scholarly journals Phylogenetic analysis of Trichostrongylus vitrinus isolates from southwest Iran

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Mohammad Amin Ghatee ◽  
Seyed Ali Asghar Malek Hosseini ◽  
Masoud Marashifard ◽  
Mehdi Karamian ◽  
Walter Robert Taylor ◽  
...  

Abstract Background Trichostrongylus is one of the most important zoonotic trichostrongylid nematodes, infecting mostly livestock. Data on its genetic characteristics are lacking in Iran. Methods We determined the phylogenetic relationships of Trichostrongylus species in three counties of Kohgiloyeh and Boyerahmad (K-B) province, southwest Iran. Small intestine and abomasum of 70 sheep and goats were investigated. Results A total of 35 isolates of Trichostrongylus worms were detected and all were genetically identified as Trichostrongylus vitrinus. Analysis of 321 bp of the internal transcribed spacer 2 (ITS2) of ribosomal DNA revealed 16 genotypes. All genotypes were single nucleotide polymorphisms, including some hypervariable points. All sequences were trimmed to 170 bp, compared with sequences on GenBank including short sequences from other endemic foci of Iran and other countries and all isolates were used to generate a maximum likelihood phylogenetic tree, which consisted of two clades A and B. Clade A included isolates from Iran, Russia, New Zealand, Australia and the UK; clade B only contained South African isolates. Most clade A isolates (north, southwest and west Iran, Russia, New Zealand, Australia and UK) were in a similar phylogenetic position. One subclade was detected in clade A (isolates from Southwest Iran, New Zealand and UK). Conclusions We hypothesize that drug resistant T. vitrinus may account for its exclusive detection in our samples. The high similarity of genotypes from Iran, New Zealand and UK may be due to their close political relationships during the colonial era. More research is needed to understand better the phylogeny of T. vitrinus and its relationship with drug resistance and human transmission.

Itinerario ◽  
2014 ◽  
Vol 38 (3) ◽  
pp. 45-58
Author(s):  
John Connor

On the outbreak of war, men from the Dominions were scattered across the British Empire. As each Dominion began recruiting their expeditionary forces at home, the issue arose whether these expatriates, especially those resident in the United Kingdom, should join the British Army or be able to enlist in their Dominion's force. Canada and New Zealand allowed recruiting for the CEF and NZEF in the UK. Many Anglophone White South Africans joined a “colonial” battalion of the Royal Fusiliers. The Australian Government refused to allow Australians in the UK to join the AIF, despite the repeated requests of the Australian expatriate community. This paper examines the questions of British and sub-Imperial Dominion identities as well as the practical policy considerations raised by this issue. It argues that there is some evidence of nascent Dominion nationalism—the Canadian High Commission in London issued what became known as “a Certificate of Canadian Citizenship” to expatriates— but that Dominion Governments generally based their decisions on this issue based on cost and domestic political considerations.


2022 ◽  
Author(s):  
◽  
Lydia Whiting

<p><b>This thesis examines the nascent, early twentieth-century New Zealand histories created by James Cowan (1870-1943), Edith Statham (1853-1951), and Horatio Gordon Robley (1840-1930). It asks how their histories of the colonial past were shaped by their own experiences and by the contexts of the period c.1863-1940. In the early twentieth-century Cowan was a journalist, best known for his publication The New Zealand Wars (1922-23). Statham was an active volunteer in the Victoria League and then a government employee, dedicated to the work of refurbishing old soldier graves. Robley was a veteran of the New Zealand Wars residing in London, known for his ethnographic collecting, publications and artwork. This thesis considers how their work converged in efforts to preserve and narrate New Zealand’s colonial history.</b></p> <p>The discussion charts the lives and careers of these three history-makers through their publications, correspondence, manuscripts, reports and newspaper reports. It begins by situating each of the history-makers within the colonial era, considering their proximity to the events they would come to memorialise. The discussion then traces the three history-makers as they stepped into the new century, their work sitting within the tensions of belonging in New Zealand at this time. What they conveyed was both a sense of a belonging to a particular geographical and cultural locale, along with a strong allegiance to empire in wake of the Anglo-South African War and the death of Queen Victoria. The discussion then considers the era when all three focused in on the conflicts of the colonial period, beginning with Statham’s soldier grave work from 1910 and ending with Cowan’s publication of The New Zealand Wars in 1923. Funding this converging work was the New Zealand government. Preserving and narrating the history had gained public and political support, partly due to the sense of urgency that the generation who had fought in the wars was fast disappearing. The degree to which this historical work was considered valuable was underscored by both government funding and public interest at the same time as the country was facing a costly and confronting world war. The discussion then traverses their attempts to continue their historical work after 1923 and in the lead up to the 1940 centenary celebrations, a period when new forms of cultural belonging and modern scholarship moved away from those that had emboldened the work of Cowan, Statham and Robley decades earlier.</p> <p>The nascent histories of Cowan, Statham and Robley represent a powerful and perplexing moment in the formation of New Zealand. They each narrated histories and public memories of and for ‘New Zealand’ in a particular context, one marked by both an intense attention to the local and a powerful imperial loyalty. Statham, having pursued a sense of progressive female citizenship in Dunedin, took up the commemoration of men who had died for empire as an extension of her public work. In doing so, Statham embodied the dichotomy of belonging in New Zealand. Cowan’s candidacy for writing an official New Zealand War history was due to his proximity to those informants who were still alive at the end of the Great War. Cowan hoped to cultivate a habit of remembering actors and events of New Zealand’s colonial past, but by rendering past conflict as resolved in the present, he only enabled the lapse into forgetting thereafter. Despite his London locale, Robley was intimately tied to New Zealand activities and aspirations over a span of 30 years. Robley was both an actor in the colonial past and a creator of its historical renderings, demonstrating that these nascent New Zealand histories were not just produced in New Zealand.</p>


