Black carbon affects the cycling of non-black carbon in soil

Black carbon (BC) is an important fraction of many soils worldwide and plays an important role in global C biogeochemistry. However, few studies have examined how it influences the mineralization of added organic matter (AOM) and its incorporation into soil physical fractions and whether BC decomposition is increased by AOM. BC-rich Anthrosols and BC-poor adjacent soils from the Central Amazon (Brazil) were incubated for 532 days either with or without addition of (13)C-isotopically different plant residue. Total C mineralization from the BC-rich Anthrosols with AOM was 25.5% (P < 0.05) lower than with mineralization from the BC-poor adjacent soils. The AOM contributed to a significantly (P < 0.05) higher proportion to the total C mineralized in the BC-rich Anthrosols (91-92%) than the BC-poor adjacent soils (69-80%). The AOM was incorporated more rapidly in BC-rich than BC-poor soils from the separated free light fraction through the intra-aggregate light fraction into the stable organo-mineral fraction and up to 340% more AOM was found in the organo-mineral fraction. This more rapid stabilization was observed despite a significantly (P < 0.05) lower metabolic quotient for BC-rich Anthrosols. The microbial biomass (MB) was up to 125% greater (P < 0.05) in BC-rich Anthrosols than BC-poor adjacent soils. To account for increased MB adsorption onto BC during fumigation extraction, a correction factor was developed via addition of a (13)C-enriched microbial culture. The recovery was found to be 21-41 % lower (P < 0.05) for BC-rich than BC-poor soils due to re-adsorption of MB onto BC. Mineralization of native soil C was enhanced to a significantly greater degree in BC-poor adjacent soils compared to BC-rich Anthrosols as a result of AOM. No positive priming by way of cometabolism due to AOM could be found for aged BC in the soils. (C) 2009 Elsevier Ltd. All rights reserved.

Taxonomic Status and Redescription of the Gillbacker Sea Catfish (Siluriformes: Ariidae: Sciades parkeri)

The Gillbacker Sea Catfish is a valid species of ariid catfish from the northeastern coast of South America. There are many synonyms In the literature for the Gillbacker Sea Catfish and even recent classifications have used different scientific names. Examination of a wide range of sizes of Individuals from different localities and examination of types and original species descriptions of Silurus parkeri, Bagrus flavescens, B. emphysetus, Arius physacanthus, A. bonneti, A. clavispinosus, and A. despaxi has lead us to the conclusion that all these names refer to the Gillbacker Sea Catfish and the valid name for the species is Sciades parkeri. The species is distinguished from all other ariid species by the following combination of features: body coloration yellow; swim bladder divided Into three chambers, posterior chamber moderately sized; nuchal plate shield-shaped, usually larger than supraocciptal process; anterior notch of nuchal plate absent; head shield exposed and granulated In orbital and postorbital regions; lateral edge of accessory patches not emarginated or shallowly notched; fleshy furrow connecting posterior nares absent; and mesial gill rakers absent from first two gill arches. Striking intraspecific and/or ontogenetic variation In eye size, maxillary-barbel length, supraoccipital-process size, nuchal-plate size and shape, and dorsal-spine thickness contributed to the numerous synonyms and misidentifications for Sciades parkeri. Bagrus albicans, described from French Guiana, has at times been listed as a synonym of Sciades parkeri. Our examination of the holotype of B. albicans, however, led us to conclude that It is a synonym of Sciades proops.

A New Species of Gymnotus (Gymnotiformes: Gymnotidae) from Rio Tiquie in Northern Brazil

