The Experts below are selected from a list of 315 Experts worldwide ranked by ideXlab platform
Sally R. Isberg - One of the best experts on this subject based on the ideXlab platform.
-
identification and characterization of micrornas mirnas and their transposable element origins in the saltwater crocodile Crocodylus porosus
Analytical Biochemistry, 2020Co-Authors: Arnab Ghosh, Sally R. Isberg, Roy N Platt, Michael W Vandewege, Rabia Tabassum, Daniel G Peterson, John W FingerAbstract:Abstract MicroRNAs (miRNAs) are 18-24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to birds, the closest extant relatives of crocodilians. Understanding gene regulation in the saltwater crocodile in the context of relatively slow genomic change thus holds potential for the investigation of genomics, evolution, and adaptation. Utilizing eleven tissue types and sixteen small RNA libraries, we report 644 miRNAs in the saltwater crocodile with > 78% of miRNAs being novel to crocodilians. We also identified potential targets for the miRNAs and analyzed the relationship of the miRNA repertoire to transposable elements (TEs). Results suggest an increased association of DNA transposons with miRNAs when compared to retrotransposons. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile. In addition, the data suggests a supporting role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.
-
unexpected lower testosterone in faster growing farmed saltwater crocodile Crocodylus porosus hatchlings
General and Comparative Endocrinology, 2016Co-Authors: John W Finger, P C Thomson, Sally R. IsbergAbstract:Abstract 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
-
Molecular identification of three novel herpesviruses found in Australian farmed saltwater crocodiles (Crocodylus porosus) and Australian captive freshwater crocodiles (Crocodylus johnstoni).
Veterinary microbiology, 2015Co-Authors: Timothy H Hyndman, Sally R. Isberg, Catherine M. Shilton, James F X Wellehan, Steven Davis, David Phalen, Lorna MelvilleAbstract: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.
-
Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
Genome Biology, 2012Co-Authors: John A St John, Amanda Y Chong, Pauline Dalzell, Christopher Moran, Arkhat Abzhanov, Jaime Gongora, Edward L. Braun, Sally R. Isberg, Lee G. Miles, Shane C BurgessAbstract: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.
-
Cross-species amplification of microsatellites in crocodilians: assessment and applications for the future
Conservation Genetics, 2009Co-Authors: Lee G. Miles, Sally R. Isberg, Stacey L. Lance, Chris Moran, Travis C. GlennAbstract:Microsatellite DNA loci have emerged as the dominant genetic tool for addressing questions associated with genetic diversity in many wildlife species, including crocodilians. Despite their usefulness, their isolation and development can be costly, as well as labour intensive, limiting their wider use in many crocodilian species. In this study, we investigate the cross-species amplification success of 82 existing microsatellites previously isolated for the saltwater crocodile ( Crocodylus porosus ) in 18 non-target crocodilian species; Alligator sinensis , Caiman Crocodylus , Caiman latirostris , Caiman yacare , Melanosuchus niger , Paleosuchus palpebrosus , Crocodylus acutus , Mecistops cataphractus , Crocodylus intermedius , Crocodylus johnstoni , Crocodylus mindorensis , Crocodylus moreletii , Crocodylus niloticus , Crocodylus novaeguineae , Crocodylus palustis , Crocodylus rhombifer , Crocodylus siamensis , and Osteolaemus tetraspis . Our results show a high level of microsatellites cross-amplification making available polymorphic markers for a range of crocodilian species previously lacking informative genetic markers.
John W Finger - One of the best experts on this subject based on the ideXlab platform.
-
identification and characterization of micrornas mirnas and their transposable element origins in the saltwater crocodile Crocodylus porosus
Analytical Biochemistry, 2020Co-Authors: Arnab Ghosh, Sally R. Isberg, Roy N Platt, Michael W Vandewege, Rabia Tabassum, Daniel G Peterson, John W FingerAbstract:Abstract MicroRNAs (miRNAs) are 18-24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to birds, the closest extant relatives of crocodilians. Understanding gene regulation in the saltwater crocodile in the context of relatively slow genomic change thus holds potential for the investigation of genomics, evolution, and adaptation. Utilizing eleven tissue types and sixteen small RNA libraries, we report 644 miRNAs in the saltwater crocodile with > 78% of miRNAs being novel to crocodilians. We also identified potential targets for the miRNAs and analyzed the relationship of the miRNA repertoire to transposable elements (TEs). Results suggest an increased association of DNA transposons with miRNAs when compared to retrotransposons. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile. In addition, the data suggests a supporting role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.
