Molecular Diagnosis of Koala Retrovirus (KoRV) in South Australian Koalas (Phascolarctos cinereus)

Koala retrovirus, a recent discovery in Australian koalas, is endogenised in 100% of northern koalas but has lower prevalence in southern populations, with lower proviral and viral loads, and an undetermined level of endogenisation. KoRV has been associated with lymphoid neoplasia, e.g., lymphoma. Recent studies have revealed high complexity in southern koala retroviral infections, with a need to clarify what constitutes positive and negative cases. This study aimed to define KoRV infection status in Mount Lofty Ranges koalas in South Australia using RNA-seq and proviral analysis (n = 216). The basis for positivity of KoRV was deemed the presence of central regions of the KoRV genome (gag 2, pol, env 1, and env 2) and based on this, 41% (89/216) koalas were positive, 57% (124/216) negative, and 2% inconclusive. These genes showed higher expression in lymph node tissue from KoRV positive koalas with lymphoma compared with other KoRV positive koalas, which showed lower, fragmented expression. Terminal regions (LTRs, partial gag, and partial env) were present in SA koalas regardless of KoRV status, with almost all (99.5%, 215/216) koalas positive for gag 1 by proviral PCR. Further investigation is needed to understand the differences in KoRV infection in southern koala populations.

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Periodontal disease in free‐ranging koalas ( Phascolarctos cinereus ) from the Mount Lofty Ranges, South Australia, and its association with koala retrovirus infection

Australian Veterinary Journal ◽

10.1111/avj.12919 ◽

2020 ◽

Vol 98 (5) ◽

pp. 200-206 ◽

Cited By ~ 2

Author(s):

RG Butcher ◽

LM Pettett ◽

J Fabijan ◽

E Ebrahimie ◽

M Mohammadi‐Dehcheshmeh ◽

...

Keyword(s):

Periodontal Disease ◽

South Australia ◽

Phascolarctos Cinereus ◽

Retrovirus Infection ◽

Free Ranging ◽

Koala Retrovirus

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Retroviral integrations contribute to elevated host cancer rates during germline invasion

Nature Communications ◽

10.1038/s41467-021-21612-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Gayle K. McEwen ◽

David E. Alquezar-Planas ◽

Anisha Dayaram ◽

Amber Gillett ◽

Rachael Tarlinton ◽

...

Keyword(s):

Endogenous Retroviruses ◽

Mutational Load ◽

Cancer Genes ◽

Phascolarctos Cinereus ◽

Cancer Prevalence ◽

Host Health ◽

Integration Sites ◽

Mammalian Genomes ◽

Retroviral Infections ◽

Koala Retrovirus

AbstractRepeated retroviral infections of vertebrate germlines have made endogenous retroviruses ubiquitous features of mammalian genomes. However, millions of years of evolution obscure many of the immediate repercussions of retroviral endogenisation on host health. Here we examine retroviral endogenisation during its earliest stages in the koala (Phascolarctos cinereus), a species undergoing germline invasion by koala retrovirus (KoRV) and affected by high cancer prevalence. We characterise KoRV integration sites (IS) in tumour and healthy tissues from 10 koalas, detecting 1002 unique IS, with hotspots of integration occurring in the vicinity of known cancer genes. We find that tumours accumulate novel IS, with proximate genes over-represented for cancer associations. We detect dysregulation of genes containing IS and identify a highly-expressed transduced oncogene. Our data provide insights into the tremendous mutational load suffered by the host during active retroviral germline invasion, a process repeatedly experienced and overcome during the evolution of vertebrate lineages.

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Reducing discards in a temperate prawn trawl fishery: a collaborative approach to bycatch research in South Australia

ICES Journal of Marine Science ◽

10.1093/icesjms/fsv147 ◽

2015 ◽

Vol 72 (9) ◽

pp. 2609-2617 ◽

Cited By ~ 4

Author(s):

Daniel Gorman ◽

Cameron Dixon

Keyword(s):

Collaborative Research ◽

Development Process ◽

South Australia ◽

Research Programme ◽

Public Perceptions ◽

Economic Sustainability ◽

Trawl Fishery ◽

Environmental Objectives ◽

Almost All ◽

Logbook Data

Abstract We present the outcomes of a collaborative research programme tasked with reducing bycatch, and thus discards in a temperate Australian prawn trawl fishery. Sea trials in the Gulf of St Vincent, South Australia, assessed the performance of a modified trawlnet that incorporated a rigid polyethylene grid and a T90-mesh codend. Compared with conventional designs, the modified net yielded marked reductions in bycatch (cumulatively >81% by weight), with pronounced decreases in sponge (92%), elasmobranchs (80%), teleost fish (71%), molluscs (61%), and crustaceans (78%). Using commercial logbook data, we estimate that the use of modified nets could reduce discards by ∼240 tons per year. This outcome was achieved with moderate declines in the catch rate (kg h−1) of the target species, Western King Prawn (mean ∼15%), of which almost all were small adults of low commercial value. Adoption of the modified net by industry was realized in March 2012, because it met environmental objectives (i.e. reducing bycatch and improving public perceptions of sustainability), reduced prawn damage, demonstrated commensurate financial returns, and engaged stakeholders throughout the development process. Overall, the project provides a useful example of bycatch research with demonstrable outcomes of improving the ecological and economic sustainability of prawn harvests.

