Identification of Cytokinin-Responsive Genes Using Microarray Meta-Analysis and RNA-Seq in Arabidopsis

Cytokinins are N6-substituted adenine derivatives that play diverse roles in plant growth and development. We sought to define a robust set of genes regulated by cytokinin as well as to query the response of genes not represented on microarrays. To this end, we performed a meta-analysis of microarray data from a variety of cytokinin-treated samples and used RNA-seq to examine cytokinin-regulated gene expression in Arabidopsis (Arabidopsis thaliana). Microarray meta-analysis using 13 microarray experiments combined with empirically defined filtering criteria identified a set of 226 genes differentially regulated by cytokinin, a subset of which has previously been validated by other methods. RNA-seq validated about 73% of the up-regulated genes identified by this meta-analysis. In silico promoter analysis indicated an overrepresentation of type-B Arabidopsis response regulator binding elements, consistent with the role of type-B Arabidopsis response regulators as primary mediators of cytokinin-responsive gene expression. RNA-seq analysis identified 73 cytokinin-regulated genes that were not represented on the ATH1 microarray. Representative genes were verified using quantitative reverse transcription-polymerase chain reaction and NanoString analysis. Analysis of the genes identified reveals a substantial effect of cytokinin on genes encoding proteins involved in secondary metabolism, particularly those acting in flavonoid and phenylpropanoid biosynthesis, as well as in the regulation of redox state of the cell, particularly a set of glutaredoxin genes. Novel splicing events were found in members of some gene families that are known to play a role in cytokinin signaling or metabolism. The genes identified in this analysis represent a robust set of cytokinin-responsive genes that are useful in the analysis of cytokinin function in plants

Probing the evolution of early-type cluster galaxies through chemical enrichment

A simple chemical enrichment model for cluster early-type galaxies is described in which the mechanisms considered in the evolutionary model are infall of primordial gas, outflows and a possible variation in the star formation efficiency. We find that - within the framework of our models - only outflows can generate a suitable range of metallicities. The chemical enrichment tracks can be combined with the latest population synthesis models to simulate clusters over a wide redshift range, for a set of toy models. The color-magnitude relation of local clusters is used as a constraint, fixing the correlation between absolute luminosity and ejected fraction of gas from outflows. It is found that the correlations between color or mass-to-light ratios and absolute luminosity are degenerate with respect to most of the input parameters. However, a significant change between monolithic and hierarchical models is predicted for redshifts z\simgt 1. The comparison between predicted and observed mass-to-light ratios yield an approximate linear bias between total and stellar masses: $M_{\rm Tot}\propto M_{\rm St}^{1.15\pm 0.08}$ in early-type galaxies. If we assume that outflows constitute the driving mechanism for the colors observed in cluster early type galaxies, the metallicity of the intracluster medium (ICM) can be linked to outflows. The color-magnitude constraint requires faint $M_V\sim -16$ galaxies to eject 85% of their gas, which means that most of the metals in the ICM may have originated in these dwarf galaxies.Comment: Accepted for publication in ApJ. Uses emulateapj.sty. 12 pages with 10 embedded EPS figure

Dirac Constraint Quantization of a Dilatonic Model of Gravitational Collapse

We present an anomaly-free Dirac constraint quantization of the string-inspired dilatonic gravity (the CGHS model) in an open 2-dimensional spacetime. We show that the quantum theory has the same degrees of freedom as the classical theory; namely, all the modes of the scalar field on an auxiliary flat background, supplemented by a single additional variable corresponding to the primordial component of the black hole mass. The functional Heisenberg equations of motion for these dynamical variables and their canonical conjugates are linear, and they have exactly the same form as the corresponding classical equations. A canonical transformation brings us back to the physical geometry and induces its quantization.Comment: 37 pages, LATEX, no figures, submitted to Physical Review

Large-scale shock-ionized and photo-ionized gas in M83: the impact of star formation

We investigate the ionization structure of the nebular gas in M83 using the line diagnostic diagram, [O III](5007 \degA)/H{\beta} vs. [S II](6716 \deg A+6731 \deg A)/H{\alpha} with the newly available narrowband images from the Wide Field Camera 3 (WFC3) of the Hubble Space Telescope (HST). We produce the diagnostic diagram on a pixel-by-pixel (0.2" x 0.2") basis and compare it with several photo- and shock-ionization models. For the photo-ionized gas, we observe a gradual increase of the log([O III]/H{\beta}) ratios from the center to the spiral arm, consistent with the metallicity gradient, as the H II regions go from super solar abundance to roughly solar abundance from the center out. Using the diagnostic diagram, we separate the photo-ionized from the shock-ionized component of the gas. We find that the shock-ionized H{\alpha} emission ranges from ~2% to about 15-33% of the total, depending on the separation criteria used. An interesting feature in the diagnostic diagram is an horizontal distribution around log([O III]/H{\beta}) ~ 0. This feature is well fit by a shock-ionization model with 2.0 Z\odot metallicity and shock velocities in the range of 250 km/s to 350 km/s. A low velocity shock component, < 200 km/s, is also detected, and is spatially located at the boundary between the outer ring and the spiral arm. The low velocity shock component can be due to : 1) supernova remnants located nearby, 2) dynamical interaction between the outer ring and the spiral arm, 3) abnormal line ratios from extreme local dust extinction. The current data do not enable us to distinguish among those three possible interpretations. Our main conclusion is that, even at the HST resolution, the shocked gas represents a small fraction of the total ionized gas emission at less than 33% of the total. However, it accounts for virtually all of the mechanical energy produced by the central starburst in M83.Comment: Accepted for publication in ApJ. aastex preprint 12pt, 21 pages, 13 figure

