Genetic mapping in polyploids

Many of our most important crop species are polyploid – an unusual phenomenon whereby each chromosome is present in multiple copies (more than the usual two copies). The most common such arrangement is tetraploidy, where each chromosome is present four times. Plant species can tolerate this condition quite well (the same cannot be said of animals or humans). In fact, polyploidy can confer certain advantages such as larger fruits and flowers, seedless fruits (useful for fruit growers) or improved tolerance to environmental stresses. However, carrying multiple copies of each chromosome complicates things, particularly when crop breeders would like to use DNA information to help inform selection decisions. This PhD project looked at how DNA information of polyploids should be best analysed, developing methods and new software tools to achieve this. We analysed DNA information from polyploid crops such as potato, rose and chrysanthemum, yielding many novel insights and important results.</p

Fear and institutions

Fear allowed early humans to adapt, evolve, and survive. When humans moved into settled communities, with more advanced means of production, the nature of fear-much like the nature of social relationships-changed. Once the means of social reproduction were secured, fear became less necessary as a survival instinct, and more useful as a heuristic device. Fear cannot be characterized as an essentially socially constructed phenomenon, or as the self-contained, individualized response to internalized traumas. The growth and nature of fear must be studied as a process that develops under its own inertia and as a phenomenon that is both shaped by and shapes its institutional setting. Fear should be understood as both structurally determined and socially transformative. This research examines fear, specifically, as it relates to neoliberalism and institutions. © 2013, Journal of Economic Issues/Association for Evolutionary Economics

The Spitzer c2d survey of Large, Nearby, Interstellar Clouds. V. Chamaeleon II Observed with IRAC

We present IRAC (3.6, 4.5, 5.8, and 8.0 micron) observations of the Chamaeleon II molecular cloud. The observed area covers about 1 square degree defined by $A_V >2$. Analysis of the data in the 2005 c2d catalogs reveals a small number of sources (40) with properties similar to those of young stellaror substellar objects (YSOs). The surface density of these YSO candidates is low, and contamination by background galaxies appears to be substantial, especially for sources classified as Class I or flat SED. We discuss this problem in some detail and conclude that very few of the candidate YSOs in early evolutionary stages are actually in the Cha II cloud. Using a refined set of criteria, we define a smaller, but more reliable, set of 24 YSO candidates.Comment: 19 pages, 10 figures, in press Ap

Sustainable management of groundwater extraction: An Australian perspective on current challenges

Study focus: Our incomplete knowledge of groundwater systems and processes imposes barriers in attempting to manage groundwater sustainably. Challenges also arise through complex institutional arrangements and decision-making processes, and the difficulty in involving stakeholders. In some areas, these difficulties have led to water table decline and impacts on groundwater users and groundwater-dependent ecosystems. However, there is potential to improve the sustainable use of groundwater resources through improvements in management practices. We discuss some of the challenges, and present survey results of research, government, and industry professionals across the groundwater sector in Australia. New hydrological insights for the region: The highest-ranked challenge identified in the survey was the difficulty in determining regional-scale volumetric water extraction limits. This is surprising given the criticism in the international literature of volumetric based approaches for groundwater management, and the decreased reliance on this approach in Australia and elsewhere in recent years. Other major challenges are the difficulty in determining and implementing maximum drawdown criteria for groundwater levels, determining water needs of ecosystems, and managing groundwater impacts on surface water. Notwithstanding these gaps in technical understanding and tools and a lack of resources for groundwater studies, improvements in stakeholder communication should enable more effective decision-making and improve compliance with regulations designed to protect groundwater and dependent ecosystems

The Spitzer c2d Survey of Large, Nearby, Interstellar Clouds. IV. Lupus Observed with MIPS

We present maps of 7.78 square degrees of the Lupus molecular cloud complex at 24, 70, and $160\:\mu$m. They were made with the Spitzer Space Telescope's Multiband Imaging Photometer for Spitzer (MIPS) instrument as part of the Spitzer Legacy Program, ``From Molecular Cores to Planet-Forming Disks'' (c2d). The maps cover three separate regions in Lupus, denoted I, III, and IV. We discuss the c2d pipeline and how our data processing differs from it. We compare source counts in the three regions with two other data sets and predicted star counts from the Wainscoat model. This comparison shows the contribution from background galaxies in Lupus I. We also create two color magnitude diagrams using the 2MASS and MIPS data. From these results, we can identify background galaxies and distinguish them from probable young stellar objects. The sources in our catalogs are classified based on their spectral energy distribution (SED) from 2MASS and Spitzer wavelengths to create a sample of young stellar object candidates. From 2MASS data, we create extinction maps for each region and note a strong corresponence between the extinction and the $160\:\mu$m emission. The masses we derived in each Lupus cloud from our extinction maps are compared to masses estimated from $^{13}$CO and C$^{18}$O and found to be similar to our extinction masses in some regions, but significantly different in others. Finally, based on our color-magnitude diagrams, we selected 12 of our reddest candidate young stellar objects for individual discussion. Five of the 12 appear to be newly-discovered YSOs.Comment: 15 pages, 17 figures, uses emulateapj.cls. Accepted for publication in ApJ. A version with high-quality figures can be found at http://peggysue.as.utexas.edu/SIRTF

Early mortality and primary causes of death in mothers of children with ID or ASD: a retrospective cohort study

