Sal-Site: Integrating new and existing ambystomatid salamander research and informational resources

Salamanders of the genus Ambystoma are a unique model organism system because they enable natural history and biomedical research in the laboratory or field. We developed Sal-Site to integrate new and existing ambystomatid salamander research resources in support of this model system. Sal-Site hosts six important resources: 1) Salamander Genome Project: an information-based web-site describing progress in genome resource development, 2) Ambystoma EST Database: a database of manually edited and analyzed contigs assembled from ESTs that were collected from A. tigrinum tigrinum and A. mexicanum, 3) Ambystoma Gene Collection: a database containing full-length protein-coding sequences, 4) Ambystoma Map and Marker Collection: an image and database resource that shows the location of mapped markers on linkage groups, provides information about markers, and provides integrating links to Ambystoma EST Database and Ambystoma Gene Collection databases, 5) Ambystoma Genetic Stock Center: a website and collection of databases that describe an NSF funded salamander rearing facility that generates and distributes biological materials to researchers and educators throughout the world, and 6) Ambystoma Research Coordination Network: a web-site detailing current research projects and activities involving an international group of researchers. Sal-Site is accessible at

Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, \u3cem\u3eAmbystoma mexicanum\u3c/em\u3e

The molecular genetic toolkit of the Mexican axolotl, a classic model organism, has matured to the point where it is now possible to identify genes for mutant phenotypes. We used a positional cloning–candidate gene approach to identify molecular bases for two historic axolotl pigment phenotypes: white and albino. White (d/d) mutants have defects in pigment cell morphogenesis and differentiation, whereas albino (a/a) mutants lack melanin. We identified in white mutants a transcriptional defect in endothelin 3 (edn3), encoding a peptide factor that promotes pigment cell migration and differentiation in other vertebrates. Transgenic restoration of Edn3 expression rescued the homozygous white mutant phenotype. We mapped the albino locus to tyrosinase (tyr) and identified polymorphisms shared between the albino allele (tyra) and tyr alleles in a Minnesota population of tiger salamanders from which the albino trait was introgressed. tyra has a 142 bp deletion and similar engineered alleles recapitulated the albinophenotype. Finally, we show that historical introgression of tyrasignificantly altered genomic composition of the laboratory axolotl, yielding a distinct, hybrid strain of ambystomatid salamander. Our results demonstrate the feasibility of identifying genes for traits in the laboratory Mexican axolotl

From Biomedicine to Natural History Research: EST Resources for Ambystomatid Aalamanders

BACKGROUND: Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum) and Eastern tiger salamander (A. tigrinum tigrinum), species with deep and diverse research histories. RESULTS: Approximately 40,000 quality cDNA sequences were isolated for these species from various tissues, including regenerating limb and tail. These sequences and an existing set of 16,030 cDNA sequences for A. mexicanum were processed to yield 35,413 and 20,599 high quality ESTs for A. mexicanum and A. t. tigrinum, respectively. Because the A. t. tigrinum ESTs were obtained primarily from a normalized library, an approximately equal number of contigs were obtained for each species, with 21,091 unique contigs identified overall. The 10,592 contigs that showed significant similarity to sequences from the human RefSeq database reflected a diverse array of molecular functions and biological processes, with many corresponding to genes expressed during spinal cord injury in rat and fin regeneration in zebrafish. To demonstrate the utility of these EST resources, we searched databases to identify probes for regeneration research, characterized intra- and interspecific nucleotide polymorphism, saturated a human - Ambystoma synteny group with marker loci, and extended PCR primer sets designed for A. mexicanum / A. t. tigrinum orthologues to a related tiger salamander species. CONCLUSIONS: Our study highlights the value of developing resources in traditional model systems where the likelihood of information transfer to multiple, closely related taxa is high, thus simultaneously enabling both laboratory and natural history research

From biomedicine to natural history research: EST resources for ambystomatid salamanders

BackgroundEstablishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum) and Eastern tiger salamander (A. tigrinum tigrinum), species with deep and diverse research histories.ResultsApproximately 40,000 quality cDNA sequences were isolated for these species from various tissues, including regenerating limb and tail. These sequences and an existing set of 16,030 cDNA sequences for A. mexicanum were processed to yield 35,413 and 20,599 high quality ESTs for A. mexicanum and A. t. tigrinum, respectively. Because the A. t. tigrinum ESTs were obtained primarily from a normalized library, an approximately equal number of contigs were obtained for each species, with 21,091 unique contigs identified overall. The 10,592 contigs that showed significant similarity to sequences from the human RefSeq database reflected a diverse array of molecular functions and biological processes, with many corresponding to genes expressed during spinal cord injury in rat and fin regeneration in zebrafish. To demonstrate the utility of these EST resources, we searched databases to identify probes for regeneration research, characterized intra- and interspecific nucleotide polymorphism, saturated a human – Ambystoma synteny group with marker loci, and extended PCR primer sets designed for A. mexicanum / A. t. tigrinum orthologues to a related tiger salamander species.ConclusionsOur study highlights the value of developing resources in traditional model systems where the likelihood of information transfer to multiple, closely related taxa is high, thus simultaneously enabling both laboratory and natural history research

The rise of oxygen and the hydrogen hourglass

Funding: the NASA Exobiology Program and the NASA National Astrobiology Institute. DCC acknowledges support from NASA Exobiology grant number NNX10AQ90G.Oxygenic photosynthesis appears to be necessary for an oxygen-rich atmosphere like Earth’s. But available geological and geochemical evidence suggest that at least 200 Myr, and possibly more than 700 Myr, elapsed between the advent of oxygenic photosynthesis and the establishment of an oxygen atmosphere. The interregnum implies that at least one other necessary condition for O2 needed to be met. Here we argue that the second condition was the oxidation of the surface and crust to the point where O2 became more stable than competing reduced gases such as CH4. The cause of Earth’s surface oxidation would be the same cause as it is for other planets with oxidized surfaces: hydrogen escape to space. The duration of the interregnum would have been determined by the rate of hydrogen escape and by the size of the reduced reservoir that needed to be oxidized before O2 became favored. We suggest that continental growth has been influenced by hydrogen escape, and we speculate that, if there must be an external bias to biological evolution, hydrogen escape can be that bias.Publisher PDFPeer reviewe

Sedimentology, chemostratigraphy and stromatolites of lower Paleoproterozoic carbonates, Turee Creek Group, Western Australia.

The ca. 2.45–2.22 Ga Turee Creek Group, Western Australia, contains carbonate-rich horizons that postdate earliest Proterozoic iron formations, bracket both Paleoproterozoic glaciogenic beds and the onset of the Great Oxidation Event (GOE), and predate ca. 2.2–2.05 Ga Lomagundi-Jatuli C-isotopic excursion(s). As such, Turee Creek carbonate strata provide an opportunity to characterize early Paleoproterozoic carbonate sedimentation and carbon cycle dynamics in the context of significant global change. Here, we report on the stratigraphy, sedimentology, petrology, carbon isotope chemostratigraphy, and stromatolite development for carbonate-rich successions within the pre-glacial part of the Kungarra Formation and the postglacial Kazput Formation. Kungarra carbonate units largely occur as laterally discontinuous beds within a thick, predominantly siliciclastic shelf deposit. While this succession contains thin microbialite horizons, most carbonates consist of patchy calcite overgrowths within a siliciclastic matrix. C-isotopic values show marked variation along a single horizon and even within hand samples, reflecting spatially and temporally variable mixing between dissolved inorganic carbon in seawater and isotopically light inorganic carbon generated via syn- and post-depositional remineralization of organic matter.In contrast, the Kazput carbonates consist of subtidal stromatolites, grainstones, and micrites deposited on a mixed carbonate–siliciclastic shelf. These carbonates exhibit moderate δ13C values of −2‰ to +1.5‰ and likely preserve a C-isotopic signature of seawater. Kazput carbonates, thus, provide some of the best available evidence that an interval of unexceptional C-isotopic values separates the Lomagundi-Jatuli C-isotopic excursion(s) from the initiation of the GOE as inferred from multiple sulfur isotopes (loss of mass independent fractionation). The Kazput Formation also contains unusual, m-scale stromatolitic buildups, which are composed of sub-mm laminae and discontinuous, convex upward lenticular precipitates up to a few mm in maximum thickness. Laminae, interpreted as microbial mat layers, contain quartz and clay minerals as well as calcite, whereas precipitate lenses consist of interlocking calcite anhedra, sometimes showing faint mm-scale banding. These cements formed either as infillings of primary voids formed by gas emission within penecontemporaneously lithified mats, or as local seafloor precipitates that formed on, or within, surface mats. It is possible that both mechanisms interacted to form the unique Kazput stromatolites. These microbialites speak to a distinctive interaction between life and environment early in the Paleoproterozoic Era