-
unexpected lower testosterone in faster growing farmed saltwater crocodile Crocodylus porosus hatchlings
General and Comparative Endocrinology, 2016Co-Authors: John W Finger, P C Thomson, Sally R. IsbergAbstract:Abstract 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
George Amato - One of the best experts on this subject based on the ideXlab platform.
-
Mitogenomic investigation reveals a cryptic lineage of Crocodylus in Cuba
Bulletin of Marine Science, 2020Co-Authors: Yoamel Milián-garcía, Jessica Castellanos-labarcena, Michael A. Russello, George AmatoAbstract:The American crocodile, Crocodylus acutus (Cuvier, 1807), is the most widely distributed crocodylian in the Americas, and coexists with the endemic and critically endangered Cuban crocodile, Crocodylus rhombifer Cuvier, 1807. Although these species are morphologically distinguishable, previous studies have shown that they are more genetically related to each other than either of them are to continental C. acutus. Here, we characterize the mitochondrial genome of Cuban C. acutus and analyze the resulting data relative to previously published whole mitochondrial genomes to reconstruct patterns of variation and phylogenetic placement within Crocodylus. We sequenced 13,776 basepairs, representing 82% of the entire genome including five (COI, COII, ATP8, ND3, ND4L) of the 13 protein-coding genes and 16 of the 22 tRNAs. Independent gene analysis of nucleotide diversity and genetic distance of Tamura-Nei demonstrated that the 16S rRNA, 12S rRNA, and COI genes are the most conserved in Crocodylus, while ND6 was the most variable (approximately 9%). Phylogenetic analysis confirmed that Cuban C. acutus forms a well-supported sister relationship with C. rhombifer, in contrast to continental C. acutus that clusters with Crocodylus intermedius Graves, 1819. The results are consistent with the hypothesis that Antillean C. acutus represents a cryptic lineage with genetic divergence at the species level. The ability to fully evaluate the taxonomic status of the Caribbean lineage of C. acutus still requires more comprehensive population samplings across the range as well as nuclear DNA sequence data. Of more immediate consequence, our results provide important information to be integrated into current Crocodylus conservation strategies in Cuba.
-
a phylogenetic hypothesis for Crocodylus crocodylia based on mitochondrial dna evidence for a trans atlantic voyage from africa to the new world
Molecular Phylogenetics and Evolution, 2011Co-Authors: Robert W Meredith, George Amato, Evon R Hekkala, John GatesyAbstract:Abstract The phylogenetic relationships among extant species of Crocodylus (Crocodylia) have been inconsistently resolved by previous systematic studies. Here we used nearly complete mitochondrial (mt) genomes (∼16,200 base pairs) for all described Crocodylus species, eight of which are new to this study, to derive a generally well-supported phylogenetic hypothesis for the genus. Model-based analyses support monophyly of all Asian + Australian species and paraphyly of Crocodylus niloticus (Nile crocodile) with a monophyletic New World clade nested within this species. Wild-caught Nile crocodiles from eastern populations group robustly with the four New World species to the exclusion of Nile crocodiles from western populations, a result that is also favored by parsimony analyses and by various subpartitions of the overall mt dataset. The fossil record of Crocodylus extends back only to the Late Miocene, while the earliest fossils assigned to C. niloticus and to New World Crocodylus are Pliocene. Therefore, in combination with paleontological evidence, mt DNA trees imply a relatively recent migration of Crocodylus from Africa to the Americas, a voyage that would have covered hundreds of miles at sea.
-
The complete mitochondrial genome of salt-water crocodile (Crocodylus porosus) and phylogeny of crocodilians.
