New Isozyme Systems for Maize (Zea mays L.): Aconitate Hydratase, Adenylate Kinase, NADH Dehydrogenase, and Shikimate Dehydrogenase

Electrophoretic variation and inheritance of four novel enzyme systems were studied in maize (Zea mays L.). A minimum of 10 genetic loci collectively encodes isozymes of aconitate hydratase (ACO; EC 4.2.1.3.), adenylate kinase (ADK; EC 2.7.4.3), NADH dehydrogenase (DIA; EC 1.6.99.-), and shikimate dehydrogenase (SAD; EC 1.1.1.25). At least four loci are responsible for the genetic control of ACO. Genetic data for two of the encoding loci, Aco1 and Aco4, demonstrated that at least two maize ACOs are active as monomers. Analysis of organellar preparations suggests that ACO1 and ACO4 are localized in the cytosolic and mitochondrial subcellular fractions, respectively. Maize ADK is encoded by a single nuclear locus, Adk1, governing monomeric enzymes that are located in the chloroplasts. Two cytosolic and two mitochondrial forms of DIA were electrophoretically resolved. Segregation analyses demonstrated that the two cytosolic isozymes are controlled by separate loci, Dia1 and Dia2, coding for products that are functional as monomers (DIA1) and dimers (DIA2). The major isozyme of SAD is apparently cytosolic, although an additional faintly staining plastid form may be present. Alleles at Sad1 are each associated with two bands that cosegregate in controlled crosses. Linkage analyses and crosses with B-A translocation stocks were effective in determining the map locations of six loci, including the previously described but unmapped locus Acp4. Several of these loci were localized to sparsely mapped regions of the genome. Dia2 and Acp4 were placed on the distal portion of the long arm of chromosome 1, 12.6 map units apart. Dia1 was localized to chromosome 2, 22.2 centimorgans (cM) from B1. Aco1 was mapped to chromosome 4, 6.2 cM from su1. Adk1 was placed on the poorly marked short arm of chromosome 6, 8.1 map units from rgd1. Less than 1% recombination was observed between Glu1 (on chromosome 10) and Sad1. In contrast to many other maize isozyme systems, there was little evidence of gene duplication or of parallel linkage relationships for these allozyme loci

Hunting Galaxies to (and for) Extinction

In studies of star-forming regions, near-infrared excess (NIRX) sources--objects with intrinsic colors redder than normal stars--constitute both signal (young stars) and noise (e.g. background galaxies). We hunt down (identify) galaxies using near-infrared observations in the Perseus star-forming region by combining structural information, colors, and number density estimates. Galaxies at moderate redshifts (z = 0.1 - 0.5) have colors similar to young stellar objects (YSOs) at both near- and mid-infrared (e.g. Spitzer) wavelengths, which limits our ability to identify YSOs from colors alone. Structural information from high-quality near-infrared observations allows us to better separate YSOs from galaxies, rejecting 2/5 of the YSO candidates identified from Spitzer observations of our regions and potentially extending the YSO luminosity function below K of 15 magnitudes where galaxy contamination dominates. Once they are identified we use galaxies as valuable extra signal for making extinction maps of molecular clouds. Our new iterative procedure: the Galaxies Near Infrared Color Excess method Revisited (GNICER), uses the mean colors of galaxies as a function of magnitude to include them in extinction maps in an unbiased way. GNICER increases the number of background sources used to probe the structure of a cloud, decreasing the noise and increasing the resolution of extinction maps made far from the galactic plane.Comment: 16 pages and 16 figures. Accepted for publication in ApJ. Full resolution version at http://www.cfa.harvard.edu/COMPLETE/papers/Foster_HuntingGalaxies.pd

Cloudshine: New Light on Dark Clouds

We present new deep near-infrared images of dark clouds in the Perseus molecular complex. These images show beautiful extended emission which we model as scattered ambient starlight and name ``cloudshine''. The brightness and color variation of cloudshine complicates the production of extinction maps, the best tracer of column density in clouds. However, since the profile of reflected light is essentially a function of mass distribution, cloudshine provides a new way to study the structure of dark clouds. Previous work has used optical scattered light to study the density profile of tenuous clouds; extending this technique into the infrared provides a high-resolution view into the interiors of very dense clouds, bypassing the complexities of using thermal dust emission, which is biased by grain temperature, or molecular tracers, which have complicated depletion patterns. As new wide-field infrared cameras are used to study star-forming regions at greater depth, cloudshine will be widely observed and should be seen as a new high-resolution tool, rather than an inconvenience.Comment: 6 pages with 3 figures, submitted to ApJ Letters v2: correct attribution of the Henyey-Greenstein function and other typos and minor word change

