Center for Crocodile Research

Noonamah, Australia

Center for Crocodile Research

Noonamah, Australia
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Jaratlerdsiri W.,University of Sydney | Deakin J.,Australian National University | Deakin J.,University of Canberra | Godinez R.M.,Harvard University | And 14 more authors.
PLoS ONE | Year: 2014

The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilianavian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (<80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs. © 2014 Jaratlerdsiri et al.


Milic N.L.,Charles Darwin University | Davis S.,Berrimah Veterinary Laboratories | Carr J.M.,Flinders University | Isberg S.,Charles Darwin University | And 3 more authors.
Developmental and Comparative Immunology | Year: 2015

A number of pathogens have been detected in crocodiles, however little is known about their ability to control these pathogens. The interferon stimulated gene (ISG), viperin, has gained attention recently as an important host protein involved in multiple arms of the immune response. Viperin in concert with a number of other ISGs was upregulated in response to viral nucleic acid mimics and sendai virus in the C. porosus cell line, LV-1, indicating an intact early innate response to viral infection in these animals for the first time. Viperin was cloned from the LV-1 cell line and shown to have similar localisation patterns as human viperin, as well as demonstrating extremely high conservation with the human orthologue, excepting at the N-terminus. Interestingly, C. porosus viperin was also able to inhibit Dengue virus replication in vitro, showing a high level of intact functionality for this protein across divergent animal species, and perhaps demonstrating its importance in the early innate response to pathogens in the animal kingdom. © 2015 Elsevier Ltd.


Hyndman T.H.,Murdoch University | Shilton C.M.,Khan Research Laboratories | Wellehan J.F.X.,Florida College | Davis S.,Khan Research Laboratories | And 4 more authors.
Veterinary Microbiology | Year: 2015

As part of a larger investigation into three emerging disease syndromes highlighted by conjunctivitis and pharyngitis, systemic lymphoid proliferation and encephalitis, and lymphonodular skin infiltrates in farmed saltwater crocodiles (Crocodylus porosus) and one emerging syndrome of systemic lymphoid proliferation in captive freshwater crocodiles (Crocodylus johnstoni), cytopathic effects (CPE), including syncytial cell formation, were observed in primary crocodile cell lines exposed to clarified tissue homogenates from affected crocodiles. Ten cell cultures with CPE were then screened for herpesviruses using two broadly-reactive herpesvirus PCRs. Amplicons were obtained from 9 of 10 cell cultures and were sequenced. Three novel herpesviruses were discovered and the phylogenetic analysis of these viruses showed there was a 63% Bayesian posterior probability value supporting these viruses clustering with the subfamily Alphaherpesvirinae, and 100% posterior probability of clustering with a clade containing the Alphaherpesvirinae and other unassigned reptile herpesviruses. It is proposed that they are named Crocodyline herpesvirus (CrHV) 1, 2 and 3. CrHV1 and 2 were only isolated from saltwater crocodiles and CrHV3 was only isolated from freshwater crocodiles. A duplex PCR was designed that was able to detect these herpesviruses in formalin-fixed paraffin-embedded tissues, a sample type that neither of the broadly-reactive PCRs was able to detect these herpesviruses in. This work describes the isolation, molecular detection and phylogeny of these novel herpesviruses but the association that they have with the emerging disease syndromes requires further investigation. © 2015 Elsevier B.V.


Chong A.Y.,University of Sydney | Kojima K.K.,Genetic Information Research Institute | Jurka J.,Genetic Information Research Institute | Ray D.A.,Mississippi State University | And 5 more authors.
Retrovirology | Year: 2014

