Dynamics of gene expression and the regulatory inference problem

From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding of transcription factor molecules to regulatory DNA. Here, we construct stochastic models of gene expression dynamics and test them on experimental time-series data of messenger-RNA concentrations. The models are used to infer biophysical parameters of gene transcription, including the statistics of transcription factor-DNA binding and the target genes controlled by a given transcription factor.Comment: revised version to appear in Europhys. Lett., new titl

Optical spectrum of the post-AGB star HD56126 in the region 4010-8790 AA

We studied in detail the optical spectrum of the post-AGB star HD56126 (IRAS07134+1005). We use high resolution spectra (R=25000 and 60000) obtained with the echelle spectrographs of the 6-m telescope. About one and a half thousand absorptions of neutral atoms and ions, absorption bands of C_2, CN, and CH molecules, and interstellar bands (DIBs) are identified in the 4010 to 8790 AA wavelength region, and the depths and radial velocities of these spectral features are measured. Differences are revealed between the variations of the radial velocities measured from spectral features of different excitation. In addition to the well-known variability of the Halpha profile, we found variations in the profiles of a number of FeII, YII, and BaII lines. We also produce an atlas of the spectrum of HD56126 and its comparison staralpha Per. The full version of the atlas is available in electronic form from Web-address: http://www.sao.ru/hq/ssl/Atlas/Atlas.htmlComment: 42 pages, 6 figure

POLLUX : a database of synthetic stellar spectra

Synthetic spectra are needed to determine fundamental stellar and wind parameters of all types of stars. They are also used for the construction of theoretical spectral libraries helpful for stellar population synthesis. Therefore, a database of theoretical spectra is required to allow rapid and quantitative comparisons to spectroscopic data. We provide such a database offering an unprecedented coverage of the entire Hertzsprung-Russell diagram. We present the POLLUX database of synthetic stellar spectra. For objects with Teff < 6 000 K, MARCS atmosphere models are computed and the program TURBOSPECTRUM provides the synthetic spectra. ATLAS12 models are computed for stars with 7 000 K <Teff <15 000 K. SYNSPEC gives the corresponding spectra. Finally, the code CMFGEN provides atmosphere models for the hottest stars (Teff > 25 000 K). Their spectra are computed with CMF_FLUX. Both high resolution (R>150 000) optical spectra in the range 3 000 to 12 000 A and spectral energy distributions extending from the UV to near--IR ranges are presented. These spectra cover the HR diagram at solar metallicity. We propose a wide variety of synthetic spectra for various types of stars in a format that is compliant with the Virtual Observatory standards. A user--friendly web interface allows an easy selection of spectra and data retrieval. Upcoming developments will include an extension to a large range of metallicities and to the near--IR high resolution spectra, as well as a better coverage of the HR diagram, with the inclusion of models for Wolf-Rayet stars and large datasets for cool stars. The POLLUX database is accessible at http://pollux.graal.univ-montp2.fr/ and through the Virtual Observatory.Comment: 9 pages, 5 figures, accepted for publication in Astronomy ans Astrophysic

Report of the High-Level Commission on Carbon Prices

The purpose of this Commission is to explore explicit carbon-pricing options and levels that would induce the change in behaviors— particularly in those driving the investments in infrastructure, technology, and equipment—needed to deliver on the temperature objective of the Paris Agreement, in a way that fosters economic growth and development, as expressed in the Sustainable Development Goals (SDGs). This report does not focus on the estimation and evaluation of the climate change impacts that would be avoided by reducing carbon emissions. While the Commission also covers other policies relevant and important to carbon-pricing design and delivery on the Paris agreement, its primary focus is on pricing. This report has been prepared based on the Commission’s assessment of the available evidence and literature as well as on its members’ judgment, developed through their extensive international policy experience. While the commissioners are in broad agreement on the overall thrust of the arguments presented in the report, they may not necessarily support every single assertion and conclusion

High-latitude supergiants: anomalies in the spectrum of LN Hya in 2010

High-resolution echelle spectra taken with the 6-m telescope in 2003-2011 are used to study features of the optical spectrum and the velocity field in the atmosphere of the semiregular variable LN Hya in detail. The weak symmetric photospheric absorptions indicate radial velocity variations from night to night (by as much as 3 km/s), resulting from small pulsations. Peculiarities and profile variations were found for strong lines of FeI, FeII, BaII, SiII, etc. The profiles of these lines were asymmetric: their short-wave wings were extended and their cores were either split or distorted by emission. During the 2010 observing season, the position and depth of the Halpha absorption component, the intensities of the short and long-wave emission components, and the intensity ratio of the latter components varied from spectrum to spectrum. Weak emissions of neutral atoms (VI, MnI, CoI, NiI, FeI) appeared in the spectrum of June 1, 2010. All these spectral peculiarities, recorded for the first time, suggest that we have detected rapid changes in the physical conditions in the upper atmospheric layers of LN Hya in 2010.Comment: 17 pages, 5 figures, 3 table

An exploration of ambigrammatic sequences in narnaviruses

Narnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are 'ambigrammatic' and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The >3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development

The multimode pulsation of the delta Scuti star V784 Cassiopeae

We present an analysis of new Johnson and Stromgren photometric and medium-resolution spectroscopic observations of the delta Scuti type variable star V784 Cassiopeae. The data were obtained in three consecutive years between 1999 and 2001. The period analysis of the light curve resulted in the detection of four frequencies ranging from 9.15 c/d to 15.90 c/d, while there is a suggestion for more, unresolved frequency components, too. The mean Stromgren indices and Hipparcos parallax were combined to calculate the following physical parameters: =7100+-100 K, log g=3.8+-0.1, M_bol=1.50+-0.15 mag. The position of the star in the HR diagram was used to derive evolutionary mass and age yielding to a consistent picture of an evolved delta Scuti star with a mixture of radial plus non-radial modes.Comment: 11 pages, 9 figures, accepted for publication in A&