Can colour vision re-evolve? Variation in the X-linked opsin locus of cathemeral Azara’s owl monkeys (Aotus azarae azarae)

Background: Do evolutionary specializations lead to evolutionary constraint? This appears plausible, particularly when specialization leads to loss of complex adaptations. In the owl monkey lineage, nocturnality clearly arose from a diurnal ancestor. This behavioural shift was accompanied by morphological changes in the eye and orbit and complete loss of colour vision via missense mutations in the gene encoding the short-wave sensitive visual pigment (SWS opsin). Interestingly, at least one subspecies of owl monkey, Azara’s owl monkey (Aotus azarae azarae), has regained activity in daylight. Given that all primate species that are active in daylight, including primarily diurnal species and species that are active during both day and night, have at least dichromatic colour vision, it seems reasonable to propose that dichromacy would be adaptive in A. a. azarae. With a disabled SWS opsin, the main avenue available for Azara’s owl monkeys to re-evolve colour vision is via a polymorphism in the intact X-linked opsin locus, which commonly occurs in other New World monkeys. To examine this possibility we assayed variation in the X-linked opsin of A. a. azarae, focusing on the three exons (3, 4 and 5) that control spectral sensitivity. Results: We found low opsin genetic variation on a population level, and no differences at the three main sites that lead to variation in spectral sensitivity in the opsins of other New World monkeys. Two rare alleles with single amino acid variants are segregating in the population, but previous functional studies indicate that these are unlikely to affect spectral sensitivity. Conclusions: Genetic constraint on the re-evolution of colour vision is likely operating in Azara’s owl monkey, which may affect the niche that this subspecies is able to occupy

Chemistry of H2O and HF Under Extreme Conditions

The predicted high pressure superionic phases of water and HF are investigated via ab initio molecular dynamics. These phases could potentially be achieved through either static compression with heating or through shock compression. We study water at densities of 2.0-3.0 g/cc (34-115 GPa) along the 2000K isotherm.We find that extremely rapid (superionic) diffusion of protons occurs in a fluid phase at pressures between 34 and 58 GPa. A transition to a stable body-centered cubic (bcc) O lattice with superionic proton conductivity is observed between 70 and 75 GPa, a much higher pressure than suggested in prior work. We find that all molecular species at pressures greater than 75 GPa are too short lived to be classified as bound states. Up to 95 GPa, we find a solid superionic phase characterized by covalent O-H bonding. Above 95 GPa, a transient network phase is found characterized by symmetric O-H hydrogen bonding with nearly 50% covalent character. Ab initio molecular dynamics simulations of HF were conducted at densities of 1.8-4.0 g/cc along the 900 K isotherm. According to our simulations, a unique form of (symmetric) hydrogen bonding could play a significant role in superionic conduction. Our work shows that superionic phases could be more prevalent in hydrogen bonded systems than previously thought, such as HCl and HBr

Simian immunodeficiency virus infection in wild-caught chimpanzees from Cameroon

Simian immunodeficiency viruses (SIVcpz) infecting chimpanzees (Pan troglodytes) in west central Africa are the closest relatives to all major variants of human immunodeficiency virus type 1 ([HIV-1]; groups M, N and O), and have thus been implicated as the source of the human infections; however, information concerning the prevalence, geographic distribution, and subspecies association of SIVcpz still remains limited. In this study, we tested 71 wild-caught chimpanzees from Cameroon for evidence of SIVcpz infection. Thirty-nine of these were of the central subspecies (Pan troglodytes troglodytes), and 32 were of the Nigerian subspecies (Pan troglodytes vellerosus), as determined by mitochondrial DNA analysis. Serological analysis determined that one P. t. troglodytes ape (CAM13) harbored serum antibodies that cross-reacted strongly with HIV-1 antigens; all other apes were seronegative. To characterize the newly identified virus, 14 partially overlapping viral fragments were amplified from fecal virion RNA and concatenated to yield a complete SIVcpz genome (9,284 bp). Phylogenetic analyses revealed that SIVcpzCAM13 fell well within the radiation of the SIVcpzPtt group of viruses, as part of a clade including all other SIVcpzPtt strains as well as HIV-1 groups M and N. However, SIVcpzCAM13 clustered most closely with SIVcpzGAB1 from Gabon rather than with SIVcpzCAM3 and SIVcpzCAM5 from Cameroon, indicating the existence of divergent SIVcpzPtt lineages within the same geographic region. These data, together with evidence of recombination among ancestral SIVcpzPtt lineages, indicate long-standing endemic infection of central chimpanzees and reaffirm a west central African origin of HIV-1. Whether P. t. vellerosus apes are naturally infected with SIVcpz requires further study

