Study of the Anatomy of the Alimentary Canal of Brochymena quadripustulata (Hemiptera:Pentatomidae)

An anatomical study of the alimentary canal and associated salivary apparatus was conducted for the pentatomid, Brochymena quadripustulata. The esophagus, ventriculus, pylorus, rectum, principal salivary glands and ducts are described and illustrated. Described structures of Brochymena quadripustulata are compared with various species of pentatomids and other hemipterans

Modelling water, sediment and nutrient fluxes from a mixed land-use catchment in New Zealand: effects of hydrologic conditions on SWAT model performance

The Soil Water Assessment Tool (SWAT) was configured for the Puarenga Stream catchment (77 km2), Rotorua, New Zealand. The catchment land use is mostly plantation forest, some of which is spray-irrigated with treated wastewater. A Sequential Uncertainty Fitting (SUFI-2) procedure was used to auto-calibrate unknown parameter values in the SWAT model which was applied to the Puarenga catchment. Discharge, sediment, and nutrient variables were then partitioned into two components (base flow and quick flow) based on hydrograph separation. A manual procedure (one-at a-time sensitivity analysis) was then used to quantify parameter sensitivity for the two hydrologically-separated regimes. Comparison of simulated daily mean discharge, sediment and nutrient concentrations with high-frequency, event-based measurements allowed the error in model predictions to be quantified. This comparison highlighted the potential for model error associated with quick-flow fluxes in flashy lower-order streams to be underestimated compared with low-frequency (e.g. monthly) measurements derived predominantly from base flow measurements. To overcome this problem we advocate the use of high-frequency, event-based monitoring data during calibration and dynamic parameter values with some dependence on discharge regime. This study has important implications for quantifying uncertainty in hydrological models, particularly for studies where model simulations are used to simulate responses of stream discharge and composition to changes in irrigation and land management

Structural characterization of CYP144A1 - a cytochrome P450 enzyme expressed from alternative transcripts in Mycobacterium tuberculosis.

Mycobacterium tuberculosis (Mtb) causes the disease tuberculosis (TB). The virulent Mtb H37Rv strain encodes 20 cytochrome P450 (CYP) enzymes, many of which are implicated in Mtb survival and pathogenicity in the human host. Bioinformatics analysis revealed that CYP144A1 is retained exclusively within the Mycobacterium genus, particularly in species causing human and animal disease. Transcriptomic annotation revealed two possible CYP144A1 start codons, leading to expression of (i) a "full-length" 434 amino acid version (CYP144A1-FLV) and (ii) a "truncated" 404 amino acid version (CYP144A1-TRV). Computational analysis predicted that the extended N-terminal region of CYP144A1-FLV is largely unstructured. CYP144A1 FLV and TRV forms were purified in heme-bound states. Mass spectrometry confirmed production of intact, His6-tagged forms of CYP144A1-FLV and -TRV, with EPR demonstrating cysteine thiolate coordination of heme iron in both cases. Hydrodynamic analysis indicated that both CYP144A1 forms are monomeric. CYP144A1-TRV was crystallized and the first structure of a CYP144 family P450 protein determined. CYP144A1-TRV has an open structure primed for substrate binding, with a large active site cavity. Our data provide the first evidence that Mtb produces two different forms of CYP144A1 from alternative transcripts, with CYP144A1-TRV generated from a leaderless transcript lacking a 5'-untranslated region and Shine-Dalgarno ribosome binding site

