Primique: automatic design of specific PCR primers for each sequence in a family

<p>Abstract</p> <p>Background</p> <p>In many contexts, researchers need specific primers for all sequences in a family such that each primer set amplifies only its target sequence and none of the others, e.g. to detect which transcription factor out of a family of very similar proteins that is present in a sample, or to design diagnostic assays for the identification of pathogen strains.</p> <p>Results</p> <p>This paper presents primique, a new graphical, user-friendly, fast, web-based tool which solves the problem: It designs specific primers for each sequence in an uploaded set. Further, a secondary set of sequences <it>not </it>to be amplified by any primer pair may be uploaded. Primers with high sequence similarity to non-target sequences are selected against. Lastly, the suggested primers may be checked against the National Center for Biotechnology Information databases for possible mis-priming.</p> <p>Conclusion</p> <p>Results are presented in interactive tables, and various primer properties are listed and displayed graphically. Any close match alignments can be displayed. Given 30 sequences, the running time of primique is about 20 seconds.</p> <p>primique can be reached via this web address: <url>http://cgi-www.daimi.au.dk/cgi-chili/primique/front.py</url></p

A Computational Pipeline for the Development of Comparative Anchor Tagged Sequence (CATS) Markers

Key points: Molecular markers that allow the transfer of map information from one species to another are vital in comparative genetics. To identify potential anchor marker sequences more efficiently, we have established a bioinformatic pipeline that combines multi-species EST- and genome- sequence data. Taking advantage of information from a few related species, comparative EST sequence analysis identifies evolutionary conserved sequences in less well-characterised species in the same family. Alignment of evolutionary conserved EST sequences with corresponding genomic sequences defines sets of PCR primer sites flanking introns. Markers identified by this procedure will be readily transferable to other species since they are selected on the basis of their common evolutionary origin. We exemplify our procedure on legumes and grasses, where model plant studies and the genome- and EST-sequence data available have a potential impact on breeding crop species

Oscillations in the Sun with SONG: Setting the scale for asteroseismic investigations

Context. We present the first high-cadence multi-wavelength radial-velocity observations of the Sun-as-a-star, carried out during 57 consecutive days using the stellar \'echelle spectrograph at the Hertzsprung SONG Telescope operating at the Teide Observatory. Aims. The aim was to produce a high-quality data set and reference values for the global helioseismic parameters {\nu_{max}}, and {\Delta \nu} of the solar p-modes using the SONG instrument. The obtained data set or the inferred values should then be used when the scaling relations are applied to other stars showing solar-like oscillations which are observed with SONG or similar instruments. Methods. We used different approaches to analyse the power spectrum of the time series to determine {\nu_{max}}; simple Gaussian fitting and heavy smoothing of the power spectrum. {\Delta\nu} was determined using the method of autocorrelation of the power spectrum. The amplitude per radial mode was determined using the method described in Kjeldsen et al. (2008). Results. We found the following values for the solar oscillations using the SONG spectrograph: {\nu_{max}} = 3141 {\pm} 12 {\mu}Hz, {\Delta\nu} = 134.98 {\pm} 0.04 {\mu}Hz and an average amplitude of the strongest radial modes of 16.6 {\pm} 0.4 cm/s. These values are consistent with previous measurements with other techniques.Comment: 5 pages, 5 figures, letter accepted for A&

