Expression of FoxC, FoxF, FoxL1, and FoxQ1 genes in the dogfish scyliorhinus canicula defines ancient and derived roles for fox genes in vertebrate development

In the human genome, members of the FoxC, FoxF, FoxL1, and FoxQ1 gene families are found in two paralagous clusters. Here we characterize all four gene families in the dogfish Seyliorhinus canicula, a member of the cartilaginous fish lineage that diverged before the radiation of osteichthyan vertebrates. We identify two FoxC genes, two FoxF genes, and single FoxQ1 and FoxL1 genes, demonstrating cluster duplication preceded the radiation of gnathostomes. The expression of all six genes was analyzed by in situ hybridization. The results show conserved expression of FoxL1, FoxF, and FoxC genes in different compartments of the mesoderm and of FoxQ1 in pharyngeal endoderm and its derivatives, confirming these as ancient sites of Fox gene expression, and also illustrate multiple cases of lineage-specific expression domains. Comparison to invertebrate chordates shows that the majority of conserved vertebrate expression domains mark tissues that are part of the primitive chordate body plan.

Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.

Human evolution, nutritional ecology and prebiotics in ancient diet

Modern studies of prebiotic non digestible carbohydrates continue to expand and demonstrate their colonic and systemic benefits. However, virtually nothing is known of their use among ancient populations. In this paper we discuss evidence for prebiotic use in the archaeological record from select areas of the world. It is suggested that members of our genus Homo would have had sufficient ecological opportunity to include prebiotic-bearing plants in diet as early as ~ 2 million years ago, but that significant dietary intake would not have taken place until the advent of technological advances that characterized the Upper Paleolithic of ~40,000 years ago. Throughout human evolution, hominid populations that diversified their diet to include prebiotic-bearing plants would have had a selective advantage over competitors.

Interference filters and coatings for mid-infrared astronomy (8-30µm)

The VISIR instrument for the European Southern Observatory (ESO) Very Large Telescope (VLT) is a thermal-infrared imager and spectrometer currently being developed by the French Service d'Astrophysique of CEA Saclay, and Dutch NFRA ASTRON Dwingeloo consortium. This cryogenic instrument will employ precision infrared bandpass filters in the N-( =7.5-14µm) and Q-( =16-28µm) band mid-IR atmospheric windows to study interstellar and circumstellar environments crucial for star and planetary formation theories. As the filters in these mid-IR wavelength ranges are of interest to many astronomical cryogenic instruments, a worldwide astronomical filter consortium was set up with participation from 12 differing institutes, each requiring instrument specific filter operating environments and optical metrology. This paper describes the design and fabrication methods used to manufacture these astronomical consortium filters, including the rationale for the selection of multilayer coating designs, temperature-dependant optical properties of the filter materials and FTIR spectral measurements showing the changes in passband and blocking performance on cooling to <50K. We also describe the development of a 7-14µm broadband antireflection coating deposited on Ge lenses and KRS-5 grisms for cryogenic operation at 40K

Pollen analysis and planted ancient woodland restoration strategies: a case study from the Wentwood, southeast Wales,UK

This paper considers the contribution of pollen analysis to conservation strategies aimed at restoring planted ancient woodland. Pollen and charcoal data are presented from organic deposits located adjacent to the Wentwood, a large planted ancient woodland in southeast Wales. Knowledge of the ecosystems preceding conifer planting can assist in restoring ancient woodlands by placing fragmented surviving ancient woodland habitats in a broader ecological, historical and cultural context. These habitats derive largely from secondary woodland that regenerated in the 3rd–5th centuries A.D. following largescale clearance of Quercus-Corylus woodland during the Romano-British period. Woodland regeneration favoured Fraxinus and Betula. Wood pasture and common land dominated the Wentwood during the medieval period until the enclosures of the 17th century. Surviving ancient woodland habitats contain an important Fagus component that probably reflects an earlier phase of planting preceding conifer planting in the 1880s. It is recommended that restoration measures should not aim to recreate static landscapes or woodland that existed under natural conditions. Very few habitats within the Wentwood can be considered wholly natural because of the long history of human impact. In these circumstances, restoration should focus on restoring those elements of the cultural landscape that are of most benefit to a range of flora and fauna, whilst taking into account factors that present significant issues for future conservation management, such as the adverse effects from projected climate change.

Cooled filters 16-42µm for FIR astronomy

The design and manufacture of dielectric-film interference filters for cooled FIR stronmy is described. The bands are 16.5-21.5µm, 17.5-19.5µm, 19.5-21.5µm and 27µm cut on. The films are PbTe/CdSe and the substrates are CdTe (some 1/2 mm thick), without absorption in the region: KRS-6 films are used for antireflection.