eight colonies studied. Furthermore, our demographic reconstructions supported severe bottlenecks with potential 10‐fold and 250‐fold declines in response to Polynesian and European hunting, respectively. Finally, we were able to assign individuals treated as unknowns to their regions of origin with high confidence (96%) using our SNP data. Our results indicate that while it may be difficult to detect population structure in species that have experienced rapid recovery, next‐generation markers and methods are powerful tools for resolving fine‐scale structure and informing conservation and management efforts.

Published
2018
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61. De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

Author

Blanchoud, Simon, Rutherford, Kim, Zondag, Lisa, Gemmell, Neil J., Wilson, Megan J., Blanchoud, Simon, Rutherford, Kim, Zondag, Lisa, Gemmell, Neil J., and Wilson, Megan J.

Abstract

Tunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. These chordates present a particularly diverse range of regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of these traits. Here we describe the genome sequencing, annotation and analysis of the Stolidobranchian Botrylloides leachii. We have produced a high-quality 159 Mb assembly, 82% of the predicted 194 Mb genome. Analysing genome size, gene number, repetitive elements, orthologs clustering and gene ontology terms show that B. leachii has a genomic architecture similar to that of most solitary tunicates, while other recently sequenced colonial ascidians have undergone genome expansion. In addition, ortholog clustering has identified groups of candidate genes for the study of colonialism and whole-body regeneration. By analysing the structure and composition of conserved gene linkages, we observed examples of cluster breaks and gene dispersions, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. We also found lineage-specific gene gain and loss within conserved cell-signalling pathways. Such examples of genetic changes within conserved cell-signalling pathways commonly associated with regeneration and development that may underlie some of the diverse regenerative abilities observed in tunicates. Overall, these results provide a novel resource for the study of tunicates and of colonial ascidians.

Published
2018

64. Additional file 6: of Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

Author

Wu, Chen, Jordan, Melissa, Newcomb, Richard, Gemmell, Neil, Bank, Sarah, Meusemann, Karen, Dearden, Peter, Duncan, Elizabeth, Sefanie Grosser, Rutherford, Kim, Gardner, Paul, Crowhurst, Ross, Steinwender, Bernd, Tooman, Leah, Stevens, Mark, and Buckley, Thomas

Abstract

Table of putative sex determination genes. (DOCX 19 kb)

Published
2017
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70. Additional file 9: of Histological and transcriptomic effects of 17Îą-methyltestosterone on zebrafish gonad development

Author

Lee, Stephanie, Horsfield, Julia, Black, Michael, Rutherford, Kim, Fisher, Amanda, and Gemmell, Neil

Subjects
animal structures, embryonic structures
Abstract

Top ten GeneGo pathways significantly enriched in pairwise comparisons of sex (testes vs. ovaries), treatment (control vs. MT-treated) and time point (40 dpf vs. 60 dpf). (DOCX 20kb)

Published
2017
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83. Identification of functional elements and regulatory circuits by Drosophila modENCODE

