Patterns may shed light not only on shell development but also on other unique and previously undescribed mechanisms of turtle development.The placement of turtles in the tree of life is 10781694 controversial. Different data sets and methodologies, even from the same authors, result in different placements. Turtles have been grouped both with the lizards (Lepidosaurs) and with birds and crocodiles (Archosaurs), generally depending on whether morphological or molecular characters, respectively, were analyzed [22,31?3]. A simple analysis of our transcriptome sequences shows that they are very similar to both lizard and bird sequences, consistent with either grouping. Given the limitations of both our transcriptome (it samples a limited set of developmental stages) and bird and lizard sequences, neither of which are `complete’, it seems unlikely that a more sophisticated analysis performed using our data will resolve this ongoing controversy. We hope that this transcriptome provides a valuable resource for the T. scripta community both for developmental studies as well as for genome annotation in the future and is of use to other biologists interested in comparative genomics.Supporting InformationTable S1 Cellular component (CC), molecular function (MF), and Gracillin web biological Licochalcone A biological activity process (BP) GO categories assigned to proteins identified in the 16985061 T. scripta embryonic transcriptome. (XLSX)AcknowledgmentsWe would like to thank Brian Haas for his advice, support, and encouragement about using Trinity for de novo transcriptome assembly, Eric Lyons for providing access to the computational resources necessary to run Trinity, and Andrew Reuther for advice on using XSEDE resources.Author ContributionsConceived and designed the experiments: NJK SFG JC KL MS EYC HEE MAF YG RMH NHH DSO KS EAS RW. Performed the experiments: NJK JC KL MS EYC HEE MAF YG RMH NHH DSO KS EAS RW. Analyzed the data: NJK SFG JC KL MS EYC HEE MAF YG RMH NHH DSO KS EAS RW. Contributed reagents/materials/analysis tools: NJK JC KL MS. Wrote the paper: NJK SFG JC KL MS EYC HEE MAF YG RMH NHH DSO KS EAS RW.
The cornea is avascular and, as such, is an “immune privileged” site. Therefore, the corneal transplant success rate is the highest among organ transplants [1?]. However, immune responses are the primary cause for graft failure in penetrating keratoplasty [3]. Interleukin-1 (IL-1) is the key cytokine participating in corneal transplant rejection [4]. In keratoplasty, increasing the IL-1 level causes antigen-presenting cell (e.g., Langerhans cells and lymphocytes) aggregation and neutrophil infiltration, leading to inflammation. Thus, antagonising the biological activity of IL-1 could effectively prolong graft survival. Interleukin-1 receptor antagonist (IL-1ra) is a natural inhibitor of IL-1. Recent studies have indicated [5?] that IL-1ra may be effective for treating the rejection of corneal transplants. Jie [9] demonstrated that thesubconjunctival injection of large doses of IL-1ra could prolong the survival of rat allografts following high-risk corneal transplantation. Although IL-1ra clearly inhibits immune and inflammatory reactions, as a natural protein, the cytokine is not stable for clinical applications, and its subconjunctival injection may increase patient suffering. In a previous study, we used genetic engineering techniques to construct a recombinant plasmid with the human IL-1ra cDNA sequence that could effectively express high levels of IL-1ra mRNA and protein in eukaryotic cells.Patterns may shed light not only on shell development but also on other unique and previously undescribed mechanisms of turtle development.The placement of turtles in the tree of life is 10781694 controversial. Different data sets and methodologies, even from the same authors, result in different placements. Turtles have been grouped both with the lizards (Lepidosaurs) and with birds and crocodiles (Archosaurs), generally depending on whether morphological or molecular characters, respectively, were analyzed [22,31?3]. A simple analysis of our transcriptome sequences shows that they are very similar to both lizard and bird sequences, consistent with either grouping. Given the limitations of both our transcriptome (it samples a limited set of developmental stages) and bird and lizard sequences, neither of which are `complete’, it seems unlikely that a more sophisticated analysis performed using our data will resolve this ongoing controversy. We hope that this transcriptome provides a valuable resource for the T. scripta community both for developmental studies as well as for genome annotation in the future and is of use to other biologists interested in comparative genomics.Supporting InformationTable S1 Cellular component (CC), molecular function (MF), and biological process (BP) GO categories assigned to proteins identified in the 16985061 T. scripta embryonic transcriptome. (XLSX)AcknowledgmentsWe would like to thank Brian Haas for his advice, support, and encouragement about using Trinity for de novo transcriptome assembly, Eric Lyons for providing access to the computational resources necessary to run Trinity, and Andrew Reuther for advice on using XSEDE resources.Author ContributionsConceived and designed the experiments: NJK SFG JC KL MS EYC HEE MAF YG RMH NHH DSO KS EAS RW. Performed the experiments: NJK JC KL MS EYC HEE MAF YG RMH NHH DSO KS EAS RW. Analyzed the data: NJK SFG JC KL MS EYC HEE MAF YG RMH NHH DSO KS EAS RW. Contributed reagents/materials/analysis tools: NJK JC KL MS. Wrote the paper: NJK SFG JC KL MS EYC HEE MAF YG RMH NHH DSO KS EAS RW.
The cornea is avascular and, as such, is an “immune privileged” site. Therefore, the corneal transplant success rate is the highest among organ transplants [1?]. However, immune responses are the primary cause for graft failure in penetrating keratoplasty [3]. Interleukin-1 (IL-1) is the key cytokine participating in corneal transplant rejection [4]. In keratoplasty, increasing the IL-1 level causes antigen-presenting cell (e.g., Langerhans cells and lymphocytes) aggregation and neutrophil infiltration, leading to inflammation. Thus, antagonising the biological activity of IL-1 could effectively prolong graft survival. Interleukin-1 receptor antagonist (IL-1ra) is a natural inhibitor of IL-1. Recent studies have indicated [5?] that IL-1ra may be effective for treating the rejection of corneal transplants. Jie [9] demonstrated that thesubconjunctival injection of large doses of IL-1ra could prolong the survival of rat allografts following high-risk corneal transplantation. Although IL-1ra clearly inhibits immune and inflammatory reactions, as a natural protein, the cytokine is not stable for clinical applications, and its subconjunctival injection may increase patient suffering. In a previous study, we used genetic engineering techniques to construct a recombinant plasmid with the human IL-1ra cDNA sequence that could effectively express high levels of IL-1ra mRNA and protein in eukaryotic cells.
