GMOD for Evolutionary Biology

The Generic Model Organism Database (GMOD, "http://gmod.org":http://gmod.org) project provides interoperable, open source software tools for managing, visualizing and annotating biological data. GMOD is also a community of people addressing common challenges with biological data. Some well known software in GMOD includes GBrowse and JBrowse for genome browsing, Apollo for genome annotation, Chado for managing data, CMap for comparative map viewing, Galaxy for workflow creation and persistence, and BioMart for warehousing biological data.

This talk will focus on three areas of particular interest to iEvoBio participants. 
1) GBrowse_syn comparative genomics viewer
2) Natural Diversity Module of the Chado database schema
3) GMOD evolutionary biology hackathon 

The GBrowse_syn comparative genomics viewer displays synteny between a reference and any number of related species. It shows inversions, duplications, and indels, and can show synteny across non-contiguous regions. It is built on the widely used GBrowse genome viewer. The Natural Diversity Module is an extension to GMOD’s Chado database schema to enable Chado to support natural diversity, population genomics, individuals, breeding, phenotypes and geolocation information. This module is the first extension to Chado to be designed by the community, rather than at one institution. We will close by soliciting nominations and ideas for a GMOD Evolutionary Biology Hackathon. This hackathon will be held November 8-12, at NESCent, which is sponsoring the event. There will be an open call for participation in August.
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Spatially resolved observations of warm ionized gas and feedback in local ULIRGs

We present VLT/VIMOS-IFU emission-line spectroscopy of a volume limited sample of 18 southern ULIRGs selected with z<0.09 and dec<10. By covering a wide range of ULIRG types, this dataset provides an important set of templates for comparison with high-redshift galaxies. We employed an automated Gaussian line fitting program to decompose the emission line profiles of Halpha, [NII], [SII], and [OI] into individual components, and chart the Halpha kinematics, and the ionized gas excitations and densities. 11/18 of our galaxies show evidence for outflowing warm ionized gas with speeds between 500 and a few 1000 km/s, with the fastest outflows associated with systems that contain an AGN. Our spatially resolved spectroscopy has allowed us to map the outflows, and in some cases determine for the first time to which nucleus the wind is associated. In three of our targets we find line components with widths >2000 km/s over spatially extended regions in both the recombination and forbidden lines; in two of these three, they are associated with a known Sy2 nucleus. Eight galaxies have clear rotating gaseous disks, and for these we measure rotation velocities, virial masses, and calculate Toomre Q parameters. We find radial gradients in the emission line ratios in a significant number of systems in our study. We attribute these gradients to changes in ionizing radiation field strength, most likely due to an increasing contribution of shocks with radius. We conclude with a detailed discussion of the results for each individual system, with reference to the existing literature. Our observations demonstrate that the complexity of the kinematics and gas properties in ULIRGs can only be disentangled with high sensitivity, spatially resolved IFU observations. Many of our targets are ideal candidates for future high spatial resolution follow-up observations.Comment: 44 pages, 8 figures, 3 tables, accepted to MNRA

Importance of private and communal lands to sustainable conservation of Africa's rhinoceroses

A new path for rhinoceros (rhino) conservation is needed. Recent data signal the alarming impact of poaching on populations in Africa's rhino stronghold, the state-run Kruger National Park (South Africa), which today supports one quarter the rhinos than a decade ago. We aggregated African rhino population data, highlighting the growing role of private and community rhino custodians, who likely now conserve >50% of Africa's rhinos. Their contribution has been enabled by a supportive policy and economic environment, but this arrangement is becoming more difficult to sustain as costs associated with protecting rhinos skyrocket and revenue-generating options become insufficient. Some privately held rhino populations are small or intensively managed, raising questions about their conservation value. As the role of private and community custodianship becomes increasingly central to the protection of Africa's remaining rhinos, its resilience must be strengthened through implementation of adaptive policies that incentivize rhino conservation. We outline policy pathways to provide an enabling environment for rhino conservation beyond state parks.Peer reviewe

