238 research outputs found
The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface
The rhizosphere is the zone of soil infuenced by a plant root and is critical for plant health and nutrient acquisition. All below ground resources must pass through this dynamic zone prior to their capture by plant roots. However, researching the undisturbed rhizosphere has proved very challenging. Here we compare the temporal changes to the intact rhizosphere pore structure during the emergence of a developing root system in diferent soils. High resolution X-ray Computed Tomography (CT) was used to quantify the impact of root development on soil structural change, at scales relevant to individual micro-pores and aggregates (µm). A comparison of micro-scale structural evolution in homogenously packed soils highlighted the impacts of a penetrating root system in changing the surrounding porous architecture and morphology. Results indicate the structural zone of infuence of a root can be more localised than previously reported (µm scale rather than mm scale). With time, growing roots signifcantly alter the soil physical environment in their immediate vicinity through reducing root-soil contact and crucially increasing porosity at the root-soil interface and not the converse as has often been postulated. This ‘rhizosphere pore structure’ and its impact on associated dynamics are discussed
Genetic characterization and phylogeography of the wild boar Sus scrofa introduced into Uruguay
The European wild boar Sus scrofa was first introduced into Uruguay, in southern South America during the early decades of the last century. Subsequently, and starting from founder populations, its range spread throughout the country and into the neighbouring Brazilian state Rio Grande do Sul. Due to the subsequent negative impact, it was officially declared a national pest. The main aim in the present study was to provide a more comprehensive scenario of wild boar differentiation in Uruguay, by using mtDNA markers to access the genetic characterization of populations at present undergoing rapid expansion. A high level of haplotype diversity, intermediate levels of nucleotide diversity and considerable population differentiation, were detected among sampled localities throughout major watercourses and catchment dams countrywide. Phylogenetic analysis revealed the existence of two different phylogroups, thereby reflecting two deliberate introduction events forming distantly genetic lineages in local wild boar populations. Our analysis lends support to the hypothesis that the invasive potential of populations emerge from introgressive hybridization with domestic pigs. On taking into account the appreciable differentiation and reduced migration between locales in wild boar populations, management strategies could be effective if each population were to be considered as a single management unit
DNA Barcoding for Community Ecology - How to Tackle a Hyperdiverse, Mostly Undescribed Melanesian Fauna
Trigonopterus weevils are widely distributed throughout Melanesia and hyperdiverse in New Guinea. They are a dominant feature in natural forests, with narrow altitudinal zonation. Their use in community ecology has been precluded by the "taxonomic impediment".
We sampled >6,500 specimens from seven areas across New Guinea; 1,002 specimens assigned to 270 morphospecies were DNA sequenced. Objective clustering of a refined dataset (excluding nine cryptic species) at 3% threshold revealed 324 genetic clusters (DNA group count relative to number of morphospecies = 20.0% overestimation of species diversity, or 120.0% agreement) and 85.6% taxonomic accuracy (the proportion of DNA groups that "perfectly" agree with morphology-based species hypotheses). Agreement and accuracy were best at an 8% threshold. GMYC analysis revealed 328 entities (21.5% overestimation) with 227 perfect GMYC entities (84.1% taxonomic accuracy). Both methods outperform the parataxonomist (19% underestimation; 31.6% taxonomic accuracy). The number of species found in more than one sampling area was highest in the Eastern Highlands and Huon (Sørensen similarity index 0.07, 4 shared species); ⅓ of all areas had no species overlap. Success rates of DNA barcoding methods were lowest when species showed a pronounced geographical structure. In general, Trigonopterus show high α and β-diversity across New Guinea.
DNA barcoding is an excellent tool for biodiversity surveys but success rates might drop when closer localities are included. Hyperdiverse Trigonopterus are a useful taxon for evaluating forest remnants in Melanesia, allowing finer-grained analyses than would be possible with vertebrate taxa commonly used to date. Our protocol should help establish other groups of hyperdiverse fauna as target taxa for community ecology. Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should help pave the road for the eventual formal naming of new species
Foundations of Black Hole Accretion Disk Theory
This review covers the main aspects of black hole accretion disk theory. We
begin with the view that one of the main goals of the theory is to better
understand the nature of black holes themselves. In this light we discuss how
accretion disks might reveal some of the unique signatures of strong gravity:
the event horizon, the innermost stable circular orbit, and the ergosphere. We
then review, from a first-principles perspective, the physical processes at
play in accretion disks. This leads us to the four primary accretion disk
models that we review: Polish doughnuts (thick disks), Shakura-Sunyaev (thin)
disks, slim disks, and advection-dominated accretion flows (ADAFs). After
presenting the models we discuss issues of stability, oscillations, and jets.