Gymnotus tiquie, new species, is described from the Rio Tiquie, a tributary of the Uaupes (Vaupes) in the upper Negro basin, Amazonas, Brazil. The new species was collected in non-floodplain (terra firme) streams, where it occurs sympatrically and syntopically with two geographically widespread congeners, the type species of the genus, G. carapo, and G. coropinae. The new species is diagnosed by a unique combination of morphometric, meristic, and osteological traits, and by a characteristic color pattern in which the dark oblique pigment bands, diverse in shape and design, are divided into band-pairs along the length of the body, in which the band-pairs are often recurved (dorsally concave), more variable, and often reticulated in the abdominal region, and in which the pale inter-bands meet at the dorsal midline along most of the length of the body. Gymnotus tiquie is a member of the G. pantherinus species group, with which it shares the presence of one (vs. two) pore in the dorsolateral portion of the preopercle (except in G. pantanal and G. anguillaris), needle-shaped (vs. conical or arrowhead-shaped) teeth on the dentary and premaxilla, and a slender body (BD 5.6-10.6% HL vs. deep 8.7-13.5%, except G. chaviro, G. curupira, G. varzea, G. chimarrao, G. maculosus, G. henni, and G. inaequilabiatus that also have a slender body). Gymnotus tiquie is most similar in overall appearance to G. cataniapo of the upper Orinoco. These two species share three unique features within the G. pantherinus group: dark band-pairs with wavy irregular margins along the length of the body, a long body cavity with 45 or more pre-caudal vertebrae, and a darkly pigmented membrane in the caudal region of the anal fin.

A new dwarf species of Proceratophrys Miranda-Ribeiro, 1920 (Anura, Cycloramphidae) from the highlands of Chapada Diamantina, Bahia, Brazil

A new species of Proceratophrys is described from the highlands of northeastern Brazil. Molecular and morphological data suggests that Proceratophrys redacta sp. nov. is sister to P. minuta, and related to P. schirchi and P. cristiceps. The new species is diagnosed by its small size, absence of rostral and palpebral appendages, sagittal ridges interrupted, absence of postocular swellings, snout vertical in profile and dorsal coloration lacking distinct ocelli. The new species represents another example of endemism for the genus Proceratophrys in Chapada Diamantina region, and of another appendageless small-sized species associated with highlands. The phylogenetic results indicate that current morphological groupings in Proceratophrys may not represent natural groups.

Compact groups of galaxies selected by stellar mass: the 2MASS compact group catalogue

We present a photometric catalogue of compact groups of galaxies (p2MCGs) automatically extracted from the Two-Micron All Sky Survey (2MASS) extended source catalogue. A total of 262 p2MCGs are identified, following the criteria defined by Hickson, of which 230 survive visual inspection (given occasional galaxy fragmentation and blends in the 2MASS parent catalogue). Only one quarter of these 230 groups were previously known compact groups (CGs). Among the 144 p2MCGs that have all their galaxies with known redshifts, 85 (59?per cent) have four or more accordant galaxies. This v2MCG sample of velocity-filtered p2MCGs constitutes the largest sample of CGs (with N = 4) catalogued to date, with both well-defined selection criteria and velocity filtering, and is the first CG sample selected by stellar mass. It is fairly complete up to Kgroup similar to 9 and radial velocity of similar to 6000?km?s-1. We compared the properties of the 78 v2MCGs with median velocities greater than 3000?km?s-1 with the properties of other CG samples, as well as those (mvCGs) extracted from the semi-analytical model (SAM) of Guo et al. run on the high-resolution Millennium-II simulation. This mvCG sample is similar (i.e. with 2/3 of physically dense CGs) to those we had previously extracted on three other SAMs run on the Millennium simulation with 125 times worse spatial and mass resolutions. The space density of v2MCGs within 6000?km?s-1 is 8.0 X 10-5?h3?Mpc-3, i.e. four times that of the Hickson sample [Hickson Compact Group (HCG)] up to the same distance and with the same criteria used in this work, but still 40?per cent less than that of mvCGs. The v2MCG constitutes the first group catalogue to show a statistically large firstsecond ranked galaxy magnitude gap according to TremaineRichstone statistics, as expected if the first ranked group members tend to be the products of galaxy mergers, and as confirmed in the mvCGs. The v2MCG is also the first observed sample to show that first-ranked galaxies tend to be centrally located, again consistent with the predictions obtained from mvCGs. We found no significant correlation of group apparent elongation and velocity dispersion in the quartets among the v2MCGs, and the velocity dispersions of apparently round quartets are not significantly larger than those of chain-like ones, in contrast to what has been previously reported in HCGs. By virtue of its automatic selection with the popular Hickson criteria, its size, its selection on stellar mass, and its statistical signs of mergers and centrally located brightest galaxies, the v2MCG catalogue appears to be the laboratory of choice to study physically dense groups of four or more galaxies of comparable luminosity.

