Merging Resource Availability with Isotope Mixing Models: The Role of Neutral Interaction Assumptions

Background: Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values. Methodology: We develop a procedure to incorporate prey availability data into Bayesian mixing models conditional on the similarity of isotope values between two prey. If a pair of prey have similar isotope values (resulting in highly uncertain mixing model results), our model increases the weight of availability data in estimating the contribution of prey to a predator's diet. We test the utility of this method in an intertidal community against independently measured feeding rates. Conclusions: Our results indicate that our weighting procedure increases the accuracy by which consumer diets can be inferred in situations where multiple prey have similar isotope values. This suggests that the exchange of formalism for predictive power is merited, particularly when the relationship between prey availability and a predator's diet cannot be assumed for all species in a system.

LIFE CYCLE AND POPULATION STRUCTURE OF AEGLA PAULENSIS (DECAPODA: ANOMURA: AEGLIDAE)

We describe growth, longevity, sex ratio, reproductive period, and recruitment of Aegla paulensis from Jaragua Stale Park, Sao Paulo, Brazil (23 degrees 27'27.9 '' S; 46 degrees 45'32.3 '' W). The population was sampled monthly (September 2007 through August 2009) with the aid of traps. Over five thousand individuals were captured, sexed, measured (carapace length = CL) and inspected for reproductive traits (females only), and then released back to the sampling site. The pattern of the reproductive cycle was strongly seasonal (austral mid autumn through late winter), with a single recruitment pulse per year. The obtained von Bertalanffy growth equations were CL = 21.25[1-e(-0.041(t + 1.250))] and CL = 16.52[1-e(-0.049(t + 1.823))] for males and females, respectively. Males (mean CL +/- SD = 11.86 +/- 2.79 mm) attain larger sizes than females (mean CL +/- SD = 10.84 +/- 2.36 mm). Aegla paulensis reproduces twice during an estimated life span of 40.2 months for females and 33.9 months for males. Temporal variation of sex ratio showed a distinctive pattern characterized by a sequence of three distinct periods that repeated from one year to another, and which suggested that a behavioral component influence the proportion of sex in adult specimens sampled with traps during reproductive and non-reproductive periods.

The Missing Part of Seed Dispersal Networks: Structure and Robustness of Bat-Fruit Interactions

Mutualistic networks are crucial to the maintenance of ecosystem services. Unfortunately, what we know about seed dispersal networks is based only on bird-fruit interactions. Therefore, we aimed at filling part of this gap by investigating bat-fruit networks. It is known from population studies that: (i) some bat species depend more on fruits than others, and (ii) that some specialized frugivorous bats prefer particular plant genera. We tested whether those preferences affected the structure and robustness of the whole network and the functional roles of species. Nine bat-fruit datasets from the literature were analyzed and all networks showed lower complementary specialization (H(2)' = 0.3760.10, mean 6 SD) and similar nestedness (NODF = 0.5660.12) than pollination networks. All networks were modular (M=0.32 +/- 0.07), and had on average four cohesive subgroups (modules) of tightly connected bats and plants. The composition of those modules followed the genus-genus associations observed at population level (Artibeus-Ficus, Carollia-Piper, and Sturnira-Solanum), although a few of those plant genera were dispersed also by other bats. Bat-fruit networks showed high robustness to simulated cumulative removals of both bats (R = 0.55 +/- 0.10) and plants (R = 0.68 +/- 0.09). Primary frugivores interacted with a larger proportion of the plants available and also occupied more central positions; furthermore, their extinction caused larger changes in network structure. We conclude that bat-fruit networks are highly cohesive and robust mutualistic systems, in which redundancy is high within modules, although modules are complementary to each other. Dietary specialization seems to be an important structuring factor that affects the topology, the guild structure and functional roles in bat-fruit networks.

Inferences of evolutionary and ecological events that influenced the population structure of Plebeia remota, a stingless bee from Brazil

The present study characterised the population genetic structure of Plebeia remota through mitochondrial DNA (mtDNA) analysis and evaluated evolutionary and ecological processes that may have contributed to the species current genetic scenario. Seventy feral nests were sampled representing four geographic regions (Cunha, Curitiba, Prudentopolis, and Blumenau). Fifteen composite mtDNA haplotypes were determined and a high genetic structure was detected among all populations. The current population structure may be a result of queen philopatry and vegetation shifts caused by palaeoclimatic changes and uplift of Brazilian coastal ranges. Finally, this study strongly suggests a revision of the taxonomic status of P. remota from the Prudentopolis region.

