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Featured researches published by Emily L. Clark.


Protoplasma | 2010

Insect endosymbionts: manipulators of insect herbivore trophic interactions?

Emily L. Clark; Alison J. Karley; Stephen F. Hubbard

Throughout their evolutionary history, insects have formed multiple relationships with bacteria. Although many of these bacteria are pathogenic, with deleterious effects on the fitness of infected insects, there are also numerous examples of symbiotic bacteria that are harmless or even beneficial to their insect host. Symbiotic bacteria that form obligate or facultative associations with insects and that are located intracellularly in the host insect are known as endosymbionts. Endosymbiosis can be a strong driving force for evolution when the acquisition and maintenance of a microorganism by the insect host results in the formation of novel structures or changes in physiology and metabolism. The complex evolutionary dynamics of vertically transmitted symbiotic bacteria have led to distinctive symbiont genome characteristics that have profound effects on the phenotype of the host insect. Symbiotic bacteria are key players in insect–plant interactions influencing many aspects of insect ecology and playing a key role in shaping the diversification of many insect groups. In this review, we discuss the role of endosymbionts in manipulating insect herbivore trophic interactions focussing on their impact on plant utilisation patterns and parasitoid biology.


Proceedings of the National Academy of Sciences of the United States of America | 2015

Population, genetic, and antigenic diversity of the apicomplexan Eimeria tenella and their relevance to vaccine development

Damer P. Blake; Emily L. Clark; Sarah E. Macdonald; Venkatachalam Thenmozhi; Krishnendu Kundu; Rajat Garg; Isa D. Jatau; Simeon Ayoade; Fumiya Kawahara; Abdalgader Moftah; Adam J. Reid; Ayotunde O. Adebambo; Ramón Álvarez Zapata; Arni S.R. Srinivasa Rao; Kumarasamy Thangaraj; P.S. Banerjee; G. Dhinakar-Raj; M. Raman; Fiona M. Tomley

Significance Sixty billion chickens are produced worldwide each year, and all are at risk from Eimeria, parasites that cause coccidiosis. Control relies widely on chemoprophylaxis, but pressure to reduce drug use in farming urges development of cost-effective vaccines. Antigens such as apical membrane antigen 1 (AMA1) offer promise as anticoccidial vaccine candidates, but experience with related apicomplexans such as Plasmodium, in which pre-existing antigenic diversity and incompatible population structure have undermined vaccine development, tempers confidence. Parasite genotyping identified enormous region-specific variation in haplotype diversity for Eimeria tenella but a contrastingly low level of polymorphism for EtAMA1. Although high levels of polyclonal Eimeria infection and hybridization indicate an ability to disseminate vaccine resistance rapidly, the low level of EtAMA1 diversity promotes vaccine development. The phylum Apicomplexa includes serious pathogens of humans and animals. Understanding the distribution and population structure of these protozoan parasites is of fundamental importance to explain disease epidemiology and develop sustainable controls. Predicting the likely efficacy and longevity of subunit vaccines in field populations relies on knowledge of relevant preexisting antigenic diversity, population structure, the likelihood of coinfection by genetically distinct strains, and the efficiency of cross-fertilization. All four of these factors have been investigated for Plasmodium species parasites, revealing both clonal and panmictic population structures with exceptional polymorphism associated with immunoprotective antigens such as apical membrane antigen 1 (AMA1). For the coccidian Toxoplasma gondii only genomic diversity and population structure have been defined in depth so far; for the closely related Eimeria species, all four variables are currently unknown. Using Eimeria tenella, a major cause of the enteric disease coccidiosis, which exerts a profound effect on chicken productivity and welfare, we determined population structure, genotype distribution, and likelihood of cross-fertilization during coinfection and also investigated the extent of naturally occurring antigenic diversity for the E. tenella AMA1 homolog. Using genome-wide Sequenom SNP-based haplotyping, targeted sequencing, and single-cell genotyping, we show that in this coccidian the functionality of EtAMA1 appears to outweigh immune evasion. This result is in direct contrast to the situation in Plasmodium and most likely is underpinned by the biology of the direct and acute coccidian life cycle in the definitive host.


