Digital gene expression analysis of the zebra finch genome

Background: In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results: Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions: Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates

The annual number of breeding adults and the effective population size of syntopic newts (Triturus cristatus, T-marmoratus)

Pond-breeding amphibians are deme-structured organisms with a population genetic structure particularly susceptible to demographic threats. We estimated the effective number of breeding adults (N-b) and the effective population size (N-e) of the European urodele amphibians Triturus cristatus (the crested newt) and T. marmoratus (the marbled newt), using temporal shifts in microsatellite allele frequencies. Eight microsatellite loci isolated from a T. cristatus library were used, five of which proved polymorphic in T. marmoratus, albeit with high frequencies of null alleles at two loci. Three ponds in western France were sampled, situated 4-10 kilometres apart and inhabited by both species. Parent-offspring cohort comparisons were used to measure N-b; samples collected at time intervals of nine or 12 years, respectively, were used to measure N-e. The adult population census size (N) was determined by mark-recapture techniques. With one exception, genetic distances (F-ST) between temporal samples were lower than among populations. N-b ranged between 10.6 and 101.8 individuals, N-e ranged between 9.6 and 13.4 individuals. For the pond where both parameters were available, N-b/N (overall range: 0.10-0.19) was marginally larger than N-e/N (overall range: 0.09-0.16), which is reflected in the temporal stability of N. In line with the observed differences in reproductive life-histories between the species, N-b/N ratios for newts were about one order of magnitude higher than for the anuran amphibian Bufo bufo. Despite of the colonization of the study area by T. cristatus only some decades ago, no significant genetic bottleneck could be detected. Our findings give rise to concerns about the long-term demographic viability of amphibian populations in situations typical for European landscapes

Isolation of Psoroptes scab mite microsatellite markers (Acari: Psoroptidae)

Nine microsatellite markers have been isolated from the scab mite,Psoroptes ovis. These markers have been tested for polymorphism in individual Psoroptes mites originating from two hosts, the European rabbit, Oryctolagus cuniculus, and sheep, Ovis aries. No definitive picture of Psoroptes species’ status or interrelationships exists. This study provides the basis for a new molecular system to elucidate the systematics of groupings within the genus Psoroptes, allowing us to clarify the population dynamics and epidemiology of the mites causing sheep scab world wide

Zero-bias molecular electronics: Exchange-correlation corrections to Landauer's formula

Standard first principles calculations of transport through single molecules miss exchange-correlation corrections to the Landauer formula. From Kubo response theory, both the Landauer formula and these corrections in the limit of zero bias are derived and calculations are presented.Comment: 4 pages, 3 figures, final version to appear in Phys. Rev. B, Rapid Communication

Global tectonic studies: Hotspots and anomalous topography

Volcanic activity on Earth and its secular variations are compared with that on other terrestrial planets. Activity at divergent, transform, and convergent plate margins is described with particular emphasis on hot spots and flood basalts. The timing and causing of uplifting above 500 meters, which in not associated with either plate boundaries or the normal nonplate margin edges of continents is considered with particular focus on the Guyana Highlands in southern Venezuela and western British Guiana, and the Brazilian Highlands in the central, eastern, and southern parts of the country. The mode and mechanism of plateau uplifting and the re-elevation of old mountain belts and subsidence of intra-continental basins are also discussed

Notes on the development of a thermistor temperature profile recorder (TPR)

A vertical temperature profile recorder, utilizing a thermistor as the temperature sensing element, has been developed for use on lakes, bays, or other enclosed or semi-enclosed bodies of water where temperature profiles in the upper 30 m are desired. Tests of the instrument indicate that it is rugged and durable, giving easily readable records accurate to ± 0.1 ° C...

Confinement effects in a guided-wave interferometer with millimeter-scale arm separation

Guided-wave atom interferometers measure interference effects using atoms held in a confining potential. In one common implementation, the confinement is primarily two-dimensional, and the atoms move along the nearly free dimension under the influence of an off-resonant standing wave laser beam. In this configuration, residual confinement along the nominally free axis can introduce a phase gradient to the atoms that limits the arm separation of the interferometer. We experimentally investigate this effect in detail, and show that it can be alleviated by having the atoms undergo a more symmetric motion in the guide. This can be achieved by either using additional laser pulses or by allowing the atoms to freely oscillate in the potential. Using these techniques, we demonstrate interferometer measurement times up to 72 ms and arm separations up to 0.42 mm with a well controlled phase, or times of 0.91 s and separations of 1.7 mm with an uncontrolled phase.Comment: 14 pages, 6 figure