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Article: Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes

Sloan, S / Jenvey, C. J / Piedrafita, D / Preston, S / Stear, M. J

BMC biotechnology. 2021 Dec., v. 21, no. 1

2021

Abstract: BACKGROUND: The purpose of this study was to develop a reliable DNA extraction protocol to use on individual Teladorsagia circumcincta nematode specimens to produce high quality DNA for genome sequencing and phylogenetic analysis. Pooled samples have ... ...

Abstract	BACKGROUND: The purpose of this study was to develop a reliable DNA extraction protocol to use on individual Teladorsagia circumcincta nematode specimens to produce high quality DNA for genome sequencing and phylogenetic analysis. Pooled samples have been critical in providing the groundwork for T. circumcincta genome construction, but there is currently no standard method for extracting high-quality DNA from individual nematodes. 11 extraction kits were compared based on DNA quality, yield, and processing time. RESULTS: 11 extraction protocols were compared, and the concentration and purity of the extracted DNA was quantified. Median DNA concentration among all methods measured on NanoDrop 2000™ ranged between 0.45–11.5 ng/μL, and on Qubit™ ranged between undetectable – 0.962 ng/μL. Median A260/280 ranged between 0.505–3.925, and median A260/230 ranged − 0.005 – 1.545. Larval exsheathment to remove the nematode cuticle negatively impacted DNA concentration and purity. CONCLUSIONS: A Schistosoma sp. DNA extraction method was determined as most suitable for individual T. circumcincta nematode specimens due to its resulting DNA concentration, purity, and relatively fast processing time.
Keywords	DNA ; Schistosoma ; Teladorsagia circumcincta ; biotechnology ; ecdysis ; genome ; larvae ; phylogeny
Language	English
Dates of publication	2021-12
Size	p. 35.
Publishing place	BioMed Central
Document type	Article
ISSN	1472-6750
DOI	10.1186/s12896-021-00695-6
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes.

Sloan, S / Jenvey, C J / Piedrafita, D / Preston, S / Stear, M J

BMC biotechnology

2021 Volume 21, Issue 1, Page(s) 35

Abstract: Background: The purpose of this study was to develop a reliable DNA extraction protocol to use on individual Teladorsagia circumcincta nematode specimens to produce high quality DNA for genome sequencing and phylogenetic analysis. Pooled samples have ... ...

Abstract	Background: The purpose of this study was to develop a reliable DNA extraction protocol to use on individual Teladorsagia circumcincta nematode specimens to produce high quality DNA for genome sequencing and phylogenetic analysis. Pooled samples have been critical in providing the groundwork for T. circumcincta genome construction, but there is currently no standard method for extracting high-quality DNA from individual nematodes. 11 extraction kits were compared based on DNA quality, yield, and processing time. Results: 11 extraction protocols were compared, and the concentration and purity of the extracted DNA was quantified. Median DNA concentration among all methods measured on NanoDrop 2000™ ranged between 0.45-11.5 ng/μL, and on Qubit™ ranged between undetectable - 0.962 ng/μL. Median A260/280 ranged between 0.505-3.925, and median A260/230 ranged - 0.005 - 1.545. Larval exsheathment to remove the nematode cuticle negatively impacted DNA concentration and purity. Conclusions: A Schistosoma sp. DNA extraction method was determined as most suitable for individual T. circumcincta nematode specimens due to its resulting DNA concentration, purity, and relatively fast processing time.
MeSH term(s)	Animals ; DNA, Helminth/genetics ; DNA, Helminth/isolation & purification ; Feces ; Genetic Techniques ; Phylogeny ; Sequence Analysis, DNA ; Sheep ; Sheep Diseases/parasitology ; Strongylida/classification ; Strongylida/genetics ; Strongylida/isolation & purification ; Strongylida Infections/parasitology ; Strongylida Infections/veterinary
Chemical Substances	DNA, Helminth
Language	English
Publishing date	2021-05-17
Publishing country	England
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1472-6750
ISSN (online)	1472-6750
DOI	10.1186/s12896-021-00695-6
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Article: Quantification of behavioural variation among sheep grazing on pasture using accelerometer sensors

Almasi, F. / Nguyen, H. / Heydarian, D. / Sohi, R. / Nikbin, S. / Jenvey, C. J. / Halliwell, E. / Ponnampalam, E. N. / Desai, A. / Jois, M. / Stear, M. J.