Locally Biased Galaxy Formation and Large Scale Structure

We examine the influence of the morphology-density(MD) relation and a wide range of simple models for biased galaxy formation on statistical measures of large scale structure. We contrast the behavior of local biasing models, in which the efficiency of galaxy formation is determined by density, geometry, or velocity dispersion of the local mass distribution, with that of non-local biasing models, in which galaxy formation is modulated coherently over scales larger than the galaxy correlation length. If morphological segregation of galaxies is governed by a local MD relation, then the correlation function of E/S0 galaxies should be steeper and stronger than that of spiral galaxies on small scales, as observed, while on large scales the correlation functions of E/S0 and spiral galaxies should have the same shape but different amplitudes. Similarly, all of our local bias models produce scale-independent amplification of the correlation function and power spectrum in the linear and mildly non-linear regimes; only a non-local biasing mechanism can alter the shape of the power spectrum on large scales. Moments of the biased galaxy distribution retain the hierarchical pattern of the mass moments, but biasing alters the values and scale-dependence of the hierarchical amplitudes S3 and S4. Pair-weighted moments of the galaxy velocity distribution are sensitive to the details of the biasing prescription. The non-linearity of the relation between galaxy density and mass density depends on the biasing prescription and the smoothing scale, and the scatter in this relation is a useful diagnostic of the physical parameters that determine the bias. Although the sensitivity of galaxy clustering statistics to the details of biasing is an obstacle to testing cosmological models, it is an asset for testing galaxy formation theories.Comment: 47 pages including 17 Figures, submitted to Ap

Think Outside the Color Box: Probabilistic Target Selection and the SDSS-XDQSO Quasar Targeting Catalog

We present the SDSS-XDQSO quasar targeting catalog for efficient flux-based quasar target selection down to the faint limit of the Sloan Digital Sky Survey (SDSS) catalog, even at medium redshifts (2.5 <~ z <~ 3) where the stellar contamination is significant. We build models of the distributions of stars and quasars in flux space down to the flux limit by applying the extreme-deconvolution method to estimate the underlying density. We convolve this density with the flux uncertainties when evaluating the probability that an object is a quasar. This approach results in a targeting algorithm that is more principled, more efficient, and faster than other similar methods. We apply the algorithm to derive low-redshift (z < 2.2), medium-redshift (2.2 <= z 3.5) quasar probabilities for all 160,904,060 point sources with dereddened i-band magnitude between 17.75 and 22.45 mag in the 14,555 deg^2 of imaging from SDSS Data Release 8. The catalog can be used to define a uniformly selected and efficient low- or medium-redshift quasar survey, such as that needed for the SDSS-III's Baryon Oscillation Spectroscopic Survey project. We show that the XDQSO technique performs as well as the current best photometric quasar-selection technique at low redshift, and outperforms all other flux-based methods for selecting the medium-redshift quasars of our primary interest. We make code to reproduce the XDQSO quasar target selection publicly available

Molecular gas in the galaxy cluster Abell 262. CO observations of UGC 1347 and other galaxies of the cluster

We present millimeter CO line emission observations of 12 galaxies within the Abell 262 cluster, together with L_FIR data, in the context of a possible molecular gas deficiency within the region of the cluster center. Several indications of the presence of such a deficiency are highlighted and connected to a model of cirrus-like cloud stripping. The model predicts a drop in the average 100 micron flux density of galaxies in the core of the cluster compared to the average 100 micron flux density in the outer regions, which is actually indicated in the IRAS data of the cluster members. This drop is explained by the decrease in the total hydrogen column density N(H) and, therefore, also includes a decrease in the molecular gas content. In addition to results for the global CO content of the galaxy sample, high-resolution interferometric CO(1-0) observations of one of the cluster members, UGC 1347, exemplify the spatial distribution of the molecular gas in a galaxy of the cluster. With these observations, it was possible to confirm the existence of a bright off-nuclear CO-emission source and to derive molecular masses and line ratios for this source and the nucleus.Comment: 14 pages, 14 figures, accepted by A&

Photometric redshifts and quasar probabilities from a single, data-driven generative model

We describe a technique for simultaneously classifying and estimating the redshift of quasars. It can separate quasars from stars in arbitrary redshift ranges, estimate full posterior distribution functions for the redshift, and naturally incorporate flux uncertainties, missing data, and multi-wavelength photometry. We build models of quasars in flux-redshift space by applying the extreme deconvolution technique to estimate the underlying density. By integrating this density over redshift one can obtain quasar flux-densities in different redshift ranges. This approach allows for efficient, consistent, and fast classification and photometric redshift estimation. This is achieved by combining the speed obtained by choosing simple analytical forms as the basis of our density model with the flexibility of non-parametric models through the use of many simple components with many parameters. We show that this technique is competitive with the best photometric quasar classification techniques---which are limited to fixed, broad redshift ranges and high signal-to-noise ratio data---and with the best photometric redshift techniques when applied to broadband optical data. We demonstrate that the inclusion of UV and NIR data significantly improves photometric quasar--star separation and essentially resolves all of the redshift degeneracies for quasars inherent to the ugriz filter system, even when included data have a low signal-to-noise ratio. For quasars spectroscopically confirmed by the SDSS 84 and 97 percent of the objects with GALEX UV and UKIDSS NIR data have photometric redshifts within 0.1 and 0.3, respectively, of the spectroscopic redshift; this amounts to about a factor of three improvement over ugriz-only photometric redshifts. Our code to calculate quasar probabilities and redshift probability distributions is publicly available