Author

Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V., Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L., Landolin, Jane M., Bristow, Christopher A., Ma, Lijia, Lin, Michael F., Washietl, Stefan, Arshinoff, Bradley I., Ay, Ferhat, Meyer, Patrick E., Robine, Nicolas, Washington, Nicole L., Di Stefano, Luisa, Berezikov, Eugene, Brown, Christopher D., Candeias, Rogerio, Carlson, Joseph W., Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y., Will, Sebastian, Alekseyenko, Artyom A., Artieri, Carlo, Booth, Benjamin W., Brooks, Angela N., Dai, Qi, Davis, Carrie A., Duff, Michael O., Feng, Xin, Gorchakov, Andrey A., Gu, Tingting, Henikoff, Jorja G., Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K., Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K., Riddle, Nicole C., Sakai, Akiko, Samsonova, Anastasia A., Sandler, Jeremy E., Schwartz, Yuri B., Sher, Noa, Spokony, Rebecca, Sturgill, David, van Baren, Marijke, Wan, Kenneth H., Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E., Brent, Michael R., Cherbas, Lucy, Elgin, Sarah C.R., Gingeras, Thomas R., Grossman, Robert, Hoskins, Roger A., Kaufman, Thomas C., Kent, William, Kuroda, Mitzi I., Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W., Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R., Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J., Celniker, Susan E., Henikoff, Steven, Karpen, Gary H., Lai, Eric C., MacAlpine, David M., Stein, Lincoln D., White, Kevin P., Kellis, Manolis, Booth, Benjamin, Comstock, Charles L.G., Dobin, Alex, Drenkow, Jorg, Dudoit, Sandrine, Dumais, Jacqueline, Fagegaltier, Delphine, Ghosh, Srinka, Hansen, Kasper D., Jha, Sonali, Langton, Laura, Lin, Wei, Miller, David, Tenney, Aaron E., Wang, Huaien, Willingham, Aarron T., Zaleski, Chris, Zhang, Dayu, Acevedo, David, Bishop, Eric P., Gadel, Sarah E., Jung, Youngsook L., Kennedy, Cameron D., Lee, Ok Kyung, Linder-Basso, Daniela, Marchetti, Sarah E., Shanower, Gregory, Nègre, Nicolas, Grossman, Robert L., Auburn, Richard, Bellen, Hugo J., Chen, Jia, Domanus, Marc H., Hanley, David, Heinz, Elizabeth, Li, Zirong, Meyer, Folker, Miller, Steven W., Morrison, Carolyn A., Scheftner, Douglas A., Senderowicz, Lionel, Shah, Parantu K., Suchy, Sarah, Tian, Feng, Venken, Koen J.T., White, Robert, Wilkening, Jared, Zieba, Jennifer, Nordman, Jared T., Orr-Weaver, Terry L., DeNapoli, Leyna C., Ding, Queying, Eng, Thomas, Kashevsky, Helena, Li, Sharon, Prinz, Joseph A., Hannon, Gregory J., Hirst, Martin, Marra, Marco, Rooks, Michelle, Zhao, Yongjun, Bryson, Terri D., Perry, Marc D., Kent, William J., Lewis, Suzanna E., Barber, Galt, Chateigner, Aurelien, Clawson, Hiram, Contrino, Sergio, Guillier, Francois, Hinrichs, Angie S., Kephart, Ellen T., Lloyd, Paul, Lyne, Rachel, McKay, Sheldon, Moore, Richard A., Mungall, Chris, Rutherford, Kim M., Ruzanov, Peter, Smith, Richard, Stinson, E. O., Zha, Zheng, Artieri, Carlo G., Malone, John H., Jiang, Lichun, Mattiuzzo, Nicolas, Feingold, Elise A., Good, Peter J., Guyer, Mark S., Lowdon, Rebecca F., Stem Cell Aging Leukemia and Lymphoma (SALL), and Restoring Organ Function by Means of Regenerative Medicine (REGENERATE)

Subjects
Transcription, Genetic, Genome, Insect, Gene regulatory network, Genomics, Genes, Insect, Computational biology, Biology, Genome, Article, Epigenesis, Genetic, Histones, Nucleosome, Animals, Drosophila Proteins, Gene Regulatory Networks, Promoter Regions, Genetic, Gene, Genetics, Multidisciplinary, Binding Sites, REDfly, Computational Biology, Molecular Sequence Annotation, Chromatin, Nucleosomes, Drosophila melanogaster, Gene Expression Regulation, RNA, Small Untranslated, Drosophila Protein, Transcription Factors
Abstract

From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation is still needed to characterize how the genome is used to help to produce a functional organism (see the Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for the Caenorhabditis elegans genome, and The modENCODE Consortium (p. 1787 ) summarize for the Drosophila melanogaster genome, full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites, and high-resolution maps of chromatin organization. Both studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Overall, the studies provide insights into the organization, structure, and function of the two genomes and provide basic information needed to guide and correlate both focused and genome-wide studies.

Published
2010

85. Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

Author

Wu, Chen, primary, Jordan, Melissa D., additional, Newcomb, Richard D., additional, Gemmell, Neil J., additional, Bank, Sarah, additional, Meusemann, Karen, additional, Dearden, Peter K., additional, Duncan, Elizabeth J., additional, Grosser, Sefanie, additional, Rutherford, Kim, additional, Gardner, Paul P., additional, Crowhurst, Ross N., additional, Steinwender, Bernd, additional, Tooman, Leah K., additional, Stevens, Mark I., additional, and Buckley, Thomas R., additional

Published
2017
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96. Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia

Author

Janes, Daniel E., primary, Organ, Christopher L., additional, Stiglec, Rami, additional, O'Meally, Denis, additional, Sarre, Stephen D., additional, Georges, Arthur, additional, Graves, Jennifer A. M., additional, Valenzuela, Nicole, additional, Literman, Robert A., additional, Rutherford, Kim, additional, Gemmell, Neil, additional, Iverson, John B., additional, Tamplin, Jeffrey W., additional, Edwards, Scott V., additional, and Ezaz, Tariq, additional

Published
2014
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97. Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

Author

Chen Wu, Jordan, Melissa D., Newcomb, Richard D., Gemmell, Neil J., Bank, Sarah, Meusemann, Karen, Dearden, Peter K., Duncan, Elizabeth J., Grosser, Sefanie, Rutherford, Kim, Gardner, Paul P., Crowhurst, Ross N., Steinwender, Bernd, Tooman, Leah K., Stevens, Mark I., and Buckley, Thomas R.