Phylogeography of the common vampire bat (Desmodus rotundus): Marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers

Background: The common vampire bat Desmodus rotundus is an excellent model organism for studying ecological vicariance in the Neotropics due to its broad geographic range and its preference for forested areas as roosting sites. With the objective of testing for Pleistocene ecological vicariance, we sequenced a mitocondrial DNA (mtDNA) marker and two nuclear markers (RAG2 and DRB) to try to understand how Pleistocene glaciations affected the distribution of intraspecific lineages in this bat. Results: Five reciprocally monophyletic clades were evident in the mitochondrial gene tree, and in most cases with high bootstrap support: Central America (CA), Amazon and Cerrado (AMC), Pantanal (PAN), Northern Atlantic Forest (NAF) and Southern Atlantic Forest (SAF). The Atlantic forest clades formed a monophyletic clade with high bootstrap support, creating an east/west division for this species in South America. On the one hand, all coalescent and non-coalescent estimates point to a Pleistocene time of divergence between the clades. On the other hand, the nuclear markers showed extensive sharing of haplotypes between distant localities, a result compatible with male-biased gene flow. In order to test if the disparity between the mitochondrial and nuclear markers was due to the difference in mutation rate and effective size, we performed a coalescent simulation to examine the feasibility that, given the time of separation between the observed lineages, even with a gene flow rate close to zero, there would not be reciprocal monophyly for a neutral nuclear marker. We used the observed values of theta and an estimated mutation rate for the nuclear marker gene to perform 1000 iterations of the simulation. The results of this simulation were inconclusive: the number of iterations with and without reciprocal monophyly of one or more clades are similar. Conclusions: We therefore conclude that the pattern exhibited by the common vampire bat, with marked geographical structure for a mitochondrial marker and no phylogeographic structure for nuclear markers is compatible with a historical scenario of complete isolation of refuge-like populations during the Pleistocene. The results on demographic history on this species is compatible with the Carnaval-Moritz model of Pleistocene vicariance, with demographic expansions in the southern Atlantic forest.

The Function and Three-Dimensional Structure of a Thromboxane A(2)/Cysteinyl Leukotriene-Binding Protein from the Saliva of a Mosquito Vector of the Malaria Parasite

The highly expressed D7 protein family of mosquito saliva has previously been shown to act as an anti-inflammatory mediator by binding host biogenic amines and cysteinyl leukotrienes (CysLTs). In this study we demonstrate that AnSt-D7L1, a two-domain member of this group from Anopheles stephensi, retains the CysLT binding function seen in the homolog AeD7 from Aedes aegypti but has lost the ability to bind biogenic amines. Unlike any previously characterized members of the D7 family, AnSt-D7L1 has acquired the important function of binding thromboxane A(2) (TXA(2)) and its analogs with high affinity. When administered to tissue preparations, AnSt-D7L1 abrogated Leukotriene C(4) (LTC(4))-induced contraction of guinea pig ileum and contraction of rat aorta by the TXA(2) analog U46619. The protein also inhibited platelet aggregation induced by both collagen and U46619 when administered to stirred platelets. The crystal structure of AnSt-D7L1 contains two OBP-like domains and has a structure similar to AeD(7). In AnSt-D7L1, the binding pocket of the C-terminal domain has been rearranged relative to AeD7, making the protein unable to bind biogenic amines. Structures of the ligand complexes show that CysLTs and TXA(2) analogs both bind in the same hydrophobic pocket of the N-terminal domain. The TXA(2) analog U46619 is stabilized by hydrogen bonding interactions of the omega-5 hydroxyl group with the phenolic hydroxyl group of Tyr 52. LTC(4) and occupies a very similar position to LTE(4) in the previously determined structure of its complex with AeD7. As yet, it is not known what, if any, new function has been acquired by the rearranged C-terminal domain. This article presents, to our knowledge, the first structural characterization of a protein from mosquito saliva that inhibits collagen mediated platelet activation.

Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies

Background: The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized. Results: We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for similar to 40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance. Conclusion: These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.

Structure of disordered gold-polymer thin films using small angle x-ray scattering

We have investigated the structure of disordered gold-polymer thin films using small angle x-ray scattering and compared the results with the predictions of a theoretical model based on two approaches-a structure form factor approach and the generalized Porod law. The films are formed of polymer-embedded gold nanoclusters and were fabricated by very low energy gold ion implantation into polymethylmethacrylate (PMMA). The composite films span (with dose variation) the transition from electrically insulating to electrically conducting regimes, a range of interest fundamentally and technologically. We find excellent agreement with theory and show that the PMMA-Au films have monodispersive or polydispersive characteristics depending on the implanted ion dose. (C) 2010 American Institute of Physics. [doi:10.1063/1.3493241]

Structure of PbTe(SiO(2))/SiO(2) multilayers deposited on Si(111)

The structure of thin films composed of a multilayer of PbTe nanocrystals embedded in SiO(2), named as PbTe(SiO(2)), between homogeneous layers of amorphous SiO(2) deposited on a single-crystal Si( 111) substrate was studied by grazing-incidence small-angle X-ray scattering (GISAXS) as a function of PbTe content. PbTe(SiO(2))/SiO(2) multilayers were produced by alternately applying plasma-enhanced chemical vapour deposition and pulsed laser deposition techniques. From the analysis of the experimental GISAXS patterns, the average radius and radius dispersion of PbTe nanocrystals were determined. With increasing deposition dose the size of the PbTe nanocrystals progressively increases while their number density decreases. Analysis of the GISAXS intensity profiles along the normal to the sample surface allowed the determination of the period parameter of the layers and a structure parameter that characterizes the disorder in the distances between PbTe layers. (C) 2010 International Union of Crystallography Printed in Singapore - all rights reserved

Local atomic structure in tetragonal pure ZrO(2) nanopowders

The local atomic structures around the Zr atom of pure (undoped) ZrO(2) nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wet-chemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO(2) nanopowders can be described by a model consisting of two oxygen subshells (4 + 4 atoms) with different Zr-O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye-Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to the z direction; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4 + 2 + 2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments.

Synchrotron X-ray powder diffraction and extended X-ray absorption fine structure spectroscopy studies on nanocrystalline ZrO(2)-CaO solid solutions

The crystal structure and the local atomic order of a series of nanocrystalline ZrO(2)-CaO solid solutions with varying CaO content were studied by synchrotron radiation X-ray powder diffraction and extended X-ray absorption fine structure (EXAFS) spectroscopy. These samples were synthesized by a pH-controlled nitrate-glycine gel-combustion process. For CaO contents up to 8 mol%, the t' form of the tetragonal phase (c/a > 1) was identified, whereas for 10 and 12 mol% CaO, the t '' form (c/a=1; oxygen anions displaced from their ideal positions in the cubic phase) was detected. Finally, the cubic phase was observed for solid solutions with CaO content of 14 mol% CaO or higher. The t'/t '' and t ''/cubic compositional boundaries were determined to be at 9 (1) and 13 (1) mol% CaO, respectively. The EXAFS study demonstrated that this transition is related to a tetragonal-to-cubic symmetry change of the first oxygen coordination shell around the Zr atoms.

Remote sensing the vertical profile of cloud droplet effective radius, thermodynamic phase, and temperature