Animal production science. 2022, v. 62, no. 15

2022

Abstract: Context Monitoring the behaviour of animals can provide early warning signs of disease or indicate loss of appetite. Also, an understanding of the variation in behaviours among animals and their distributions is essential for meaningful statistical ... ...

Abstract	Context Monitoring the behaviour of animals can provide early warning signs of disease or indicate loss of appetite. Also, an understanding of the variation in behaviours among animals and their distributions is essential for meaningful statistical inference. Therefore, quantifying the variation of behaviours is of both biological and statistical interest. Aim The objectives of this study were to determine the distributions and quantify the variation among animals with respect to the times spent grazing, ruminating, idling, walking, and licking. Methods The activities of 147 (male=67, female=80) Merino lambs at 10–11months of age on a commercial farm in Edenhope, Victoria, Australia were recorded for 26days, using ActiGraph accelerometer sensors attached to the left side of the sheep’s muzzle. The male and female sheep were kept in separate paddocks. A Support Vector Machine algorithm was used to differentiate sheep behaviour into six categories: grazing, ruminating, idling, walking, licking, and other activities. The distributions of behaviours were analysed using energy statistics-based tests and Generalised Additive Models for Location, Scale, and Shape (GAMLSS). Different distributions were compared using Akaike Information Criterion (AIC) values. Key results Among the distributions that were considered, we found that times spent ruminating in both male and female sheep populations as well as idling in male sheep were best described by the skew exponential type 2 distribution. Grazing, walking and licking behaviours were best described by the Box–Cox t distribution. The distribution of time spent grazing was symmetrical and unimodal in males, and adequately modelled by a normal distribution, but the distribution in females had a prominent left skew. Also, we found that females typically grazed for a longer time than males. However, males spent more time ruminating than grazing. Conclusions The time spent by the animal in each activity varied during the day. Within each population, the variation among animals in the time spent grazing was best described by a Box–Cox t distribution. Implications This study has enhanced our understanding of grazing behaviour and will facilitate more appropriate analyses of the causes of variation among animals in grazing behaviour.
Keywords	Merino ; accelerometers ; actigraphy ; animal production ; anorexia ; commercial farms ; energy ; females ; males ; normal distribution ; pastures ; sheep ; statistical inference ; support vector machines ; Australia
Language	English
Size	p. 1527-1538.
Publishing place	CSIRO Publishing
Document type	Article
ZDB-ID	2472524-9
ISSN	1836-5787 ; 1836-0939
ISSN (online)	1836-5787
ISSN	1836-0939
DOI	10.1071/AN21464
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Article ; Online: Immunoglobulins as Biomarkers for Gastrointestinal Nematodes Resistance in Small Ruminants: A systematic review.

Aboshady, H M / Stear, M J / Johansson, A / Jonas, E / Bambou, J C

Scientific reports

2020 Volume 10, Issue 1, Page(s) 7765

Abstract: The rise of anthelmintic resistance worldwide has led to the development of alternative control strategies for gastrointestinal nematodes (GIN) infections, which are one of the main constraints on the health of grazing small ruminants. Presently, ... ...

Abstract	The rise of anthelmintic resistance worldwide has led to the development of alternative control strategies for gastrointestinal nematodes (GIN) infections, which are one of the main constraints on the health of grazing small ruminants. Presently, breeding schemes rely mainly on fecal egg count (FEC) measurements on infected animals which are time-consuming and requires expertise in parasitology. Identifying and understanding the role of immunoglobulins in the mechanisms of resistance could provide a more efficient and sustainable method of identifying nematode-resistant animals for selection. In this study we review the findings on immunoglobulin response to GIN in the literature published to date (june 2019) and discuss the potential to use immunoglobulins as biomarkers. The literature review revealed 41 studies which measured at least one immunoglobulin: 35 focused on lamb immune response (18 used non-naïve lambs) and 7 on yearlings. In this review we propose a conceptual model summarizing the role of immunoglobulins in resistance to GIN. We highlight the need for more carefully designed and documented studies to allow comparisons across different populations on the immunoglobulin response to GIN infection.
MeSH term(s)	Animals ; Biomarkers ; Disease Resistance/immunology ; Gastrointestinal Diseases/immunology ; Gastrointestinal Diseases/parasitology ; Goats ; Immunoglobulin Isotypes/immunology ; Immunoglobulins/immunology ; Nematode Infections/immunology ; Nematode Infections/parasitology ; Ruminants ; Sheep
Chemical Substances	Biomarkers ; Immunoglobulin Isotypes ; Immunoglobulins
Language	English
Publishing date	2020-05-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-64775-x
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Article ; Online: Differences between female and castrated male lambs in susceptibility to natural, predominantly Teladorsagia circumcincta infection.