Molecular and Electronic Structure of the Peptide Subunit of Geobacter sulfurreducens Conductive Phi from First Principles

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved a-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pain was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's alpha-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

On the Limit of Frequency of Electrochemical Oscillators and Its Relationship to Kinetic Parameters

The class of electrochemical oscillators characterized by a partially hidden negative differential resistance in an N-shaped current potential curve encompasses a myriad of experimental examples. We present a comprehensive methodological analysis of the oscillation frequency of this class of systems and discuss its dependence on electrical and kinetic parameters. The analysis is developed from a skeleton ordinary differential equation model, and an equation for the oscillation frequency is obtained. Simulations are carried out for a model system, namely, the nickel electrodissolution, and the numerical results are confirmed by experimental data on this system. In addition, the treatment is further applied to the electro-oxidation of ethylene glycol where unusually large oscillation frequencies have been reported. Despite the distinct chemistry underlying the oscillatory dynamics of these systems, a very good agreement between experiments and theoretical predictions is observed. The application of the developed theory is suggested as an important step for primary kinetic characterization.

Molecular phylogeny and morphometric analyses reveal deep divergence between Amazonia and Atlantic Forest species of Dendrophryniscus

Dendrophryniscus is an early diverging clade of bufonids represented by few small-bodied species distributed in Amazonia and the Atlantic Forest. We used mitochondrial (414 bp of 12S, 575 bp of 16S genes) and nuclear DNA (785 bp of RAG-1) to investigate phylogenetic relationships and the timing of diversification within the genus. These molecular data were gathered from 23 specimens from 19 populations, including eight out of the 10 nominal species of the genus as well as Rhinella boulengeri. Analyses also included sequences of representatives of 18 other bufonid genera that were publically available. We also examined morphological characters to analyze differences within Dendrophryniscus. We found deep genetic divergence between an Amazonian and an Atlantic Forest clade, dating back to Eocene. Morphological data corroborate this distinction. We thus propose to assign the Amazonian species to a new genus, Amazonella. The species currently named R. boulengeri, which has been previously assigned to the genus Rhamphophryne, is shown to be closely related to Dendrophryniscus species. Our findings illustrate cryptic trends in bufonid morphological evolution, and point to a deep history of persistence and diversification within the Amazonian and Atlantic rainforests. We discuss our results in light of available paleoecological data and the biogeographic patterns observed in other similarly distributed groups. (C) 2011 Elsevier Inc. All rights reserved.

Demographic processes in the montane Atlantic rainforest: Molecular and cytogenetic evidence from the endemic frog Proceratophrys boiei

Historical climatic refugia predict genetic diversity in lowland endemics of the Brazilian Atlantic rainforest. Yet, available data reveal distinct biological responses to the Last Glacial Maximum (LGM) conditions across species of different altitudinal ranges. We show that species occupying Brazil's montane forests were significantly less affected by LGM conditions relative to lowland specialists, but that pre-Pleistocene tectonics greatly influenced their geographic variation. Our conclusions are based on palaeoclimatic distribution models, molecular sequences of the cytochrome b, 16S, and RAG-1 genes, and karyotype data for the endemic frog Proceratophrys boiei. DNA and chromosomal data identify in P. boiei at least two broadly divergent phylogroups, which have not been distinguished morphologically. Cytogenetic results also indicate an area of hybridization in southern Sao Paulo. The location of the phylogeographic break broadly matches the location of a NW-SE fault, which underwent reactivation in the Neogene and led to remarkable landscape changes in southeastern Brazil. Our results point to different mechanisms underpinning diversity patterns in lowland versus montane tropical taxa, and help us to understand the processes responsible for the large number of narrow endemics currently observed in montane areas of the southern Atlantic forest hotspot. (C) 2011 Elsevier Inc. All rights reserved.