Prospectus, September 2, 1974

FACULTY, STUDENTS CONQUER REGISTRATION; Enrollment Procedures Eased By Mail; Dr. Staerkel Welcomes Student Body; Lonnie & The Lugnutz Top Activities; All-College Cookout And Activity Day Schedule; Meeting Set For Prospectus Jobs; Campus Artist Needed For Cartoon Series; StuGo Prexy, Karen Coleman, Offers Welcome; Adjusting To College Life; Parking Regulations; Convocations Plans Activities; Debaters Defend Championships; Music Director Ernie Hoffman Looking For Interested Students; Athletic Season Review; Fast Freddy\u27s Football Forecast; Kirby Wins Babe Ruth Scholarship; Don Grothe New Links Coach; Classified Ads; Here Are Your P/C Student Officers; SIMS Lecture Sept. 10; P/C Bridge Club Opens Season In Sunday Session; Prospectus Staff Salary Increase; M*A*S*H Headlines Film Season; StuGo Works Through Summer; Theatre Troupe To Hold Auditionshttps://spark.parkland.edu/prospectus_1974/1011/thumbnail.jp

The Radio-Optical Correlation in Steep-Spectrum Quasars

Using complete samples of steep-spectrum quasars, we present evidence for a correlation between radio and optical luminosity which is not caused by selection effects, nor caused by an orientation dependence (such as relativistic beaming), nor a byproduct of cosmic evolution. We argue that this rules out models of jet formation in which there are no parameters in common with the production of the optical continuum. This is arguably the most direct evidence to date for a close link between accretion onto a black hole and the fuelling of relativistic jets. The correlation also provides a natural explanation for the presence of aligned optical/radio structures in only the most radio luminous high-redshift galaxies.Comment: MNRAS in press. Uses BoxedEPS (included

Understanding Infrared Galaxy Populations: the SWIRE Legacy Survey

We discuss spectral energy distributions, photometric redshifts, redshift distributions, luminosity functions, source-counts and the far infrared to optical luminosity ratio for sources in the SWIRE Legacy Survey. The spectral energy distributions of selected SWIRE sources are modelled in terms of a simple set of galaxy and quasar templates in the optical and near infrared, and with a set of dust emission templates (cirrus, M82 starburst, Arp 220 starburst, and AGN dust torus) in the mid infrared. The optical data, together with the IRAC 3.6 and 4.5 mu data, have been used to determine photometric redshifts. For galaxies with known spectroscopic redshifts there is a notable improvement in the photometric redshift when the IRAC data are used, with a reduction in the rms scatter from 10% in (1+z) to 5%. While further spectroscopic data are needed to confirm this result, the prospect of determining good photometric redshifts for the 2 million extragalactic objects in SWIRE is excellent. The distribution of the different infrared sed types in the L{ir}/L{opt} versus L{ir} plane, where L{ir} and L{opt} are the infrared and optical bolometric luminosities, is discussed. Source-counts at 24, 70 and 160 mu are discussed, and luminosity functions at 3.6 and 24 mu are presented.Comment: 8 pages, 14 figures, to appear in proceedings of 'Spitzer IR Diagnostics Conference, Nov 14-16, 2005

Timeline analysis and wavelet multiscale analysis of the AKARI All-Sky Survey at 90 micron

We present a careful analysis of the point source detection limit of the AKARI All-Sky Survey in the WIDE-S 90 $\mu$m band near the North Ecliptic Pole (NEP). Timeline Analysis is used to detect IRAS sources and then a conversion factor is derived to transform the peak timeline signal to the interpolated 90 $\mu$m flux of a source. Combined with a robust noise measurement, the point source flux detection limit at S/N $>5$ for a single detector row is $1.1\pm0.1$ Jy which corresponds to a point source detection limit of the survey of $\sim$0.4 Jy. Wavelet transform offers a multiscale representation of the Time Series Data (TSD). We calculate the continuous wavelet transform of the TSD and then search for significant wavelet coefficients considered as potential source detections. To discriminate real sources from spurious or moving objects, only sources with confirmation are selected. In our multiscale analysis, IRAS sources selected above $4\sigma$ can be identified as the only real sources at the Point Source Scales. We also investigate the correlation between the non-IRAS sources detected in Timeline Analysis and cirrus emission using wavelet transform and contour plots of wavelet power spectrum. It is shown that the non-IRAS sources are most likely to be caused by excessive noise over a large range of spatial scales rather than real extended structures such as cirrus clouds.Comment: 16 pages, 19 figures, 5 tables, accepted for publication in MNRA