Following our review of the analytic work, we take a parallel approach in
reviewing numerical studies of black hole accretion disks. We finish with a few
select applications that highlight particular astrophysical applications:
measurements of black hole mass and spin, black hole vs. neutron star accretion
disks, black hole accretion disk spectral states, and quasi-periodic
oscillations (QPOs).Comment: 91 pages, 23 figures, final published version available at
http://www.livingreviews.org/lrr-2013-
Accreting Millisecond X-Ray Pulsars
Accreting Millisecond X-Ray Pulsars (AMXPs) are astrophysical laboratories
without parallel in the study of extreme physics. In this chapter we review the
past fifteen years of discoveries in the field. We summarize the observations
of the fifteen known AMXPs, with a particular emphasis on the multi-wavelength
observations that have been carried out since the discovery of the first AMXP
in 1998. We review accretion torque theory, the pulse formation process, and
how AMXP observations have changed our view on the interaction of plasma and
magnetic fields in strong gravity. We also explain how the AMXPs have deepened
our understanding of the thermonuclear burst process, in particular the
phenomenon of burst oscillations. We conclude with a discussion of the open
problems that remain to be addressed in the future.Comment: Review to appear in "Timing neutron stars: pulsations, oscillations
and explosions", T. Belloni, M. Mendez, C.M. Zhang Eds., ASSL, Springer;
[revision with literature updated, several typos removed, 1 new AMXP added
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Detection of cosmic structures using the bispectrum phase. II. First results from application to cosmic reionization using the Hydrogen Epoch of Reionization Array
Characterizing the epoch of reionization (EoR) at via the
redshifted 21 cm line of neutral Hydrogen (HI) is critical to modern
astrophysics and cosmology, and thus a key science goal of many current and planned low-frequency radio telescopes. The primary challenge to detecting this signal is the overwhelmingly bright foreground emission at these frequencies, placing stringent requirements on the knowledge of the instruments and inaccuracies in analyses. Results from these experiments have largely been limited not by thermal sensitivity but by systematics, particularly caused by the inability to calibrate the instrument to high accuracy. The interferometric bispectrum phase is immune to antenna-based calibration and errors therein, and presents an independent alternative to detect the EoR HI fluctuations while largely avoiding calibration systematics. Here, we provide a demonstration of this technique on a subset of data from the Hydrogen Epoch of Reionization Array (HERA) to place approximate constraints on the IGM brightness temperature. From this limited data, at we infer "" upper limits on the IGM brightness temperature to be "pseudo" mK at Mpc (data-limited) and
"pseudo" mK at
Mpc (noise-limited). The "pseudo" units denote only an approximate and not an exact correspondence to the actual distance scales and brightness temperatures. By propagating models in parallel to the data analysis, we confirm that the dynamic range required to separate the cosmic HI signal from the foregrounds is similar to that in standard approaches, and the power spectrum of the bispectrum phase is still data-limited (at dynamic range) indicating scope for further improvement in sensitivity as the array build-out continues
Imaging and Modeling Data from the Hydrogen Epoch of Reionization Array
We analyze data from the Hydrogen Epoch of Reionization Array. This is the
third in a series of papers on the closure phase delay-spectrum technique
designed to detect the HI 21cm emission from cosmic reionization. We present
the details of the data and models employed in the power spectral analysis, and
discuss limitations to the process. We compare images and visibility spectra
made with HERA data, to parallel quantities generated from sky models based on
the GLEAM survey, incorporating the HERA telescope model. We find reasonable
agreement between images made from HERA data, with those generated from the
models, down to the confusion level. For the visibility spectra, there is broad
agreement between model and data across the full band of MHz. However,
models with only GLEAM sources do not reproduce a roughly sinusoidal spectral
structure at the tens of percent level seen in the observed visibility spectra
on scales MHz on 29 m baselines. We find that this structure is
likely due to diffuse Galactic emission, predominantly the Galactic plane,
filling the far sidelobes of the antenna primary beam. We show that our current
knowledge of the frequency dependence of the diffuse sky radio emission, and
the primary beam at large zenith angles, is inadequate to provide an accurate
reproduction of the diffuse structure in the models. We discuss implications
due to this missing structure in the models, including calibration, and in the
search for the HI 21cm signal, as well as possible mitigation techniques
Understanding the HERA Phase i receiver system with simulations and its impact on the detectability of the EoR delay power spectrum
The detection of the Epoch of Reionization (EoR) delay power spectrum using a
"foreground avoidance method" highly depends on the instrument chromaticity.
The systematic effects induced by the radio-telescope spread the foreground
signal in the delay domain, which contaminates the EoR window theoretically
observable. Applied to the Hydrogen Epoch of Reionization Array (HERA), this
paper combines detailed electromagnetic and electrical simulations in order to
model the chromatic effects of the instrument, and quantify its frequency and
time responses. In particular, the effects of the analogue receiver,
transmission cables, and mutual coupling are included. These simulations are
able to accurately predict the intensity of the reflections occurring in the
150-m cable which links the antenna to the back-end. They also show that
electromagnetic waves can propagate from one dish to another one through large
sections of the array due to mutual coupling. The simulated system time
response is attenuated by a factor after a characteristic delay which
depends on the size of the array and on the antenna position. Ultimately, the
system response is attenuated by a factor after 1400 ns because of the
reflections in the cable, which corresponds to characterizable
-modes above 0.7 at 150 MHz. Thus, this new
study shows that the detection of the EoR signal with HERA Phase I will be more
challenging than expected. On the other hand, it improves our understanding of
the telescope, which is essential to mitigate the instrument chromaticity
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