Background: Crocodilians are thought to be hosts to a diverse and divergent complement of endogenous retroviruses (ERVs) but a comprehensive investigation is yet to be performed. The recent sequencing of three crocodilian genomes provides an opportunity for a more detailed and accurate representation of the ERV diversity that is present in these species. Here we investigate the diversity, distribution and evolution of ERVs from the genomes of three key crocodilian species, and outline the key processes driving crocodilian ERV proliferation and evolution. Results: ERVs and ERV related sequences make up less than 2% of crocodilian genomes. We recovered and described 45 ERV groups within the three crocodilian genomes, many of which are species specific. We have also revealed a new class of ERV, ERV4, which appears to be common to crocodilians and turtles, and currently has no characterised exogenous counterpart. For the first time, we formally describe the characteristics of this ERV class and its classification relative to other recognised ERV and retroviral classes. This class shares some sequence similarity and sequence characteristics with ERV3, although it is phylogenetically distinct from the other ERV classes. We have also identified two instances of gene capture by crocodilian ERVs, one of which, the capture of a host KIT-ligand mRNA has occurred without the loss of an ERV domain. Conclusions: This study indicates that crocodilian ERVs comprise a wide variety of lineages, many of which appear to reflect ancient infections. In particular, ERV4 appears to have a limited host range, with current data suggesting that it is confined to crocodilians and some lineages of turtles. Also of interest are two ERV groups that demonstrate evidence of host gene capture. This study provides a framework to facilitate further studies into non-mammalian vertebrates and highlights the need for further studies into such species. © 2014 Chong et al.; licensee BioMed Central.


Lott M.J.,Macquarie University | Hose G.C.,Macquarie University | Isberg S.R.,Center for Crocodile Research | Power M.L.,Macquarie University
Parasitology Research | Year: 2014

Paratrichosoma-associated helminthiasis has been identified in saltwater crocodiles under intensive farming conditions. The development of sustainable integrated management practices is dependent on a detailed understanding of Paratrichosoma population genetics and infection dynamics. This study investigated the genetic relationships of Paratrichosoma sp in a population of commercially farmed saltwater crocodiles, Crocodylus porosus, in northern Australia. 18S ribosomal RNA gene sequence data were obtained from Paratrichosoma sp eggs present in the epidermis of infected animals. A high level of genetic diversity was distributed within the Paratrichosoma sp population (241 variable positions in the 1094 bp alignment), indicating an accelerated rate of nucleotide base-pair substitutions in this genus of nematodes. Several possible environmental correlates of the incidence and intensity of helminthiasis, including season, rainfall, and mean monthly temperature, were investigated by visual inspection of crocodile skins. Stepwise logistic regression revealed a significant negative linear relationship (P = 0.011, R2 = 32.69 %) between mean monthly rainfall and the incidence of monthly Paratrichosoma-associated helminthiasis. Variation in the severity of Paratrichosoma-associated helminthiasis could not be explained by any of the independent environmental variables included within an ordinal regression analysis. The large genetic diversity in these nematodes indicates a high probability of anthelmintic resistant alleles occurring in the population. We discuss how the spread of these alleles may be mitigated by adopting targeted treatment protocols. © 2014, Springer-Verlag Berlin Heidelberg.


Jaratlerdsiri W.,University of Sydney | Isberg S.R.,University of Sydney | Isberg S.R.,Center for Crocodile Research | Higgins D.P.,University of Sydney | And 2 more authors.
PLoS ONE | Year: 2014

Major Histocompatibility Complex (MHC) class II genes encode for molecules that aid in the presentation of antigens to helper T cells. MHC characterisation within and between major vertebrate taxa has shed light on the evolutionary mechanisms shaping the diversity within this genomic region, though little characterisation has been performed within the Order Crocodylia. Here we investigate the extent and effect of selective pressures and trans-species polymorphism on MHC class II α and β evolution among 20 extant species of Crocodylia. Selection detection analyses showed that diversifying selection influenced MHC class II β diversity, whilst diversity within MHC class II α is the result of strong purifying selection. Comparison of translated sequences between species revealed the presence of twelve trans-species polymorphisms, some of which appear to be specific to the genera Crocodylus and Caiman. Phylogenetic reconstruction clustered MHC class II α sequences into two major clades representing the families Crocodilidae and Alligatoridae. However, no further subdivision within these clades was evident and, based on the observation that most MHC class II α sequences shared the same transspecies polymorphisms, it is possible that they correspond to the same gene lineage across species. In contrast, phylogenetic analyses of MHC class II β sequences showed a mixture of subclades containing sequences from Crocodilidae and/or Alligatoridae, illustrating orthologous relationships among those genes. Interestingly, two of the subclades containing sequences from both Crocodilidae and Alligatoridae shared specific trans-species polymorphisms, suggesting that they may belong to ancient lineages pre-dating the divergence of these two families from the common ancestor 85-90 million years ago. The results presented herein provide an immunogenetic resource that may be used to further assess MHC diversity and functionality in Crocodylia. © 2014 Jaratlerdsiri et al.


