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276 results on '"Hertz-Fowler, Christiane"'

2. Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis

Author

Initiative, International Glossina Genome, Attardo, Geoffrey M, Abila, Patrick P, Auma, Joanna E, Baumann, Aaron A, Benoit, Joshua B, Brelsfoard, Corey L, Ribeiro, José MC, Cotton, James A, Pham, Daphne QD, Darby, Alistair C, Van Den Abbeele, Jan, Denlinger, David L, Field, Linda M, Nyanjom, Steven RG, Gaunt, Michael W, Geiser, Dawn L, Gomulski, Ludvik M, Haines, Lee R, Hansen, Immo A, Jones, Jeffery W, Kibet, Caleb K, Kinyua, Johnson K, Larkin, Denis M, Lehane, Michael J, Rio, Rita VM, Macdonald, Sandy J, Macharia, Rosaline W, Malacrida, Anna R, Marco, Heather G, Marucha, Kevin K, Masiga, Daniel K, Meuti, Megan E, Mireji, Paul O, Obiero, George FO, Koekemoer, Jacobus JO, Okoro, Chinyere K, Omedo, Irene A, Osamor, Victor C, Balyeidhusa, Apollo SP, Peyton, Justin T, Price, David P, Quail, Michael A, Ramphul, Urvashi N, Rawlings, Neil D, Riehle, Michael A, Robertson, Hugh M, Sanders, Mandy J, Scott, Maxwell J, Dashti, Zahra Jalali Sefid, Snyder, Anna K, Srivastava, Tulika P, Stanley, Eleanor J, Swain, Martin T, Hughes, Daniel ST, Tarone, Aaron M, Taylor, Todd D, Telleria, Erich L, Thomas, Gavin H, Walshe, Deirdre P, Wilson, Richard K, Winzerling, Joy J, Acosta-Serrano, Alvaro, Aksoy, Serap, Arensburger, Peter, Aslett, Martin, Bateta, Rosemary, Benkahla, Alia, Berriman, Matthew, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christoffels, Alan, Falchetto, Marco, Friedrich, Markus, Fu, Shuhua, Gäde, Gerd, Githinji, George, Gregory, Richard, Hall, Neil, Harkins, Gordon, Hattori, Masahira, Hertz-Fowler, Christiane, Hide, Winston, Hu, Wanqi, Imanishi, Tadashi, Inoue, Noboru, Jonas, Mario, Kawahara, Yoshihiro, Koffi, Mathurin, Kruger, Adele, Lawson, Daniel, Lehane, Stella, Lehväslaiho, Heikki, Luiz, Thiago, Makgamathe, Mmule, Malele, Imna, Manangwa, Oliver, Manga, Lucien, and Megy, Karyn

Subjects
Vector-Borne Diseases, Genetics, Prevention, Infectious Diseases, Biotechnology, 2.2 Factors relating to the physical environment, Aetiology, Infection, Good Health and Well Being, Animals, Blood, Feeding Behavior, Female, Genes, Insect, Genome, Insect, Insect Proteins, Insect Vectors, Microbiota, Molecular Sequence Annotation, Molecular Sequence Data, Reproduction, Salivary Glands, Sensation, Sequence Analysis, DNA, Symbiosis, Trypanosoma, Trypanosomiasis, African, Tsetse Flies, Wolbachia, International Glossina Genome Initiative, General Science & Technology
Abstract

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.

Published
2014

3. The Genome of the Kinetoplastid Parasite, Leishmania major

Author

Ivens, Alasdair C., Peacock, Christopher S., Worthey, Elizabeth A., Murphy, Lee, Aggarwal, Gautam, Berriman, Matthew, Sisk, Ellen, Rajandream, Marie-Adele, Adlem, Ellen, Aert, Rita, Anupama, Atashi, Apostolou, Zina, Attipoe, Philip, Bason, Nathalie, Bauser, Christopher, Beck, Alfred, Beverley, Stephen M., Bianchettin, Gabriella, Borzym, Katja, Bothe, Gordana, Bruschi, Carlo V., Collins, Matt, Cadag, Eithon, Ciarloni, Laura, Clayton, Christine, Cronin, Ann, Cruz, Angela K., Davies, Robert M., De Gaudenzi, Javier, Dobson, Deborah E., Duesterhoeft, Andreas, Fazelina, Gholam, Fosker, Nigel, Frasch, Alberto Carlos, Fraser, Audrey, Fuchs, Monika, Gabel, Claudia, Goble, Arlette, Goffeau, André, Harris, David, Hertz-Fowler, Christiane, Hilbert, Helmut, Horn, David, Huang, Yiting, Klages, Sven, Knights, Andrew, Kube, Michael, Larke, Natasha, Litvin, Lyudmila, Lord, Angela, Louie, Tin, Marra, Marco, Masuy, David, Matthews, Keith, Michaeli, Shulamit, Mottram, Jeremy C., Müller-Auer, Silke, Munden, Heather, Nelson, Siri, Norbertczak, Halina, Oliver, Karen, O'Neil, Susan, Pentony, Martin, Pohl, Thomas M., Price, Claire, Purnelle, Bénédicte, Quail, Michael A., Rabbinowitsch, Ester, Reinhardt, Richard, Rieger, Michael, Rinta, Joel, Robben, Johan, Robertson, Laura, Ruiz, Jeronimo C., Rutter, Simon, Saunders, David, Schäfer, Melanie, Schein, Jacquie, Schwartz, David C., Seeger, Kathy, Seyler, Amber, Sharp, Sarah, Shin, Heesun, Sivam, Dhileep, Squares, Rob, Squares, Steve, Tosato, Valentina, Vogt, Christy, Volckaert, Guido, Wambutt, Rolf, Warren, Tim, Wedler, Holger, Woodward, John, Zhou, Shiguo, Zimmermann, Wolfgang, Smith, Deborah F., Blackwell, Jenefer M., Stuart, Kenneth D., Barrell, Bart, and Myler, Peter J.

Published
2005

4. Comparative Genomics of Trypanosomatid Parasitic Protozoa

Author

El-Sayed, Najib M., Myler, Peter J., Blandin, Gaëlle, Berriman, Matthew, Crabtree, Jonathan, Aggarwal, Gautam, Caler, Elisabet, Renauld, Hubert, Worthey, Elizabeth A., Hertz-Fowler, Christiane, Ghedin, Elodie, Peacock, Christopher, Bartholomeu, Daniella C., Haas, Brian J., Tran, Anh-Nhi, Wortman, Jennifer R., Angiuoli, Samuel, Anupama, Atashi, Badger, Jonathan, Bringaud, Frederic, Cadag, Eithon, Carlton, Jane M., Cerqueira, Gustavo C., Creasy, Todd, Delcher, Arthur L., Djikeng, Appolinaire, Embley, T. Martin, Hauser, Christopher, Ivens, Alasdair C., Kummerfeld, Sarah K., Pereira-Leal, Jose B., Nilsson, Daniel, Peterson, Jeremy, Salzberg, Steven L., Shallom, Joshua, Silva, Joana C., Sundaram, Jaideep, Westenberger, Scott, White, Owen, Melville, Sara E., Donelson, John E., Andersson, Björn, Stuart, Kenneth D., and Hall, Neil