Non-molecular Phases of H2O and HF Under Detonation-like Conditions

Energetic materials are known to produce simple molecular species, such as HF and H{sub 2}O, during detonation. The behavior of such species under conditions of simultaneous high pressure and temperature are unknown. The predicted high pressure superionic phases of water and HF are investigated via ab initio molecular dynamics. We study water at densities of 2.0-3.0 g/cc (34 -115 GPa) along the 2000 K isotherm. We find that extremely rapid (superionic) diffusion of protons occurs in a fluid phase at pressures between 34 and 58 GPa. A transition to a stable body-centered cubic (bcc) O lattice with superionic proton conductivity is observed between 70 and 75 GPa. We find that all molecular species at pressures greater than 75 GPa are too short lived to be classified as bound states. Up to 95 GPa, we find a solid superionic phase characterized by covalent O-H bonding. Above 95 GPa, a transient network phase is found characterized by symmetric O-OH hydrogen bonding with nearly 50% covalent character. Ab initio molecular dynamics H simulations of HF were conducted at densities of 1.8-4.0 g/cc along the 900 K isotherm. According to our simulations, a unique form of (symmetric) hydrogen bonding could play a significant role in superionic conduction. Our work shows that the Chapman-Jouget and Zeldovich-von Neumann Doring (ZND) states of some energetic materials are close to the molecular to non-molecular transition

The Spitzer c2d Survey of Large, Nearby, Interstellar Clouds. I. Chamaeleon II Observed with MIPS

We present maps of over 1.5 square degrees in Chamaeleon (Cha) II at 24, 70, and 160 micron observed with the Spitzer Space Telescope Multiband Imaging Photometer for Spitzer (MIPS) and a 1.2 square degree millimeter map from SIMBA on the Swedish-ESO Submillimetre Telescope (SEST). The c2d Spitzer Legacy Team's data reduction pipeline is described in detail. Over 1500 24 micron sources and 41 70 micron sources were detected by MIPS with fluxes greater than 10-sigma. More than 40 potential YSOs are identified with a MIPS and 2MASS color-color diagram and by their spectral indices, including two previously unknown sources with 24 micron excesses. Our new SIMBA millimeter map of Cha II shows that only a small fraction of the gas is in compact structures with high column densities. The extended emission seen by MIPS is compared with previous CO observations. Some selected interesting sources, including two detected at 1 mm, associated with Cha II are discussed in detail and their SEDs presented. The classification of these sources using MIPS data is found to be consistent with previous studies.Comment: 44 pages, 12 figures (1 color), to be published in Ap

A multi-wavelength analysis for interferometric (sub-)mm observations of protoplanetary disks: radial constraints on the dust properties and the disk structure

Theoretical models of grain growth predict dust properties to change as a function of protoplanetary disk radius, mass, age and other physical conditions. We lay down the methodology for a multi-wavelength analysis of (sub-)mm and cm continuum interferometric observations to constrain self-consistently the disk structure and the radial variation of the dust properties. The computational architecture is massively parallel and highly modular. The analysis is based on the simultaneous fit in the uv-plane of observations at several wavelengths with a model for the disk thermal emission and for the dust opacity. The observed flux density at the different wavelengths is fitted by posing constraints on the disk structure and on the radial variation of the grain size distribution. We apply the analysis to observations of three protoplanetary disks (AS 209, FT Tau, DR Tau) for which a combination of spatially resolved observations in the range ~0.88mm to ~10mm is available (from SMA, CARMA, and VLA), finding evidence of a decreasing maximum dust grain size (a_max) with radius. We derive large a_max values up to 1 cm in the inner disk between 15 and 30 AU and smaller grains with a_max~1 mm in the outer disk (R > 80AU). In this paper we develop a multi-wavelength analysis that will allow this missing quantity to be constrained for statistically relevant samples of disks and to investigate possible correlations with disk or stellar parameters.Comment: 19 pages, 15 figures, accepted for publication in A&