Abuargob, O / Stear, M J

Veterinary parasitology

2014 Volume 205, Issue 3-4, Page(s) 588–594

Abstract: The difference between castrated male lambs and entire female lambs in susceptibility to gastrointestinal nematode infection was investigated in a flock of Scottish Blackface sheep. Castrated male lambs had higher faecal egg counts, higher body weights, ... ...

Abstract	The difference between castrated male lambs and entire female lambs in susceptibility to gastrointestinal nematode infection was investigated in a flock of Scottish Blackface sheep. Castrated male lambs had higher faecal egg counts, higher body weights, lower parasite-specific plasma IgA activity and more adult nematodes. There were no detectable differences in the length of adult Teladorsagia circumcincta. Heavier egg shedding by males was associated with greater worm burdens. The difference in plasma IgA activity may have been a consequence of larger numbers of adult nematodes inhibiting the transfer of mucosal IgA to the plasma. At least part of the sex difference in egg production could be a consequence of males ingesting larger amounts of grass and hence numbers of infective larvae because of their larger size. The differences between castrated males and females contribute to the observed variation in nematode egg production in naturally infected lambs.
MeSH term(s)	Animals ; Disease Susceptibility ; Feces/parasitology ; Female ; Gastrointestinal Diseases/epidemiology ; Gastrointestinal Diseases/parasitology ; Gastrointestinal Diseases/veterinary ; Immunoglobulin A/blood ; Male ; Parasite Egg Count/veterinary ; Sex Factors ; Sheep ; Sheep Diseases/epidemiology ; Sheep Diseases/immunology ; Sheep Diseases/parasitology ; Trichostrongyloidea/immunology ; Trichostrongyloidea/isolation & purification ; Trichostrongyloidiasis/epidemiology ; Trichostrongyloidiasis/parasitology ; Trichostrongyloidiasis/veterinary
Chemical Substances	Immunoglobulin A
Language	English
Publishing date	2014-09-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	196831-2
ISSN	1873-2550 ; 0304-4017
ISSN (online)	1873-2550
ISSN	0304-4017
DOI	10.1016/j.vetpar.2014.08.024
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Article: Bioinformatic analysis of eosinophil activity and its implications for model and target species

Jenvey, C.J / Alenizi, D / Almasi, F / Cairns, C / Holmes, A / Sloan, S / Stear, M.J

Parasitology. 2020 Apr., v. 147, no. 4

2020

Abstract: Eosinophils are important immune cells that have been implicated in resistance to gastrointestinal nematode (GIN) infections in both naturally and experimentally infected sheep. Proteins of particular importance appear to be IgA-Fc alpha receptor (FcαRI), ...

Abstract	Eosinophils are important immune cells that have been implicated in resistance to gastrointestinal nematode (GIN) infections in both naturally and experimentally infected sheep. Proteins of particular importance appear to be IgA-Fc alpha receptor (FcαRI), C-C chemokine receptor type 3 (CCR3), proteoglycan 3 (PRG3, major basic protein 2) and EPX (eosinophil peroxidase). We used known human nucleotide sequences to search the ruminant genomes, followed by translation to protein and sequence alignments to visualize differences between sequences and species. Where a sequence was retrieved for cow, but not for sheep and goat, this was used additionally as a reference sequence. In this review, we show that eosinophil function varies among host species. Consequently, investigations into the mechanisms of ruminant immune responses to GIN should be conducted using the natural host. Specifically, we address differences in protein sequence and structure for eosinophil proteins.
Keywords	CCR3 receptor ; amino acid sequences ; bioinformatics ; cows ; eosinophils ; gastrointestinal nematodes ; genome ; goats ; hosts ; humans ; immune response ; models ; nucleotide sequences ; peroxidase ; proteoglycans ; sequence alignment ; sheep ; translation (genetics)
Language	English
Dates of publication	2020-04
Size	p. 393-400.
Publishing place	Cambridge University Press
Document type	Article
ZDB-ID	207627-5
ISSN	1469-8161 ; 0031-1820
ISSN (online)	1469-8161
ISSN	0031-1820
DOI	10.1017/S0031182019001768
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Article ; Online: Efficacy of treatment of cattle for liver fluke at housing: influence of differences in flukicidal activity against juvenile Fasciola hepatica.