2022 ◽  
Author(s):  
◽  
Lydia Whiting

<p><b>This thesis examines the nascent, early twentieth-century New Zealand histories created by James Cowan (1870-1943), Edith Statham (1853-1951), and Horatio Gordon Robley (1840-1930). It asks how their histories of the colonial past were shaped by their own experiences and by the contexts of the period c.1863-1940. In the early twentieth-century Cowan was a journalist, best known for his publication The New Zealand Wars (1922-23). Statham was an active volunteer in the Victoria League and then a government employee, dedicated to the work of refurbishing old soldier graves. Robley was a veteran of the New Zealand Wars residing in London, known for his ethnographic collecting, publications and artwork. This thesis considers how their work converged in efforts to preserve and narrate New Zealand’s colonial history.</b></p> <p>The discussion charts the lives and careers of these three history-makers through their publications, correspondence, manuscripts, reports and newspaper reports. It begins by situating each of the history-makers within the colonial era, considering their proximity to the events they would come to memorialise. The discussion then traces the three history-makers as they stepped into the new century, their work sitting within the tensions of belonging in New Zealand at this time. What they conveyed was both a sense of a belonging to a particular geographical and cultural locale, along with a strong allegiance to empire in wake of the Anglo-South African War and the death of Queen Victoria. The discussion then considers the era when all three focused in on the conflicts of the colonial period, beginning with Statham’s soldier grave work from 1910 and ending with Cowan’s publication of The New Zealand Wars in 1923. Funding this converging work was the New Zealand government. Preserving and narrating the history had gained public and political support, partly due to the sense of urgency that the generation who had fought in the wars was fast disappearing. The degree to which this historical work was considered valuable was underscored by both government funding and public interest at the same time as the country was facing a costly and confronting world war. The discussion then traverses their attempts to continue their historical work after 1923 and in the lead up to the 1940 centenary celebrations, a period when new forms of cultural belonging and modern scholarship moved away from those that had emboldened the work of Cowan, Statham and Robley decades earlier.</p> <p>The nascent histories of Cowan, Statham and Robley represent a powerful and perplexing moment in the formation of New Zealand. They each narrated histories and public memories of and for ‘New Zealand’ in a particular context, one marked by both an intense attention to the local and a powerful imperial loyalty. Statham, having pursued a sense of progressive female citizenship in Dunedin, took up the commemoration of men who had died for empire as an extension of her public work. In doing so, Statham embodied the dichotomy of belonging in New Zealand. Cowan’s candidacy for writing an official New Zealand War history was due to his proximity to those informants who were still alive at the end of the Great War. Cowan hoped to cultivate a habit of remembering actors and events of New Zealand’s colonial past, but by rendering past conflict as resolved in the present, he only enabled the lapse into forgetting thereafter. Despite his London locale, Robley was intimately tied to New Zealand activities and aspirations over a span of 30 years. Robley was both an actor in the colonial past and a creator of its historical renderings, demonstrating that these nascent New Zealand histories were not just produced in New Zealand.</p>


2015 ◽  
Vol 59 (4) ◽  
pp. 66-82
Author(s):  
Christiaan Beyers

In the context of transitional justice, how does the reinvented state come to be assumed as a social fact? South African land restitution interpellates victims of apartheid- and colonial-era forced removals as claimants, moral and legal subjects of a virtuous 'new' state. In the emotional narratives of loss and suffering called forth in land claim forms, the state is addressed as a subject capable of moral engagement. Claim forms also 'capture' affects related to the event of forced removals as an unstable political resource. However, within an ultimately legal and bureaucratic process, the desire for recognition is typically not reciprocated. Moreover, material settlements are indefinitely delayed due to political and institutional complications. The resulting disillusionment is counterweighed by persistent aspirations for state redress.


