A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Arenas Gomez, C. M., Woodcock, M. R., Smith, J. J., Voss, S. R., & Delgado, J. P. A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia. Data in Brief, 29, (2020): 105256, doi:10.1016/j.dib.2020.105256.The amphibian order Caudata, contains several important model species for biological research. However, there is need to generate transcriptome data from representative species of the primary salamander families. Here we describe a de novo reference transcriptome for a terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). We employed paired-end (PE) illumina RNA sequencing to assemble a de novo reference transcriptome for B. vallecula. Assembled transcripts were compared against sequences from other vertebrate taxa to identify orthologous genes, and compared to the transcriptome of a close plethodontid relative (Bolitoglossa ramosi) to identify commonly expressed genes in the skin. This dataset should be useful to future comparative studies aimed at understanding important biological process, such as immunity, wound healing, and the production of antimicrobial compounds.This work was funded by a research grant from COLCIENCIAS 569 (GRANT 027-2103) and CODI (Programa Sostenibilidad) 2013–2014 of the University of Antioquia. A PhD fellowship to the first author, Claudia Arenas was funded by the COLCIENCIAS 567 Grant. We thank the lab of Juan Fernando Alzate from the University of Antioquia for their help in developing our bioinformatic methodological approach. We thank Andrea Gómez and Melisa Hincapie for their help in animal collection and husbandry

Network Analysis and Comparative Phylogenomics of MicroRNAs and their Respective Messenger RNA Targets Using Twelve Drosophila species

MicroRNAs represent a special class of small (~21–25 nucleotides) non-coding RNA molecules which exert powerful post-transcriptional control over gene expression in eukaryotes. Indeed microRNAs likely represent the most abundant class of regulators in animal gene regulatory networks. This study describes the recovery and network analyses of a suite of homologous microRNA targets recovered through two different prediction methods for whole gene regions across twelve Drosophila species. Phylogenetic criteria under an accepted tree topology were used as a reference frame to 1) make inference into microRNA-target predictions, 2) study mathematical properties of microRNA-gene regulatory networks, 3) and conduct novel phylogenetic analyses using character data derived from weighted edges of the microRNA-target networks. This study investigates the evidences of natural selection and phylogenetic signatures inherent within the microRNA regulatory networks and quantifies time and mutation necessary to rewire a microRNA regulatory network. Selective factors that appear to operate upon seed aptamers include cooperativity (redundancy) of interactions and transcript length. Topological analyses of microRNA regulatory networks recovered significant enrichment for a motif possessing a redundant link in all twelve species sampled. This would suggest that optimization of the whole interactome topology itself has been historically subject to natural selection where resilience to attack have offered selective advantage. It seems that only a modest number of microRNA–mRNA interactions exhibit conservation over Drosophila cladogenesis. The decrease in conserved microRNA-target interactions with increasing phylogenetic distance exhibited a cure typical of a saturation phenomena. Scale free properties of a network intersection of microRNA target predictions methods were found to transect taxonomic hierarchy

Using Transcriptomics to Enable a Plethodontid Salamander (\u3cem\u3eBolitoglossa ramosi\u3c/em\u3e) for Limb Regeneration Research

Background: Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. To gain a broader perspective on the molecular basis of limb regeneration and enhance the molecular toolkit of an emerging plethodontid salamander (Bolitoglossa ramosi), we used RNA-Seq to generate a de novo reference transcriptome and identify differentially expressed genes during limb regeneration. Results: Using paired-end Illumina sequencing technology and Trinity assembly, a total of 433,809 transcripts were recovered and we obtained functional annotation for 142,926 non-redundant transcripts of the B. ramosi de novo reference transcriptome. Among the annotated transcripts, 602 genes were identified as differentially expressed during limb regeneration. This list was further processed to identify a core set of genes that exhibit conserved expression changes between B. ramosi and the Mexican axolotl (Ambystoma mexicanum), and presumably their common ancestor from approximately 180 million years ago. Conclusions: We identified genes from B. ramosi that are differentially expressed during limb regeneration, including multiple conserved protein-coding genes and possible putative species-specific genes. Comparative analyses reveal a subset of genes that show similar patterns of expression with ambystomatid species, which highlights the importance of developing comparative gene expression data for studies of limb regeneration among salamanders

A morphological and mtDNA analysis of the badlands tiger beetle, Cicindela (s. str.) decemnotata Say, 1817 (Coleoptera: Carabidae: Cicindelinae) with the description of three new subspecies

We conducted a morphological and mtDNA analysis of Cicindela decemnotata Say (Coleoptera: Carabidae: Cicindelinae) populations from throughout its geographic range to determine the extent of variation within the species and to assess the validity of subspecific names. The morphological study included an analysis of traditional subspecific characters including elytral color and maculations. These results provided evidence for the recognition of four subspecies of C. decemnotata, three of which are new: 1. C. d. decemnotata Say usually with green to dark green dorsal coloration and complete elytral maculations; it is widely distributed from Canada south to northern New Mexico and west into southern Utah and Idaho; 2. C. d. meriwetheri n. ssp. is distinguished by its bright green to green dorsal coloration, elytral maculation characterized by a thin middle band, a lack of humeral maculations, and a small number of genal setae; it has a restricted distribution from eastern Washington north to south central British Columbia; 3. C. d. bonnevillensis n. ssp. is distinguished by a combination of green to green-purple dorsal coloration and its greatly reduced elytral maculations; it is restricted to the area of ancient Lake Bonneville in north central Utah; 4. C. d. montevolans n. ssp. is distinguished by a predominately red-purple dorsal color and greatly reduced elytral maculations; its distribution is restricted to high elevations of the Bear River Mountains of northeastern Utah and southeastern Idaho. We also analyzed the mitochondrial haplotypes for cob and cox1 genes for one to six individuals from each of the six populations. This molecular analysis indicated recently diverged but discrete groups within C. decemnotata that are compatible with the subspecies distinctions postulated from morphology. These shallow molecular divergences within C. decemnotata are best explained by rapid phylogenetic radiation in the recent geological past in the wake of postglacial recession