Published
2005

5. The Genome of the African Trypanosome Trypanosoma brucei

Author

Berriman, Matthew, Ghedin, Elodie, Hertz-Fowler, Christiane, Blandin, Gaëlle, Renauld, Hubert, Bartholomeu, Daniella C., Lennard, Nicola J., Caler, Elisabet, Hamlin, Nancy E., Haas, Brian, Böhme, Ulrike, Hannick, Linda, Aslett, Martin A., Shallom, Joshua, Marcello, Lucio, Hou, Lihua, Wickstead, Bill, Arrowsmith, Claire, Atkin, Rebecca J., Barron, Andrew J., Bringaud, Frederic, Brooks, Karen, Carrington, Mark, Cherevach, Inna, Chillingworth, Tracey-Jane, Churcher, Carol, Clark, Louise N., Corton, Craig H., Cronin, Ann, Davies, Rob M., Doggett, Jonathon, Djikeng, Appolinaire, Feldblyum, Tamara, Field, Mark C., Fraser, Audrey, Goodhead, Ian, Hance, Zahra, Harper, David, Harris, Barbara R., Hauser, Heidi, Hostetler, Jessica, Ivens, Al, Jagels, Kay, Johnson, David, Johnson, Justin, Jones, Kristine, Kerhornou, Arnaud X., Koo, Hean, Larke, Natasha, Landfear, Scott, Larkin, Christopher, Leech, Vanessa, Line, Alexandra, Lord, Angela, MacLeod, Annette, Mooney, Paul J., Moule, Sharon, Morgan, Gareth W., Mungall, Karen, Norbertczak, Halina, Ormond, Doug, Pai, Grace, Peacock, Chris S., Peterson, Jeremy, Quail, Michael A., Rabbinowitsch, Ester, Rajandream, Marie-Adele, Reitter, Chris, Salzberg, Steven L., Sanders, Mandy, Schobel, Seth, Sharp, Sarah, Simmonds, Mark, Simpson, Anjana J., Tallon, Luke, Tait, Andrew, Tivey, Adrian R., Van Aken, Susan, Walker, Danielle, Wanless, David, Wang, Shiliang, White, Brian, White, Owen, Whitehead, Sally, Woodward, John, Wortman, Jennifer, Adams, Mark D., Embley, T. Martin, Gull, Keith, Ullu, Elisabetta, Barry, J. David, Fairlamb, Alan H., Opperdoes, Fred, Barrell, Barclay G., Donelson, John E., Hall, Neil, Fraser, Claire M., Melville, Sara E., and El-Sayed, Najib M.

Published
2005

6. Genome-wide subcellular protein localisation in the flagellate parasite Trypanosoma brucei

Author

Billington, Karen, Halliday, Clare, Madden, Ross, Dyer, Philip, Carrington, Mark, Vaughan, Sue, Hertz-Fowler, Christiane, Dean, Samuel, Sunter, Jack D., Wheeler, Richard John, Gull, Keith, Billington, Karen, Halliday, Clare, Madden, Ross, Dyer, Philip, Carrington, Mark, Vaughan, Sue, Hertz-Fowler, Christiane, Dean, Samuel, Sunter, Jack D., Wheeler, Richard John, and Gull, Keith

Abstract

Trypanosoma brucei is a model trypanosomatid, an important group of human, animal and plant unicellular parasites. Understanding their complex cell architecture and life cycle is challenging because, as with most eukaryotic microbes, ~50% of genome-encoded proteins have completely unknown functions. Here, using fluorescence microscopy and cell lines expressing endogenously tagged proteins, we mapped the subcellular localization of 89% of the T. brucei proteome, a resource we call TrypTag. We provide clues to function and define lineage-specific organelle adaptations for parasitism, mapping the ultraconserved cellular architecture of eukaryotes, including the first comprehensive ‘cartographic’ analysis of the eukaryotic flagellum, which is vital for morphogenesis and pathology. To demonstrate the power of this resource, we identify novel organelle subdomains and changes in molecular composition through the cell cycle. TrypTag is a transformative resource, important for hypothesis generation for both eukaryotic evolutionary molecular cell biology and fundamental parasite cell biology.

Published
2023

8. VEuPathDB:The eukaryotic pathogen, vector and host bioinformatics resource center

Author

Amos, Beatrice, Aurrecoechea, Cristina, Barba, Matthieu, Barreto, Ana, Basenko, Evelina Y., Bażant, Wojciech, Belnap, Robert, Blevins, Ann S., Böhme, Ulrike, Brestelli, John, Brunk, Brian P., Caddick, Mark, Callan, Danielle, Campbell, Lahcen, Christensen, Mikkel B., Christophides, George K., Crouch, Kathryn, Davis, Kristina, Debarry, Jeremy, Doherty, Ryan, Duan, Yikun, Dunn, Michael, Falke, Dave, Fisher, Steve, Flicek, Paul, Fox, Brett, Gajria, Bindu, Giraldo-Calderón, Gloria I., Harb, Omar S., Harper, Elizabeth, Hertz-Fowler, Christiane, Hickman, Mark J., Howington, Connor, Hu, Sufen, Humphrey, Jay, Iodice, John, Jones, Andrew, Judkins, John, Kelly, Sarah A., Kissinger, Jessica C., Kwon, Dae Kun, Lamoureux, Kristopher, Lawson, Daniel, Li, Wei, Lies, Kallie, Lodha, Disha, Long, Jamie, MacCallum, Robert M., Maslen, Gareth, McDowell, Mary Ann, Nabrzyski, Jaroslaw, Roos, David S., Rund, Samuel S.C., Schulman, Stephanie Wever, Shanmugasundram, Achchuthan, Sitnik, Vasily, Spruill, Drew, Starns, David, Stoeckert, Christian J., Tomko, Sheena Shah, Wang, Haiming, Warrenfeltz, Susanne, Wieck, Robert, Wilkinson, Paul A., Xu, Lin, Zheng, Jie, Amos, Beatrice, Aurrecoechea, Cristina, Barba, Matthieu, Barreto, Ana, Basenko, Evelina Y., Bażant, Wojciech, Belnap, Robert, Blevins, Ann S., Böhme, Ulrike, Brestelli, John, Brunk, Brian P., Caddick, Mark, Callan, Danielle, Campbell, Lahcen, Christensen, Mikkel B., Christophides, George K., Crouch, Kathryn, Davis, Kristina, Debarry, Jeremy, Doherty, Ryan, Duan, Yikun, Dunn, Michael, Falke, Dave, Fisher, Steve, Flicek, Paul, Fox, Brett, Gajria, Bindu, Giraldo-Calderón, Gloria I., Harb, Omar S., Harper, Elizabeth, Hertz-Fowler, Christiane, Hickman, Mark J., Howington, Connor, Hu, Sufen, Humphrey, Jay, Iodice, John, Jones, Andrew, Judkins, John, Kelly, Sarah A., Kissinger, Jessica C., Kwon, Dae Kun, Lamoureux, Kristopher, Lawson, Daniel, Li, Wei, Lies, Kallie, Lodha, Disha, Long, Jamie, MacCallum, Robert M., Maslen, Gareth, McDowell, Mary Ann, Nabrzyski, Jaroslaw, Roos, David S., Rund, Samuel S.C., Schulman, Stephanie Wever, Shanmugasundram, Achchuthan, Sitnik, Vasily, Spruill, Drew, Starns, David, Stoeckert, Christian J., Tomko, Sheena Shah, Wang, Haiming, Warrenfeltz, Susanne, Wieck, Robert, Wilkinson, Paul A., Xu, Lin, and Zheng, Jie

Abstract

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC., The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

