Design and Initial Performance of SHARP, a Polarimeter for the SHARC-II Camera at the Caltech Submillimeter Observatory

We have developed a fore-optics module that converts the SHARC-II camera at the Caltech Submillimeter Observatory into a sensitive imaging polarimeter at wavelengths of 350 and 450 microns. We refer to this module as "SHARP". SHARP splits the incident radiation into two orthogonally polarized beams that are then re-imaged onto opposite ends of the 32 x 12 pixel detector array in SHARC-II. A rotating half-wave plate is used just upstream from the polarization-splitting optics. The effect of SHARP is to convert SHARC-II into a dual-beam 12 x 12 pixel polarimeter. A novel feature of SHARP's design is the use of a crossed grid in a submillimeter polarimeter. Here we describe the detailed optical design of SHARP and present results of tests carried out during our first few observing runs. At 350 microns, the beam size (9 arcseconds), throughput (75%), and instrumental polarization (< 1%) are all very close to our design goals.Comment: submitted to Applied Optic

Far-infrared polarimetry from the Stratospheric Observatory for Infrared Astronomy

Multi-wavelength imaging polarimetry at far-infrared wavelengths has proven to be an excellent tool for studying the physical properties of dust, molecular clouds, and magnetic fields in the interstellar medium. Although these wavelengths are only observable from airborne or space-based platforms, no first-generation instrument for the Stratospheric Observatory for Infrared Astronomy (SOFIA) is presently designed with polarimetric capabilities. We study several options for upgrading the High-resolution Airborne Wideband Camera (HAWC) to a sensitive FIR polarimeter. HAWC is a 12 x 32 pixel bolometer camera designed to cover the 53 - 215 micron spectral range in 4 colors, all at diffraction-limited resolution (5 - 21 arcsec). Upgrade options include: (1) an external set of optics which modulates the polarization state of the incoming radiation before entering the cryostat window; (2) internal polarizing optics; and (3) a replacement of the current detector array with two state-of-the-art superconducting bolometer arrays, an upgrade of the HAWC camera as well as polarimeter. We discuss a range of science studies which will be possible with these upgrades including magnetic fields in star-forming regions and galaxies and the wavelength-dependence of polarization.Comment: 12 pages, 5 figure

Statistical Assessment of Shapes and Magnetic Field Orientations in Molecular Clouds through Polarization Observations

We present a novel statistical analysis aimed at deriving the intrinsic shapes and magnetic field orientations of molecular clouds using dust emission and polarization observations by the Hertz polarimeter. Our observables are the aspect ratio of the projected plane-of-the-sky cloud image, and the angle between the mean direction of the plane-of-the-sky component of the magnetic field and the short axis of the cloud image. To overcome projection effects due to the unknown orientation of the line-of-sight, we combine observations from 24 clouds, assuming that line-of-sight orientations are random and all are equally probable. Through a weighted least-squares analysis, we find that the best-fit intrinsic cloud shape describing our sample is an oblate disk with only small degrees of triaxiality. The best-fit intrinsic magnetic field orientation is close to the direction of the shortest cloud axis, with small (~24 deg) deviations toward the long/middle cloud axes. However, due to the small number of observed clouds, the power of our analysis to reject alternative configurations is limited.Comment: 14 pages, 8 figures, accepted for publication in MNRA

New Results on the Submillimeter Polarization Spectrum of the Orion Molecular Cloud

We have used the SHARP polarimeter at the Caltech Submillimeter Observatory to map the polarization at wavelengths of 350 and 450 micron in a ~2 x 3 arcmin region of the Orion Molecular Cloud. The map covers the brightest region of the OMC-1 ridge including the Kleinmann-Low (KL) nebula and the submillimeter source Orion-south. The ratio of 450-to-350 micron polarization is ~ 1.3 +/- 0.3 in the outer parts of the cloud and drops by a factor of 2 towards KL. The outer cloud ratio is consistent with measurements in other clouds at similar wavelengths and confirms previous measurements placing the minimum of the polarization ratio in dusty molecular clouds at a wavelength ~ 350 micron.Comment: 7 pages, 6 figures, submitted to ApJ Let

A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus

<p>Abstract</p> <p>Background</p> <p>A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of <it>Eucalyptus</it>, a genus that includes over 700 species, some of which are used worldwide in plantation forestry. Nevertheless, the average marker density achieved with current technologies remains at the level of a few hundred markers per population. Furthermore, the transferability of markers produced with most existing technology across species and pedigrees is usually very limited. High throughput, combined with wide genome coverage and high transferability are necessary to increase the resolution, speed and utility of molecular marker technology in eucalypts. We report the development of a high-density DArT genome profiling resource and demonstrate its potential for genome-wide diversity analysis and linkage mapping in several species of <it>Eucalyptus</it>.</p> <p>Findings</p> <p>After testing several genome complexity reduction methods we identified the <it>Pst</it>I/<it>Taq</it>I method as the most effective for <it>Eucalyptus </it>and developed 18 genomic libraries from <it>Pst</it>I/<it>Taq</it>I representations of 64 different <it>Eucalyptus </it>species. A total of 23,808 cloned DNA fragments were screened and 13,300 (56%) were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the <it>E. grandis </it>tree whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees.</p> <p>Conclusions</p> <p>This operational DArT array will deliver 1,000-2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees and thus provide high genome coverage. This array will also provide a high-throughput platform for population genetics and phylogenetics in <it>Eucalyptus</it>. The transferability of DArT across species and pedigrees is particularly valuable for a large genus such as <it>Eucalyptus </it>and will facilitate the transfer of information between different studies. Furthermore, the DArT marker array will provide a high-resolution link between phenotypes in populations and the <it>Eucalyptus </it>reference genome, which will soon be completed.</p

Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon

Widespread species spanning strong environmental (e.g., climatic) gradients frequently display morphological and physiological adaptations to local conditions. Some adaptations are common to different species that occupy similar environments. However, the genomic architecture underlying such convergent traits may not be the same between species. Using genomic data from previous studies of three widespread eucalypt species that grow along rainfall gradients in southern Australia, our probabilistic approach provides evidence that adaptation to aridity is a genome-wide phenomenon, likely to involve multiple and diverse genes, gene families and regulatory regions that affect a multitude of complex genetic and biochemical processes

Climate-adjusted provenancing: A strategy for climate-resilient ecological restoration

Investments in ecological restoration are estimated at $US 2 trillion per annum worldwide and are increasing rapidly (Cunningham, 2008; Williams et al., 2014). These investments are occurring in an environment of accelerated climate change that is projected to continue into the next century, yet they currently take little account of such change. This has significant implications for the long-term success of restoration plantings across millions of hectares, with germplasm used in current restoration efforts potentially poorly-adapted to future climates. New approaches that optimize the climate-resilience of these restoration efforts are thus essential (Breed et al., 2013; Williams et al., 2014; Havens et al., 2015)..

CMBPol Mission Concept Study: Prospects for polarized foreground removal

In this report we discuss the impact of polarized foregrounds on a future CMBPol satellite mission. We review our current knowledge of Galactic polarized emission at microwave frequencies, including synchrotron and thermal dust emission. We use existing data and our understanding of the physical behavior of the sources of foreground emission to generate sky templates, and start to assess how well primordial gravitational wave signals can be separated from foreground contaminants for a CMBPol mission. At the estimated foreground minimum of ~100 GHz, the polarized foregrounds are expected to be lower than a primordial polarization signal with tensor-to-scalar ratio r=0.01, in a small patch (~1%) of the sky known to have low Galactic emission. Over 75% of the sky we expect the foreground amplitude to exceed the primordial signal by about a factor of eight at the foreground minimum and on scales of two degrees. Only on the largest scales does the polarized foreground amplitude exceed the primordial signal by a larger factor of about 20. The prospects for detecting an r=0.01 signal including degree-scale measurements appear promising, with 5 sigma_r ~0.003 forecast from multiple methods. A mission that observes a range of scales offers better prospects from the foregrounds perspective than one targeting only the lowest few multipoles. We begin to explore how optimizing the composition of frequency channels in the focal plane can maximize our ability to perform component separation, with a range of typically 40 < nu < 300 GHz preferred for ten channels. Foreground cleaning methods are already in place to tackle a CMBPol mission data set, and further investigation of the optimization and detectability of the primordial signal will be useful for mission design.Comment: 42 pages, 14 figures, Foreground Removal Working Group contribution to the CMBPol Mission Concept Study, v2, matches AIP versio

Polarisation Observations of VY Canis Majoris Water Vapour 5{32}-4{41} 620.701 GHz Maser Emission with HIFI

CONTEXT: Water vapour maser emission from evolved oxygen-rich stars remains poorly understood. Additional observations, including polarisation studies and simultaneous observation of different maser transitions may ultimately lead to greater insight. AIMS: We have aimed to elucidate the nature and structure of the VY CMa water vapour masers in part by observationally testing a theoretical prediction of the relative strengths of the 620.701 GHz and the 22.235 GHz maser components of ortho water vapour. METHODS: In its high-resolution mode (HRS) the Herschel Heterodyne Instrument for the Infrared (HIFI) offers a frequency resolution of 0.125 MHz, corresponding to a line-of-sight velocity of 0.06 km/s, which we employed to obtain the strength and linear polarisation of maser spikes in the spectrum of VY CMa at 620.701 GHz. Simultaneous ground based observations of the 22.235 GHz maser with the Max-Planck-Institut f\"ur Radioastronomie 100-meter telescope at Effelsberg, provided a ratio of 620.701 GHz to 22.235 GHz emission. RESULTS:We report the first astronomical detection to date of water vapour maser emission at 620.701 GHz. In VY CMa both the 620.701 and the 22.235 GHz polarisation are weak. At 620.701 GHz the maser peaks are superposed on what appears to be a broad emission component, jointly ejected asymmetrically from the star. We observed the 620.701 GHz emission at two epochs 21 days apart, both to measure the potential direction of linearly polarised maser components and to obtain a measure of the longevity of these components. Although we do not detect significant polarisation levels in the core of the line, they rise up to approximately 6% in its wings