Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>Riboswitches are mRNA elements that change conformation when bound to small molecules. They are known to be key regulators of biosynthetic pathways in both prokaryotes and eukaryotes.</p> <p>Presentation of the Hypothesis</p> <p>The hypothesis presented here is that riboswitches function as receptors in hormone perception. We propose that riboswitches initiate or integrate signaling cascades upon binding to classic signaling molecules. The molecular interactions for ligand binding and gene expression control would be the same as for biosynthetic pathways, but the context and the cadre of ligands to consider is dramatically different. The hypothesis arose from the observation that a compound used to identify adenine binding RNA sequences is chemically similar to the classic plant hormone, or growth regulator, cytokinin. A general tenet of the hypothesis is that riboswitch-binding metabolites can be used to make predictions about chemically related signaling molecules. In fact, all cell permeable signaling compounds can be considered as potential riboswitch ligands. The hypothesis is plausible, as demonstrated by a cursory review of the transcriptome and genome of the model plant <it>Arabidopsis thaliana </it>for transcripts that <it>i) </it>contain an adenine aptamer motif, and <it>ii) </it>are also predicted to be cytokinin-regulated. Here, one gene, <it>CRK10 </it>(for <it>Cysteine-rich Receptor-like Kinase 10</it>, At4g23180), contains an adenine aptamer-related sequence and is down-regulated by cytokinin approximately three-fold in public gene expression data. To illustrate the hypothesis, implications of cytokinin-binding to the <it>CRK10 </it>mRNA are discussed.</p> <p>Testing the hypothesis</p> <p>At the broadest level, screening various cell permeable signaling molecules against random RNA libraries and comparing hits to sequence and gene expression data bases could determine how broadly the hypothesis applies. Specific cases, such as <it>CRK10 </it>presented here, will require experimental validation of direct ligand binding, altered RNA conformation, and effect on gene expression. Each case will be different depending on the signaling pathway and the physiology involved.</p> <p>Implications of the hypothesis</p> <p>This would be a very direct signal perception mechanism for regulating gene expression; rivaling animal steroid hormone receptors, which are frequently ligand dependent transcription initiation factors. Riboswitch-regulated responses could occur by modulating target RNA stability, translatability, and alternative splicing - all known expression platforms used in riboswitches. The specific illustration presented, <it>CRK10</it>, implies a new mechanism for the perception of cytokinin, a classic plant hormone. Experimental support for the hypothesis would add breadth to the growing list of important functions attributed to riboswitches.</p> <p>Reviewers</p> <p>This article was reviewed by Anthony Poole, Rob Knight, Mikhail Gelfand.</p

Student Engineers from RWU Capture Top Honors in FAA Competition

Two teams of students awarded for innovative aviation solutions to improve jetway lighting, runway debris removal

High Speed photometry of faint Cataclysmic Variables: I. V359 Cen, XZ Eri, HY Lup, V351 Pup, V630 Sgr, YY Tel, CQ Vel, CE-315

The first results of a photometric survey of faint Cataclysmic Variables are presented. V359 Cen is an SU UMa star with a period of 112 min. Even though observed at quiescence, the mass transfer rate in this old nova may be sufficiently high that in such a short period system (with its implied small mass ratio) the disc may be excited into an elliptical shape with the result that the observed brightness modulation gives a superhump period rather than an orbital period. XZ Eri is an eclipsing dwarf nova with an orbital period (P(orb)) of 88.1 min. HY Lup has only slight variability. V351 Pup, the remnant of Nova Puppis 1991, has P(orb) = 2.837 h and a light curve that strongly resembles that of the magnetic Nova Cyg 1975. V630 Sgr is the first nova remnant that has both positive superhumps (P(sh) = 2.980 h) and eclipses (P(orb) = 2.831 h). The YY Tel identification is somewhat uncertain. The correct identification for CQ Vel is provided from discovery of its flickering activity. The light curve of CE-315, a recently discovered AM CVn star, shows similarities to that of GP Com, with no apparent orbital modulation.Comment: 8 pages, 12 figures, accepted for publication in MNRA

High speed photometry of faint cataclysmic variables - VI. Car2, V1040 Cen, Ha 075648, IL Nor (Nova Nor 1893), HS Pup (Nova Pup 1963), SDSS J2048-06, CSS 081419-005022 and CSS 112634-100210

We have observed 8 faint cataclysmic variable stars photometrically. The nova-like Car2 was extensively sampled but showed little variability. V1040 Cen was observed near the end of a dwarf nova outburst and possessed dwarf nova and quasi-periodic oscillations. Ha 075648 has strong large amplitude flickering and a possible orbital modulation at 3.49 h. The correct identification for the nova remnant IL Nor (Nova Nor 1893) has been established. HS Pup (Nova Pup 1963) has a possible orbital period of 3.244 h. SDSS J2048-06 is a low mass transfer dwarf nova that in quiescence shows slow variations at 7.67 h (though poorly sampled with our observations) and an orbital modulation at 87.26 min. The dwarf nova CSS 081419-005022 has an orbital period of 1.796 h and the eclipsing dwarf nova CSS 112634-100210 has an orbital period of 1.8581 h.Comment: 7 pages, 15 figures. Accepted for publication in MNRA

High speed photometry of faint Cataclysmic Variables: II. RS Car, V365 Car,] V436 Car, AP Cru, RR Cha, BI Ori, CM Phe and V522 Sgr