Subjects
COLLEMBOLA, NUCLEOTIDE sequencing, METHYLATION, HORIZONTAL gene transfer, GENOMICS, DEVELOPMENTAL biology, PHYSIOLOGY
Abstract

Background: The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. Results: Our genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and sequencing coverage of ~180x. DNA elements, LTRs and simple repeats and LINEs formed the largest components and SINEs were very rare. Phylogenomics (370,877 amino acids) placed H. duospinosa within the Neanuridae. We recovered orthologs of the conserved sex determination genes thought to play a role in sex determination. Analysis of CpG content suggested the absence of DNA methylation, and consistent with this we were unable to detect orthologs of the DNA methyltransferase enzymes. The small subunit rRNA gene contained a possible retrotransposon. The Hox gene complex was broken over two scaffolds. For chemosensory ability, at least 15 and 18 ionotropic glutamate and gustatory receptors were identified, respectively. However, we were unable to identify any odorant receptors or their obligate co-receptor Orco. Twenty-three chitinase-like genes were identified from the assembly. Members of this multigene family may play roles in the digestion of fungal cell walls, a common food source for these saproxylic organisms. We also detected 59 and 96 genes that blasted to bacteria and fungi, respectively, but were located on scaffolds that otherwise contained arthropod genes. Conclusions: The genome of H. duospinosa contains some unusual features including a Hox complex broken over two scaffolds, in a different manner to other arthropod species, a lack of odorant receptor genes and an apparent lack of environmentally responsive DNA methylation, unlike many other arthropods. Our detection of candidate horizontal gene transfer candidates confirms that this phenomenon is occurring across Collembola. These findings allow us to narrow down the regions of the arthropod phylogeny where key innovations have occurred that have facilitated the evolutionary success of Hexapoda. [ABSTRACT FROM AUTHOR]

Published
2017
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98. Histological and transcriptomic effects of 17α-methyltestosterone on zebrafish gonad development.

Author

Ling Jie Lee, Stephanie, Horsfield, Julia A., Black, Michael A., Rutherford, Kim, Fisher, Amanda, and Gemmell, Neil J.

Subjects
METHYLTESTOSTERONE, ZEBRA danio, GONAD development, ANDROGENS, AROMATASE inhibitors
Abstract

Background: Sex hormones play important roles in teleost ovarian and testicular development. In zebrafish, ovarian differentiation appears to be dictated by an oocyte-derived signal via Cyp19a1a aromatase-mediated estrogen production. Androgens and aromatase inhibitors can induce female-to-male sex reversal, however, the mechanisms underlying gonadal masculinisation are poorly understood. We used histological analyses together with RNA sequencing to characterise zebrafish gonadal transcriptomes and investigate the effects of 17α-methyltestosterone on gonadal differentiation. Results: At a morphological level, 17α-methyltestosterone (MT) masculinised gonads and accelerated spermatogenesis, and these changes were paralleled in masculinisation and de-feminisation of gonadal transcriptomes. MT treatment upregulated expression of genes involved in male sex determination and differentiation (amh, dmrt1, gsdf and wt1a) and those involved in 11-oxygenated androgen production (cyp11c1 and hsd11b2). It also repressed expression of ovarian development and folliculogenesis genes (bmp15, gdf9, figla, zp2.1 and zp3b). Furthermore, MT treatment altered epigenetic modification of histones in zebrafish gonads. Contrary to expectations, higher levels of cyp19a1a or foxl2 expression in control ovaries compared to MT-treated testes and control testes were not statistically significant during early gonad development (40 dpf). Conclusion: Our study suggests that both androgen production and aromatase inhibition are important for androgen-induced gonadal masculinisation and natural testicular differentiation in zebrafish. [ABSTRACT FROM AUTHOR]

Published
2017
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100. PomBase 2015: updates to the fission yeast database

Author

McDowall, Mark D., primary, Harris, Midori A., additional, Lock, Antonia, additional, Rutherford, Kim, additional, Staines, Daniel M., additional, Bähler, Jürg, additional, Kersey, Paul J., additional, Oliver, Stephen G., additional, and Wood, Valerie, additional

Published
2014
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