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Using non-invasive sampling methods to determine the prevalence and distribution of Chlamydia pecorum and koala retrovirus in a remnant koala population with conservation importance

Wildlife Research ◽

10.1071/wr17184 ◽

2018 ◽

Vol 45 (4) ◽

pp. 366 ◽

Cited By ~ 1

Author(s):

Faye Wedrowicz ◽

Jennifer Mosse ◽

Wendy Wright ◽

Fiona E. Hogan

Keyword(s):

Native Species ◽

Conservation Strategies ◽

The South ◽

Phascolarctos Cinereus ◽

Urogenital Infection ◽

Non Invasive ◽

Chlamydia Pecorum ◽

Genetic Sampling ◽

Pathogen Prevalence ◽

Koala Retrovirus

Context Pathogenic infections are an important consideration for the conservation of native species, but obtaining such data from wild populations can be expensive and difficult. Two pathogens have been implicated in the decline of some koala (Phascolarctos cinereus) populations: urogenital infection with Chlamydia pecorum and koala retrovirus subgroup A (KoRV-A). Pathogen data for a wild koala population of conservation importance in South Gippsland, Victoria are essentially absent. Aims This study uses non-invasive sampling of koala scats to provide prevalence and genotype data for C. pecorum and KoRV-A in the South Gippsland koala population, and compares pathogen prevalence between wild koalas and koalas in rescue shelters. Methods C. pecorum and KoRV-A provirus were detected by PCR of DNA isolated from scats collected in the field. Pathogen genetic variation was investigated using DNA sequencing of the C. pecorum ompA and KoRV-A env genes. Key results C. pecorum and KoRV-A were detected in 61% and 27% of wild South Gippsland individuals tested, respectively. KoRV-A infection tended to be higher in shelter koalas compared with wild koalas. In contrast with other Victorian koala populations sampled, greater pathogen diversity was present in South Gippsland. Conclusions In the South Gippsland koala population, C. pecorum is widespread and common whereas KoRV appears less prevalent than previously thought. Further work exploring the dynamics of these pathogens in South Gippsland koalas is warranted and may help inform future conservation strategies for this important population. Implications Non-invasive genetic sampling from scats is a powerful method for obtaining data regarding pathogen prevalence and diversity in wildlife. The use of non-invasive methods for the study of pathogens may help fill research gaps in a way that would be difficult or expensive to achieve using traditional methods.

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Residency and movement dynamics of southern rock lobster (Jasus edwardsii) after a translocation event

Marine and Freshwater Research ◽

10.1071/mf13334 ◽

2015 ◽

Vol 66 (7) ◽

pp. 623 ◽

Cited By ~ 2

Author(s):

Adrian Linnane ◽

Shane Penny ◽

Peter Hawthorne ◽

Matthew Hoare

Keyword(s):

Large Scale ◽

South Australia ◽

Rock Lobster ◽

Directed Movement ◽

Translocation Event ◽

South West ◽

Movement Dynamics ◽

Close Proximity ◽

Jasus Edwardsii ◽

Almost All

Previous movement studies on the southern rock lobster (Jasus edwardsii) have all involved releasing tagged animals at the point of capture. In 2007, 5298 lobsters, in total, were tagged and translocated from an offshore site (>100-m depth) to two inshore sites (<20-m depth) in South Australia. After a period of 735 days, 510 (9.6%) had been recaptured. The majority of translocated lobsters were located within close proximity to the release points, with 306 (60%) having moved <5km. Of the remainder, 133 (26%) were recaptured within 5–10km, with a further 71 (14%) individuals having moved >10km. Movement patterns were highly directional in nature, with individuals consistently travelling in a south-west bearing, regardless of distance moved. In almost all cases, movement was from inshore to offshore sites, with female lobsters travelling significantly further (mean 5.66km ±6.41s.d.) than males (mean 5.02km ±9.66s.d.). The results are consistent with previous large-scale tagging studies of J. edwardsii, which indicated high residency levels but with occasional directed movement by some individuals.