Short time scale photometric properties of eight faint Cataclysmic Variable (CV) stars are presented. Nova Carinae 1895 (RS Car) has a photometric modulation at 1.977 h which could be either an orbital or a superhump period. Nova Carinae 1948 (V365 Car) shows flickering, but any orbital modulation has a period in excess of 6 h. The nova-like variable and X-ray source V436 Car has an orbital modulation at P(orb) = 4.207 h, no detectable period near 2.67 h (which had previously given it a possible intermediate polar classification), and Dwarf Nova Oscillations (DNOs) at ~40 s. Nova Crucis 1936 (AP Cru) has a double humped ellipsoidal modulation at P(orb) = 5.12 h and a stable modulation at 1837 s characteristic of an intermediate polar. Nova Chamaeleontis 1953 (RR Cha) is an ecliping system with P(orb) = 3.362 h, but at times shows negative superhumps at 3.271 h and positive superhumps at 3.466 h. In addition it has a stable period at 1950 s, characteristic of an intermediate polar. BI Ori is a dwarf nova which we observed at quiescence and outburst without detecting any orbital modulation. CM Phe is a nova-like variable for which we confirm Hoard, Wachter & Kim-Quijano's (2001) value of P(orb) = 6.454 h. We have identified the remnant of Nova Saggitarii 1931 (V522 Sgr) with a flickering source ~2.2 mag fainter than the previously proposed candidate (which we find to be non-variable).Comment: 10 pages, 18 figures, accepted for publication in MNRAS. Figures 3, 4 and 8 are available at full resolution at http://mensa.ast.uct.ac.za/~pwoud

Evidence for Infrared-Faint Radio Sources as z > 1 Radio-Loud AGN

Infrared-Faint Radio Sources (IFRSs) are a class of radio objects found in the Australia Telescope Large Area Survey (ATLAS) which have no observable mid-infrared counterpart in the Spitzer Wide-area Infrared Extragalactic (SWIRE) survey. The extended Chandra Deep Field South now has even deeper Spitzer imaging (3.6 to 70 micron) from a number of Legacy surveys. We report the detections of two IFRS sources in IRAC images. The non-detection of two other IFRSs allows us to constrain the source type. Detailed modeling of the SED of these objects shows that they are consistent with high redshift (z > 1) AGN.Comment: 10 pages, 7 figures, accepted for publication in Ap

A subcutaneous adipose tissue-liver signalling axis controls hepatic gluconeogenesis.

The search for effective treatments for obesity and its comorbidities is of prime importance. We previously identified IKK-ε and TBK1 as promising therapeutic targets for the treatment of obesity and associated insulin resistance. Here we show that acute inhibition of IKK-ε and TBK1 with amlexanox treatment increases cAMP levels in subcutaneous adipose depots of obese mice, promoting the synthesis and secretion of the cytokine IL-6 from adipocytes and preadipocytes, but not from macrophages. IL-6, in turn, stimulates the phosphorylation of hepatic Stat3 to suppress expression of genes involved in gluconeogenesis, in the process improving glucose handling in obese mice. Preliminary data in a small cohort of obese patients show a similar association. These data support an important role for a subcutaneous adipose tissue-liver axis in mediating the acute metabolic benefits of amlexanox on glucose metabolism, and point to a new therapeutic pathway for type 2 diabetes

57 second oscillations in Nova Centauri 1986 (V842 Cen)

High speed photometry in 2008 shows that the light curve of V842 Cen possesses a coherent modulation at 56.825 s, with sidebands at 56.598 s and 57.054 s. These have appeared since this nova remnant was observed in 2000 and 2002. We deduce that the dominant signal is the rotation period of the white dwarf primary and the sidebands are caused by reprocessing from a surface moving with an orbital period of 3.94 h. Thus V842 Cen is an intermediate polar (IP) of the DQ Herculis subclass, is the fastest rotating white dwarf among the IPs and is the third fastest known in a cataclysmic variable. As in other IPs we see no dwarf nova oscillations, but there are often quasi-periodic oscillations in the range 350 - 1500 s. There is a strong brightness modulation with a period of 3.78 h, which we attribute to negative superhumps, and there is an even stronger signal at 2.886 h which is of unknown origin but is probably a further example of that seen in GW Lib and some other systems. We used the Swift satellite to observe V842 Cen in the ultra-violet and in X-rays, although no periodic modulation was detected in the short observations. The X-ray luminosity of this object appears to be much lower than that of other IPs in which the accretion region is directly visible.Comment: 6 pages, 10 figures, accepted for publication in MNRA

The Growth of Black Holes from Population III Remnants in the Renaissance Simulations

The formation of stellar mass black holes from the remnants of Population III stars provides a source of initial black hole seeds with the potential to grow into intermediate or, in rare cases, possibly supermassive black holes. We use the Renaissance simulation suite to follow the growth of over 15,000 black holes born into mini-haloes in the early Universe. We compute the evolution of the black holes by post-processing individual remnant Population III star particles in the Renaissance simulation snapshots. The black holes populate haloes from 10$^{6}$ M$_{\odot}$ up to 10$^{9}$ M$_{\odot}$. We find that all of the black holes display very inefficient growth. On average the black holes increase their initial mass by a factor 10$^{-5}$, with the most active black holes increasing their mass by approximately 10%. Only a single black hole experiences any period of super-Eddington accretion, but the duration is very short and not repeated. Furthermore, we find no correlation of black hole accretion with halo mass in the mass range sampled. Within most haloes, we identify clumps of cool, dense gas for which accretion rates would be high, but instances of black holes encountering these clumps are rare and short-lived. Star formation competes with black hole growth by consuming available gas and driving down accretion rates through feedback. We conclude that the black holes born from Population III remnants do not form a significant population of intermediate mass black holes in the early Universe and will need to wait until later times to undergo significant accretion, if at all.Comment: 12 pages, 9 figures, accepted for publication in MNRA