Investigation of the protein osteocalcin of Camelops hesternus: Sequence, structure and phylogenetic implications

Ancient DNA sequences offer an extraordinary opportunity to unravel the evolutionary history of ancient organisms. Protein sequences offer another reservoir of genetic information that has recently become tractable through the application of mass spectrometric techniques. The extent to which ancient protein sequences resolve phylogenetic relationships, however, has not been explored. We determined the osteocalcin amino acid sequence from the bone of an extinct Camelid (21 ka, Camelops hesternus) excavated from Isleta Cave, New Mexico and three bones of extant camelids: bactrian camel (Camelus bactrianus); dromedary camel (Camelus dromedarius) and guanaco (Llama guanacoe) for a diagenetic and phylogenetic assessment. There was no difference in sequence among the four taxa. Structural attributes observed in both modern and ancient osteocalcin include a post-translation modification, Hyp₉, deamidation of Gln₃₅ and Gln₃₉, and oxidation of Met₃₆. Carbamylation of the N-terminus in ancient osteocalcin may result in blockage and explain previous difficulties in sequencing ancient proteins via Edman degradation.A phylogenetic analysis using osteocalcin sequences of 25 vertebrate taxa was conducted to explore osteocalcin protein evolution and the utility of osteocalcin sequences for delineating phylogenetic relationships. The maximum likelihood tree closely reflected generally recognized taxonomic relationships. For example, maximum likelihood analysis recovered rodents, birds and, within hominins, the Homo-Pan-Gorilla trichotomy. Within Artiodactyla, character state analysis showed that a substitution of Pro₄ for His₄ defines the Capra-Ovis clade within Artiodactyla. Homoplasy in our analysis indicated that osteocalcin evolution is not a perfect indicator of species evolution. Limited sequence availability prevented assigning functional significance to sequence changes. Our preliminary analysis of osteocalcin evolution represents an initial step towards a complete character analysis aimed at determining the evolutionary history of this functionally significant protein. We emphasize that ancient protein sequencing and phylogenetic analyses using amino acid sequences must pay close attention to post-translational modifications, amino acid substitutions due to diagenetic alteration and the impacts of isobaric amino acids on mass shifts and sequence alignments.     

Ocean Mixed-Layer Depth and Current Variation Estimated From Imagery of Surfactant Streaks

The ability of high-resolution imaging systems to resolve small-scale structure on the ocean surface suggests the possibility of using characteristics of Langmuir circulation to map the surface mixed-layer depth and near-surface current. We illustrate this using synthetic aperture radar and infrared imagery that are collected across the edge of the Gulf Stream (GS), which reveals surfactant streaks, or ldquowindrows,rdquo that are induced by Langmuir circulation. Based on changes in the windrow spacing and orientation, the mixed layer is estimated to deepen from 7 to 12 m across the edge of the GS and the current to increase from about 1 to 2 m/s. These spatial changes compare reasonably well with independent data, suggesting that the approach is plausible. It may also be possible to extract additional environmental information from the windrows.     

Late Holocene Mediterranean coastal change along the Tiber Delta and Roman occupation of the Laurentine shore, central Italy

A line of Roman villas once dominated the Mediterranean coastline to the south of the Tiber river mouth near Ostia in central Italy. The Roman remains, which were constructed within a series of dune ridges, now lie up to 900 m from the current shoreline as a result of the continued evolution of the Tiber delta in response to postglacial sea level rise, sediment inputs from the Tiber river catchment and tectonic uplift. Infrared stimulated luminescence (IRSL) ages of potassium-rich feldspars extracted from dune sands are in good agreement with the independent age control provided by the Roman structures and allow us to hypothesise an increase in aggradation rates of five times since the end of the period of Roman occupation compared with the earlier Holocene.     

Factors influencing the release of dissolved organic carbon and dissolved forms of nitrogen from a small upland headwater during autumn runoff events

