Darwin, Australia
Darwin, Australia

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St John J.A.,University of California at Santa Cruz | Braun E.L.,University of Florida | Isberg S.R.,Porosus Pty Ltd | Isberg S.R.,University of Sydney | And 47 more authors.
Genome Biology | Year: 2012

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described. © 2012 BioMed Central Ltd.

Chong A.Y.-Y.,University of Sydney | Atkinson S.J.,University of Sydney | Isberg S.,Porosus Pty Ltd | Gongora J.,University of Sydney
Mobile DNA | Year: 2012

Background: Endogenous retroviruses (ERVs) are remnants of exogenous retroviruses that have integrated into the nuclear DNA of a germ-line cell. Here we present the results of a survey into the ERV complement of Crocodylus porosus, the saltwater crocodile, representing 45 individuals from 17 sampling locations in the Northern Territory of Australia. These retroelements were compared with published ERVs from other species of Crocodylia (Crocodilians; alligators, caimans, gharials and crocodiles) as well as representatives from other vertebrates. This study represents one of the first in-depth studies of ERVs within a single reptilian species shedding light on the diversity of ERVs and proliferation mechanisms in crocodilians. Results: Analyses of the retroviral pro-pol gene region have corroborated the presence of two major clades of ERVs in C. porosus and revealed 18 potentially functional fragments out of the 227 recovered that encode intact pro-pol ORFs. Interestingly, we have identified some patterns of diversification among those ERVs as well as a novel sequence that suggests the presence of an additional retroviral genus in C. porosus. In addition, considerable diversity but low genetic divergence within one of the C. porosus ERV lineages was identified. Conclusions: We propose that the ERV complement of C. porosus has come about through a combination of recent infections and replication of ancestral ERVs. Strong purifying selection acting on these clades suggests that this activity is recent or still occurring in the genome of this species. The discovery of potentially functional elements is an interesting development that warrants further investigation. © 2012 Chong et al.; licensee BioMed Central Ltd.

Finger J.W.J.,University of Georgia | Finger J.W.J.,Porosus Pty Ltd | Isberg S.R.,University of Georgia
CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources | Year: 2012

The immune function of crocodilians is understudied but is of interest for medical, ecological and evolutionary purposes. Crocodiles share a common ancestor with birds, comprising the archosaurian lineage, so they are an important link in our understanding of immune system evolution. As top trophic carnivores, they inhabit temperate and tropical climates in their semiaquatic environment. However, they are also ectothermic, whereby environmental temperatures affect their physiological processes, including immune function, adding to the complexity of research in this area. Anecdotal observations and recent research have augmented enthusiasm in the realm of crocodilian immunology. Despite comprising both adaptive and innate systems, most research has investigated the innate system, which comprises peptides, proteins and leucocytes functioning in defence. Herein, we provide an overview into the innate immune system of the crocodile and areas for further research. © CAB International 2012.

Finger Jr. J.W.,University of Georgia | Finger Jr. J.W.,Porosus Pty Ltd. | Gogal Jr. R.M.,University of Georgia
Archives of Environmental Contamination and Toxicology | Year: 2013

Endocrine-disrupting chemicals (EDCs) alter cellular and organ system homeostasis by interfering with the body's normal physiologic processes. Numerous studies have identified environmental estrogens as modulators of EDC-related processes in crocodilians, notably in sex determination. Other broader studies have shown that environmental estrogens dysregulate normal immune function in mammals, birds, turtles, lizards, fish, and invertebrates; however, the effects of such estrogenic exposures on alligator immune function have not been elucidated. Alligators occupy a top trophic status, which may give them untapped utility as indicators of environmental quality. Environmental estrogens are also prevalent in the waters they occupy. Understanding the effects of these EDCs on alligator immunity is critical for managing and assessing changes in their health and is thus the focus of this review. © Springer Science+Business Media New York 2013.

