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

DGB 40 ft parachute Final report

Structural design and performance tests on disk gap-band parachute for supersonic planetary entr

Single Molecule Study of the Intrinsically Disordered FG-Repeat Nucleoporin 153

AbstractNucleoporins (Nups), which are intrinsically disordered, form a selectivity filter inside the nuclear pore complex, taking a central role in the vital nucleocytoplasmic transport mechanism. These Nups display a complex and nonrandom amino-acid architecture of phenylalanine glycine (FG)-repeat clusters and intra-FG linkers. How such heterogeneous sequence composition relates to function and could give rise to a transport mechanism is still unclear. Here we describe a combined chemical biology and single-molecule fluorescence approach to study the large human Nup153 FG-domain. In order to obtain insights into the properties of this domain beyond the average behavior, we probed the end-to-end distance (RE) of several ∼50-residues long FG-repeat clusters in the context of the whole protein domain. Despite the sequence heterogeneity of these FG-clusters, we detected a reoccurring and consistent compaction from a relaxed coil behavior under denaturing conditions (RE/RE,RC = 0.99 ± 0.15 with RE,RC corresponding to ideal relaxed coil behavior) to a collapsed state under native conditions (RE/RE,RC = 0.79 ± 0.09). We then analyzed the properties of this protein on the supramolecular level, and determined that this human FG-domain was in fact able to form a hydrogel with physiological permeability barrier properties

High accuracy measure of atomic polarizability in an optical lattice clock

Despite being a canonical example of quantum mechanical perturbation theory, as well as one of the earliest observed spectroscopic shifts, the Stark effect contributes the largest source of uncertainty in a modern optical atomic clock through blackbody radiation. By employing an ultracold, trapped atomic ensemble and high stability optical clock, we characterize the quadratic Stark effect with unprecedented precision. We report the ytterbium optical clock's sensitivity to electric fields (such as blackbody radiation) as the differential static polarizability of the ground and excited clock levels: 36.2612(7) kHz (kV/cm)^{-2}. The clock's fractional uncertainty due to room temperature blackbody radiation is reduced an order of magnitude to 3 \times 10^{-17}.Comment: 5 pages, 3 figures, 2 table