The Color Variability of Quasars

We quantify quasar color-variability using an unprecedented variability database - ugriz photometry of 9093 quasars from SDSS Stripe 82, observed over 8 years at ~60 epochs each. We confirm previous reports that quasars become bluer when brightening. We find a redshift dependence of this blueing in a given set of bands (e.g. g and r), but show that it is the result of the flux contribution from less-variable or delayed emission lines in the different SDSS bands at different redshifts. After correcting for this effect, quasar color-variability is remarkably uniform, and independent not only of redshift, but also of quasar luminosity and black hole mass. The color variations of individual quasars, as they vary in brightness on year timescales, are much more pronounced than the ranges in color seen in samples of quasars across many orders of magnitude in luminosity. This indicates distinct physical mechanisms behind quasar variability and the observed range of quasar luminosities at a given black hole mass - quasar variations cannot be explained by changes in the mean accretion rate. We do find some dependence of the color variability on the characteristics of the flux variations themselves, with fast, low-amplitude, brightness variations producing more color variability. The observed behavior could arise if quasar variability results from flares or ephemeral hot spots in an accretion disc.Comment: Accepted for publication in ApJ - in press, 17 pages, 14 figures - v2: abstract typo corrected & reference clean-u

Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors.

The essential enzyme CYP121 is a target for drug development against antibiotic resistant strains of Mycobacterium tuberculosis. A triazol-1-yl phenol fragment 1 was identified to bind to CYP121 using a cascade of biophysical assays. Synthetic merging and optimization of 1 produced a 100-fold improvement in binding affinity, yielding lead compound 2 (KD = 15 μM). Deconstruction of 2 into its component retrofragments allowed the group efficiency of structural motifs to be assessed, the identification of more LE scaffolds for optimization and highlighted binding affinity hotspots. Structure-guided addition of a metal-binding pharmacophore onto LE retrofragment scaffolds produced low nanomolar (KD = 15 nM) CYP121 ligands. Elaboration of these compounds to target binding hotspots in the distal active site afforded compounds with excellent selectivity against human drug-metabolizing P450s. Analysis of the factors governing ligand potency and selectivity using X-ray crystallography, UV-vis spectroscopy, and native mass spectrometry provides insight for subsequent drug development.MEK was supported by a Commonwealth (University of Cambridge) Scholarship awarded in conjunction with the Cambridge Commonwealth Trust and Cambridge Overseas Trust. AGC and KJM were supported by grants from the BBSRC (Grant No: BB/I019669/1 and BB/I019227/1). GGJ received funding from the Ogden Trust and the Isaac Newton Trust administered through the University of Cambridge Bursary Scheme. DSCH was supported by a Croucher Cambridge International Scholarship awarded in conjunction between the Croucher Foundation and the Cambridge Overseas Trust. SAH was supported by an Oliphant Cambridge Australia Scholarship (App No: 10132070) awarded by the Cambridge Commonwealth Trust. The contributions of LBM and LPSC were supported by funds from the Francis Crick Institute, which receives its core funding principally from Wellcome Trust, Cancer Research UK, and the UK Medical Research Council (to LPSC - MC_UP_A253_1111) and funds from FAPESP, CNPq and CAPES-PDSE (to LBM - 2011/21232-1, 140079/2013-0, 99999.003125/2014-09).This is the final version of the article. It first appeared from the American Chemical Society via http://dx.doi.org/10.1021/acs.jmedchem.6b0000