Jaratlerdsiri W.,University of Sydney | Isberg S.R.,University of Sydney | Isberg S.R.,Porosus Pty. Ltd. | Higgins D.P.,University of Sydney | Gongora J.,University of Sydney
Immunogenetics | Year: 2012

Saltwater crocodiles are in high demand for the production of luxury fashion items. However, their susceptibility to disease incurs substantial losses and it is hoped to be able to genetically select these animals for disease resistance. So far, this has only been enabled by phenotypic selection. Investigating the major histocompatibility complex (MHC) could provide insight into the ability of an individual to respond to pathogens acting as a selective pressure on the host. Here, we assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 3 among 42 saltwater crocodiles from nine river basins in the Northern Territory, Australia. We generated 640 sequences using cloning and sequencing methods and identified 43 MHC variants among them. Phylogenetic analyses clustered these variants into two major clades, which may suggest two gene lineages. We found the number of variants within an individual varying between one and seven, indicating that there are at least four gene loci in this species. Selection detection analyses revealed an elevated ratio of nonsynonymous to synonymous substitutions (mean∈=∈1.152 per codon), suggesting balancing selection. Population differentiation analyses revealed that the MHC did not show structuring among the river basins, and there were some shared variants among them. This may be a result of possible gene flow and/or similar selection pressures among populations. These findings provide background knowledge to identify potential MHC markers, which could be used for selecting genetically variable individuals for future disease associations. All MHC class I exon 3 sequences reported in this paper were submitted to the GenBank database with following accession numbers: HQ008785-HQ008789, HQ008791-HQ008798, HQ008808-HQ008815, HQ008824, HQ008826-HQ008830, HQ008835, HQ008839, HQ008842-HQ008850, and JX023536-JX023540. © 2012 Springer-Verlag.

Luck N.L.,University of Sydney | Thomas K.C.,University of Sydney | Morin-Adeline V.E.,University of Sydney | Barwick S.,University of Sydney | And 78 more authors.
Australian Journal of Zoology | Year: 2012

The saltwater crocodile is distributed throughout south-east Asia and Australia. In Australia, it is most abundant in the Northern Territory and Queensland, where it is sustainably farmed for its skins and meat. The aim of this study was to elucidate the relationships and genetic structure among saltwater crocodiles from the Northern Territory of Australia using mitochondrial control region sequences from 61 individuals, representing nine river basins and six of unknown origin, as well as published sequences from other regions. Eight mitochondrial control region haplotypes were identified among both published and novel sequences. Three of the haplotypes appear to be restricted to specimens from northern Australia, with a single haplotype being the most widely dispersed across all river basins. Although Analysis of Molecular Variance provides some support for differentiation among river basins, the frequency of shared haplotypes among these geographical units and median-joining network analysis do not support a clear genetic structure or phylogeographic pattern for saltwater crocodiles in the Northern Territory. The results of this study will assist in furthering our understanding of the genetic diversity of wild saltwater crocodile populations used for ranching in the Northern Territory, as well as providing a framework for assessing the origin of unknown specimens in the future. © 2012 CSIRO.

Shilton C.,Berrimah Veterinary Laboratories | Brown G.P.,University of Sydney | Chambers L.,Berrimah Veterinary Laboratories | Benedict S.,Berrimah Veterinary Laboratories | And 4 more authors.
Veterinary Pathology | Year: 2014

Extremely poor growth of some individuals within a birth cohort (runting) is a significant problem in crocodile farming. We conducted a pathological investigation to determine if infectious disease is associated with runting in farmed saltwater crocodiles (Crocodylus porosus) and to look for evidence of other etiologies. In each of 2005 and 2007, 10 normal and 10 runt crocodiles, with an average age of 5.5 months and reared under identical conditions, were sampled. Laboratory testing included postmortem; histological examination of a wide variety of tissues (with quantitation of features that were noted subjectively to be different between groups); hematology; serum biochemistry (total protein, albumin, globulins, total calcium, phosphorus, and iron); bacterial culture of liver and spleen (2005 only); viral culture of liver, thymus, tonsil, and spleen using primary crocodile cell lines (2007 only); and serum corticosterone (2007 only). The only evidence of infectious disease was mild cutaneous poxvirus infection in 45% of normal and 40% of runt crocodiles and rare intestinal coccidia in 5% of normal and 15% of runt crocodiles. Bacterial and viral culture did not reveal significant differences between the 2 groups. However, runt crocodiles exhibited significant (P <.05) increases in adrenocortical cell cytoplasmic vacuolation and serum corticosterone, decreased production of bone (osteoporosis), and reduced lymphoid populations in the spleen, tonsil, and thymus. Runts also exhibited moderate anemia, hypoalbuminemia, and mild hypophosphatemia. Taken together, these findings suggest an association between runting and a chronic stress response (hyperactivity of the hypothalamic-pituitary-adrenal axis). © The Author(s) 2014.

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