Forbes, A B / Reddick, D / Stear, M J

The Veterinary record

2015 Volume 176, Issue 13, Page(s) 333

Abstract: Flukicides are commonly administered at housing to cattle that have grazed fluke-infected pastures or that have been purchased from endemic areas. The choice of product is determined by numerous factors, one of which is the stages of Fasciola hepatica ... ...

Abstract	Flukicides are commonly administered at housing to cattle that have grazed fluke-infected pastures or that have been purchased from endemic areas. The choice of product is determined by numerous factors, one of which is the stages of Fasciola hepatica that are killed. Flukicides can be categorised into three main groups: (A) those that kill all juvenile stages and adults; (B) those that kill juveniles from six to eight weeks of age and adults and (C) those that kill adults only. This study was conducted on a commercial beef farm in Scotland and was designed to compare the efficacy of flukicides from each of these three classes in terms of their effects on faecal egg output, coproantigen and liveweight gain. The majority of animals in the untreated control group were positive for coproantigen, fluke eggs or both throughout the study duration of 16 weeks. Egg reappearance interval following housing treatment was eight weeks for clorsulon and 13 weeks for nitroxynil, though patent infections in both groups developed in only a small minority of animals; no fluke eggs were recovered from cattle treated with triclabendazole. Coproantigen was detected four weeks before the reappearance of fluke eggs in the dung. Animals treated with flukicides had significantly fewer faecal samples positive for eggs (P<0.006) and coproantigen (P<0.05) following treatment compared with the controls. Despite differences in the efficacy profiles among the flukicide-treated groups, there were no significant differences (P>0.05) in growth rates among any of the four treatment groups. There was, however, a significant negative association (P<0.001) between fluke positivity at housing and subsequent growth performance, irrespective of treatment group.
MeSH term(s)	Animals ; Anthelmintics/pharmacology ; Anthelmintics/therapeutic use ; Cattle ; Cattle Diseases/drug therapy ; Fasciola hepatica/drug effects ; Fasciola hepatica/growth & development ; Fascioliasis/drug therapy ; Fascioliasis/veterinary ; Feces/parasitology ; Housing, Animal ; Parasite Egg Count/veterinary ; Treatment Outcome
Chemical Substances	Anthelmintics
Language	English
Publishing date	2015-03-28
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial ; Research Support, Non-U.S. Gov't
ZDB-ID	390015-0
ISSN	2042-7670 ; 0042-4900
ISSN (online)	2042-7670
ISSN	0042-4900
DOI	10.1136/vr.102720
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Article ; Online: Combatting African Animal Trypanosomiasis (AAT) in livestock: The potential role of trypanotolerance.

Yaro, M / Munyard, K A / Stear, M J / Groth, D M

Veterinary parasitology

2016 Volume 225, Page(s) 43–52

Abstract: African Animal Trypanosomiasis (AAT) is endemic in at least 37 of the 54 countries in Africa. It is estimated to cause direct and indirect losses to the livestock production industry in excess of US$ 4.5 billion per annum. A century of intervention has ... ...

Abstract	African Animal Trypanosomiasis (AAT) is endemic in at least 37 of the 54 countries in Africa. It is estimated to cause direct and indirect losses to the livestock production industry in excess of US$ 4.5 billion per annum. A century of intervention has yielded limited success, owing largely to the extraordinary complexity of the host-parasite interaction. Trypanotolerance, which refers to the inherent ability of some African livestock breeds, notably Djallonke sheep, N'Dama cattle and West African Dwarf goats, to withstand a trypanosomiasis challenge and still remain productive without any form of therapy, is an economically sustainable option for combatting this disease. Yet trypanotolerance has not been adequately exploited in the fight against AAT. In this review, we describe new insights into the genetic basis of trypanotolerance and discuss the potential of exploring this phenomenon as an integral part of the solution for AAT, particularly, in the context of African animal production systems.
MeSH term(s)	Africa ; Animal Husbandry ; Animals ; Breeding ; Disease Resistance/genetics ; Livestock/parasitology ; Trypanosomiasis, African/genetics ; Trypanosomiasis, African/veterinary
Language	English
Publishing date	2016-07-30
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	196831-2
ISSN	1873-2550 ; 0304-4017
ISSN (online)	1873-2550
ISSN	0304-4017
DOI	10.1016/j.vetpar.2016.05.003
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Article ; Online: Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment.