Cloud-aerosol interaction is a key issue in the climate system, affecting the water cycle, the weather, and the total energy balance including the spatial and temporal distribution of latent heat release. Information on the vertical distribution of cloud droplet microphysics and thermodynamic phase as a function of temperature or height, can be correlated with details of the aerosol field to provide insight on how these particles are affecting cloud properties and their consequences to cloud lifetime, precipitation, water cycle, and general energy balance. Unfortunately, today's experimental methods still lack the observational tools that can characterize the true evolution of the cloud microphysical, spatial and temporal structure in the cloud droplet scale, and then link these characteristics to environmental factors and properties of the cloud condensation nuclei. Here we propose and demonstrate a new experimental approach (the cloud scanner instrument) that provides the microphysical information missed in current experiments and remote sensing options. Cloud scanner measurements can be performed from aircraft, ground, or satellite by scanning the side of the clouds from the base to the top, providing us with the unique opportunity of obtaining snapshots of the cloud droplet microphysical and thermodynamic states as a function of height and brightness temperature in clouds at several development stages. The brightness temperature profile of the cloud side can be directly associated with the thermodynamic phase of the droplets to provide information on the glaciation temperature as a function of different ambient conditions, aerosol concentration, and type. An aircraft prototype of the cloud scanner was built and flew in a field campaign in Brazil. The CLAIM-3D (3-Dimensional Cloud Aerosol Interaction Mission) satellite concept proposed here combines several techniques to simultaneously measure the vertical profile of cloud microphysics, thermodynamic phase, brightness temperature, and aerosol amount and type in the neighborhood of the clouds. The wide wavelength range, and the use of multi-angle polarization measurements proposed for this mission allow us to estimate the availability and characteristics of aerosol particles acting as cloud condensation nuclei, and their effects on the cloud microphysical structure. These results can provide unprecedented details on the response of cloud droplet microphysics to natural and anthropogenic aerosols in the size scale where the interaction really happens.

Charm and longitudinal structure functions within the Kharzeev-Levin-Nardi model

We use the Kharzeev-Levin-Nardi (KLN) model of the low x gluon distributions to fit recent HERA data on F(L) and F(2)(c)(F(2)(b)). Having checked that this model gives a good description of the data, we use it to predict F(L) and F(2)(c) to be measured in a future electron-ion collider. The results are similar to those obtained with the de Florian-Sassot and Eskola-Paukkunen-Salgado nuclear gluon distributions. The conclusion of this exercise is that the KLN model, simple as it is, may still be used as an auxiliary tool to make estimates for both heavy-ion and electron-ion collisions.

Electron dephasing scattering rate in two-dimensional GaAs/InGaAs heterostructures with embedded InAs quantum dots

We report a comprehensive study of weak-localization and electron-electron interaction effects in a GaAs/InGaAs two-dimensional electron system with nearby InAs quantum dots, using measurements of the electrical conductivity with and without magnetic field. Although both the effects introduce temperature dependent corrections to the zero magnetic field conductivity at low temperatures, the magnetic field dependence of conductivity is dominated by the weak-localization correction. We observed that the electron dephasing scattering rate tau(-1)(phi), obtained from the magnetoconductivity data, is enhanced by introducing quantum dots in the structure, as expected, and obeys a linear dependence on the temperature and elastic mean free path, which is against the Fermi-liquid model. (c) 2008 American Institute of Physics. [DOI: 10.1063/1.2996034]

The Importance of Protein-Protein Interactions on the pH-Induced Conformational Changes of Bovine Serum Albumin: A Small-Angle X-Ray Scattering Study

The combined effects of concentration and pH on the conformational states of bovine serum albumin (BSA) are investigated by small-angle x-ray scattering. Serum albumins, at physiological conditions, are found at concentrations of similar to 35-45 mg/mL (42 mg/mL in the case of humans). In this work, BSA at three different concentrations (10, 25, and 50 mg/mL) and pH values (2.0-9.0) have been studied. Data were analyzed by means of the Global Fitting procedure, with the protein form factor calculated from human serum albumin (HSA) crystallographic structure and the interference function described, considering repulsive and attractive interaction potentials within a random phase approximation. Small-angle x-ray scattering data show that BSA maintains its native state from pH 4.0 up to 9.0 at all investigated concentrations. A pH-dependence of the absolute net protein charge is shown and the charge number per BSA is quantified to 10(2), 8(l), 13(2), 20(2), and 26(2) for pH values 4.0, 5.4, 7.0, 8.0, and 9.0, respectively. The attractive potential diminishes as BSA concentration increases. The coexistence of monomers and dimers is observed at 50 mg/mL and pH 5.4, near the BSA isoelectric point. Samples at pH 2.0 show a different behavior, because BSA overall shape changes as a function of concentration. At 10 mg/mL, BSA is partially unfolded and a strong repulsive protein-protein interaction occurs due to the high amount of exposed charge. At 25 and 50 mg/mL, BSA undergoes some refolding, which likely results in a molten-globule state. This work concludes by confirming that the protein concentration plays an important role on the pH-unfolded BSA state, due to a delicate compromise between interaction forces and crowding effects.