Finger J.W.,University of Georgia | Finger J.W.,University of Sydney | Finger J.W.,Center for Crocodile Research | Thomson P.C.,University of Sydney | And 5 more authors.
General and Comparative Endocrinology | Year: 2015

To determine reference levels for on-farm stressors on immune responsiveness and growth rate, 253 hatchling crocodiles from 11 known breeding pairs were repeatedly measured and blood sampled during their first year. Plasma corticosterone (CORT) was used to quantify baseline stress levels in captive animals and were found to be lower (mean 1.83. ±. SE 0.16. ng/mL) than previously reported in saltwater crocodile hatchlings. Two tests of immune function were also conducted. Innate constitutive immunity was assessed using bacterial killing assays (BKA) against two bacterial species: Escherichia coli and Providencia rettgeri, whereby the latter causes considerable economic loss to industry from septicaemic mortalities. Although the bactericidal capabilities were different at approximately 4. months old (32. ±. 3% for E. coli and 16. ±. 4% for P. rettgeri), the differences had disappeared by approximately 9. months old (58. ±. 2% and 68. ±. 6%, respectively). To assess immune responsiveness to a novel antigen, the inflammatory swelling response caused by phytohaemagglutinin (PHA) injection was assessed but was only significantly different between Samplings 1 and 3 (5% LSD). There were no significant clutch effects for CORT or PHA but there were for both BKA traits. CORT was not significantly associated with growth (head length) or the immune parameters except for P. rettgeri BKA where higher CORT levels were associated with better bactericidal capability. As such, these results suggest that the crocodiles in this study are not stressed, therefore endorsing the management strategies adopted within the Australian industry Code of Practice. © 2015 Elsevier Inc.


Finger Jr J.W.,University of Georgia | Finger Jr J.W.,University of Sydney | Adams A.L.,Khan Research Laboratories | Thomson P.C.,University of Sydney | And 7 more authors.
Australian Journal of Zoology | Year: 2013

Immune responsiveness, the ability of an organism to effectively respond immunologically following antigenic exposure, is an essential component of life history, as organisms require effective immune functionality in order to grow, survive and reproduce. However, immune status is also associated with concomitant trade-offs in these physiological functions. Herein we demonstrate the validation of phytohaemagglutinin (PHA) injection in saltwater crocodiles, Crocodylus porosus, to assess cellular immune responsiveness. Following injection of 2mgmL-1 PHA into the hind toe webbing, we observed a peak swelling response 12h after injection, with PHA inducing increased thickness compared with webs injected with phosphate-buffered saline (PBS) (F5,518&=145.13, P<0.001). Subsequent injections increased responsiveness relative to the primary injection response (F5,290=2. 92, P≤0.029), suggesting that PHA exposure induced immunological memory, a tenet of acquired immunity. Histological examination revealed that PHA-injected toe webs displayed increased numbers of leukocytes (granulocytes, macrophages, and lymphocytes) relative to PBS-injected webs, with peak leukocytic infiltrate observed 12h after injection. We suggest the use of PHA injection in crocodilians as a measure of cellular immune responsiveness in agricultural (production and animal welfare), ecological, and toxicological contexts. © 2013 CSIRO.


Finger J.W.,University of Georgia | Finger J.W.,University of Sydney | Finger J.W.,Center for Crocodile Research | Finger J.W.,Auburn University | And 3 more authors.
General and Comparative Endocrinology | Year: 2016

Agricultural production of the saltwater crocodile (Crocodylus porosus) is an emergent industry in northern Australia with many of the factors affecting production remaining unknown. In this study, we sought to expand upon our previous findings of reference corticosterone and immune function by reporting baseline sex hormone levels [testosterone (TEST) and estradiol (ESTR)] and their association with growth. This was achieved by sampling 253 hatchling crocodiles repeatedly at 3, 6, and 9 months of age. Sampling age had a significant effect on both TEST (p<. 0.001) and ESTR (p<. 0.001) suggesting climatic/abiotic factors have an influence even in prepubescent crocodiles. Stress, as measured by plasma corticosterone, had no detectable effect on plasma ESTR or TEST levels. Unexpectedly however, TEST was higher in slower-growing crocodiles, which is contrary to what has been reported for the American alligator. ESTR was not associated with growth. © 2015 Elsevier Inc.

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