Published
2022

10. Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species

Author

Jackson, Andrew P., Berry, Andrew, Aslett, Martin, Allison, Harriet C., Burton, Peter, Vavrova-Anderson, Jana, Brown, Robert, Browne, Hilary, Corton, Nicola, Hauser, Heidi, Gamble, John, Gilderthorp, Ruth, Marcello, Lucio, McQuillan, Jacqueline, Otto, Thomas D., Quail, Michael A., Sanders, Mandy J., van Tonder, Andries, Ginger, Michael L., Field, Mark C., Barry, J. David, Hertz-Fowler, Christiane, and Berriman, Matthew

Published
2012

11. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

Author

Amos, Beatrice, primary, Aurrecoechea, Cristina, additional, Barba, Matthieu, additional, Barreto, Ana, additional, Basenko, Evelina Y, additional, Bażant, Wojciech, additional, Belnap, Robert, additional, Blevins, Ann S, additional, Böhme, Ulrike, additional, Brestelli, John, additional, Brunk, Brian P, additional, Caddick, Mark, additional, Callan, Danielle, additional, Campbell, Lahcen, additional, Christensen, Mikkel B, additional, Christophides, George K, additional, Crouch, Kathryn, additional, Davis, Kristina, additional, DeBarry, Jeremy, additional, Doherty, Ryan, additional, Duan, Yikun, additional, Dunn, Michael, additional, Falke, Dave, additional, Fisher, Steve, additional, Flicek, Paul, additional, Fox, Brett, additional, Gajria, Bindu, additional, Giraldo-Calderón, Gloria I, additional, Harb, Omar S, additional, Harper, Elizabeth, additional, Hertz-Fowler, Christiane, additional, Hickman, Mark J, additional, Howington, Connor, additional, Hu, Sufen, additional, Humphrey, Jay, additional, Iodice, John, additional, Jones, Andrew, additional, Judkins, John, additional, Kelly, Sarah A, additional, Kissinger, Jessica C, additional, Kwon, Dae Kun, additional, Lamoureux, Kristopher, additional, Lawson, Daniel, additional, Li, Wei, additional, Lies, Kallie, additional, Lodha, Disha, additional, Long, Jamie, additional, MacCallum, Robert M, additional, Maslen, Gareth, additional, McDowell, Mary Ann, additional, Nabrzyski, Jaroslaw, additional, Roos, David S, additional, Rund, Samuel S C, additional, Schulman, Stephanie Wever, additional, Shanmugasundram, Achchuthan, additional, Sitnik, Vasily, additional, Spruill, Drew, additional, Starns, David, additional, Stoeckert, Christian J, additional, Tomko, Sheena Shah, additional, Wang, Haiming, additional, Warrenfeltz, Susanne, additional, Wieck, Robert, additional, Wilkinson, Paul A, additional, Xu, Lin, additional, and Zheng, Jie, additional

Published
2021
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12. Genome Assemblies across the Diverse Evolutionary Spectrum of Leishmania Protozoan Parasites

Author

Warren, Wesley C., primary, Akopyants, Natalia S., additional, Dobson, Deborah E., additional, Hertz-Fowler, Christiane, additional, Lye, Lon-Fye, additional, Myler, Peter J., additional, Ramasamy, Gowthaman, additional, Shanmugasundram, Achchuthan, additional, Silva-Franco, Fatima, additional, Steinbiss, Sascha, additional, Tomlinson, Chad, additional, Wilson, Richard K., additional, and Beverley, Stephen M., additional

Published
2021
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13. TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei

Author

Shameer, Sanu, Logan-Klumpler, Flora J., Vinson, Florence, Cottret, Ludovic, Merlet, Benjamin, Achcar, Fiona, Boshart, Michael, Berriman, Matthew, Breitling, Rainer, Bringaud, Frédéric, Bütikofer, Peter, Cattanach, Amy M., Bannerman-Chukualim, Bridget, Creek, Darren J., Crouch, Kathryn, de Koning, Harry P., Denise, Hubert, Ebikeme, Charles, Fairlamb, Alan H., Ferguson, Michael A. J., Ginger, Michael L., Hertz-Fowler, Christiane, Kerkhoven, Eduard J., Mäser, Pascal, Michels, Paul A. M., Nayak, Archana, Nes, David W., Nolan, Derek P., Olsen, Christian, Silva-Franco, Fatima, Smith, Terry K., Taylor, Martin C., Tielens, Aloysius G. M., Urbaniak, Michael D., van Hellemond, Jaap J., Vincent, Isabel M., Wilkinson, Shane R., Wyllie, Susan, Opperdoes, Fred R., Barrett, Michael P., and Jourdan, Fabien

Published
2015
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15. High-depth African genomes inform human migration and health

Author

Choudhury, Ananyo, Aron, Shaun, Botigué, Laura R., Sengupta, Dhriti, Botha, Gerrit, Bensellak, Taoufik, Wells, Gordon, Kumuthini, Judit, Shriner, Daniel, Fakim, Yasmina J., Ghoorah, Anisah W., Dareng, Eileen, Odia, Trust, Falola, Oluwadamilare, Adebiyi, Ezekiel, Hazelhurst, Scott, Mazandu, Gaston, Nyangiri, Oscar A., Mbiyavanga, Mamana, Benkahla, Alia, Kassim, Samar K., Mulder, Nicola, Adebamowo, Sally N., Chimusa, Emile R., Muzny, Donna, Metcalf, Ginger, Gibbs, Richard A., TrypanoGEN Research Group, Rotimi, Charles, Ramsay, Michèle, Adeyemo, Adebowale A., Lombard, Zané, Hanchard, Neil A., Matovu, Enock, Bucheton, Bruno, Hertz-Fowler, Christiane, Koffi, Mathurin, Macleod, Annette, Mumba-Ngoyi, Dieudonne, Noyes, Harry, Simo, Gustave, Simuunza, Martin, Botigué, Laura, Adebamowo, Clement, Agongo, Godfred, Boua, Romuald P., Oduro, Abraham, Sorgho, Hermann, Landouré, Guida, Cissé, Lassana, Diarra, Salimata, Samassékou, Oumar, Anabwani, Gabriel, Matshaba, Mogomotsi, Joloba, Moses, Kekitiinwa, Adeodata, Mardon, Graeme, Mpoloka, Sununguko W., Kyobe, Samuel, Mlotshwa, Busisiwe, Mwesigwa, Savannah, Retshabile, Gaone, Williams, Lesedi, Wonkam, Ambroise, Moussa, Ahmed, Adu, Dwomoa, Ojo, Akinlolu, Burke, David, Salako, Babatunde O., Awadalla, Philip, Bruat, Vanessa, and Gbeha, Elias

Abstract

The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals—comprising 50 ethnolinguistic groups, including previously unsampled populations—to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.

Published
2020

16. Additional file 2 of Copy number variation in human genomes from three major ethno-linguistic groups in Africa

Author

Nyangiri, Oscar A., Noyes, Harry, Mulindwa, Julius, Hamidou Ilboudo, Kabore, Justin Windingoudi, Ahouty, Bernardin, Koffi, Mathurin, Asina, Olivier Fataki, Dieudonne Mumba, Ofon, Elvis, Simo, Gustave, Magambo Phillip Kimuda, Enyaru, John, Alibu, Vincent Pius, Kelita Kamoto, Chisi, John, Simuunza, Martin, Camara, Mamadou, Sidibe, Issa, MacLeod, Annette, Bucheton, Bruno, Hall, Neil, Hertz-Fowler, Christiane, and Matovu, Enock

Abstract

Additional file 2. Correlation of GenomeSTRiP and cn.MOPS and supplementary figures.