Ab initio Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions

We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot

CARMA Large Area Star Formation Survey: Project Overview with Analysis of Dense Gas Structure and Kinematics in Barnard 1

We present details of the CARMA Large Area Star Formation Survey (CLASSy), while focusing on observations of Barnard 1. CLASSy is a CARMA Key Project that spectrally imaged N2H+, HCO+, and HCN (J=1-0 transitions) across over 800 square arcminutes of the Perseus and Serpens Molecular Clouds. The observations have angular resolution near 7" and spectral resolution near 0.16 km/s. We imaged ~150 square arcminutes of Barnard 1, focusing on the main core, and the B1 Ridge and clumps to its southwest. N2H+ shows the strongest emission, with morphology similar to cool dust in the region, while HCO+ and HCN trace several molecular outflows from a collection of protostars in the main core. We identify a range of kinematic complexity, with N2H+ velocity dispersions ranging from ~0.05-0.50 km/s across the field. Simultaneous continuum mapping at 3 mm reveals six compact object detections, three of which are new detections. A new non-binary dendrogram algorithm is used to analyze dense gas structures in the N2H+ position-position-velocity (PPV) cube. The projected sizes of dendrogram-identified structures range from about 0.01-0.34 pc. Size-linewidth relations using those structures show that non-thermal line-of-sight velocity dispersion varies weakly with projected size, while rms variation in the centroid velocity rises steeply with projected size. Comparing these relations, we propose that all dense gas structures in Barnard 1 have comparable depths into the sky, around 0.1-0.2 pc; this suggests that over-dense, parsec-scale regions within molecular clouds are better described as flattened structures rather than spherical collections of gas. Science-ready PPV cubes for Barnard 1 molecular emission are available for download.Comment: Accepted to The Astrophysical Journal (ApJ), 51 pages, 27 figures (some with reduced resolution in this preprint); Project website is at http://carma.astro.umd.edu/class

On the structure of the transition disk around TW Hya

For over a decade, the structure of the inner cavity in the transition disk of TW Hydrae has been a subject of debate. Modeling the disk with data obtained at different wavelengths has led to a variety of proposed disk structures. Rather than being inconsistent, the individual models might point to the different faces of physical processes going on in disks, such as dust growth and planet formation. Our aim is to investigate the structure of the transition disk again and to find to what extent we can reconcile apparent model differences. A large set of high-angular-resolution data was collected from near-infrared to centimeter wavelengths. We investigated the existing disk models and established a new self-consistent radiative-transfer model. A genetic fitting algorithm was used to automatize the parameter fitting. Simple disk models with a vertical inner rim and a radially homogeneous dust composition from small to large grains cannot reproduce the combined data set. Two modifications are applied to this simple disk model: (1) the inner rim is smoothed by exponentially decreasing the surface density in the inner ~3 AU, and (2) the largest grains (>100 um) are concentrated towards the inner disk region. Both properties can be linked to fundamental processes that determine the evolution of protoplanetary disks: the shaping by a possible companion and the different regimes of dust-grain growth, respectively. The full interferometric data set from near-infrared to centimeter wavelengths requires a revision of existing models for the TW Hya disk. We present a new model that incorporates the characteristic structures of previous models but deviates in two key aspects: it does not have a sharp edge at 4 AU, and the surface density of large grains differs from that of smaller grains. This is the first successful radiative-transfer-based model for a full set of interferometric data.Comment: 22 pages, 12 figures, accepted for publication in Astronomy & Astrophysic