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2. Recent advances in functional research in Giardia intestinalis

Author

Jex, Aaron R, Svärd, Staffan, Hagen, Kari D, Starcevich, Hannah, Emery, Samantha J, Balan, Balu, Nosala, Chris, and Dawson, Scott C

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Genetics, Human Genome, Biotechnology, Bioengineering, 1.1 Normal biological development and functioning, Computational Biology, Giardia lamblia, Research, Bioinformatics, CRISPr, Functional research, Giardia, Molecular biology, Microbiology, Veterinary Sciences, Medical Microbiology, Mycology & Parasitology, Veterinary sciences
Abstract

This review considers current advances in tools to investigate the functional biology of Giardia, it's coding and non-coding genes, features and cellular and molecular biology. We consider major gaps in current knowledge of the parasite and discuss the present state-of-the-art in its in vivo and in vitro cultivation. Advances in in silico tools, including for the modelling non-coding RNAs and genomic elements, as well as detailed exploration of coding genes through inferred homology to model organisms, have provided significant, primary level insight. Improved methods to model the three-dimensional structure of proteins offer new insights into their function, and binding interactions with ligands, other proteins or precursor drugs, and offer substantial opportunities to prioritise proteins for further study and experimentation. These approaches can be supplemented by the growing and highly accessible arsenal of systems-based methods now being applied to Giardia, led by genomic, transcriptomic and proteomic methods, but rapidly incorporating advanced tools for detection of real-time transcription, evaluation of chromatin states and direct measurement of macromolecular complexes. Methods to directly interrogate and perturb gene function have made major leaps in recent years, with CRISPr-interference now available. These approaches, coupled with protein over-expression, fluorescent labelling and in vitro and in vivo imaging, are set to revolutionize the field and herald an exciting time during which the field may finally realise Giardia's long proposed potential as a model parasite and eukaryote.

Published
2020

3. Epidemiological evaluation of sewage surveillance as a tool to detect the presence of COVID-19 cases in a low case load setting

Author

Black, Jim, Aung, Phyo, Nolan, Monica, Roney, Emma, Poon, Rachael, Hennessy, Daneeta, Crosbie, Nicholas D., Deere, Dan, Jex, Aaron R., John, Nijoy, Baker, Louise, Scales, Peter J., Usher, Shane P., McCarthy, David T., Schang, Christelle, Schmidt, Jonathan, Myers, Steven, Begue, Natacha, Kaucner, Christine, Thorley, Bruce, Druce, Julian, Monis, Paul, Lau, Melody, and Sarkis, Suzie

Published
2021
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9. Transcriptome and histone epigenome of Plasmodium vivax salivary-gland sporozoites point to tight regulatory control and mechanisms for liver-stage differentiation in relapsing malaria

Author

Muller, Ivo, Jex, Aaron R., Kappe, Stefan H.I., Mikolajczak, Sebastian A., Sattabongkot, Jetsumon, Patrapuvich, Rapatbhorn, Lindner, Scott, Flannery, Erika L., Koepfli, Cristian, Ansell, Brendan, Lerch, Anita, Emery-Corbin, Samantha J., Charnaud, Sarah, Smith, Jeffrey, Merrienne, Nicolas, Swearingen, Kristian E., Moritz, Robert L., Petter, Michaela, Duffy, Michael F., and Chuenchob, Vorada

Published
2019
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11. Hookworms dynamically respond to loss of Type 2 immune pressure

Author

Ferguson, Annabel A., primary, Inclan-Rico, Juan M., additional, Lu, Dihong, additional, Bobardt, Sarah D., additional, Hung, LiYin, additional, Gouil, Quentin, additional, Baker, Louise, additional, Ritchie, Matthew E., additional, Jex, Aaron R., additional, Schwarz, Erich M., additional, Rossi, Heather L., additional, Nair, Meera G., additional, Dillman, Adler R., additional, and Herbert, De’Broski R., additional

Published
2023
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15. The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus

Author

Schwarz, Erich M, Korhonen, Pasi K, Campbell, Bronwyn E, Young, Neil D, Jex, Aaron R, Jabbar, Abdul, Hall, Ross S, Mondal, Alinda, Howe, Adina C, Pell, Jason, Hofmann, Andreas, Boag, Peter R, Zhu, Xing-Quan, Gregory, T Ryan, Loukas, Alex, Williams, Brian A, Antoshechkin, Igor, Brown, C Titus, Sternberg, Paul W, and Gasser, Robin B