Veterinary Parasitology | 2014

An optimised protocol for molecular identification of Eimeria from chickens

Saroj Kumar; Rajat Garg; Abdalgader Moftah; Emily L. Clark; Sarah E. Macdonald; Abdul Chaudhry; Olivier Sparagano; P.S. Banerjee; Krishnendu Kundu; Fiona M. Tomley; Damer P. Blake

Molecular approaches supporting identification of Eimeria parasites infecting chickens have been available for more than 20 years, although they have largely failed to replace traditional measures such as microscopy and pathology. Limitations of microscopy-led diagnostics, including a requirement for specialist parasitological expertise and low sample throughput, are yet to be outweighed by the difficulties associated with accessing genomic DNA from environmental Eimeria samples. A key step towards the use of Eimeria species-specific PCR as a sensitive and reproducible discriminatory tool for use in the field is the production of a standardised protocol that includes sample collection and DNA template preparation, as well as primer selection from the numerous PCR assays now published. Such a protocol will facilitate development of valuable epidemiological datasets which may be easily compared between studies and laboratories. The outcome of an optimisation process undertaken in laboratories in India and the UK is described here, identifying four steps. First, samples were collected into a 2% (w/v) potassium dichromate solution. Second, oocysts were enriched by flotation in saturated saline. Third, genomic DNA was extracted using a QIAamp DNA Stool mini kit protocol including a mechanical homogenisation step. Finally, nested PCR was carried out using previously published primers targeting the internal transcribed spacer region 1 (ITS-1). Alternative methods tested included sample processing in the presence of faecal material, DNA extraction using a traditional phenol/chloroform protocol, the use of SCAR multiplex PCR (one tube and two tube versions) and speciation using the morphometric tool COCCIMORPH for the first time with field samples.


Molecular and Biochemical Parasitology | 2012

EmaxDB: Availability of a first draft genome sequence for the apicomplexan Eimeria maxima.

Damer P. Blake; Halimah Alias; Karen J. Billington; Emily L. Clark; Mohd Noor Mat-Isa; Ahmad Fuad Hilmi Mohamad; Mohd Rashdi Mohd-Amin; Yea Ling Tay; Adrian L. Smith; Fiona M. Tomley; Kiew Lian Wan

Apicomplexan parasites are serious pathogens of animals and man that cause diseases including coccidiosis, malaria and toxoplasmosis. The importance of these parasites has prompted the establishment of genomic resources in support of developing effective control strategies. For the Eimeria species resources have developed most rapidly for the reference Eimeria tenella Houghton strain (http://www.genedb.org/Homepage/Etenella). The value of these resources can be enhanced by comparison with related parasites. The well characterised immunogenicity and genetic diversity associated with Eimeria maxima promote its use in genetics-led studies on coccidiosis and recommended its selection for sequencing. Using a combination of sequencing technologies a first draft assembly and annotation has been produced for an E. maxima Houghton strain-derived clone (EmaxDB; http://www.genomemalaysia.gov.my/emaxdb/). The assembly of a draft genome sequence for E. maxima provides a resource for comparative studies with Eimeria and related parasites as demonstrated here through the identification of genes predicted to encode microneme proteins in E. maxima.


International Journal for Parasitology | 2016

Cryptic Eimeria genotypes are common across the southern but not northern hemisphere

Emily L. Clark; Sarah E. Macdonald; V. Thenmozhi; Krishnendu Kundu; Rajat Garg; Saroj Kumar; Simeon Ayoade; Kimberly Fornace; Isa D. Jatau; Abdalgader Moftah; Matthew J. Nolan; N.R. Sudhakar; Ayotunde O. Adebambo; Idris A. Lawal; Ramón Álvarez Zapata; Joseph A. Awuni; H. David Chapman; Esron D. Karimuribo; Claire M. Mugasa; Boniface Namangala; Jonathan Rushton; Xun Suo; Kumarasamy Thangaraj; Arni S.R. Srinivasa Rao; A. K. Tewari; P.S. Banerjee; G. Dhinakar Raj; M. Raman; Fiona M. Tomley; Damer P. Blake

Graphical abstract


PLOS Genetics | 2017

A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

Emily L. Clark; Stephen J. Bush; Mary E. B. McCulloch; Iseabail L. Farquhar; Rachel Young; Lucas Lefevre; Clare Pridans; Hiu-Gwen Tsang; Chunlei Wu; Cyrus Afrasiabi; Mick Watson; Bruce Whitelaw; Tom C. Freeman; Kim M. Summers; Alan Archibald; David A. Hume

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of ‘guilt by association’ was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.