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Gene Expression Does Not Support the Developmental Hourglass Model in Three Animals with Spiralian Development

Molecular Biology and Evolution ◽

10.1093/molbev/msz065 ◽

2019 ◽

Vol 36 (7) ◽

pp. 1373-1383 ◽

Cited By ~ 1

Author(s):

Longjun Wu ◽

Kailey E Ferger ◽

J David Lambert

Keyword(s):

Gene Expression ◽

Large Fraction ◽

Molecular Data ◽

Development Stage ◽

Data Sets ◽

Rna Seq ◽

Developmental Evolution ◽

Phylotypic Stage ◽

Hourglass Model ◽

Almost All

Abstract It has been proposed that animals have a pattern of developmental evolution resembling an hourglass because the most conserved development stage—often called the phylotypic stage—is always in midembryonic development. Although the topic has been debated for decades, recent studies using molecular data such as RNA-seq gene expression data sets have largely supported the existence of periods of relative evolutionary conservation in middevelopment, consistent with the phylotypic stage and the hourglass concepts. However, so far this approach has only been applied to a limited number of taxa across the tree of life. Here, using established phylotranscriptomic approaches, we found a surprising reverse hourglass pattern in two molluscs and a polychaete annelid, representatives of the Spiralia, an understudied group that contains a large fraction of metazoan body plan diversity. These results suggest that spiralians have a divergent midembryonic stage, with more conserved early and late development, which is the inverse of the pattern seen in almost all other organisms where these phylotranscriptomic approaches have been reported. We discuss our findings in light of proposed reasons for the phylotypic stage and hourglass model in other systems.

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Fluorescence In Situ Hybridization (FISH) Analysis of the Locations of the Oligonucleotides 5S rDNA, (AGGGTTT)3, and (TTG)6 in Three Genera of Oleaceae and Their Phylogenetic Framework

Genes ◽

10.3390/genes10050375 ◽

2019 ◽

Vol 10 (5) ◽

pp. 375 ◽

Cited By ~ 4

Author(s):

Xiaomei Luo ◽

Juncheng Liu

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

5S Rdna ◽

Fish Analysis ◽

Cytogenetic Map ◽

Ligustrum Lucidum ◽

Starting Point ◽

Central Regions ◽

Almost All

We report the cytogenetic map for a collection of species in the Oleaceae, and test similarities among the karyotypes relative to their known species phylogeny. The oligonucleotides 5S ribosomal DNA (rDNA), (AGGGTTT)3, and (TTG)6 were used as fluorescence in situ hybridization (FISH) probes to locate the corresponding chromosomes in three Oleaceae genera: Fraxinus pennsylvanica, Syringa oblata, Ligustrum lucidum, and Ligustrum × vicaryi. Forty-six small chromosomes were identified in four species. (AGGGTTT)3 signals were observed on almost all chromosome ends of four species, but (AGGGTTT)3 played no role in distinguishing the chromosomes but displayed intact chromosomes and could thus be used as a guide for finding chromosome counts. (TTG)6 and 5S rDNA signals discerned several chromosomes located at subterminal or central regions. Based on the similarity of the signal pattern (mainly in number and location and less in intensity) of the four species, the variations in the 5S rDNA and (TTG)6 distribution can be ordered as L. lucidum < L. × vicaryi < F. pennsylvanica < S. oblata. Variations have observed in the three genera. The molecular cytogenetic data presented here might serve as a starting point for further larger-scale elucidation of the structure of the Oleaceae genome, and comparison with the known phylogeny of Oleaceae family.

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Dispersal of Silver Gulls, Larus novaehollandiae Stephens, from Breeding Colonies in South Australia

Wildlife Research ◽

10.1071/wr9850279 ◽

1985 ◽

Vol 12 (2) ◽

pp. 279 ◽

Cited By ~ 2

Author(s):

JR Ottaway ◽

R Carrick ◽

MD Murray

Keyword(s):

South Australia ◽

High Status ◽

Dispersal Patterns ◽

North West ◽

Significant Difference ◽

Rubbish Dumps ◽

The Difference ◽

Dispersal Distances ◽

Almost All ◽

The City

Dispersal of Larus novaehollandiae Stephens, from 10 colonies in South Australia, was studied during 1968-8 1 by means of bands designed for identification of free-living, uncaptured individuals. Dispersal patterns were characteristic of each colony, even for three colonies which were, at most, 10 km apart. Almost all dispersal records came from the area between Adelaide and Melbourne, and within 30 km of the coast. After breeding, the majority of gulls disperse eastwards; however, dispersal from each colony was correlated with a shift of gull population into areas where food was available from human sources such as rubbish dumps. From colonies 80 km south-east of Adelaide, a major human population, the predominant winter dispersal of these gulls was north-west, into the city and suburbs. The maximum direct-line dispersal distances recorded for 95% of the 3133 resighted gulls were <458 km. The greatest direct-line distance recorded was 1430 km. Overall, there was no significant difference in the mean dispersal distances of juveniles and adults, although at distances >480 km significantly more juveniles (<2y) were seen than adults (>2y). This involved only 2.5% of the total number of birds resighted. It is suggested that older, dominant birds maintain high status at preferred feeding places, and juveniles are possibly more erratic in their movements, as they search for food. This would account for the difference in the dispersal ofjuveniles and adults from a particular colony, and also for the significantly higher proportion of juveniles found at extreme distances from their natal colonies.

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