INTRODUCTION: Mothers of children with intellectual disability or autism spectrum disorder (ASD) have poorer health than other mothers. Yet no research has explored whether this poorer health is reflected in mortality rates or whether certain causes of death are more likely. We aimed to calculate the hazard ratios for death and for the primary causes of death in mothers of children with intellectual disability or ASD compared to other mothers. METHODS: The study population comprised all mothers of live-born children in Western Australia from 1983-2005. We accessed state-wide databases which enabled us to link socio-demographic details, birth dates, diagnoses of intellectual disability or ASD in the children and dates and causes of death for all mothers who had died prior to 2011. Using Cox Regression with death by any cause and death by each of the three primary causes as the event of interest, we calculated hazard ratios for death for mothers of children intellectual disability or ASD compared to other mothers. RESULTS AND DISCUSSION: During the study period, mothers of children with intellectual disability or ASD had more than twice the risk of death. Mothers of children with intellectual disability were 40% more likely to die of cancer; 150% more likely to die of cardiovascular disease and nearly 200% more likely to die from misadventure than other mothers. Due to small numbers, only hazard ratios for cancer were calculated for mothers of children with ASD. These mothers were about 50% more likely to die from cancer than other mothers. Possible causes and implications of our results are discussed. CONCLUSION: Similar studies, pooling data from registries elsewhere, would improve our understanding of factors increasing the mortality of mothers of children with intellectual disability or ASD. This would allow the implementation of informed services and interventions to improve these mothers' longevity

Massive star formation and feedback in W49A: The source of our Galaxy's most luminous water maser outflow

We present high spatial resolution mid-IR images of the ring of UCHII regions in W49A obtained at Gemini North, allowing us to identify the driving source of its powerful H2O maser outflow. These data also confirm our previous report that several radio sources in the ring are undetected in the mid-IR because they are embedded deep inside the cloud core. We locate the source of the water maser outflow at the position of the compact mid-IR peak of source G (source G:IRS1). This IR source is not coincident with any identified compact radio continuum source, but is coincident with a hot molecular core, so we propose that G:IRS1 is a hot core driving an outflow analogous to the wide-angle bipolar outflow in OMC-1. G:IRS1 is at the origin of a larger bipolar cavity and CO outflow. The water maser outflow is orthogonal to the bipolar CO cavity, so the masers probably reside near its waist in the cavity walls. Models of the IR emission require a massive protostar of 45Msun, 3e5Lsun, and an effective envelope accretion rate of 1e-3Msun/yr. Feedback from the central star could potentially drive the H2O maser outflow, but it has insufficient radiative momentum to have driven the large-scale CO outflow, requiring that this massive star had an active accretion disk over the past 10^4 yr. Combined with the spatialy resolved morphology in IR images, G:IRS1 in W49 provides compelling evidence for a massive protostar that formed by accreting from a disk, accompanied by a bipolar outflow.Comment: 14 pages, MNRAS accepte

The Spitzer c2d Survey of Nearby Dense Cores: II: Discovery of a Low Luminosity Object in the "Evolved Starless Core" L1521F

We present Spitzer Space Telescope observations of the "evolved starless core" L1521F which reveal the presence of a very low luminosity object (L < 0.07 Lsun). The object, L1521F-IRS, is directly detected at mid-infrared wavelengths (>5 micron) but only in scattered light at shorter infrared wavelengths, showing a bipolar nebula oriented east-west which is probably tracing an outflow cavity. The nebula strongly suggests that L1521F-IRS is embedded in the L1521F core. Thus L1521F-IRS is similar to the recently discovered L1014-IRS and the previously known IRAM 04191 in its substellar luminosity and dense core environment. However these objects differ significantly in their core density, core chemistry, and outflow properties, and some may be destined to be brown dwarfs rather than stars.Comment: 10 pages with 3 figures, accepted by ApJ Letter

The Spitzer c2d Survey of Nearby Dense Cores: I: First Direct Detection of the Embedded Source in IRAM 04191+1522

We report the first detections of the Class 0 protostellar source IRAM 04191+1522 at wavelengths shortward of 60 microns with the Spitzer Space Telescope. We see extended emission in the Spitzer images that suggests the presence of an outflow cavity in the circumstellar envelope. We combine the Spitzer observations with existing data to form a complete dataset ranging from 3.6 to 1300 microns and use these data to construct radiative transfer models of the source. We conclude that the internal luminosity of IRAM 04191+1522, defined to be the sum of the luminosity from the internal sources (a star and a disk), is L_int = 0.08 +/- 0.04 L_sun, placing it among the lowest luminosity protostars known. Though it was discovered before the launch of the Spitzer Space Telescope, IRAM 04191+1522 falls within a new class of Very Low Luminosity Objects being discovered by Spitzer. Unlike the two other well-studied objects in this class, which are associated either with weak, compact outflows or no outflows at all, IRAM 04191+1522 has a well-defined molecular outflow with properties consistent with those expected based on relations derived from higher luminosity (L_int > 1 L_sun) protostars. We discuss the difficulties in understanding IRAM 04191+1522 in the context of the standard model of star formation, and suggest a possible explanation for the very low luminosity of this source.Comment: Accepted for publication in the Astrophysical Journal. 39 pages, 9 figures. See http://peggysue.as.utexas.edu/SIRTF/ for high-resolution figure