We identify and assess the relative importance of the principal factors influencing the release of dissolved organic carbon (DOC) and dissolved forms of nitrogen (N) from a small upland headwater dominated by podzolic soils during a sequence of autumn runoff events. We achieve this by subjecting high‐resolution hydrometeorological and hydrochemical data to an R‐mode principal component factor analysis and a stepwise multivariate regression analysis. We find that the release of DOC and N is influenced by four principal factors, namely event magnitude, soil water flow through the Bs horizon, the length of time since the soil profile was last flushed, and rewetting of the H horizon. The release of DOC and dissolved organic nitrogen (DON) is most strongly influenced by the combination of event magnitude and soil water flow through the Bs horizon, and to a lesser extent by the length of time since the soil profile was last flushed. Rewetting of the H horizon also influences the release of DOC, but this is not the case for DON. The release of nitrate (NO₃‐N) is most strongly influenced by the combination of the length of time since the soil profile was last flushed and rewetting of the H horizon, and to a lesser extent by event magnitude. Soil water flow through the Bs horizon does not influence the release of NO₃‐N. We argue that the mechanisms by which the above factors influence the release of DOC and N are probably strongly associated with moisture‐dependent biological activity, which governs the turnover of organic matter in the soil and limits the availability of NO₃‐N in the soil for leaching. We conclude that the release of DOC and N from upland headwaters dominated by podzolic soils is largely controlled by the variable interaction of hydrometeorological factors and moisture‐dependent biological processes, and that a shift in climate towards drier summers and wetter winters may result in the release of DOC and N becoming increasingly variable and more episodic in the future. Copyright © 2006 John Wiley & Sons, Ltd.     

Crossover from capillary fingering to compact invasion for two-phase drainage with stable viscosity ratios

Motivated by a wide range of applications from enhanced oil recovery to carbon dioxide sequestration, we have developed a two-dimensional, pore-level model of immiscible drainage, incorporating viscous, capillary, and gravitational effects. This model has been validated quantitatively, in the very different limits of zero viscosity ratio and zero capillary number; flow patterns from modeling agree well with experiment. For a range of stable viscosity ratios (μ_injected/μ_displaced ? 1), we have increased the capillary number, N_c, and studied the way in which the flows deviate from capillary fingering (the fractal flow of invasion percolation) and become compact for realistic capillary numbers. Results exhibiting this crossover from capillary fingering to compact invasion are presented for the average position of the injected fluid, the fluid–fluid interface, the saturation and fractional flow profiles, and the relative permeabilities. The agreement between our results and earlier theoretical predictions [Blunt M, King MJ, Scher H. Simulation and theory of two-phase flow in porous media. Phys Rev A 1992;46:7680–99; Lenormand R. Flow through porous media: limits of fractal patterns. Proc Roy Soc A 1989;423:159–68; Wilkinson D. Percolation effects in immiscible displacement. Phys Rev A 1986;34:1380–90; Xu B, Yortsos YC, Salin D. Invasion Percolation with viscous forces. Phys Rev E 1998;57:739–51] supports the validity of these general theoretical arguments, which were independent of the details of the porous media in both two and three dimensions.     

The expansion of the giant filamentary shell, DEM 171, in the Magellanic Bridge

The giant filamentary shell, DEM 171, is found to be expanding at approximately 37 km s⁻¹. A supernova and stellar wind origin are both explored as possible causes for the expanding shell. A stellar wind origin would imply a mass-loss rate of the order of 10⁻⁵ M_⊙ yr⁻¹, indicating that it could be caused by a Wolf–Rayet star. A number of blue stars are found to lie within the shell and one is identified as a Wolf–Rayet candidate.     

A demographic approach to monitoring the health of coral reefs

Inshore coral reefs adjacent to the wet tropics in North Queensland, Australia, are regularly exposed to flood plumes from coastal river systems. Changes in the nature of these plumes have been linked to the declining health of coral reefs in the region. The effect of flood plumes on the health of inshore corals was investigated by quantifying aspects of the demography of populations of corymbose and digitate Acropora at three groups of Island reefs along a gradient of exposure and decreasing water quality (High Island >Frankland's >Fitzroy). The size-structures of colonies, the rates of sexual recruitment, and the growth and survival of juveniles, all varied among the Island reefs. Juvenile and adult sized colonies were far more abundant at the Fitzroy Island reefs, than at the High or Frankland Island reefs that were more exposed to flood plumes. Additionally, there were up to eight times as many sexual recruits at the Fitzroy Island reefs, compared with the High Island reefs. However, the rates of growth and survival of the juvenile sized corals at the Fitzroy Island reefs were lower than at the more exposed reefs. The comparatively low abundance of adult corals at the exposed reefs is most likely due to their histories of disturbance from crown-of-thorns and coral bleaching, but the lack of subsequent recovery due to their low levels of larval recruitment. If a stock-recruitment relationship is typical for these groups of reefs, then the low rates of recruitment may be linked to the low density of adult colonies. Alternately, direct or indirect effects of chronic exposure to poor water quality may have resulted in less suitable substrata for larval settlement. We discuss these results and provide examples of how information about population structure and dynamics can be used in simple matrix models to quantify the current and future health of populations of corals under various scenarios.