Published
2020
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17. Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens

Author

Roos David, Nwaka Solomon, Berriman Matt, Hertz-Fowler Christiane, Crowther Greg, Ralph Stuart, Doyle Maria, Shanmugam Dhanasekaran, Carmona Santiago, Overington John, Magariños María Paula, Van Voorhis Wes, and Agüero Fernán

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Published
2010
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18. Comparative genomics of trypanosomatid parasitic protozoa

Author

Sayed, Najib M. El-, Myler, Peter J., Blandin, Gaelle, Berriman, Matthew, Crabtree, Jonathan, Aggarwal, Gautam, Caler, Elisabet, Renauld, Hubert, Worthey, Elizabeth A., Hertz-Fowler, Christiane, Ghedin, Elodie, Peacock, Christopher, Bartholomeu, Daniella C., Haas, Brian J., Tran, Anh-Nhi, Wortman, Jennifer R., Alsmark, U. Cecilia M., Angiuoli, Samuel, Anupama, Atashi, Badger, Jonathan, Bringaud, Frederic, Cadag, Eithon, Carlton, Jane M., Cerqueira, Gustavo C., Creasy, Todd, Delcher, Arthur L., Djikeng, Appolinaire, Embley, T. Martin, Hauser, Christopher, Ivens, Alasdair C., Kummerfeld, Sarah K., Pereira-Leal, Jose B., Nilsson, Daniel, Peterson, Jeremy, Salzberg, Steven L., Shallom, Joshua, Silva, Joana C., Sundaram, Jaideep, Westenberger, Scott, White, Owen, Melville, Sara E., Donelson, John E., Andersson, Bjorn, Stuart, Kenneth D., and Hall, Neil

Subjects
Leishmaniasis -- Genetic aspects, Trypanosoma cruzi -- Genetic aspects, Trypanosoma brucei -- Genetic aspects, Science and technology, Genetic aspects
Abstract

A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that--along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions--have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont., The protozoan pamogens Leishmania major, Trypanosoma cruzi, and Trypanosoma brucei (family Trypanosomatidae, order Kinetoplastida) collectively cause disease and death in millions of humans and countless infections in other mammals, primarily [...]

Published
2005

19. GeneDB—an annotation database for pathogens

Author

Logan-Klumpler, Flora J., De Silva, Nishadi, Boehme, Ulrike, Rogers, Matthew B., Velarde, Giles, McQuillan, Jacqueline A., Carver, Tim, Aslett, Martin, Olsen, Christian, Subramanian, Sandhya, Phan, Isabelle, Farris, Carol, Mitra, Siddhartha, Ramasamy, Gowthaman, Wang, Haiming, Tivey, Adrian, Jackson, Andrew, Houston, Robin, Parkhill, Julian, Holden, Matthew, Harb, Omar S., Brunk, Brian P., Myler, Peter J., Roos, David, Carrington, Mark, Smith, Deborah F., Hertz-Fowler, Christiane, and Berriman, Matthew

Published
2012
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20. High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation

Author

Mulindwa, Julius, primary, Noyes, Harry, additional, Ilboudo, Hamidou, additional, Pagani, Luca, additional, Nyangiri, Oscar, additional, Kimuda, Magambo Phillip, additional, Ahouty, Bernardin, additional, Asina, Olivier Fataki, additional, Ofon, Elvis, additional, Kamoto, Kelita, additional, Kabore, Justin Windingoudi, additional, Koffi, Mathurin, additional, Ngoyi, Dieudonne Mumba, additional, Simo, Gustave, additional, Chisi, John, additional, Sidibe, Issa, additional, Enyaru, John, additional, Simuunza, Martin, additional, Alibu, Pius, additional, Jamonneau, Vincent, additional, Camara, Mamadou, additional, Tait, Andy, additional, Hall, Neil, additional, Bucheton, Bruno, additional, MacLeod, Annette, additional, Hertz-Fowler, Christiane, additional, Matovu, Enock, additional, Mumba, Dieuodonne, additional, Alibu, Vincent P., additional, Macleod, Annette, additional, Hertzfowler, Christianne, additional, Elliot, Alison, additional, Bishop, Ozlem, additional, Mulindwa, Julius, additional, Ahouty, Bernadin, additional, and Kabore, Justin, additional

Published
2020
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21. Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma

Author

Thornton, Sophie, primary, Coupland, Sarah, additional, Olohan, Lisa, additional, Sibbring, Julie, additional, Kenny, John, additional, Hertz-Fowler, Christiane, additional, Liu, Xuan, additional, Haldenby, Sam, additional, Heimann, Heinrich, additional, Hussain, Rumana, additional, Kipling, Natalie, additional, Taktak, Azzam, additional, and Kalirai, Helen, additional

Published
2020
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22. Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom

Author

Haldenby, Sam, primary, Bronowski, Christina, additional, Nelson, Charlotte, additional, Kenny, John, additional, Martinez-Rodriguez, Carmen, additional, Chaudhuri, Roy, additional, Williams, Nicola J., additional, Forbes, Ken, additional, Strachan, Norval J., additional, Pulman, Jane, additional, Winstanley, Ian N., additional, Corless, Caroline E., additional, Humphrey, Tom J., additional, Bolton, Frederick J., additional, O’Brien, Sarah J., additional, Hall, Neil, additional, Hertz-Fowler, Christiane, additional, and Winstanley, Craig, additional

Published
2020
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23. TriTrypDB: a functional genomic resource for the Trypanosomatidae

Author

Aslett, Martin, Aurrecoechea, Cristina, Berriman, Matthew, Brestelli, John, Brunk, Brian P., Carrington, Mark, Depledge, Daniel P., Fischer, Steve, Gajria, Bindu, Gao, Xin, Gardner, Malcolm J., Gingle, Alan, Grant, Greg, Harb, Omar S., Heiges, Mark, Hertz-Fowler, Christiane, Houston, Robin, Innamorato, Frank, Iodice, John, Kissinger, Jessica C., Kraemer, Eileen, Li, Wei, Logan, Flora J., Miller, John A., Mitra, Siddhartha, Myler, Peter J., Nayak, Vishal, Pennington, Cary, Phan, Isabelle, Pinney, Deborah F., Ramasamy, Gowthaman, Rogers, Matthew B., Roos, David S., Ross, Chris, Sivam, Dhileep, Smith, Deborah F., Srinivasamoorthy, Ganesh, Stoeckert, Christian J., Jr, Subramanian, Sandhya, Thibodeau, Ryan, Tivey, Adrian, Treatman, Charles, Velarde, Giles, and Wang, Haiming

Published
2010
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24. The genome of the blood fluke Schistosoma mansoni

Author

Berriman, Matthew, Haas, Brian J., LoVerde, Philip T., Wilson, Alan R., Dillon, Gary P., Cerqueira, Gustavo C., Mashiyama, Susan T., Al-Lazikani, Bissan, Andrade, Luiza F., Ashton, Peter D., Aslett, Martin A., Bartholomeu, Daniella C., Blandin, Gaelle, Caffrey, Conor R., Coghlan, Avril, Coulson, Richard, Day, Tim A., Delcher, Art, DeMarco, Ricardo, Djikeng, Appolinaire, Eyre, Tina, Gamble, John A., Ghedin, Elodie, Gu, Yong, Hertz-Fowler, Christiane, Hirai, Hirohisha, Hirai, Yuriko, Houston, Robin, Ivens, Alasdair, Johnston, David A., Lacerda, Daniela, Macedo, Camila D., McVeigh, Paul, Ning, Zemin, Oliveira, Guilherme, Overington, John P., Parkhill, Julian, Pertea, Mihaela, Pierce, Raymond J., Protasio, Anna V., Quail, Michael A., Rajandream, Marie-Adèle, Rogers, Jane, Sajid, Mohammed, Salzberg, Steven L., Stanke, Mario, Tivey, Adrian R., White, Owen, Williams, David L., Wortman, Jennifer, Wu, Wenjie, Zamanian, Mostafa, Zerlotini, Adhemar, Fraser-Liggett, Claire M., Barrell, Barclay G., and El-Sayed, Najib M.