Systematic Evaluation of Extraction Methods for Multiplatform-Based Metabotyping: Application to the Fasciola hepatica Metabolome

Combining data from multiple analytical platforms is essential for comprehensive study of the molecular phenotype (metabotype) of a given biological sample. The metabolite profiles generated are intrinsically dependent on the analytical platforms, each requiring optimization of instrumental parameters, separation conditions, and sample extraction to deliver maximal biological information. An in-depth evaluation of extraction protocols for characterizing the metabolome of the hepatobiliary fluke Fasciola hepatica, using ultra performance liquid chromatography and capillary electrophoresis coupled with mass spectroscopy is presented. The spectrometric methods were characterized by performance, and metrics of merit were established, including precision, mass accuracy, selectivity, sensitivity, and platform stability. Although a core group of molecules was common to all methods, each platform contributed a unique set, whereby 142 metabolites out of 14,724 features were identified. A mixture design revealed that the chloroform:methanol:water proportion of 15:59:26 was globally the best composition for metabolite extraction across UPLC-MS and CE-MS platforms accommodating different columns and ionization modes. Despite the general assumption of the necessity of platform-adapted protocols for achieving effective metabotype characterization, we show that an appropriately designed single extraction procedure is able to fit the requirements of all technologies. This may constitute a paradigm shift in developing efficient protocols for high-throughput metabolite profiling with more-general analytical applicability.

Reconnection studies under different types of turbulence driving

We study a model of fast magnetic reconnection in the presence of weak turbulence proposed by Lazarian and Vishniac (1999) using three-dimensional direct numerical simulations. The model has been already successfully tested in Kowal et al. (2009) confirming the dependencies of the reconnection speed V-rec on the turbulence injection power P-inj and the injection scale l(inj) expressed by a constraint V-rec similar to P(inj)(1/2)l(inj)(3/4)and no observed dependency on Ohmic resistivity. In Kowal et al. (2009), in order to drive turbulence, we injected velocity fluctuations in Fourier space with frequencies concentrated around k(inj) = 1/l(inj), as described in Alvelius (1999). In this paper, we extend our previous studies by comparing fast magnetic reconnection under different mechanisms of turbulence injection by introducing a new way of turbulence driving. The new method injects velocity or magnetic eddies with a specified amplitude and scale in random locations directly in real space. We provide exact relations between the eddy parameters and turbulent power and injection scale. We performed simulations with new forcing in order to study turbulent power and injection scale dependencies. The results show no discrepancy between models with two different methods of turbulence driving exposing the same scalings in both cases. This is in agreement with the Lazarian and Vishniac (1999) predictions. In addition, we performed a series of models with varying viscosity nu. Although Lazarian and Vishniac (1999) do not provide any prediction for this dependence, we report a weak relation between the reconnection speed with viscosity, V-rec similar to nu(-1/4).

Analysis, manufacture and characterization of Ni/Cu functionally graded structures

In this work, an experimental and numerical analysis and characterization of functionally graded structures (FGSs) is developed. Nickel (Ni) and copper (Cu) materials are used as basic materials in the numerical modeling and experimental characterization. For modeling, a MATLAB finite element code is developed, which allows simulation of harmonic and modal analysis considering the graded finite element formulation. For experimental characterization, Ni-Cu FGSs are manufactured by using spark plasma sintering technique. Hardness and Young's modulus are found by using microindentation and ultrasonic measurements, respectively. The effective gradation of Ni/Cu FGS is addressed by means of optical microscopy, energy dispersive spectrometry, scanning electron microscopy and hardness testing. For the purpose of comparing modeling and experimental results, the hardness curve, along the gradation direction, is used for identifying the gradation profile; accordingly, the experimental hardness curve is used for approximating the Young's modulus variation and the graded finite element modeling is used for verification. For the first two resonance frequency values, a difference smaller than 1% between simulated and experimental results is obtained. (C) 2012 Elsevier Ltd. All rights reserved.