Yaro, M / Munyard, K A / Morgan, E / Allcock, R J N / Stear, M J / Groth, D M

BMC genomics

2019 Volume 20, Issue 1, Page(s) 816

Abstract: Background: The Djallonke sheep is well adapted to harsh environmental conditions, and is relatively resistant to Haemonchosis and resilient to animal trypanosomiasis. The larger Sahelian sheep, which cohabit the same region, is less well adapted to ... ...

Abstract	Background: The Djallonke sheep is well adapted to harsh environmental conditions, and is relatively resistant to Haemonchosis and resilient to animal trypanosomiasis. The larger Sahelian sheep, which cohabit the same region, is less well adapted to these disease challenges. Haemonchosis and Trypanosomiasis collectively cost the worldwide animal industry billions of dollars in production losses annually. Results: Here, we separately sequenced and then pooled according to breed the genomes from five unrelated individuals from each of the Djallonke and Sahelian sheep breeds (sourced from Ghana), at greater than 22-fold combined coverage for each breed. A total of approximately 404 million (97%) and 343 million (97%) sequence reads from the Djallonke and Sahelian breeds respectively, were successfully mapped to the sheep reference genome Oar v3.1. We identified approximately 11.1 million and 10.9 million single nucleotide polymorphisms (SNPs) in the Djallonke and Sahelian breeds, with approximately 15 and 16% respectively of these not previously reported in sheep. Multiple regions of reduced heterozygosity were also found; 70 co-localised within genomic regions harbouring genes that mediate disease resistance, immune response and adaptation in sheep or cattle. Thirty- three of the regions of reduced heterozygosity co-localised with previously reported genes for resistance to haemonchosis and trypanosomiasis. Conclusions: Our analyses suggest that these regions of reduced heterozygosity may be signatures of selection for these economically important diseases.
MeSH term(s)	Adaptation, Physiological/genetics ; Animals ; Breeding ; Chromosomes, Mammalian/genetics ; Disease Resistance/genetics ; Female ; Genomics ; Heterozygote ; Male ; Polymorphism, Single Nucleotide ; Sheep/genetics ; Sheep/immunology ; Sheep/microbiology ; Sheep/physiology ; Tropical Climate ; Trypanosomiasis/immunology
Language	English
Publishing date	2019-11-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-019-6198-8
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Article ; Online: Bioinformatic analysis of eosinophil activity and its implications for model and target species.

Jenvey, C J / Alenizi, D / Almasi, F / Cairns, C / Holmes, A / Sloan, S / Stear, M J

Parasitology

2019 Volume 147, Issue 4, Page(s) 393–400

Abstract	Eosinophils are important immune cells that have been implicated in resistance to gastrointestinal nematode (GIN) infections in both naturally and experimentally infected sheep. Proteins of particular importance appear to be IgA-Fc alpha receptor (FcαRI), C-C chemokine receptor type 3 (CCR3), proteoglycan 3 (PRG3, major basic protein 2) and EPX (eosinophil peroxidase). We used known human nucleotide sequences to search the ruminant genomes, followed by translation to protein and sequence alignments to visualize differences between sequences and species. Where a sequence was retrieved for cow, but not for sheep and goat, this was used additionally as a reference sequence. In this review, we show that eosinophil function varies among host species. Consequently, investigations into the mechanisms of ruminant immune responses to GIN should be conducted using the natural host. Specifically, we address differences in protein sequence and structure for eosinophil proteins.
MeSH term(s)	Animals ; Cattle ; Cattle Diseases/immunology ; Computational Biology/methods ; Eosinophils/immunology ; Gastrointestinal Diseases/immunology ; Gastrointestinal Diseases/veterinary ; Goat Diseases/immunology ; Goats ; Humans ; Nematode Infections/immunology ; Nematode Infections/veterinary ; Sheep ; Sheep Diseases/immunology ; Sheep, Domestic
Language	English
Publishing date	2019-12-16
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	207627-5
ISSN	1469-8161 ; 0031-1820
ISSN (online)	1469-8161
ISSN	0031-1820
DOI	10.1017/S0031182019001768
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