Journal of Genetics and Genomics, 2007Co-Authors: Yan Li, Xuefeng Ji, Xiaobing Wu, George AmatoAbstract:Abstract The nucleotide sequence of the complete mitochondrial DNA (mtDNA) molecule of the salt-water crocodile ( Crocodylus porosus ) was determined in this article. The molecule is 16,917 base pairs (bp) in length, and codes for 22 tRNAs, 13 protein-coding genes, 2 rRNAs, as well as a control region (D-loop), as is characteristic for mitochondrial genomes of other metazoans. The gene order conforms to that of other crocodilians sequenced, but the arrangement of some tRNA genes differs from other vertebrates. It shows that the gene order of crocodilians is remarkably conserved. In this study, the relationships among crocodilians were examined in the phylogenetic analysis based on the control conserved regions of 17 crocodilians. The results suggest that the gharial ( Gavialis gangeticus ) joins the false gharial ( Tomistoma schlegelii ) on a common branch, and then constitutes a sister group to traditional Crocodylidae. Thus, the result supports that G. gangeticus belongs to Crocodylidae. The analyses also suggest that the African slender-snouted crocodile ( Crocodylus cataphractus ) can be treated as an isolated genus, and constitutes a sister group to Crocodylus .
-
molecular evidence for species level divergence in african nile crocodiles Crocodylus niloticus laurenti 1786
Comptes Rendus Palevol, 2003Co-Authors: Andreas Schmitz, George Amato, Evon R Hekkala, Patrick Mansfeld, Tara Shine, Hemmo Nickel, Wolfgang BohmeAbstract:Abstract Relationships of the newly discovered dwarf crocodiles from Mauritania were inferred from mitochondrial 12S sequences. Specimens from 13 different Crocodylus niloticus populations (from East Africa, West Africa and Madagascar) were compared. Additional representatives of the genus Crocodylus (one from Africa and one from Australia), the African genus Osteolaemus and the South American alligatorid Paleosuchus palpebrosus (as outgroup) were included in the analysis. Maximum-likelihood and Bayesian analyses yielded relationships that were strikingly different from currently prevailing phylogenetic hypotheses. Both analyses consistently revealed two groups, one consisting of the monophyletic West- and Central African populations and the other of a paraphyletic group containing the East African and Madagascan populations. High genetic divergence between those groups indicates separation on the species level. Furthermore ‘C’ cataphractus is clearly shown not to be a member of the genus Crocodylus. The resulting nomenclatural changes are discussed. To cite this article: A. Schmitz et al., C. R. Palevol 2 (2003).
A Nielan - One of the best experts on this subject based on the ideXlab platform.
-
chrysosporium anamorph of nannizziopsis vriesii associated with fatal cutaneous mycoses in the salt water crocodile Crocodylus porosus
Medical Mycology, 2002Co-Authors: A D Thomas, L Sigler, S Peucker, J H Norton, A NielanAbstract:The Chrysosporium anamorph of Nannizziopsis vriesii, recently identified as the cause of cutaneous infections in chameleons and brown tree snakes, was associated with skin infections and deaths in saltwater crocodile (Crocodylus porosus) hatchlings on two separate occasions 3 years apart (1994 and 1997). In all, 48 animals died from the infection. All hatchlings came from the same farm in northern Queensland, Australia.
Ikramul Haque - One of the best experts on this subject based on the ideXlab platform.
-
complete mitochondrial genome sequences of three Crocodylus species and their comparison within the order crocodylia
Gene, 2011Co-Authors: P. R. Meganathan, Bhawna Dubey, Mark A Batzer, Ikramul HaqueAbstract:Abstract Crocodylus is the largest genus within the Order Crocodylia consisting of eleven species. This paper reports the complete mitochondrial genome sequences of three Crocodylus species, Crocodylus moreletii , Crocodylus johnstoni and Crocodylus palustris , and compares the newly obtained mitochondrial DNA sequences with other crocodilians, available in the public databases. The mitochondrial genomes of C. moreletii , C. johnstoni and C. palustris are 16,827 bp, 16,851 bp and 16,852 bp in length, respectively. These mitochondrial genomes consist of 13 protein coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region. The mitochondrial genomes of all the Crocodylus species, studied herein show identical characteristics in terms of nucleotide composition and codon usage, suggestive of the existence of analogous evolutionary patterns within the genus, Crocodylus . The synonymous and non-synonymous substitution rates for all the protein coding genes of Crocodylus were observed in between 0.001 and 0.275 which reveal the prevalence of purifying selection in these genes. The phylogenetic analyses based on complete mitochondrial DNA data substantiate the previously established crocodilian phylogeny. This study provides a better understanding of the crocodilian mitochondrial genome and the data described herein will prove useful for future studies concerning crocodilian mitochondrial genome evolution.