The Effects of Processing Non-Timber Forest Products and Trade Partnerships on People's Well-Being and Forest Conservation in Amazonian Societies

This study evaluated whether processing non-timber forest products (NTFPs) and establishing trade partnerships between forest communities and companies enhance the outcomes of NTFP commercialization. In particular, we evaluated whether product processing, partnerships, or their combination was associated with a number of outcomes related to the well-being of forest inhabitants and forest conservation. We based our analyses on ethnographic and quantitative data (i.e., survey and systematic observations) gathered at seven communities from five societies of the Brazilian and Bolivian Amazon. Our results indicated that product processing and partnerships do not represent a silver bullet able to improve the results of NTFP commercialization in terms of well-being and conservation indicators. Compared with cases without interventions, households adopting partnerships but not product processing were most often associated with improved economic proxies of well-being (total income, NTFP income, food consumption and gender equality in income). In comparison, the combination of product processing and partnerships was associated with similar outcomes. Unexpectedly, product processing alone was associated with negative outcomes in the economic indicators of well-being. All of the investigated strategies were associated with less time spent in social and cultural activities. With respect to forest conservation, the strategies that included a partnership with or without processing produced similar results: while household deforestation tended to decrease, the hunting impact increased. Processing alone was also associated with higher levels of hunting, though it did not reduce deforestation. Our results indicate that establishing partnerships may enhance the outcomes of NTFP trade in terms of the financial outcomes of local communities, but practitioners need to use caution when adopting the processing strategy and they need to evaluate potential negative results for indicators of social and cultural activities. With respect to conservation, the three strategies are promising for reducing deforestation, but more pervasive impacts, such as hunting, might increase.

Evidence that a single bioluminescent system is shared by all known bioluminescent fungal lineages

Since the early 20th century, many researchers have attempted to determine how fungi are able to emit light. The first successful experiment was obtained using the classical luciferin-luciferase test that consists of mixing under controlled conditions hot (substrate/luciferin) and cold (enzyme/luciferase) water extracts prepared from bioluminescent fungi. Failures by other researchers to reproduce those experiments using different species of fungi lead to the hypothesis of a non-enzymatic luminescent pathway. Only recently, the involvement of a luciferase in this system was proven, thus confirming its enzymatic nature. Of the 100 000 described species in Kingdom Fungi, only 71 species are known to be luminescent and they are distributed unevenly amongst four distantly related lineages. The question we address is whether the mechanism of bioluminescence is the same in all four evolutionary lineages suggesting a single origin of luminescence in the Fungi, or whether each lineage has a unique mechanism for light emission implying independent origins. We prepared hot and cold extracts of numerous species representing the four bioluminescent fungal lineages and performed cross-reactions (luciferin x luciferase) in all possible combinations using closely related non-luminescent species as controls. All cross-reactions with extracts from luminescent species yielded positive results, independent of lineage, whereas no light was emitted in cross-reactions with extracts from non-luminescent species. These results support the hypothesis that all four lineages of luminescent fungi share the same type of luciferin and luciferase, that there is a single luminescent mechanism in the Fungi, and that fungal luciferin is not a ubiquitous molecule in fungal metabolism.

Galaxy triplets in Sloan Digital Sky Survey Data Release 7-I. Catalogue

We present a new catalogue of galaxy triplets derived from the Sloan Digital Sky Survey (SDSS) Data Release 7. The identification of systems was performed considering galaxies brighter than Mr=-20.5 and imposing constraints over the projected distances, radial velocity differences of neighbouring galaxies and isolation. To improve the identification of triplets, we employed a data pixelization scheme, which allows us to handle large amounts of data as in the SDSS photometric survey. Using spectroscopic and photometric data in the redshift range 0.01 =z= 0.40, we obtain 5901 triplet candidates. We have used a mock catalogue to analyse the completeness and contamination of our methods. The results show a high level of completeness ( 80 per cent) and low contamination ( 5 per cent). By using photometric and spectroscopic data, we have also addressed the effects of fibre collisions in the spectroscopic sample. We have defined an isolation criterion considering the distance of the triplet brightest galaxy to the closest neighbour cluster, to describe a global environment, as well as the galaxies within a fixed aperture, around the triplet brightest galaxy, to measure the local environment. The final catalogue comprises 1092 isolated triplets of galaxies in the redshift range 0.01 =z= 0.40. Our results show that photometric redshifts provide very useful information, allowing us to complete the sample of nearby systems whose detection is affected by fibre collisions, as well as extending the detection of triplets to large distances, where spectroscopic redshifts are not available.