Author(s):  
Julian W. Tang ◽  
Oliver T.R. Toovey ◽  
Kirsty N. Harvey ◽  
David D.S. Hui
Keyword(s):  

Author(s):  
Simon F Lashmar ◽  
Donagh P Berry ◽  
Rian Pierneef ◽  
Farai C Muchadeyi ◽  
Carina Visser

Abstract A major obstacle in applying genomic selection (GS) to uniquely adapted local breeds in less-developed countries has been the cost of genotyping at high densities of single nucleotide polymorphisms (SNP). Cost reduction can be achieved by imputing genotypes from lower to higher densities. Locally adapted breeds tend to be admixed and exhibit a high degree of genomic heterogeneity thus necessitating the optimization of SNP selection for downstream imputation. The aim of this study was to quantify the achievable imputation accuracy for a sample of 1,135 South African (SA) Drakensberger using several custom-derived lower-density panels varying in both SNP density and how the SNP were selected. From a pool of 120,608 genotyped SNP, subsets of SNP were chosen 1) at random, 2) with even genomic dispersion, 3) by maximizing the mean minor allele frequency (MAF), 4) using a combined score of MAF and linkage disequilibrium (LD), 5) using a partitioning-around-medoids (PAM) algorithm, and finally 6) using a hierarchical LD-based clustering algorithm. Imputation accuracy to higher density improved as SNP density increased; animal-wise imputation accuracy defined as the within-animal correlation between the imputed and actual alleles ranged from 0.625 to 0.990 when 2,500 randomly selected SNP were chosen versus a range of 0.918 to 0.999 when 50,000 randomly selected SNP were used. At a panel density of 10,000 SNP, the mean (standard deviation) animal-wise allele concordance rate was 0.976 (0.018) versus 0.982 (0.014) when the worst (i.e., random) as opposed to the best (i.e., combination of MAF and LD) SNP selection strategy was employed. A difference of 0.071 units was observed between the mean correlation-based accuracy of imputed SNP categorized as low (0.01&lt;MAF≤0.1) versus high MAF (0.4&lt;MAF≤0.5). Greater mean imputation accuracy was achieved for SNP located on autosomal extremes when these regions were populated with more SNP. The presented results suggested that genotype imputation can be a practical cost-saving strategy for indigenous breeds such as the South African Drakensberger. Based on the results, a genotyping panel consisting of approximately 10,000 SNP selected based on a combination of MAF and LD would suffice in achieving a less than 3% imputation error rate for a breed characterized by genomic admixture on the condition that these SNP are selected based on breed-specific selection criteria.


Biomedicines ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 808
Author(s):  
Laura Pérez-Lago ◽  
Teresa Aldámiz-Echevarría ◽  
Rita García-Martínez ◽  
Leire Pérez-Latorre ◽  
Marta Herranz ◽  
...  

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13–15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1–2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.


2021 ◽  
Vol 22 (4) ◽  
pp. 1695
Author(s):  
Bruno O. Villoutreix ◽  
Vincent Calvez ◽  
Anne-Geneviève Marcelin ◽  
Abdel-Majid Khatib

SARS-CoV-2 exploits angiotensin-converting enzyme 2 (ACE2) as a receptor to invade cells. It has been reported that the UK and South African strains may have higher transmission capabilities, eventually in part due to amino acid substitutions on the SARS-CoV-2 Spike protein. The pathogenicity seems modified but is still under investigation. Here we used the experimental structure of the Spike RBD domain co-crystallized with part of the ACE2 receptor, several in silico methods and numerous experimental data reported recently to analyze the possible impacts of three amino acid replacements (Spike K417N, E484K, N501Y) with regard to ACE2 binding. We found that the N501Y replacement in this region of the interface (present in both the UK and South African strains) should be favorable for the interaction with ACE2, while the K417N and E484K substitutions (South African strain) would seem neutral or even unfavorable. It is unclear if the N501Y substitution in the South African strain could counterbalance the K417N and E484K Spike replacements with regard to ACE2 binding. Our finding suggests that the UK strain should have higher affinity toward ACE2 and therefore likely increased transmissibility and possibly pathogenicity. If indeed the South African strain has a high transmission level, this could be due to the N501Y replacement and/or to substitutions in regions located outside the direct Spike–ACE2 interface but not so much to the K417N and E484K replacements. Yet, it should be noted that amino acid changes at Spike position 484 can lead to viral escape from neutralizing antibodies. Further, these amino acid substitutions do not seem to induce major structural changes in this region of the Spike protein. This structure–function study allows us to rationalize some observations made for the UK strain but raises questions for the South African strain.


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