FDR Explorer

AbstractIn this paper we describe the internal structures of FDR, the refinement model checker for Hoare's Communicating Sequential Processes (CSP), as well as an Application Programming Interface (API) allowing one to interact more closely with, and have fine grained control over, FDR's behaviour and data structures. With such information it is possible to create optimised CSP code to perform refinement checks that are more space/time efficient, hence enabling the analysis of more complex and data intensive specifications. This information is very valuable for both CSP users and tools that automatically generate CSP code, such as those related to security analysis generating test-cases as CSP processes. We also present a simple example of using the tool. Finally, we show how one can transform FDR's graph format into a graph notation (e.g., JGraph), hence enabling visualisation of Labelled Transition Systems (LTS) of CSP specifications

For and against ownership: William Godwin's theory of property

© 2009 University of Notre Dame. 12 month embargo by the publisher. Article will be released in April 2010.This article offers an interpretation of British philosopher William Godwin's theory of property ownership, as outlined in his Enquiry Concerning Political Justice. Godwin's work can be read as presenting an incoherent account of property rights, which, on the one hand, justifies its existence on seemingly utilitarian grounds while, on the other, impugns its legitimacy on egalitarian grounds. But the contradiction apparent in Godwin's position is actually illusory and can in fact be plausibly interpreted as comprising a coherent two-level understanding of political morality, wherein the right to own private property is best comprehended as a “right to do wrong.

Inner wellbeing: concept and validation of a new approach to subjective perceptions of wellbeing-India

© The Author(s) 2013. This article is published with open access at Springerlink.com. This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.This paper describes the conceptual development of a multi-domain, psychosocial model of 'Inner Wellbeing' (IWB) and assesses the construct validity of the scale designed to measure it. IWB expresses what people think and feel they are able to be and do. Drawing together scholarship in wellbeing and international development it is grounded in field research in marginalised, rural communities in the global South. Results from research in India at two points in time (2011 and 2013) are reported. At Time 1 (n = 287), we were unable to confirm an eight-factor, correlated model as distinct yet interrelated domains. However, at Time 2 (n = 335), we were able to confirm a revised, seven-factor correlated model with economic confidence, agency and participation, social connections, close relationships, physical and mental health, competence and self-worth, and values and meaning (five items per domain) as distinct yet interrelated domains. In particular, at Time 2, a seven-factor, correlated model provided a significantly better fit to the data than did a one-factor model.This work is supported by the Economic and Social Research Council/Department for International Development Joint Scheme for Research on International Development (Poverty Alleviation) grant number RES-167-25-0507 ES/H033769/1. Special thanks are due to Chaupal and Gangaram Paikra, Pritam Das, Usha Kujur, Kanti Minjh, Susanna Siddiqui, and Dinesh Tirkey

Refinement Modal Logic

In this paper we present {\em refinement modal logic}. A refinement is like a bisimulation, except that from the three relational requirements only `atoms' and `back' need to be satisfied. Our logic contains a new operator 'all' in addition to the standard modalities 'box' for each agent. The operator 'all' acts as a quantifier over the set of all refinements of a given model. As a variation on a bisimulation quantifier, this refinement operator or refinement quantifier 'all' can be seen as quantifying over a variable not occurring in the formula bound by it. The logic combines the simplicity of multi-agent modal logic with some powers of monadic second-order quantification. We present a sound and complete axiomatization of multi-agent refinement modal logic. We also present an extension of the logic to the modal mu-calculus, and an axiomatization for the single-agent version of this logic. Examples and applications are also discussed: to software verification and design (the set of agents can also be seen as a set of actions), and to dynamic epistemic logic. We further give detailed results on the complexity of satisfiability, and on succinctness

HDAC Regulates Transcription at the Outset of Axolotl Tail Regeneration

Tissue regeneration is associated with complex changes in gene expression and post-translational modifications of proteins, including transcription factors and histones that comprise chromatin. We tested 172 compounds designed to target epigenetic mechanisms in an axolotl (Ambystoma mexicanum) embryo tail regeneration assay. A relatively large number of compounds (N = 55) inhibited tail regeneration, including 18 histone deacetylase inhibitors (HDACi). In particular, romidepsin, an FDA-approved anticancer drug, potently inhibited tail regeneration when embryos were treated continuously for 7 days. Additional experiments revealed that romidepsin acted within a very narrow, post-injury window. Romidepsin treatment for only 1-minute post amputation inhibited regeneration through the first 7 days, however after this time, regeneration commenced with variable outgrowth of tailfin tissue and abnormal patterning. Microarray analysis showed that romidepsin altered early, transcriptional responses at 3 and 6-hour post-amputation, especially targeting genes that are implicated in tumor cell death, as well as genes that function in the regulation of transcription, cell differentiation, cell proliferation, pattern specification, and tissue morphogenesis. Our results show that HDAC activity is required at the time of tail amputation to regulate the initial transcriptional response to injury and regeneration

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