Published
2009
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27. 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

28. 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

29. The structure of a conserved telomeric region associated with variant antigen loci in the blood parasite Trypanosoma congolense

Author

Abbas, Ali Hadi, Pereira, Sara Silva, D'Archivio, Simon, Wickstead, Bill, Morrison, Liam J, Hall, Neil, Hertz-Fowler, Christiane, Darby, Alistair C, and Jackson, Andrew P

Subjects
telomere, parasitic diseases, antigenic variation, Trypanosoma congolens, variant surface glycoprotein, expression site, ESAG
Abstract

African trypanosomiasis is a vector-borne disease of humans and livestock caused by African trypanosomes (Trypanosoma spp.). Survival in the vertebrate bloodstream depends on antigenic variation of Variant Surface Glycoproteins (VSG) coating the parasite surface. In T. brucei, a model for antigenic variation, monoallelic VSG expression originates from dedicated VSG expression sites (VES). T. brucei VES have a conserved structure consisting of a telomeric VSG locus downstream of unique, repeat sequences and an independent promoter. Additional protein-coding sequences, known as 'Expression Site Associated Genes (ESAGs)', are also often present and are implicated in diverse, bloodstream-stage functions. T. congolense is a related veterinary pathogen, also displaying VSG-mediated antigenic variation. A T. congolense VES has not been described, making it unclear if regulation of VSG expression is conserved between species. Here, we describe a conserved telomeric region associated with VSG loci from long-read DNA sequencing of two T. congolense strains, which consists of a distal repeat, conserved non-coding elements and other genes besides the VSG; although these are not orthologous to T. brucei ESAGs. Most conserved telomeric regions are associated with accessory minichromosomes, but the same structure may also be associated with megabase chromosomes. We propose that this region represents the T. congolense VES, and through comparison with T. brucei, we discuss the parallel evolution of antigenic switching mechanisms, and unique adaptation of the T. brucei VES for developmental regulation of bloodstream-stage genes. Hence, we provide a basis for understanding antigenic switching in T. congolense and the origins of the African trypanosome VES.

Published
2018

30. No evidence for association between APOL1 kidney disease risk alleles and Human African Trypanosomiasis in two Ugandan populations

Author

Kimuda, Magambo Phillip, Noyes, Harry, Mulindwa, Julius, Enyaru, John, Alibu, Vincent Pius, Sidibe, Issa, Mumba Ngoyi, Dieuodonne, Hertz-Fowler, Christiane, MacLeod, Annette, Tastan Bishop, Özlem, and Matovu, Enock

Subjects
parasitic diseases
Abstract

Background:\ud \ud Human African trypanosomiasis (HAT) manifests as an acute form caused by Trypanosoma brucei rhodesiense (Tbr) and a chronic form caused by Trypanosoma brucei gambiense (Tbg). Previous studies have suggested a host genetic role in infection outcomes, particularly for APOL1. We have undertaken candidate gene association studies (CGAS) in a Ugandan Tbr and a Tbg HAT endemic area, to determine whether polymorphisms in IL10, IL8, IL4, HLAG, TNFA, TNX4LB, IL6, IFNG, MIF, APOL1, HLAA, IL1B, IL4R, IL12B, IL12R, HP, HPR, and CFH have a role in HAT.\ud Methodology and results:\ud \ud We included 238 and 202 participants from the Busoga Tbr and Northwest Uganda Tbg endemic areas respectively. Single Nucleotide Polymorphism (SNP) genotype data were analysed in the CGAS. The study was powered to find odds ratios > 2 but association testing of the SNPs with HAT yielded no positive associations i.e. none significant after correction for multiple testing. However there was strong evidence for no association with Tbr HAT and APOL1 G2 of the size previously reported in the Kabermaido district of Uganda.\ud Conclusions/Significance:\ud \ud A recent study in the Soroti and Kaberamaido focus in Central Uganda found that the APOL1 G2 allele was strongly associated with protection against Tbr HAT (odds ratio = 0.2, 95% CI: 0.07 to 0.48, p = 0.0001). However, in our study no effect of G2 on Tbr HAT was found, despite being well powered to find a similar sized effect (OR = 0.9281, 95% CI: 0.482 to 1.788, p = 0.8035). It is possible that the G2 allele is protective from Tbr in the Soroti/Kabermaido focus but not in the Iganga district of Busoga, which differ in ethnicity and infection history. Mechanisms underlying HAT infection outcome and virulence are complex and might differ between populations, and likely involve several host, parasite or even environmental factors.

Published
2018

31. Macrophage migrating inhibitory factor expression is associated with Trypanosoma brucei gambiense infection and is controlled by trans-acting expression quantitative trait loci in the Guinean population

Author

Kaboré, Justin Windingoudi, primary, Camara, Oumou, additional, Ilboudo, Hamidou, additional, Capewell, Paul, additional, Clucas, Caroline, additional, Cooper, Anneli, additional, Kaboré, Jacques, additional, Camara, Mamadou, additional, Jamonneau, Vincent, additional, Hertz-Fowler, Christiane, additional, Bélem, Adrien Marie Gaston, additional, Matovu, Enock, additional, Macleod, Annette, additional, Sidibé, Issa, additional, Noyes, Harry, additional, and Bucheton, Bruno, additional

Published
2019
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32. Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections

Author

Jayaraman, Siddharth, primary, Harris, Claire, additional, Paxton, Edith, additional, Donachie, Anne-Marie, additional, Vaikkinen, Heli, additional, McCulloch, Richard, additional, Hall, James P. J., additional, Kenny, John, additional, Lenzi, Luca, additional, Hertz-Fowler, Christiane, additional, Cobbold, Christina, additional, Reeve, Richard, additional, Michoel, Tom, additional, and Morrison, Liam J., additional

Published
2019
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33. A polymorphism in the haptoglobin, haptoglobin related protein locus is associated with risk of human sleeping sickness within Cameroonian populations

Author

Ofon, Elvis, Noyes, Harry, Mulindwa, Julius, Ilboudo, Hamidou, Simuunza, Martin, Eboo, Vincent, Njiokou, Flobert, Koffi, Mathurin, Bucheton, Bruno, Fogue, Pythagore, Hertz-Fowler, Christiane, MacLeod, Annette, Simo, Gustave, Grp, TrypanoGEN Res, and Consortium, H3Africa