Gas and Dust Associated with the Strange, Isolated, Star BP Piscium

We have carried out a multiwavelength observational campaign demonstrating some of the remarkable properties of the infrared-bright variable star BP Psc. Surrounded by a compact dusty, gaseous disk, this little-studied late-G (or early-K) type star emits about 75% of its detected energy flux at infrared wavelengths. Evidence for accretion of gas in conjunction with narrow bi-polar jets and Herbig-Haro objects is apparently consistent with classification of BP Psc as a pre-main sequence star, as postulated in most previous studies. If young, then BP Psc would be one of the nearest and oldest known classical T Tauri stars. However, such an evolutionary classification encounters various problems that are absent or much less severe if BP Psc is instead a luminosity class III post-main sequence star. In this case, it would be the first known example of a first ascent giant surrounded by a massive molecular disk with accompanying rapid gas accretion and prominent jets and HH objects. In this model, the genesis of the massive dusty gaseous disk could be a consequence of the envelopment of a low mass companion star. Properties in the disk may be conducive to the current formation of planets, a gigayear or more after the formation of BP Psc itself.Comment: Accepted for Astrophysical Journal New version with minor changes: includes fixing a typo on the 3rd line of the paragraph that follows Equa 4 and adding a new reference (Nordhaus and Blackman 2006

Taking the Measure of the Universe: Precision Astrometry with SIM PlanetQuest

Precision astrometry at microarcsecond accuracy has application to a wide range of astrophysical problems. This paper is a study of the science questions that can be addressed using an instrument that delivers parallaxes at about 4 microarcsec on targets as faint as V = 20, differential accuracy of 0.6 microarcsec on bright targets, and with flexible scheduling. The science topics are drawn primarily from the Team Key Projects, selected in 2000, for the Space Interferometry Mission PlanetQuest (SIM PlanetQuest). We use the capabilities of this mission to illustrate the importance of the next level of astrometric precision in modern astrophysics. SIM PlanetQuest is currently in the detailed design phase, having completed all of the enabling technologies needed for the flight instrument in 2005. It will be the first space-based long baseline Michelson interferometer designed for precision astrometry. SIM will contribute strongly to many astronomical fields including stellar and galactic astrophysics, planetary systems around nearby stars, and the study of quasar and AGN nuclei. SIM will search for planets with masses as small as an Earth orbiting in the `habitable zone' around the nearest stars using differential astrometry, and could discover many dozen if Earth-like planets are common. It will be the most capable instrument for detecting planets around young stars, thereby providing insights into how planetary systems are born and how they evolve with time. SIM will observe significant numbers of very high- and low-mass stars, providing stellar masses to 1%, the accuracy needed to challenge physical models. Using precision proper motion measurements, SIM will probe the galactic mass distribution and the formation and evolution of the Galactic halo. (abridged)Comment: 54 pages, 28 figures, uses emulateapj. Submitted to PAS

Two-Component Elements Mediate Interactions between Cytokinin and Salicylic Acid in Plant Immunity

Recent studies have revealed an important role for hormones in plant immunity. We are now beginning to understand the contribution of crosstalk among different hormone signaling networks to the outcome of plant–pathogen interactions. Cytokinins are plant hormones that regulate development and responses to the environment. Cytokinin signaling involves a phosphorelay circuitry similar to two-component systems used by bacteria and fungi to perceive and react to various environmental stimuli. In this study, we asked whether cytokinin and components of cytokinin signaling contribute to plant immunity. We demonstrate that cytokinin levels in Arabidopsis are important in determining the amplitude of immune responses, ultimately influencing the outcome of plant–pathogen interactions. We show that high concentrations of cytokinin lead to increased defense responses to a virulent oomycete pathogen, through a process that is dependent on salicylic acid (SA) accumulation and activation of defense gene expression. Surprisingly, treatment with lower concentrations of cytokinin results in increased susceptibility. These functions for cytokinin in plant immunity require a host phosphorelay system and are mediated in part by type-A response regulators, which act as negative regulators of basal and pathogen-induced SA–dependent gene expression. Our results support a model in which cytokinin up-regulates plant immunity via an elevation of SA–dependent defense responses and in which SA in turn feedback-inhibits cytokinin signaling. The crosstalk between cytokinin and SA signaling networks may help plants fine-tune defense responses against pathogens

Jaguar Densities across Human-Dominated Landscapes in Colombia: The Contribution of Unprotected Areas to Long Term Conservation

Large carnivores such as jaguars (Panthera onca) are species of conservation concern because they are suffering population declines and are keystone species in their ecosystems. Their large area requirements imply that unprotected and ever-increasing agricultural regions can be important habitats as they allow connectivity and dispersal among core protected areas. Yet information on jaguar densities across unprotected landscapes it is still scarce and crucially needed to assist management and range-wide conservation strategies. Our study provides the first jaguar density estimates of Colombia in agricultural regions which included cattle ranching, the main land use in the country, and oil palm cultivation, an increasing land use across the Neotropics. We used camera trapping across two agricultural landscapes located in the Magdalena River valley and in the Colombian llanos (47–53 stations respectively; >2000 trap nights at both sites) and classic and spatially explicit capture-recapture models with the sex of individuals as a covariate. Density estimates were 2.52±0.46–3.15±1.08 adults/100 km2 in the Magdalena valley, whereas 1.12±0.13–2.19±0.99 adults/100 km2 in the Colombian llanos, depending on analysis used. We suggest that jaguars are able to live across unprotected human-use areas and co-exist with agricultural landscapes including oil-palm plantations if natural areas and riparian habitats persist in the landscape and hunting of both jaguar and prey is limited. In the face of an expanding agriculture across the tropics we recommend land-use planning, adequate incentives, regulations, and good agricultural practices for range-wide jaguar connectivity and survival