-
molecular phylogenetic analyses of genus Crocodylus eusuchia crocodylia crocodylidae and the taxonomic position of Crocodylus porosus
Molecular Phylogenetics and Evolution, 2010Co-Authors: P. R. Meganathan, Bhawna Dubey, Mark A Batzer, Ikramul HaqueAbstract:The genus Crocodylus consists of 11 species including the largest living reptile, Crocodylus porosus. The current understanding of the intrageneric relationships between the members of the genus Crocodylus is sparse. Even though members of this genus have been included in many phylogenetic analyses, different molecular approaches have resulted in incongruent trees leaving the phylogenetic relationships among the members of Crocodylus unresolved inclusive of the placement of C. porosus. In this study, the complete mitochondrial genome sequences along with the partial mitochondrial gene sequences and a nuclear gene, C-mos were utilized to infer the intrageneric relationships among Crocodylus species with a special emphasis on the phylogenetic position of C. porosus. Four different phylogenetic methods, Neighbour Joining, Maximum Parsimony, Maximum Likelihood and Bayesian inference, were utilized to reconstruct the crocodilian phylogeny. The uncorrected pairwise distances computed in the study, show close proximity of C. porosus to C. siamensis and the tree topologies thus obtained, also consistently substantiated this relationship with a high statistical support. In addition, the relationship between C. acutus and C. intermedius was retained in all the analyses. The results of the current phylogenetic study support the well established intergeneric crocodilian phylogenetic relationships. Thus, this study proposes the sister relationship between C. porosus and C. siamensis and also suggests the close relationship of C. acutus to C. intermedius within the genus Crocodylus.
-
Molecular identification of Indian crocodile species: PCR-RFLP method for forensic authentication
Journal of Forensic Sciences, 2009Co-Authors: P. R. Meganathan, Bhawna Dubey, Ikramul HaqueAbstract:South East Asian countries are known for illegal poaching and trade of crocodiles clandestinely, to be used in skin, medicinal, and cosmetic industries. Besides crocodiles being listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora, India has its Wildlife Protection Act, 1972 for conservation of crocodile species. Hitherto, lack of any rapid and reliable technique for examinations of crocodile-based crime exhibits such as skin, bones, etc. has been a major problem for an effective promulgation of law on illegal trade. DNA-based identification of species using PCR-RFLP technique for an apt identification of all the three Indian crocodile species namely, Crocodylus porosus, Crocodylus palustris and Gavialis gangeticus is presented here. A 628 bp segment of cytochrome b gene was amplified using novel primers followed by restriction digestion with three enzymes i.e., HaeIII, MboI, and MwoI, separately and in combination. The technique has produced a species-specific pattern for identifying the three crocodile species individually, which fulfills the requirement for its forensic application. It is expected that the technique will prove handy in identification of all the three Indian crocodile species and strengthen conservation efforts.
-
Molecular identification of crocodile species using novel primers for forensic analysis
Conservation Genetics, 2009Co-Authors: P. R. Meganathan, Bhawna Dubey, Ikramul HaqueAbstract:All crocodilians are under varying degrees of threat due to over exploitation and these species have been listed in Appendix I or II of CITES. The lack of molecular techniques for the identification of confiscated samples makes it difficult to enforce the law. Conclusive forensic identification of species requires a complete gene sequence which is difficult in case of degraded samples. We have developed two novel sets of primers to amplify two partial cytochrome b gene sequences of 6 crocodile species i.e. Crocodylus palustris, Crocodylus porosus, Crocodylus siamensis, Crocodylus niloticus, Gavialis gangeticus and Caiman crocodilus. These partial sequences were edited to give a complete cyt b gene sequence, which can be used as an effective tool for forensic authentication of crocodile species. A phylogeny of crocodile species was reconstructed using these sequences. The described primers hold great promise in forensic identification of crocodile species, which can aid in the effective enforcement of law and conservation of these ancient species.