Subjects
Male, 0301 basic medicine, Heredity, Trypanosoma brucei gambiense, Biochemistry, Geographical Locations, Gene Frequency, Risk Factors, Zoonoses, Medicine and Health Sciences, Cameroon, Child, Aged, 80 and over, Protozoans, Genetics, biology, lcsh:Public aspects of medicine, Haptoglobin, Neglected Diseases, Eukaryota, Middle Aged, 3. Good health, Genetic Mapping, Infectious Diseases, Female, Research Article, Neglected Tropical Diseases, Adult, Trypanosoma, Genotyping, medicine.medical_specialty, lcsh:Arctic medicine. Tropical medicine, Adolescent, Genotype, lcsh:RC955-962, Variant Genotypes, Locus (genetics), Single-nucleotide polymorphism, Research and Analysis Methods, Polymorphism, Single Nucleotide, African Trypanosomiasis, Molecular Genetics, Young Adult, 03 medical and health sciences, Antigens, Neoplasm, Trypanosomiasis, Molecular genetics, Parasitic Diseases, medicine, Humans, SNP, Genetic Predisposition to Disease, Molecular Biology Techniques, Molecular Biology, Alleles, Genetic Association Studies, Aged, Protozoan Infections, Plasma Proteins, Haptoglobins, Organisms, Public Health, Environmental and Occupational Health, Biology and Life Sciences, Proteins, lcsh:RA1-1270, Tropical Diseases, Parasitic Protozoans, Minor allele frequency, Trypanosomiasis, African, 030104 developmental biology, Genetic Loci, Case-Control Studies, Asymptomatic Diseases, People and Places, Africa, Immunology, biology.protein, Asymptomatic carrier
Abstract

Background Human African Trypanosomiasis (HAT) is a neglected disease targeted for elimination as a public health problem by 2020. Elimination requires a better understanding of the epidemiology and clinical evolution of HAT. In addition to the classical clinical evolution of HAT, asymptomatic carriers and spontaneous cure have been reported in West Africa. A genetic component to human susceptibility to HAT has been suggested to explain these newly observed responses to infection. In order to test for genetic associations with infection response, genetic polymorphism in 17 genes were tested (APOL1, IL1B, IL4, IL4R, IL6, IL8, IL12B, IL12RB1, IL10, TNFA, INFG, MIF, HLA-G, HLA-A, HP, HPR and CFH). Methodology A case-control study was performed on 180 blood samples collected from 56 cases and 124 controls from Cameroon. DNA was extracted from blood samples. After quality control, 25 samples (24 controls and 1 case) were eliminated. The genotyping undertaken on 155 individuals including 55 cases and 100 controls were investigated at 96 loci (88 SNPs and 8 indels) located on 17 genes. Associations between these loci and HAT were estimated via a case-control association test. Results Analyses of 64 SNPs and 4 indels out of 96 identified in the selected genes reveal that the minor allele (T) of rs8062041 in haptoglobin (HP) appeared to be protective against HAT (p = 0.0002395, OR 0.359 (CI95 [0.204–0.6319])); indicating higher frequency in cases compared to controls. This minor allele with adjusted p value of 0.0163 is associated with a lower risk (protective effect) of developing sleeping sickness. Conclusion The haptoglobin related protein HPR and HP are tightly linked and both are duplicated in some people and may lead to higher activity. This increased production could be responsible of the protection associated with rs8062041 even though this SNP is within HP., Author summary Human African trypanosomiasis (HAT) or sleeping sickness is a neglected tropical disease targeted for elimination by 2020. This elimination requires a better understanding of the epidemiology and clinical evolution of this disease. Beside the classical clinical evolution, asymptomatic carriers, seropositive and spontaneous cure of infected persons have been reported in West Africa. Arguments in favor of human genetic susceptibility to HAT have been raised to explain this variability in clinical presentation. This study investigated the genetic polymorphism of 17 genes between controls and sleeping sickness patients in Southern Cameroon in order to improve our knowledge of human susceptibility to trypanosome infections. We identified single nucleotide polymorphisms and indels in 17 selected genes involved in immune responses and carried out a case-control candidate gene association study and demonstrated differences between variants associated with the disease. From these genes, only haptoglobin (HP) at the SNP rs8062041 was found to have polymorphisms which were strongly associated with trypanosomiasis. The minor allele (T) at this SNP position appeared to be protective against HAT (p = 0.0002395, OR 0.359 (CI95 [0.204–0.6319])) reducing the risk of developing disease approximately threefold. The haptoglobin related protein (HPR) is adjacent to HP and is a component of the Trypanolytic factor that kills trypanosomes. The HP and HPR locus is duplicated in some people. The rs8062041 variant may be associated with this duplication and it is possible that increased production of HPR is the cause of the protection associated with rs8062041. The results reported here will contribute to the knowledge of the role of human genetics in disease progression, and thus lead to the identification of novel biomarkers which could involve development of new diagnostics, treatments and intervention strategies.

Published
2017

34. Introducing the TrypanoGEN biobank: A valuable resource for the elimination of human African trypanosomiasis

Author

Ilboudo, Hamidou, Noyes, Harry, Mulindwa, Julius, Kimuda, Magambo Phillip, Koffi, Mathurin, Kabore, Justin Windingoudi, Ahouty, Bernadin, Ngoyi, Dieudonne Mumba, Fataki, Olivier, Simo, Gustave, Ofon, Elvis, Enyaru, John, Chisi, John, Kamoto, Kelita, Simuunza, Martin, Alibu, Vincent P, Lejon, Veerle, Jamonneau, Vincent, Macleod, Annette, Camara, Mamadou, Bucheton, Bruno, Hertz-Fowler, Christiane, Sidibe, Issa, Matovu, Enock, Grp, TrypanoGEN Res, and Consortium, H3Africa

Subjects
0301 basic medicine, Aging, Geographical Locations, Plasma, Environmental protection, Zoonoses, Medicine and Health Sciences, African trypanosomiasis, Uganda, Cameroon, Biological Specimen Banks, Aged, 80 and over, lcsh:Public aspects of medicine, Genomics, Middle Aged, Biobank, Infectious Diseases, Neglected Tropical Diseases, Adult, Resource (biology), lcsh:Arctic medicine. Tropical medicine, Adolescent, lcsh:RC955-962, Zambia, Biology, African Trypanosomiasis, 03 medical and health sciences, Young Adult, Trypanosomiasis, medicine, Parasitic Diseases, Genome-Wide Association Studies, Genetics, Humans, Genetic Predisposition to Disease, Disease Eradication, Environmental planning, Africa South of the Sahara, Aged, Symposium, Protozoan Infections, Public Health, Environmental and Occupational Health, Biology and Life Sciences, Computational Biology, Human Genetics, lcsh:RA1-1270, DNA, medicine.disease, Tropical Diseases, Genome Analysis, 030104 developmental biology, Trypanosomiasis, African, People and Places, Africa, Parasitology
Abstract

No abstract available.

Published
2017

35. Application of Long Read Sequencing to Determine Expressed Antigen Diversity inTrypanosoma BruceiInfections

Author

Jayaraman, Siddharth, primary, Harris, Claire, additional, Paxton, Edith, additional, Donachie, Anne-Marie, additional, Vaikkinen, Heli, additional, McCulloch, Richard, additional, Hall, James P. J., additional, Kenny, John, additional, Lenzi, Luca, additional, Hertz-Fowler, Christiane, additional, Cobbold, Christina, additional, Reeve, Richard, additional, Michoel, Tom, additional, and Morrison, Liam J., additional

Published
2018
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37. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

Author

Basenko, Evelina, primary, Pulman, Jane, additional, Shanmugasundram, Achchuthan, additional, Harb, Omar, additional, Crouch, Kathryn, additional, Starns, David, additional, Warrenfeltz, Susanne, additional, Aurrecoechea, Cristina, additional, Stoeckert, Christian, additional, Kissinger, Jessica, additional, Roos, David, additional, and Hertz-Fowler, Christiane, additional

Published
2018
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38. Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus

Author

Craig, Thomas, primary, Holland, Richard, additional, D’Amore, Rosalinda, additional, Johnson, James R., additional, McCue, Hannah V., additional, West, Anthony, additional, Zulkower, Valentin, additional, Tekotte, Hille, additional, Cai, Yizhi, additional, Swan, Daniel, additional, Davey, Robert P, additional, Hertz-Fowler, Christiane, additional, Hall, Anthony, additional, and Caddick, Mark, additional

Published
2017
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39. No evidence for association with APOL1 kidney disease risk alleles and Human African Trypanosomiasis in two Ugandan populations

Author

Kimuda, Magambo Phillip, primary, Noyes, Harry, additional, Mulindwa, Julius, additional, Enyaru, John, additional, Alibu, Vincent Pius, additional, Sidibe, Issa, additional, Mumba, Dieuodonne, additional, Hertz-Fowler, Christiane, additional, MacLeod, Annette, additional, Bishop, Özlem Tastan, additional, and Matovu, Enock, additional

Published
2017
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41. Association between IL1 gene polymorphism and human African trypanosomiasis in populations of sleeping sickness foci of southern Cameroon.