The COMPLETE Nature of the Warm Dust Ring in Perseus

The Perseus molecular cloud complex is a ~30pc long chain of molecular clouds most well-known for the two star-forming clusters NGC1333 and IC348 and the well-studied outflow source in B5. However, when studied at mid- to far-infrared wavelengths the region is dominated by a ~10pc diameter shell of warm dust, likely generated by an HII region caused by the early B-star HD278942. Using a revised calibration technique the COMPLETE team has produced high-sensitivity temperature and column-density maps of the Perseus region from IRAS Sky Survey Atlas (ISSA) 60 and 100um data. In this paper, we combine the ISSA based dust-emission maps with other observations collected as part of the COMPLETE Survey, along with archival H-alpha and MSX observations. Molecular line observations from FCRAO and extinction maps constructed by applying the NICER method to the 2MASS catalog provide independent estimates of the ``true'' column-density of the shell. H-alpha emission in the region of the shell confirms that it is most likely an HII region located behind the cloud complex, and 8um data from MSX indicates that the shell may be interacting with the cloud. Finally, the two polarisation components previously seen towards background stars in the region can be explained by the association of the stronger component with the shell. If confirmed, this would be the first observation of a parsec-scale swept-up magnetic field.Comment: Accepted by ApJ. Figures have been compressed - full resolution version available at http://cfa-www.harvard.edu/COMPLETE/results.htm

Repeatability and reliability of exploratory behavior in proactive and reactive zebrafsh, Danio rerio

Behavioral responses to novel situations often vary and can belong to a suite of correlated behaviors. Characteristic behaviors of different personality types (e.g. stress coping styles) are generally consistent across contexts and time. Here, we compare the repeatability and reliability of exploratory behaviors between zebrafsh strains selectively bred to display contrasting behavioral responses to stressors that represent the proactive-reactive axis. Specifically, we measure exploratory behavior of individual fish in an open field test over five weeks. We quantified the stationary time, average swimming speed and time spent by a fish in the center area. We found a number of strain differences for each behavioral measure. Stationary time was the most repeatable and reliable measure for assessing proactive-reactive behavioral differences. Reactive zebrafish generally showed the highest reliability and repeatability of exploratory behavior compared to proactive zebrafish and a separate wild caught strain. Given the increased interest in the evolutionary consequences and proximate mechanisms of consistent individual differences, it will be important to continue to investigate how different selective pressures may influence expression of stress coping styles and their effects on the consistency of an animal’s behavior

Coupling Control Variates for Markov Chain Monte Carlo

We show that Markov couplings can be used to improve the accuracy of Markov chain Monte Carlo calculations in some situations where the steady-state probability distribution is not explicitly known. The technique generalizes the notion of control variates from classical Monte Carlo integration. We illustrate it using two models of nonequilibrium transport

Evidence for Grain Growth in Molecular Clouds: A Bayesian Examination of the Extinction Law in Perseus

We investigate the shape of the extinction law in two $1^{\circ}$ square fields of the Perseus molecular cloud complex. We combine deep red-optical (r, i and z band) observations obtained using Megacam on the MMT with UKIRT (United Kingdom Infrared Telescope) Infrared Deep Sky Survey near-infrared (J, H and K band) data to measure the colours of background stars. We develop a new hierarchical Bayesian statistical model, including measurement error, intrinsic colour variation, spectral type and dust reddening, to simultaneously infer parameters for individual stars and characteristics of the population. We implement an efficient Markov chain Monte Carlo algorithm utilizing generalized Gibbs sampling to compute coherent probabilistic inferences. We find a strong correlation between the extinction $(A_V)$ and the slope of the extinction law (parametrized by $R_V)$. Because the majority of the extinction towards our stars comes from the Perseus molecular cloud, we interpret this correlation as evidence of grain growth at moderate optical depths. The extinction law changes from the ‘diffuse’ value of $R_V \sim 3$ to the 'dense cloud' value of $R_V \sim 5$ as the column density rises from $A_V = 2$ to 10 mag. This relationship is similar for the two regions in our study, despite their different physical conditions, suggesting that dust grain growth is a fairly universal process.Astronom

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion

Gene regulatory interactions underlying the early stages of non-genotoxic carcinogenesis are poorly understood. Here, we have identified key candidate regulators of phenobarbital (PB)-mediated mouse liver tumorigenesis, a well-characterized model of non-genotoxic carcinogenesis, by applying a new computational modeling approach to a comprehensive collection of in vivo gene expression studies. We have combined our previously developed motif activity response analysis (MARA), which models gene expression patterns in terms of computationally predicted transcription factor binding sites with singular value decomposition (SVD) of the inferred motif activities, to disentangle the roles that different transcriptional regulators play in specific biological pathways of tumor promotion. Furthermore, transgenic mouse models enabled us to identify which of these regulatory activities was downstream of constitutive androstane receptor and β-catenin signaling, both crucial components of PB-mediated liver tumorigenesis. We propose novel roles for E2F and ZFP161 in PB-mediated hepatocyte proliferation and suggest that PB-mediated suppression of ESR1 activity contributes to the development of a tumor-prone environment. Our study shows that combining MARA with SVD allows for automated identification of independent transcription regulatory programs within a complex in vivo tissue environment and provides novel mechanistic insights into PB-mediated hepatocarcinogenesi