HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).
Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.
Conclusions: HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes

The Sunyaev-Zeldovich Effect at 1 and 2 mm towards ROSAT Clusters

An observing campaign was devoted to the search for the Sunyaev-Zeldovich (S-Z) effect towards X-ray ROSAT Clusters in the millimetric spectral domain. A double channel (1.2 and 2 {\it mm}) photometer was installed at the focus of the 15m Swedish ESO Submillimeter Telescope (SEST) in Chile in september 1994 and 1995 and observations of the targets S1077, A2744, S295 and RXJ0658-5557 were gathered. Detections were found for A2744 at 1 {\it mm} and in both channels (at 1.2 and 2 {\it mm}) towards RXJ0658-5557. For the first time there is evidence for the S-Z enhancement and both the latter and the decrement were detected on the same source. We discuss astrophysical and systematic effects which could give origin to these signals.Comment: 6 pg Latex file (style file included) including 1 ps figure, XVIth Moriond Astrophysics Meeting "The Anisotropies of the Cosmic Microwave Background", Les Arcs, Savoie-France, March 16-23 199

The abundance of boron in evolved A- and B-type stars

Boron abundances in A- and B-type stars may be a successful way to track evolutionary effects in these hot stars. The light elements -- Li, Be, and B -- are tracers of exposure to temperatures more moderate than those in which the H-burning CN-cycle operates. Thus, any exposure of surface stellar layers to deeper layers will affect these light element abundances. Li and Be are used in this role in investigations of evolutionary processes in cool stars, but are not observable in hotter stars. An investigation of boron, however, is possible through the B II 1362=C5 resonance line. We have gathered high resolution spectra from the IUE database of A- and B-type stars near 10~M_\odot for which nitrogen abundances have been determined (by Gies & Lambert, 1992, and Venn 1995). The B II 1362=C5 line is blended throughout the temperature range of this program, requiring spectrum syntheses to recover the boron abundances. For no star could we synthesize the 1362=C5 region using the meteoritic/solar boron abundance of log(B) =3D 2.88 (Anders & Grevesse 1989); a lower boron abundance was necessary which may reflect evolutionary effects (e.g., mass loss or mixing near the main-sequence), the natal composition of the star forming regions, or a systematic error in the analyses (e.g., non-LTE effects). Regardless of the initial boron abundance, and despite the possibility of non-LTE effects, it seems clear that boron is severely depleted in some stars. It may be that the nitrogen and boron abundances are anticorrelated, as would be expected from mixing between the H-burning and outer stellar layers. If, as we suspect, a residue of boron is present in the A-type supergiants, we may exclude a scenario in which mixing occurs continuously between the surface and the dee

Quasispecies evolution in general mean-field landscapes

I consider a class of fitness landscapes, in which the fitness is a function of a finite number of phenotypic "traits", which are themselves linear functions of the genotype. I show that the stationary trait distribution in such a landscape can be explicitly evaluated in a suitably defined "thermodynamic limit", which is a combination of infinite-genome and strong selection limits. These considerations can be applied in particular to identify relevant features of the evolution of promoter binding sites, in spite of the shortness of the corresponding sequences.Comment: 6 pages, 2 figures, Europhysics Letters style (included) Finite-size scaling analysis sketched. To appear in Europhysics Letter

Probing the interiors of the ice giants: Shock compression of water to 700 GPa and 3.8 g/ccm

Recently there has been tremendous increase in the number of identified extra-solar planetary systems. Our understanding of their formation is tied to exoplanet internal structure models, which rely upon equations of state of light elements and compounds like water. Here we present shock compression data for water with unprecedented accuracy that shows water equations of state commonly used in planetary modeling significantly overestimate the compressibility at conditions relevant to planetary interiors. Furthermore, we show its behavior at these conditions, including reflectivity and isentropic response, is well described by a recent first-principles based equation of state. These findings advocate this water model be used as the standard for modeling Neptune, Uranus, and "hot Neptune" exoplanets, and should improve our understanding of these types of planets.Comment: Accepted to Phys. Rev. Lett.; supplementary material attached including 2 figures and 2 tables; to view attachments, please download and extract the gzipped tar source file listed under "Other formats

A Deep VLA survey at 20cm of the ISO ELAIS survey regions

We have used the Very Large Array(VLA) in C configuration to carry out a sensitive 20cm radio survey of regions of sky that have been surveyed in the Far Infra-Red over the wavelength range 5-200 microns with ISO as part of the European Large Area ISO Survey(ELAIS). As usual in surveys based on a relatively small number of overlapping VLA pointings the flux limit varies over the area surveyed. The survey has a flux limit that varies from a 5$\sigma$ limit of 0.135mJy over an area of 0.12deg$^2$ to a 5$\sigma$ limit of 1.15mJy or better over the whole region covered of 4.22 deg$^2$. In this paper we present the radio catalogue of 867 sources. These regions of sky have previously been surveyed to shallow flux limits at 20cm with the VLA as part of the VLA D configuration NVSS(FWHM=45 arcsec) and VLA B configuration FIRST(FWHM=5 arcsec) surveys. We have carried out a a detailed comparison of the reliability of our own survey and these two independent surveys in order to assess the reliability and completeness of each survey.Comment: 19 pages, 24 figures, submitted to MNRAS, also available in http://www.ast.cam.ac.uk/~ciliegi/elais/paper

Onto better TRAILs for cancer treatment

Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), also known as Apo-2 ligand (Apo2L), is a member of the TNF cytokine superfamily. By cross-linking TRAIL-Receptor (TRAIL-R) 1 or TRAIL-R2, also known as death receptors 4 and 5 (DR4 and DR5), TRAIL has the capability to induce apoptosis in a wide variety of tumor cells while sparing vital normal cells. The discovery of this unique property among TNF superfamily members laid the foundation for testing the clinical potential of TRAIL-R-targeting therapies in the cancer clinic. To date, two of these therapeutic strategies have been tested clinically: (i) recombinant human TRAIL and (ii) antibodies directed against TRAIL-R1 or TRAIL-R2. Unfortunately, however, these TRAIL-R agonists have basically failed as most human tumors are resistant to apoptosis induction by them. It recently emerged that this is largely due to the poor agonistic activity of these agents. Consequently, novel TRAIL-R-targeting agents with increased bioactivity are currently being developed with the aim of rendering TRAIL-based therapies more active. This review summarizes these second-generation novel formulations of TRAIL and other TRAIL-R agonists, which exhibit enhanced cytotoxic capacity toward cancer cells, thereby providing the potential of being more effective when applied clinically than first-generation TRAIL-R agonists