Author

Ofon, Elvis, Noyes, Harry, Ebo’o Eyanga, Vincent, Njiokou, Flobert, Koffi, Mathurin, Fogue, Pythagore, Hertz-Fowler, Christiane, MacLeod, Annette, Matovu, Enock, Simo, Gustave, and null, null

Subjects
AFRICAN trypanosomiasis, DISEASES
Abstract

Background: Human African Trypanosomiasis (HAT) is a neglected tropical disease caused by infections due to Trypanosoma brucei subspecies. In addition to the well-established environmental and behavioural risks of becoming infected, there is evidence for a genetic component to the response to trypanosome infection. We undertook a candidate gene case-control study to investigate genetic associations further. Methodology: We genotyped one polymorphism in each of seven genes (IL1A, IL1RN, IL4RN, IL6, HP, HPR, and HLA-G) in 73 cases and 250 controls collected from 19 ethno-linguistic subgroups stratified into three major ethno-linguistic groups, 2 pooled ethno-linguistic groups and 11 ethno-linguistic subgroups from three Cameroonian HAT foci. The seven polymorphic loci tested consisted of three SNPs, three variable numbers of tandem repeat (VNTR) and one INDEL. Results: We found that the genotype (TT) and minor allele (T) of IL1A gene as well as the genotype 1A3A of IL1RN were associated with an increased risk of getting Trypanosoma brucei gambiense and develop HAT when all data were analysed together and also when stratified by the three major ethno-linguistic groups, 2 pooled ethno-linguistic subgroups and 11 ethno-linguistic subgroups. Conclusion: This study revealed that one SNP rs1800794 of IL1A and one VNTR rs2234663 of IL1RN were associated with the increased risk to be infected by Trypanosoma brucei gambiense and develop sleeping sickness in southern Cameroon. The minor allele T and the genotype TT of SNP rs1800794 in IL1A as well as the genotype 1A3A of IL1RN rs2234663 VNTR seem to increase the risk of getting Trypanosoma brucei gambiense infections and develop sleeping sickness in southern Cameroon. [ABSTRACT FROM AUTHOR]

Published
2019
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42. Current challenges of research on filamentous fungi in relation to human welfare and a sustainable bio-economy: a white paper

Author

Meyer, Vera, Andersen, Mikael Rørdam, Brakhage, Axel A., Braus, Gerhard H., Caddick, Mark X., Cairns, Timothy C., de Vries, Ronald P., Haarmann, Thomas, Hansen, Kim, Hertz-Fowler, Christiane, Krappmann, Sven, Mortensen, Uffe Hasbro, Peñalva, Miguel A., Ram, Arthur F. J., Head, Ritchie M., Meyer, Vera, Andersen, Mikael Rørdam, Brakhage, Axel A., Braus, Gerhard H., Caddick, Mark X., Cairns, Timothy C., de Vries, Ronald P., Haarmann, Thomas, Hansen, Kim, Hertz-Fowler, Christiane, Krappmann, Sven, Mortensen, Uffe Hasbro, Peñalva, Miguel A., Ram, Arthur F. J., and Head, Ritchie M.

Abstract

The EUROFUNG network is a virtual centre of multidisciplinary expertise in the field of fungal biotechnology. The first academic-industry Think Tank was hosted by EUROFUNG to summarise the state of the art and future challenges in fungal biology and biotechnology in the coming decade. Currently, fungal cell factories are important for bulk manufacturing of organic acids, proteins, enzymes, secondary metabolites and active pharmaceutical ingredients in white and red biotechnology. In contrast, fungal pathogens of humans kill more people than malaria or tuberculosis. Fungi are significantly impacting on global food security, damaging global crop production, causing disease in domesticated animals, and spoiling an estimated 10 % of harvested crops. A number of challenges now need to be addressed to improve our strategies to control fungal pathogenicity and to optimise the use of fungi as sources for novel compounds and as cell factories for large scale manufacture of bio-based products. This white paper reports on the discussions of the Think Tank meeting and the suggestions made for moving fungal bio(techno)logy forward.

Published
2016

43. Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis : International Glossina Genome Initiative

Author

Watanabe, Junichi, Hattori, Masahira, Berriman, Matthew, Lehane, Michael, Hall, Neil, Solano, Philippe, Aksoy, Serap, Hide, Winston, Touré, Yeya, Attardo, Geoffrey, Darby, Alistair, Toyoda, Atsushi, Hertz-Fowler, Christiane, Larkin, Denis, Cotton, James, Sanders, Mandy, Swain, Martin, Quail, Michael, Inoue, Noboru, Ravel, Sophie, Taylor, Todd, Srivastava, Tulika, Sharma, Vineet, Warren, Wesley, Wilson, Richard, Suzuki, Yutaka, Lawson, Daniel, Hughes, Daniel, Megy, Karyn, Masiga, Daniel, Mireji, Paul, Hansen, Immo, Van Den Abbeele, Jan, Benoit, Joshua, Bourtzis, Kostas, Obiero, George, Robertson, Hugh, Jones, Jeffery, Zhou, Jing-Jiang, Field, Linda, Friedrich, Markus, Nyanjom, Steven, Telleria, Erich, Caljon, Guy, Ribeiro, José, Acosta-Serrano, Alvaro, Ooi, Cher-Pheng, Rose, Clair, Price, David, Haines, Lee, Christoffels, Alan, Sim, Cheolho, Pham, Daphne, Denlinger, David, Geiser, Dawn, Omedo, Irene, Winzerling, Joy, Peyton, Justin, Marucha, Kevin, Jonas, Mario, Meuti, Megan, Rawlings, Neil, Zhang, Qirui, Macharia, Rosaline, Michalkova, Veronika, Dashti, Zahra, Baumann, Aaron, Gäde, Gerd, Marco, Heather, Caers, Jelle, Schoofs, Liliane, Riehle, Michael, Hu, Wanqi, Tu, Zhijian, Tarone, Aaron, Malacrida, Anna, Kibet, Caleb, Scolari, Francesca, Koekemoer, Jacobus, Willis, Judith, Gomulski, Ludvik, Falchetto, Marco, Scott, Maxwell, Fu, Shuhua, Sze, Sing-Hoi, Luiz, Thiago, Weiss, Brian, Walshe, Deirdre, Wang, Jingwen, Wamalwa, Mark, Mwangi, Sarah, Ramphul, Urvashi, Snyder, Anna, Brelsfoard, Corey, Thomas, Gavin, Tsiamis, George, Arensburger, Peter, Rio, Rita, Macdonald, Sandy, Panji, Sumir, Kruger, Adele, Benkahla, Alia, Balyeidhusa, Apollo, Msangi, Atway, Okoro, Chinyere, Stephens, Dawn, Stanley, Eleanor, Mpondo, Feziwe, Wamwiri, Florence, Mramba, Furaha, Siwo, Geoffrey, Githinji, George, Harkins, Gordon, Murilla, Grace, Lehväslaiho, Heikki, Malele, Imna, Auma, Joanna, Kinyua, Johnson, Ouma, Johnson, Okedi, Loyce, Manga, Lucien, Aslett, Martin, Koffi, Mathurin, Gaunt, Michael, Makgamathe, Mmule, Mulder, Nicola, Manangwa, Oliver, Abila, Patrick, Wincker, Patrick, Gregory, Richard, Bateta, Rosemary, Sakate, Ryuichi, Ommeh, Sheila, Lehane, Stella, Imanishi, Tadashi, Osamor, Victor, and Kawahara, Yoshihiro

