Development of an unbiased statistical method for the analysis of unigenic evolution

BACKGROUND: Unigenic evolution is a powerful genetic strategy involving random mutagenesis of a single gene product to delineate functionally important domains of a protein. This method involves selection of variants of the protein which retain function, followed by statistical analysis comparing expected and observed mutation frequencies of each residue. Resultant mutability indices for each residue are averaged across a specified window of codons to identify hypomutable regions of the protein. As originally described, the effect of changes to the length of this averaging window was not fully eludicated. In addition, it was unclear when sufficient functional variants had been examined to conclude that residues conserved in all variants have important functional roles. RESULTS: We demonstrate that the length of averaging window dramatically affects identification of individual hypomutable regions and delineation of region boundaries. Accordingly, we devised a region-independent chi-square analysis that eliminates loss of information incurred during window averaging and removes the arbitrary assignment of window length. We also present a method to estimate the probability that conserved residues have not been mutated simply by chance. In addition, we describe an improved estimation of the expected mutation frequency. CONCLUSION: Overall, these methods significantly extend the analysis of unigenic evolution data over existing methods to allow comprehensive, unbiased identification of domains and possibly even individual residues that are essential for protein function

METIS - the Mid-infrared E-ELT Imager and Spectrograph

METIS, the Mid-infrared ELT Imager and Spectrograph (formerly called MIDIR), is a proposed instrument for the European Extremely Large Telescope (E-ELT), currently undergoing a phase-A study. The study is carried out within the framework of the ESO-sponsored E-ELT instrumentation studies. METIS will be designed to cover the E-ELT science needs at wavelengths longward of 3um, where the thermal background requires different operating schemes. In this paper we discuss the main science drivers from which the instrument baseline has been derived. Specific emphasis has been given to observations that require very high spatial and spectral resolution, which can only be achieved with a ground-based ELT. We also discuss the challenging aspects of background suppression techniques, adaptive optics in the mid-IR, and telescope site considerations. The METIS instrument baseline includes imaging and spectroscopy at the atmospheric L, M, and N bands with a possible extension to Q band imaging. Both coronagraphy and polarimetry are also being considered. However, we note that the concept is still not yet fully consolidated. The METIS studies are being performed by an international consortium with institutes from the Netherlands, Germany, France, United Kingdom, and Belgium.Comment: 15 pages, to be published in Proc SPIE 7014: Ground-based & Airborne Instrumentation for Astronomy I

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

A population of high-redshift type-2 quasars-I. Selection criteria and optical spectra

Peer reviewe

Development of an unbiased statistical method for the analysis of unigenic evolution-0

<p><b>Copyright information:</b></p><p>Taken from "Development of an unbiased statistical method for the analysis of unigenic evolution"</p><p>BMC Bioinformatics 2006;7():150-150.</p><p>Published online 17 Mar 2006</p><p>PMCID:PMC1434776.</p><p>Copyright © 2006 Behrsin et al; licensee BioMed Central Ltd.</p> of individual residues was averaged over a window of 1, 5, 11 or 25 codons. The hypo- or hypermutability was then plotted as a bar in the center of the specified window and the window was shifted downstream one codon at a time. Individual hypomutable regions, designated A, B, C, and D are indicated on the plot for the 11 codon window. For comparison, the difference between mutability calculated by previous methods (5) and mutability as described in this manuscript is also shown (circles)

Development of an unbiased statistical method for the analysis of unigenic evolution-1

<p><b>Copyright information:</b></p><p>Taken from "Development of an unbiased statistical method for the analysis of unigenic evolution"</p><p>BMC Bioinformatics 2006;7():150-150.</p><p>Published online 17 Mar 2006</p><p>PMCID:PMC1434776.</p><p>Copyright © 2006 Behrsin et al; licensee BioMed Central Ltd.</p>d against region length and amino acid residue number. Calculations were performed as described in the text. Only regions that are significant at the 0.005 level are plotted; the whole window is plotted whenever this significance level is achieved. If a residue is involved in more than one significant region of the same length, the region with the highest χvalue is plotted. Colours indicate χof the region and range from deep red (χ> 15, corresponding to α < 0.0001) to pale green (χ> 8, α < 0.005). Four hypomutable regions approximating regions A-D (Figure 1) are evident