Comparative analyses of multi-species sequences from targeted genomic regions

The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.     

Morphological integration in the cranium during anuran metamorphosis

We examined the role of thyroid hormone in mediating morphological integration between cranial cartilage and bone during anuran metamorphosis. Exogenous T3 applied to premetamorphic tadpoles (Bombina orientalis) via intracranial implants of plastic micropellets precociously induced typical metamorphic changes in both tissues, but also dissociated the relative timing of developmental events between them. Morphological integration between the two primary cranial tissues is achieved in part by each tissue responding independently to endocrine factors and does not reflect a tight developmental coupling between them.     

Chemical reduction of three-dimensional silica micro-assemblies into microporous silicon replicas

The carbothermal reduction of silica into silicon requires the use of temperatures well above the silicon melting point (> or =2,000 degrees C). Solid silicon has recently been generated directly from silica at much lower temperatures (< or =850 degrees C) via electrochemical reduction in molten salts. However, the silicon products of such electrochemical reduction did not retain the microscale morphology of the starting silica reactants. Here we demonstrate a low-temperature (650 degrees C) magnesiothermic reduction process for converting three-dimensional nanostructured silica micro-assemblies into microporous nanocrystalline silicon replicas. The intricate nanostructured silica microshells (frustules) of diatoms (unicellular algae) were converted into co-continuous, nanocrystalline mixtures of silicon and magnesia by reaction with magnesium gas. Selective magnesia dissolution then yielded an interconnected network of silicon nanocrystals that retained the starting three-dimensional frustule morphology. The silicon replicas possessed a high specific surface area (>500 m(2) g(-1)), and contained a significant population of micropores (< or =20 A). The silicon replicas were photoluminescent, and exhibited rapid changes in impedance upon exposure to gaseous nitric oxide (suggesting a possible application in microscale gas sensing). This process enables the syntheses of microporous nanocrystalline silicon micro-assemblies with multifarious three-dimensional shapes inherited from biological or synthetic silica templates for sensor, electronic, optical or biomedical applications.     

The genomic basis of adaptive evolution in threespine sticklebacks

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.     

Expression of a mammalian Na-H exchanger in muscle fibres of the giant barnacle

It is now well established that the internal pH (pHi) of mammalian cells is regulated by means of a plasma membrane transport system that exchanges extracellular Na+ for intracellular H+ (ref. 1). Furthermore, modulation of the activity of the Na-H exchanger seems to have a crucial role in the action of various mitogens and growth factors. The possibility that such a mammalian Na-H exchanger might be efficiently expressed in a giant invertebrate cell was suggested to us by recent results of Barnard and Miledi and colleagues, who demonstrated in frog oocytes the expression of various plasma membrane channels that presumably were encoded by the mammalian messenger RNA wih which the oocytes had been injected. We used muscle fibres of the giant barnacle, which normally have no demonstrable Na-H exchanger activity, and report here that, when injected with poly(A)+ RNA isolated from rabbit liver, the muscle fibres express a Na-H exchanger. No such expression is observed, however, when the injected material is pretreated with ribonuclease A. As hepatocytes are known to possess a Na-H exchanger, the most straightforward interpretation of our data is that a mammalian Na-H exchanger has been expressed in the muscle fibre of an invertebrate.