Environmental Entomology | 2012

How Conserved are the Bacterial Communities Associated with Aphids? A Detailed Assessment of the Brevicoryne brassicae (Hemiptera: Aphididae) Using 16S rDNA

Emily L. Clark; Tim J. Daniell; J. Wishart; Stephen F. Hubbard; Alison J. Karley

ABSTRACT Aphids harbor a community of bacteria that include obligate and facultative endosymbionts belonging to the Enterobacteriaceae along with opportunistic, commensal, or pathogenic bacteria. This study represents the first detailed analysis of the identity and diversity of the bacterial community associated with the cabbage aphid, Brevicoryne brassicae (L.). 16S rDNA sequence analysis revealed that the community of bacteria associated with B. brassicae was diverse, with at least four different bacterial community types detected among aphid lines, collected from widely dispersed sites in Northern Britain. The bacterial sequence types isolated from B. brassicae showed little similarity to any bacterial endosymbionts characterized in insects; instead, they were closely related to freeliving extracellular bacterial species that have been isolated from the aphid gut or that are known to be present in the environment, suggesting that they are opportunistic bacteria transmitted between the aphid gut and the environment. To quantify variation in bacterial community between aphid lines, which was driven largely by differences in the proportions of two dominant bacterial orders, the Pseudomonales and the Enterobacteriales, we developed a novel real-time (Taqman) qPCR assay. By improving our knowledge of aphid microbial ecology, and providing novel molecular tools to examine the presence and function of the microbial community, this study forms the basis of further research to explore the influence of the extracellular bacterial community on aphid fitness, pest status, and susceptibility to control by natural enemies.


PLOS ONE | 2013

Occurrence of Eimeria Species Parasites on Small-Scale Commercial Chicken Farms in Africa and Indication of Economic Profitability

Kimberly Fornace; Emily L. Clark; Sarah E. Macdonald; Boniface Namangala; Esron D. Karimuribo; Joseph A. Awuni; Olaf Thieme; Damer P. Blake; Jonathan Rushton

Small-scale commercial poultry production is emerging as an important form of livestock production in Africa, providing sources of income and animal protein to many poor households, yet the occurrence and impact of coccidiosis on this relatively new production system remains unknown. The primary objective of this study was to examine Eimeria parasite occurrence on small-scale commercial poultry farms in Ghana, Tanzania and Zambia. Additionally, farm economic viability was measured by calculating the farm gross margin and enterprise budget. Using these economic measures as global assessments of farm productivity, encompassing the diversity present in regional husbandry systems with a measure of fundamental local relevance, we investigated the detection of specific Eimeria species as indicators of farm profitability. Faecal samples and data on production parameters were collected from small-scale (less than 2,000 birds per batch) intensive broiler and layer farms in peri-urban Ghana, Tanzania and Zambia. All seven Eimeria species recognised to infect the chicken were detected in each country. Furthermore, two of the three genetic variants (operational taxonomic units) identified previously in Australia have been described outside of Australia for the first time. Detection of the most pathogenic Eimeria species associated with decreased farm profitability and may be considered as an indicator of likely farm performance. While a causal link remains to be demonstrated, the presence of highly pathogenic enteric parasites may pose a threat to profitable, sustainable small-scale poultry enterprises in Africa.


Journal of Biosciences | 2012

Genetic mapping and coccidial parasites: past achievements and future prospects

Emily L. Clark; Damer P. Blake

Coccidial parasites including Cryptosporidium parvum, Cyclospora cayetanensis, Neospora caninum, Toxoplasma gondii and the Eimeria species can cause severe disease of medical and veterinary importance. As many as one-third of the human population may carry T. gondii infection, and Eimeria are thought to cost the global poultry production industry in excess of US


Trends in Parasitology | 2017

Are Eimeria Genetically Diverse, and Does It Matter?

Emily L. Clark; Fiona M. Tomley; Damer P. Blake

2 billion per annum. Despite their significance, effective vaccines are scarce and have been confined to the veterinary field. As sequencing and genotyping technologies continue to develop, genetic mapping remains a valuable tool for the identification of genes that underlie phenotypic traits of interest and the assembly of contiguous genome sequences. For the coccidian, cross-fertilization still requires in vivo infection, a feature of their life cycle which limits the use of genetic mapping strategies. Importantly, the development of population-based approaches has now removed the need to isolate clonal lines for genetic mapping of selectable traits, complementing the classical clone-based techniques. To date, four coccidial species, representing three genera, have been investigated using genetic mapping. In this review we will discuss recent progress with these species and examine the prospects for future initiatives.

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Damer P. Blake

Royal Veterinary College

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Krishnendu Kundu

Indian Veterinary Research Institute

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