Subjects
Veterinary Sciences, Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Biotechnology, Immunization, Orphan Drug, Human Genome, Rare Diseases, Infectious Diseases, Vaccine Related, Biodefense, Prevention, Infection, Animals, Anthelmintics, Antigens, Helminth, Drug Resistance, Female, Gene Expression Regulation, Genes, Helminth, Genome Size, Genome, Helminth, Haemonchiasis, Haemonchus, Helminth Proteins, Host-Parasite Interactions, Life Cycle Stages, Male, Peptide Hydrolases, Sheep, Sheep Diseases, Transcriptome, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe barber's pole worm, Haemonchus contortus, is one of the most economically important parasites of small ruminants worldwide. Although this parasite can be controlled using anthelmintic drugs, resistance against most drugs in common use has become a widespread problem. We provide a draft of the genome and the transcriptomes of all key developmental stages of H. contortus to support biological and biotechnological research areas of this and related parasites.ResultsThe draft genome of H. contortus is 320 Mb in size and encodes 23,610 protein-coding genes. On a fundamental level, we elucidate transcriptional alterations taking place throughout the life cycle, characterize the parasite's gene silencing machinery, and explore molecules involved in development, reproduction, host-parasite interactions, immunity, and disease. The secretome of H. contortus is particularly rich in peptidases linked to blood-feeding activity and interactions with host tissues, and a diverse array of molecules is involved in complex immune responses. On an applied level, we predict drug targets and identify vaccine molecules.ConclusionsThe draft genome and developmental transcriptome of H. contortus provide a major resource to the scientific community for a wide range of genomic, genetic, proteomic, metabolomic, evolutionary, biological, ecological, and epidemiological investigations, and a solid foundation for biotechnological outcomes, including new anthelmintics, vaccines and diagnostic tests. This first draft genome of any strongylid nematode paves the way for a rapid acceleration in our understanding of a wide range of socioeconomically important parasites of one of the largest nematode orders.

Published
2013

19. Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum

Author

Corsi, Giulia I., Tichkule, Swapnil, Sannella, Anna Rosa, Vatta, Paolo, Asnicar, Francesco, Segata, Nicola, Jex, Aaron R., van Oosterhout, Cock, Cacciò, Simone M., Corsi, Giulia I., Tichkule, Swapnil, Sannella, Anna Rosa, Vatta, Paolo, Asnicar, Francesco, Segata, Nicola, Jex, Aaron R., van Oosterhout, Cock, and Cacciò, Simone M.

Abstract

Cryptosporidium parvum is a globally distributed zoonotic pathogen and a major cause of diarrhoeal disease in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human- and ruminant-derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and most are probably recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long-term evolutionary consequences of these events. Our results suggest that increased globalization and close human-animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host–parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.

Published
2023

23. A communal catalogue reveals Earths multiscale microbial diversity

Author

Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vzquez-Baeza, Yoshiki, Gonzlez, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Martinez, L. Margarita, Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, OBrien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia

Subjects
Observations, Environmental aspects, Biodiversity -- Observations -- Environmental aspects, Microbial colonies -- Environmental aspects, Biological diversity -- Observations -- Environmental aspects
Abstract

Author(s): Luke R. Thompson [1, 2, 3]; Jon G. Sanders [1]; Daniel McDonald [1]; Amnon Amir [1]; Joshua Ladau [4]; Kenneth J. Locey [5]; Robert J. Prill [6]; Anupriya Tripathi [...], Our growing awareness of the microbial worlds importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earths microbial diversity.

Published
2017
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27. Recent advances in candidate-gene and whole-genome approaches to the discovery of anthelmintic resistance markers and the description of drug/receptor interactions

Author

Kotze, Andrew C., Hunt, Peter W., Skuce, Philip, von Samson-Himmelstjerna, Georg, Martin, Richard J., Sager, Heinz, Krücken, Jürgen, Hodgkinson, Jane, Lespine, Anne, Jex, Aaron R., Gilleard, John S., Beech, Robin N., Wolstenholme, Adrian J., Demeler, Janina, Robertson, Alan P., Charvet, Claude L., Neveu, Cedric, Kaminsky, Ronald, Rufener, Lucien, Alberich, Melanie, Menez, Cecile, and Prichard, Roger K.

Published
2014
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32. VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses

Author

Tichkule, Swapnil, primary, Myung, Yoochan, additional, Naung, Myo T, additional, Ansell, Brendan R E, additional, Guy, Andrew J, additional, Srivastava, Namrata, additional, Mehra, Somya, additional, Cacciò, Simone M, additional, Mueller, Ivo, additional, Barry, Alyssa E, additional, van Oosterhout, Cock, additional, Pope, Bernard, additional, Ascher, David B, additional, and Jex, Aaron R, additional

Published
2022
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