Abstract

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology. ispartof: Science vol:344 issue:6182 pages:380-386 ispartof: location:United States status: published

Published
2014

44. EuPathDB: the eukaryotic pathogen genomics database resource

Author

Aurrecoechea, Cristina, primary, Barreto, Ana, additional, Basenko, Evelina Y., additional, Brestelli, John, additional, Brunk, Brian P., additional, Cade, Shon, additional, Crouch, Kathryn, additional, Doherty, Ryan, additional, Falke, Dave, additional, Fischer, Steve, additional, Gajria, Bindu, additional, Harb, Omar S., additional, Heiges, Mark, additional, Hertz-Fowler, Christiane, additional, Hu, Sufen, additional, Iodice, John, additional, Kissinger, Jessica C., additional, Lawrence, Cris, additional, Li, Wei, additional, Pinney, Deborah F., additional, Pulman, Jane A., additional, Roos, David S., additional, Shanmugasundram, Achchuthan, additional, Silva-Franco, Fatima, additional, Steinbiss, Sascha, additional, Stoeckert, Christian J., additional, Spruill, Drew, additional, Wang, Haiming, additional, Warrenfeltz, Susanne, additional, and Zheng, Jie, additional

Published
2016
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45. Current challenges of research on filamentous fungi in relation to human welfare and a sustainable bio-economy: a white paper

Author

Meyer, Vera, primary, Andersen, Mikael R., additional, Brakhage, Axel A., additional, Braus, Gerhard H., additional, Caddick, Mark X., additional, Cairns, Timothy C., additional, de Vries, Ronald P., additional, Haarmann, Thomas, additional, Hansen, Kim, additional, Hertz-Fowler, Christiane, additional, Krappmann, Sven, additional, Mortensen, Uffe H., additional, Peñalva, Miguel A., additional, Ram, Arthur F. J., additional, and Head, Ritchie M., additional

Published
2016
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46. GeneMill: A 21st century platform for innovation

Author

Johnson, James R., primary, D'Amore, Rosalinda, additional, Thain, Simon C., additional, Craig, Thomas, additional, McCue, Hannah V., additional, Hertz-Fowler, Christiane, additional, Hall, Neil, additional, and Hall, Anthony J.W., additional

Published
2016
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47. Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach

Author

Aljabr, Waleed, primary, Touzelet, Olivier, additional, Pollakis, Georgios, additional, Wu, Weining, additional, Munday, Diane C., additional, Hughes, Margaret, additional, Hertz-Fowler, Christiane, additional, Kenny, John, additional, Fearns, Rachel, additional, Barr, John N., additional, Matthews, David A., additional, and Hiscox, Julian A., additional

Published
2016
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49. TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei

Author

LS Biochemie van parasieten, B&C BRC-SIB-TR, Regenerative Medicine, Stem Cells & Cancer, Shameer, Sanu, Logan-Klumpler, Flora J, Vinson, Florence, Cottret, Ludovic, Merlet, Benjamin, Achcar, Fiona, Boshart, Michael, Berriman, Matthew, Breitling, Rainer, Bringaud, Frédéric, Bütikofer, Peter, Cattanach, Amy M, Bannerman-Chukualim, Bridget, Creek, Darren J, Crouch, Kathryn, de Koning, Harry P, Denise, Hubert, Ebikeme, Charles, Fairlamb, Alan H, Ferguson, Michael A J, Ginger, Michael L, Hertz-Fowler, Christiane, Kerkhoven, Eduard J, Mäser, Pascal, Michels, Paul A M, Nayak, Archana, Nes, David W, Nolan, Derek P, Olsen, Christian, Silva-Franco, Fatima, Smith, Terry K, Taylor, Martin C, Tielens, Aloysius G M, Urbaniak, Michael D, van Hellemond, Jaap J, Vincent, Isabel M, Wilkinson, Shane R, Wyllie, Susan, Opperdoes, Fred R, Barrett, Michael P, Jourdan, Fabien, LS Biochemie van parasieten, B&C BRC-SIB-TR, Regenerative Medicine, Stem Cells & Cancer, Shameer, Sanu, Logan-Klumpler, Flora J, Vinson, Florence, Cottret, Ludovic, Merlet, Benjamin, Achcar, Fiona, Boshart, Michael, Berriman, Matthew, Breitling, Rainer, Bringaud, Frédéric, Bütikofer, Peter, Cattanach, Amy M, Bannerman-Chukualim, Bridget, Creek, Darren J, Crouch, Kathryn, de Koning, Harry P, Denise, Hubert, Ebikeme, Charles, Fairlamb, Alan H, Ferguson, Michael A J, Ginger, Michael L, Hertz-Fowler, Christiane, Kerkhoven, Eduard J, Mäser, Pascal, Michels, Paul A M, Nayak, Archana, Nes, David W, Nolan, Derek P, Olsen, Christian, Silva-Franco, Fatima, Smith, Terry K, Taylor, Martin C, Tielens, Aloysius G M, Urbaniak, Michael D, van Hellemond, Jaap J, Vincent, Isabel M, Wilkinson, Shane R, Wyllie, Susan, Opperdoes, Fred R, Barrett, Michael P, and Jourdan, Fabien

Published
2015

50. Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty

Author

Carnes, Jason, Anupama, Atashi, Balmer, Olivier, Jackson, Andrew, Lewis, Michael, Brown, Rob, Cestari, Igor, Desquesnes, Marc, Gendrin, Claire, Hertz-Fowler, Christiane, Imamura, Hideo, Ivens, Alasdair, Koreny, Ludek, Lai, De-Hua, MacLeod, Annette, McDermott, Suzanne M., Merritt, Chris, Monnerat, Severine, Moon, Wonjong, Myler, Peter, Phan, Isabelle, Ramasamy, Gowthaman, Sivam, Dhileep, Lun, Zhao-Rong, Lukes, Julius, Stuart, Ken, Schnaufer, Achim, Carnes, Jason, Anupama, Atashi, Balmer, Olivier, Jackson, Andrew, Lewis, Michael, Brown, Rob, Cestari, Igor, Desquesnes, Marc, Gendrin, Claire, Hertz-Fowler, Christiane, Imamura, Hideo, Ivens, Alasdair, Koreny, Ludek, Lai, De-Hua, MacLeod, Annette, McDermott, Suzanne M., Merritt, Chris, Monnerat, Severine, Moon, Wonjong, Myler, Peter, Phan, Isabelle, Ramasamy, Gowthaman, Sivam, Dhileep, Lun, Zhao-Rong, Lukes, Julius, Stuart, Ken, and Schnaufer, Achim

Abstract

Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase c subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

Published
2015

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