The mass and age of the first SONG target: the red giant 46 LMi

Context. The Stellar Observation Network Group (SONG) is an initiative to build a worldwide network of 1m telescopes with high-precision radial-velocity spectrographs. Here we analyse the first radial-velocity time series of a red-giant star measured by the SONG telescope at Tenerife. The asteroseismic results demonstrate a major increase in the achievable precision of the parameters for red-giant stars obtainable from ground-based observations. Reliable tests of the validity of these results are needed, however, before the accuracy of the parameters can be trusted. Aims. We analyse the first SONG time series for the star 46 LMi, which has a precise parallax and an angular diameter measured from interferometry, and therefore a good determination of the stellar radius. We use asteroseismic scaling relations to obtain an accurate mass, and modelling to determine the age. Methods. A 55-day time series of high-resolution, high S/N spectra were obtained with the first SONG telescope. We derive the asteroseismic parameters by analysing the power spectrum. To give a best guess on the large separation of modes in the power spectrum, we have applied a new method which uses the scaling of Kepler red-giant stars to 46 LMi. Results. Several methods have been applied: classical estimates, seismic methods using the observed time series, and model calculations to derive the fundamental parameters of 46 LMi. Parameters determined using the different methods are consistent within the uncertainties. We find the following values for the mass M (scaling), radius R (classical), age (modelling), and surface gravity (combining mass and radius): M = 1.09 ± 0.04 M⊙, R = 7.95 ± 0.11 R⊙ age t = 8.2 ± 1.9 Gy, and log g = 2.674 ± 0.013. Conclusions. The exciting possibilities for ground-based asteroseismology of solar-like oscillations with a fully robotic network have been illustrated with the results obtained from just a single site of the SONG network. The window function is still a severe problem which will be solved when there are more nodes in the network

MASCARA-2 b: A hot Jupiter transiting the mV=7.6m_V=7.6 A-star HD185603

In this paper we present MASCARA-2 b, a hot Jupiter transiting the $m_V=7.6$ A2 star HD 185603. Since early 2015, MASCARA has taken more than 1.6 million flux measurements of the star, corresponding to a total of almost 3000 hours of observations, revealing a periodic dimming in the flux with a depth of $1.3\%$. Photometric follow-up observations were performed with the NITES and IAC80 telescopes and spectroscopic measurements were obtained with the Hertzsprung SONG telescope. We find MASCARA-2 b orbits HD 185603 with a period of $3.474119^{+0.000005}_{-0.000006}~\rm{days}$ at a distance of $0.057 \pm 0.006~\rm{AU}$, has a radius of $1.83 \pm 0.07~\rm{R}_{\rm{J}}$ and place a $99\%$ upper limit on the mass of $< 17~\rm{M}_{\rm{J}}$. HD 185603 is a rapidly rotating early-type star with an effective temperature of $8980^{+90}_{-130}~\rm{K}$ and a mass and radius of $1.89^{+0.06}_{-0.05}~M_\odot$, $1.60 \pm 0.06~R_\odot$, respectively. Contrary to most other hot Jupiters transiting early-type stars, the projected planet orbital axis and stellar spin axis are found to be aligned with $\lambda=0.6 \pm 4^\circ$. The brightness of the host star and the high equilibrium temperature, $2260 \pm 50~\rm{K}$, of MASCARA-2 b make it a suitable target for atmospheric studies from the ground and space. Of particular interest is the detection of TiO, which has recently been detected in the similarly hot planets WASP-33 b and WASP-19 b.Comment: 8 pages, 4 figures, Accepted for publication in A&

Can legume systeny be useful in guiding the introgression of wild genes into cultivated peanut?

Edição dos resumos do Workshop, Porto Alegre, RS, 2007

Can legume synteny be useful in guiding the introgression of wild genes into cultivated peanut?

Edição do International Workshop Integrating Genomics Into Plant Breeding, Porto Alegre, out. 2007

Lidar-Based Relative Position Estimation and Tracking for Multi-Robot Systems

Relative positioning systems play a vital role in current multi-robot systems. We present a self-contained detection and tracking approach, where a robot estimates a distance (range) and an angle (bearing) to another robot using measurements extracted from the raw data provided by two laser range finders. We propose a method based on the detection of circular features with least-squares fitting and filtering out outliers using a map-based selection. We improve the estimate of the relative robot position and reduce its uncertainty by feeding measurements into a Kalman filter, resulting in an accurate tracking system. We evaluate the performance of the algorithm in a realistic indoor environment to demonstrate its robustness and reliability

Process evaluation for stressor reduction interventions in sport

Stressor reduction interventions may have the potential to improve the well-being of those involved in sport. Organizational psychologists have used these primary interventions in various performance domains. The authors describe the stressor reduction design and implementation processes, and the contexts in which they occur, that impact on these interventions. The authors then examine how process evaluation methods can be applied during stressor reduction in sport settings. Process evaluation requires the frequent collection of data about intervention experiences and events from multiple sources using a mixed-methods approach. The article contains practical recommendations for sport psychologists who implement stressor reduction interventions