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Sal-Site: Research Resources for the Mexican Axolotl

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Salamanders in Regeneration Research

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1290))

Abstract

Sal-Site serves axolotl research efforts by providing Web access to genomic data and information, and living stocks that are reared and made available by the Ambystoma Genetic Stock Center (AGSC). In this chapter, we detail how investigators can search for genes of interest among Sal-Site resources to identify orthologous nucleotide and protein-coding sequences, determine genome positions within the Ambystoma meiotic map, and obtain estimates of gene expression. In the near future, additional genomic resources will be made available for the axolotl, including a listing of genes that are partially or wholly contained within Bacterial Artificial Chromosome (BAC) vectors, a prioritized collection of deeply sequenced BAC clones, chromosome-specific assemblies of genomic DNA, and transgenic axolotls that are engineered using TALENs and CRISPRs. Also, services provided by the AGSC will be expanded to include microinjection of user constructs into single cell embryos and distribution of axolotl tissues, DNA, and RNA. In conclusion, Sal-Site is a useful resource that generates, shares, and evolves Ambystoma associated information and databases to serve research and education.

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References

  1. Putta S, Smith JJ, Walker JA, Rondet M, Weisrock DW, Monaghan JR, Kump DK, King DC, Maness NJ, Habermann B, Tanaka EM, Bryant SV, Gardiner DM, Parichy DM, Voss SR (2004) From biomedicine to natural history research: EST resources for ambystomatid salamanders. BMC Genomics 5:54

    Article  Google Scholar 

  2. Smith JJ, Putta S, Walker JA, Kump DK, Samuels AK, Monaghan JR, Weisrock DW, Staben C, Voss SR (2005) Sal-Site: integrating new and existing ambystomatid salamander research and informational resources. BMC Genomics 6:181

    Article  Google Scholar 

  3. Voss SR, Kump DK, Putta S, Pauly N, Reynolds A, Henry RJ, Smith JJ et al (2011) Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res 21:1306–1312

    Article  CAS  Google Scholar 

  4. Smith JJ, Putta S, Zhu W, Pao GM, Verma IM, Hunter T, Bryant SV, Gardiner DM, Harkins TT, Voss SR (2009) Genic regions of a large salamander genome contain long introns and novel genes. BMC Genomics 10:19

    Article  CAS  Google Scholar 

  5. Voss SR, Prudic KL, Oliver JC, Shaffer HB (2003) Candidate gene analysis of metamorphic timing in ambystomatid salamanders. Mol Ecol 12:1217–1223

    Article  CAS  Google Scholar 

  6. Dixon JE, Allegrucci C, Redwood C, Kump DC, Bian Y, Chatfield J, Chen Y-S, Sottile V, Voss SR, Alberio R, Johnson AD (2010) Axolotl Nanog activity in mouse embryonic stem cells demonstrates that ground state pluripotency is conserved from urodele amphibians to mammals. Development 137:2973–2980

    Article  CAS  Google Scholar 

  7. Tapia N, Reinhardt P, Duemmler A, Wu G, Araúzo-Bravo MJ, Esch D, Greber B, Cojocaru V, Rascon CA, Tazaki A, Kump K, Voss R, Tanaka EM, Schöler HR (2012) Reprogramming to pluripotency is an ancient trait of vertebrate Oct4 and Pou2 proteins. Nat Commun 3:1279

    Article  Google Scholar 

  8. Voss SR, Shaffer HB (1997) Adaptive evolution via a major gene effect: paedomorphosis in the Mexican axolotl. Proc Natl Acad Sci USA 94:14185–14189

    Article  CAS  Google Scholar 

  9. Voss SR, Smith JJ (2005) Evolution of salamander life cycles: a major-effect quantitative trait locus contributes to discrete and continuous variation for metamorphic timing. Genetics 170:275–281

    Article  CAS  Google Scholar 

  10. Johnson CK, Voss SR (2013) Salamander paedomorphosis: linking thyroid hormone to life history and life cycle evolution. Curr Top Dev Biol 103:229–258

    Article  CAS  Google Scholar 

  11. Page RB, Boley MA, Kump DK, Voss SR (2013) Genomics of a metamorphic timing QTL: met1 maps to a unique genomic position and regulates morph and species-specific patterns of brain transcription. Genome Biol Evol 5:1716–1730

    Article  Google Scholar 

  12. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  Google Scholar 

  13. Huggins P, Johnson CK, Schoergendorfer A, Putta S, Bathke AC, Stromberg AJ, Voss SR (2012) Identification of differentially expressed thyroid hormone responsive genes from the brain of the Mexican Axolotl (Ambystoma mexicanum). Comp Biochem Physiol C Toxicol Pharmacol 155:128–135

    Article  CAS  Google Scholar 

  14. Irizarry RA, Hobbs B, Collin F, Beazer Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high-density oligonucleotide array probe level data. Biostatistics 4:249–264

    Article  Google Scholar 

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Correspondence to S. Randal Voss .

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Baddar, N.W.A.H., Woodcock, M.R., Khatri, S., Kump, D.K., Voss, S.R. (2015). Sal-Site: Research Resources for the Mexican Axolotl. In: Kumar, A., Simon, A. (eds) Salamanders in Regeneration Research. Methods in Molecular Biology, vol 1290. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2495-0_25

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  • DOI: https://doi.org/10.1007/978-1-4939-2495-0_25

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2494-3

  • Online ISBN: 978-1-4939-2495-0

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